Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold150
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1465027
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.31
Warning! 98465 characters in sequence are not A, C, G, or T
File 8 of 9
Found at i:1260958 original size:28 final size:28
Alignment explanation
Indices: 1260926--1260995 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 28
1260916 TCACAACCGA
* ** *
1260926 GGATACTCCAACCTCGTTATTTCAT-CGG
1 GGATACTCCAACCCCGTTACCTC-TGAGG
1260954 GGATACTCCAACCCCGTTACCTCTGAGG
1 GGATACTCCAACCCCGTTACCTCTGAGG
1260982 GGATACTCCAACCC
1 GGATACTCCAACCC
1260996 TGGCTTTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
27 1 0.03
28 36 0.97
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.24
Consensus pattern (28 bp):
GGATACTCCAACCCCGTTACCTCTGAGG
Found at i:1260975 original size:204 final size:209
Alignment explanation
Indices: 1260612--1261048 Score: 715
Period size: 204 Copynumber: 2.1 Consensus size: 209
1260602 AATTGTTCAT
1260612 AATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGGTACT
1 AATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGGTACT
*
1260677 CCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGGATACTCCAACCTCATTAT
66 -C-ACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAACCGAGGATACTCCAACCTCATTAT
*
1260742 TTCATCGGGGATACTCCAACCCTGTTACCTCCGAGGGGATACTCCAACCCCAGCTTTATTTCCAA
129 TTCATCGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCAGCTTTATTTCCAA
1260807 AATATTGATTTC-CAC
194 AATATTGATTTCTCAC
*
1260822 AATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACTAATTTTCCTTTAATC-GGGG-A-T
1 AATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGGTACT
* *
1260884 -AC-CCGATTTTATTTCCAAAAAACATCAATTTTTCACAACCGAGGATACTCCAACCTCGTTATT
66 CACTCCGATTTTATTTCC-AAAAACACCAATTTTTCACAACCGAGGATACTCCAACCTCATTATT
* **
1260947 TCATCGGGGATACTCCAACCCCGTTACCTCTGAGGGGATACTCCAACCCTGGCTTTATTTCCAAA
130 TCATCGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCAGCTTTATTTCCAAA
*
1261012 ATATTGATTTCTCAT
195 ATATTGATTTCTCAC
*
1261027 AATTGGGGATACTCCAACCCCG
1 AATCGGGGATACTCCAACCCCG
1261049 TTATTTTCGA
Statistics
Matches: 215, Mismatches: 10, Indels: 9
0.92 0.04 0.04
Matches are distributed among these distances:
203 14 0.07
204 117 0.54
205 23 0.11
207 1 0.00
208 1 0.00
209 4 0.02
210 55 0.26
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.31
Consensus pattern (209 bp):
AATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGGTACT
CACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAACCGAGGATACTCCAACCTCATTATTT
CATCGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCAGCTTTATTTCCAAAA
TATTGATTTCTCAC
Found at i:1261061 original size:79 final size:80
Alignment explanation
Indices: 1260951--1261153 Score: 216
Period size: 79 Copynumber: 2.6 Consensus size: 80
1260941 GTTATTTCAT
** **
1260951 CGGGGATACTCCAACCCCGTTA-CCTCTGAGGGGATACTCCAACCCT-GGCTTTATTTCCAAAAT
1 CGGGGATACTCCAACCCCGTTATTTTC-GAGGGGATACTCCAACCCTCGATTTTA-TTCCAAAAT
* * *
1261014 -ATTGATTTCTCATAAT
64 CATCGATTTCTCACAAC
* * **
1261030 TGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAA-TCTCGATTTTATTCCCTAATCA
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCTCGATTTTATTCCAAAATCA
* *
1261094 TCGATTTTTTACAAC
66 TCGATTTCTCACAAC
* * *
1261109 CGGGGATACTCCAACCCTGTTATTTTCAAGGGGACACTCCAACCC
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCC
1261154 CGTTACTATC
Statistics
Matches: 102, Mismatches: 18, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
78 9 0.09
79 90 0.88
80 3 0.03
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.31
Consensus pattern (80 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCTCGATTTTATTCCAAAATCA
TCGATTTCTCACAAC
Found at i:1263222 original size:4 final size:4
Alignment explanation
Indices: 1263213--1263239 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1263203 TTTTGAGGTG
1263213 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1263240 GTTCTGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:1270016 original size:78 final size:78
Alignment explanation
Indices: 1269906--1270111 Score: 243
Period size: 78 Copynumber: 2.6 Consensus size: 78
1269896 GAGATAATAA
* * * * * * *
1269906 CGGGGTTGGAGTGTTCCCTTGAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATGA
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-A
*
1269971 -TTAGAAAAAAAAT
65 CTTAGAAAAAAAAC
* *
1269984 CGGGATTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATAC
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAC
* * * *
1270049 TTTGGGAATAAAGC
66 -TTAGAAAAAAAAC
* *
1270063 CGGGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGAT
1270112 GAAATAACAA
Statistics
Matches: 108, Mismatches: 18, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
77 1 0.01
78 54 0.50
79 53 0.49
ACGTcount: A:0.29, C:0.17, G:0.30, T:0.24
Consensus pattern (78 bp):
CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAC
TTAGAAAAAAAAC
Found at i:1270119 original size:28 final size:28
Alignment explanation
Indices: 1270063--1270134 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 28
1270053 GGAATAAAGC
** *
1270063 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
1270091 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
**
1270119 CAAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
1270135 TCGACTGTGA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.25, C:0.19, G:0.33, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:1270357 original size:263 final size:263
Alignment explanation
Indices: 1270012--1270512 Score: 756
Period size: 263 Copynumber: 1.9 Consensus size: 263
1270002 TCGAAAATAA
* * * *
1270012 CGGGGTTGGAGTATCCCCAATTATGAGAAATCAATACTTTGGGAATAAAGCCGGGGTTGGAGTAT
1 CGGGGTTGGAATATCCCCAATTATGAAAAATCAATACTTTAGAAATAAAGCCGGGGTTGGAGTAT
* *
1270077 CCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAAT-AACAAGGTTGGAGTATCCTCGACT
66 CCCCTCGGAAATAACGGGGTTGGAGTATCCCCGAT--AATCAACAAGGTTGGAGTATCCCCGACT
1270141 GTGAA-AAATTGGT-ATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATT
129 GTGAAGAAATTGGTGATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAA-GAAAATT
* * *
1270204 GGTGTTTCGAAAATAAAACCGGGGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAA
193 AGTGTTTCGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAA
1270269 TAAAAC
258 TAAAAC
* * * *
1270275 CGGGGTTGGAATATCCCCGATTATGAAAAATTAATATTTTAGAAATAAAGTCGGGGTTGGAGTAT
1 CGGGGTTGGAATATCCCCAATTATGAAAAATCAATACTTTAGAAATAAAGCCGGGGTTGGAGTAT
* ** *
1270340 CCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATTATCAACGGGGTTGGAGTATCCCCGATTGT
66 CCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATAATCAACAAGGTTGGAGTATCCCCGACTGT
* *
1270405 GAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTATAGAAAATTAGT
131 GAAGAAATTGGTGATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGAAAATTAGT
* * *
1270470 GTTTTGAAAATAAAATCGGAGTTGGAATATCCTCGATTGTGGA
196 GTTTCGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGA
1270513 GAATTGATAA
Statistics
Matches: 213, Mismatches: 22, Indels: 6
0.88 0.09 0.02
Matches are distributed among these distances:
261 2 0.01
262 25 0.12
263 146 0.69
264 40 0.19
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (263 bp):
CGGGGTTGGAATATCCCCAATTATGAAAAATCAATACTTTAGAAATAAAGCCGGGGTTGGAGTAT
CCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATAATCAACAAGGTTGGAGTATCCCCGACTGT
GAAGAAATTGGTGATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGAAAATTAGT
GTTTCGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAA
AAC
Found at i:1270390 original size:27 final size:26
Alignment explanation
Indices: 1270326--1270402 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 26
1270316 GAAATAAAGT
*
1270326 CGGGGTTGGAGTATCCCCTCGGA-AATAA
1 CGGGGTTGGAGTAT-CCC-C-GATTATAA
1270354 CGGGGTTGGAGTATCCCCGATTATCAA
1 CGGGGTTGGAGTATCCCCGATTAT-AA
1270381 CGGGGTTGGAGTATCCCCGATT
1 CGGGGTTGGAGTATCCCCGATT
1270403 GTGAAGAAAT
Statistics
Matches: 46, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
25 2 0.04
26 3 0.07
27 27 0.59
28 14 0.30
ACGTcount: A:0.21, C:0.22, G:0.32, T:0.25
Consensus pattern (26 bp):
CGGGGTTGGAGTATCCCCGATTATAA
Found at i:1270489 original size:51 final size:52
Alignment explanation
Indices: 1270122--1270507 Score: 234
Period size: 52 Copynumber: 7.4 Consensus size: 52
1270112 GAAATAACAA
* * * * * *
1270122 GGTTGGAGTATCCTCGACTGT-GAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATAGAAAAATTAGT-GTTTTGAAAATAAAATCGG
* * * * * *
1270174 AGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTCGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATTATAGAAAAATTAGTGTTTTGAAAATAAAATCGG
* * * *
1270226 GGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTT-AGCAATAAAACCGG
1 GGTTGGAGTATCCCCGATTATAGAAAAATTAGTGTTTTGA-AAATAAAATCGG
* * * *
1270278 GGTTGGAATATCCCCGATTAT-GAAAAATTAATATTTT-AGAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATAGAAAAATTAGTGTTTTGA-AAATAAAATCGG
* **** * *** ** *
1270329 GGTTGGAGTATCCCCTCGGA-AATA-ACGGGGTTGGAGTATCCCCGATTAT-CAA-CGG
1 GGTTGGAGTAT-CCC-C-GATTATAGA-AAAATT--AGTGT-TTTGAAAATAAAATCGG
* * *
1270384 GGTTGGAGTATCCCCGATTGT-GAAGAAATTGGTGTTTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATAGAA-AAATTAGTG--TTTTGAAAATAAAATCGG
*
1270438 AGTTGGAGTATCCCCGATTATAG-AAAATTAGTGTTTTGAAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATAGAAAAATTAGTGTTTTGAAAATAAAATCGG
* * *
1270489 AGTTGGAATATCCTCGATT
1 GGTTGGAGTATCCCCGATT
1270508 GTGGAGAATT
Statistics
Matches: 255, Mismatches: 60, Indels: 39
0.72 0.17 0.11
Matches are distributed among these distances:
51 72 0.28
52 100 0.39
53 30 0.12
54 30 0.12
55 15 0.06
56 5 0.02
57 2 0.01
58 1 0.00
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.30
Consensus pattern (52 bp):
GGTTGGAGTATCCCCGATTATAGAAAAATTAGTGTTTTGAAAATAAAATCGG
Found at i:1272902 original size:13 final size:13
Alignment explanation
Indices: 1272884--1272909 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1272874 ACAAAGATCC
1272884 ATGTATCGATACA
1 ATGTATCGATACA
1272897 ATGTATCGATACA
1 ATGTATCGATACA
1272910 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1272905 original size:33 final size:33
Alignment explanation
Indices: 1272863--1272929 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1272853 AAAATTTCCA
***
1272863 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
1272896 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
1272929 A
1 A
1272930 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:1272973 original size:19 final size:18
Alignment explanation
Indices: 1272949--1273016 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
1272939 CAGTAGCTAA
1272949 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
1272968 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
1272983 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
1273000 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
1273017 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:1272989 original size:13 final size:13
Alignment explanation
Indices: 1272971--1272995 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1272961 ACAATACTTA
1272971 TGTATCGATACAT
1 TGTATCGATACAT
1272984 TGTATCGATACA
1 TGTATCGATACA
1272996 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1272993 original size:32 final size:32
Alignment explanation
Indices: 1272952--1273014 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1272942 TAGCTAATTA
*
1272952 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
1272984 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
1273015 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:1273851 original size:28 final size:28
Alignment explanation
Indices: 1273820--1273906 Score: 65
Period size: 28 Copynumber: 3.1 Consensus size: 28
1273810 TGAGGAGTAA
1273820 AAAGTGCCACCAACTCGTGTGGGCTTTG
1 AAAGTGCCACCAACTCGTGTGGGCTTTG
** ** *
1273848 AAAG-GCGTCCTGCTC-TTTGAGGAC--TG
1 AAAGTGCCACCAACTCGTGTG-GG-CTTTG
*
1273874 AAAGGTGCCACCAACTTGTGTGGGCTTTG
1 AAA-GTGCCACCAACTCGTGTGGGCTTTG
1273903 AAAG
1 AAAG
1273907 GTGTACTGCT
Statistics
Matches: 41, Mismatches: 11, Indels: 14
0.62 0.17 0.21
Matches are distributed among these distances:
26 8 0.20
27 11 0.27
28 14 0.34
29 8 0.20
ACGTcount: A:0.23, C:0.22, G:0.30, T:0.25
Consensus pattern (28 bp):
AAAGTGCCACCAACTCGTGTGGGCTTTG
Found at i:1273895 original size:55 final size:55
Alignment explanation
Indices: 1273800--1274422 Score: 938
Period size: 55 Copynumber: 11.3 Consensus size: 55
1273790 ATAAAGTGTA
* * * * * * *
1273800 TCCTTCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAA-AGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1273855 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* *
1273910 TACTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
1273965 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* * *
1274020 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGGGTGGGCTTTGAA-AAGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
*
1274075 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
1274130 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1274185 TCCTGCTCTTTG-GAGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAG-GACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
1274240 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* * *
1274295 TCTTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGGGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
*
1274350 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1274405 TCCTGCTCTTTGAGGACT
1 TCCTGCTCTTTGAGGACT
1274423 AAAAAGCGGA
Statistics
Matches: 526, Mismatches: 29, Indels: 26
0.91 0.05 0.04
Matches are distributed among these distances:
54 19 0.04
55 490 0.93
56 17 0.03
ACGTcount: A:0.20, C:0.20, G:0.31, T:0.29
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
Found at i:1275434 original size:17 final size:18
Alignment explanation
Indices: 1275390--1275454 Score: 51
Period size: 19 Copynumber: 3.5 Consensus size: 18
1275380 TAAGTAGGTT
*
1275390 TTTTCTTTTCTCTCTTTTTC
1 TTTT-TTTTGTCT-TTTTTC
* *
1275410 TTTGTTTTGT-TTTTTTG
1 TTTTTTTTGTCTTTTTTC
* *
1275427 TTTTTTTTCCTCTTTTTTT
1 TTTTTTTT-GTCTTTTTTC
1275446 TTTTTTTTG
1 TTTTTTTTG
1275455 AAGAGAAGGT
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
17 12 0.33
18 2 0.06
19 19 0.53
20 3 0.08
ACGTcount: A:0.00, C:0.12, G:0.06, T:0.82
Consensus pattern (18 bp):
TTTTTTTTGTCTTTTTTC
Found at i:1283885 original size:78 final size:78
Alignment explanation
Indices: 1283775--1283980 Score: 234
Period size: 78 Copynumber: 2.6 Consensus size: 78
1283765 GAGATAATAA
* * * * * * *
1283775 CGGGGTTGGAGTGTTCCCTTGAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATGA
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-A
*
1283840 -TTAGAAAAAAAAT
65 CTTAGAAAAAAAAC
* *
1283853 CGGGATTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATAC
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAC
* * * *
1283918 TTTGGGAATAAAGC
66 -TTAGAAAAAAAAC
* * *
1283932 CGGGGTTGGAGTATCCCTTCGGAAGTAACGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGAT
1283981 GAAATAACAA
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
77 1 0.01
78 54 0.50
79 52 0.49
ACGTcount: A:0.29, C:0.17, G:0.30, T:0.24
Consensus pattern (78 bp):
CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAC
TTAGAAAAAAAAC
Found at i:1283965 original size:79 final size:78
Alignment explanation
Indices: 1283775--1283977 Score: 230
Period size: 79 Copynumber: 2.6 Consensus size: 78
1283765 GAGATAATAA
* * ** * *
1283775 CGGGGTTGGAGTGTTCCCTT-GAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATG
1 CGGGGTTGGAGT-ATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATG
*
1283839 ATTAGAAAAAAAAT
65 ATTAGAAAAAAAAC
* *
1283853 CGGGATTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAAT-A
1 CGGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATGA
* * * *
1283917 CTTTGGGAATAAAGC
66 --TTAGAAAAAAAAC
* *
1283932 CGGGGTTGGAGTATCCCTTCGGAAGTAACGGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCC
1283978 GATGAAATAA
Statistics
Matches: 105, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
77 6 0.06
78 49 0.47
79 50 0.48
ACGTcount: A:0.29, C:0.17, G:0.30, T:0.24
Consensus pattern (78 bp):
CGGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATGA
TTAGAAAAAAAAC
Found at i:1283988 original size:28 final size:27
Alignment explanation
Indices: 1283932--1284003 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 27
1283922 GGAATAAAGC
*
1283932 CGGGGTTGGAGTATCCCTTCGGAAGTAA
1 CGGGGTTGGAGTATCCC-TCGGAAATAA
1283960 CGGGGTTGGAGTATCCC-CGATGAAATAA
1 CGGGGTTGGAGTATCCCTCG--GAAATAA
**
1283988 CAAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
1284004 TCGACTGTGA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
26 2 0.05
28 37 0.95
ACGTcount: A:0.25, C:0.18, G:0.33, T:0.24
Consensus pattern (27 bp):
CGGGGTTGGAGTATCCCTCGGAAATAA
Found at i:1284087 original size:52 final size:51
Alignment explanation
Indices: 1284026--1284375 Score: 162
Period size: 51 Copynumber: 6.7 Consensus size: 51
1284016 AATTGGTATT
* *
1284026 TTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTGGTG
1 TTTGAAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTAGTG
* * **
1284077 TTTCGAAAATAAAACCGGGGTTGGAGTATCCCCGATT-GTGGAAAAATTAGTG
1 TTT-GAAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGG-AAAATTAGTG
* * * * * * * *
1284129 TTTTAGCAATAAAACCGG-GTTGGAATATCCCCGATT-ATGAAAAATTAATA
1 TTTGA-AAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTAGTG
* * * * * ** *
1284179 TTTTAGAAATAAAGTCGGGGTTGGAGTATCCCCTCGGAAATAACGG--GGTTGGAGTA
1 TTTGA-AAATAAAATCGGAGTTGGAGTAT-CCC-C-G-ATTAAAGGAAAATT--AGTG
** ** * * * *
1284235 TCCCCGATGAT-CAA-CGGGGTTGGAGTATCCCCGATTGTGAA-G-AAATTGGTG
1 T--TTGAAAATAAAATCGGAGTTGGAGTATCCCCGA-T-TAAAGGAAAATTAGTG
* *
1284286 TTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTATA-GAAAATTAGTG
1 ---TTTGAAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTAGTG
* *
1284339 TTTTGAAAATAAAATCGGAGTTGGAATATCCTCGATT
1 -TTTGAAAATAAAATCGGAGTTGGAGTATCCCCGATT
1284376 GTGGAGAATT
Statistics
Matches: 227, Mismatches: 50, Indels: 44
0.71 0.16 0.14
Matches are distributed among these distances:
50 23 0.10
51 71 0.31
52 64 0.28
53 17 0.07
54 26 0.11
55 16 0.07
56 7 0.03
57 2 0.01
58 1 0.00
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (51 bp):
TTTGAAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTAGTG
Found at i:1284231 original size:262 final size:262
Alignment explanation
Indices: 1283883--1284380 Score: 750
Period size: 262 Copynumber: 1.9 Consensus size: 262
1283873 GAAAATAACG
* * * *
1283883 GGGTTGGAGTATCCCCAATTATGAGAAATCAATACTTTGGGAATAAAGCCGGGGTTGGAGTATCC
1 GGGTTGGAATATCCCCAATTATGAAAAATCAATACTTTAGAAATAAAGCCGGGGTTGGAGTATCC
* * *
1283948 CTTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAAT-AACAAGGTTGGAGTATCCTCGACTGT
66 CCTCGGAAATAACGGGGTTGGAGTATCCCCGATG--ATCAACAAGGTTGGAGTATCCCCGACTGT
*
1284012 GAA-AAATTGGT-ATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTGG
129 GAAGAAATTGGTGATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAA-GAAAATTAG
* *
1284075 TGTTTCGAAAATAAAACCGGGGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATA
193 TGTTTCGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATA
1284140 AAACC
258 AAACC
* * * *
1284145 GGGTTGGAATATCCCCGATTATGAAAAATTAATATTTTAGAAATAAAGTCGGGGTTGGAGTATCC
1 GGGTTGGAATATCCCCAATTATGAAAAATCAATACTTTAGAAATAAAGCCGGGGTTGGAGTATCC
** *
1284210 CCTCGGAAATAACGGGGTTGGAGTATCCCCGATGATCAACGGGGTTGGAGTATCCCCGATTGTGA
66 CCTCGGAAATAACGGGGTTGGAGTATCCCCGATGATCAACAAGGTTGGAGTATCCCCGACTGTGA
* *
1284275 AGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTATAGAAAATTAGTGT
131 AGAAATTGGTGATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGAAAATTAGTGT
* * *
1284340 TTTGAAAATAAAATCGGAGTTGGAATATCCTCGATTGTGGA
196 TTCGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGA
1284381 GAATTGATAA
Statistics
Matches: 211, Mismatches: 22, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
260 2 0.01
261 25 0.12
262 144 0.68
263 40 0.19
ACGTcount: A:0.32, C:0.13, G:0.27, T:0.28
Consensus pattern (262 bp):
GGGTTGGAATATCCCCAATTATGAAAAATCAATACTTTAGAAATAAAGCCGGGGTTGGAGTATCC
CCTCGGAAATAACGGGGTTGGAGTATCCCCGATGATCAACAAGGTTGGAGTATCCCCGACTGTGA
AGAAATTGGTGATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGAAAATTAGTGT
TTCGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAA
CC
Found at i:1284258 original size:27 final size:26
Alignment explanation
Indices: 1284194--1284269 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 26
1284184 GAAATAAAGT
1284194 CGGGGTTGGAGTATCCCCTCGGA-AATAA
1 CGGGGTTGGAGTAT-CCC-C-GATAATAA
*
1284222 CGGGGTTGGAGTATCCCCGATGATCAA
1 CGGGGTTGGAGTATCCCCGATAAT-AA
1284249 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
1284270 TGTGAAGAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
25 2 0.04
26 3 0.07
27 26 0.58
28 14 0.31
ACGTcount: A:0.21, C:0.22, G:0.34, T:0.22
Consensus pattern (26 bp):
CGGGGTTGGAGTATCCCCGATAATAA
Found at i:1284357 original size:51 final size:52
Alignment explanation
Indices: 1283992--1284375 Score: 223
Period size: 52 Copynumber: 7.3 Consensus size: 52
1283982 AAATAACAAG
* * * * * *
1283992 GTTGGAGTATCCTCGACTGT-GAAAAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATAGAAAAATTAGT-GTTTTGAAAATAAAATCGGA
* * * * * *
1284044 GTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTCGAAAATAAAACCGGG
1 GTTGGAGTATCCCCGATTATAGAAAAATTAGTGTTTTGAAAATAAAATCGGA
* * * *
1284096 GTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTT-AGCAATAAAACCGG-
1 GTTGGAGTATCCCCGATTATAGAAAAATTAGTGTTTTGA-AAATAAAATCGGA
* * * * *
1284147 GTTGGAATATCCCCGATTAT-GAAAAATTAATATTTT-AGAAATAAAGTCGGG
1 GTTGGAGTATCCCCGATTATAGAAAAATTAGTGTTTTGA-AAATAAAATCGGA
* **** * *** ** * *
1284198 GTTGGAGTATCCCCTCGGA-AATA-ACGGGGTTGGAGTATCCCCGATGAT-CAA-CGGG
1 GTTGGAGTAT-CCC-C-GATTATAGA-AAAATT--AGTGT-TTTGAAAATAAAATCGGA
* * *
1284253 GTTGGAGTATCCCCGATTGT-GAAGAAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATAGAA-AAATTAGTG--TTTTGAAAATAAAATCGGA
1284307 GTTGGAGTATCCCCGATTATAG-AAAATTAGTGTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATAGAAAAATTAGTGTTTTGAAAATAAAATCGGA
* *
1284358 GTTGGAATATCCTCGATT
1 GTTGGAGTATCCCCGATT
1284376 GTGGAGAATT
Statistics
Matches: 253, Mismatches: 59, Indels: 41
0.72 0.17 0.12
Matches are distributed among these distances:
50 25 0.10
51 64 0.25
52 81 0.32
53 30 0.12
54 30 0.12
55 15 0.06
56 5 0.02
57 2 0.01
58 1 0.00
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.30
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTATAGAAAAATTAGTGTTTTGAAAATAAAATCGGA
Found at i:1286757 original size:13 final size:13
Alignment explanation
Indices: 1286739--1286764 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1286729 ACAAAGATCC
1286739 ATGTATCGATACA
1 ATGTATCGATACA
1286752 ATGTATCGATACA
1 ATGTATCGATACA
1286765 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1286760 original size:33 final size:33
Alignment explanation
Indices: 1286718--1286784 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1286708 AAAATTTCCA
***
1286718 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
1286751 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
1286784 A
1 A
1286785 TTCCTTGGCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:1286827 original size:19 final size:18
Alignment explanation
Indices: 1286803--1286870 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
1286793 CAGTAGCTAA
1286803 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
1286822 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
1286837 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
1286854 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
1286871 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:1286843 original size:13 final size:13
Alignment explanation
Indices: 1286825--1286849 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1286815 ACAATACTTA
1286825 TGTATCGATACAT
1 TGTATCGATACAT
1286838 TGTATCGATACA
1 TGTATCGATACA
1286850 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1286847 original size:32 final size:32
Alignment explanation
Indices: 1286806--1286868 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1286796 TAGCTAATTA
*
1286806 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
1286838 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
1286869 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:1287103 original size:13 final size:13
Alignment explanation
Indices: 1287085--1287110 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1287075 ACAAAGATCC
1287085 ATGTATCGATACA
1 ATGTATCGATACA
1287098 ATGTATCGATACA
1 ATGTATCGATACA
1287111 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1287106 original size:33 final size:33
Alignment explanation
Indices: 1287064--1287130 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1287054 AAAATTTCCA
***
1287064 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
1287097 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
1287130 A
1 A
1287131 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:1287174 original size:19 final size:18
Alignment explanation
Indices: 1287150--1287217 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
1287140 CAGTAGCTAA
1287150 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
1287169 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
1287184 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
1287201 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
1287218 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:1287190 original size:13 final size:13
Alignment explanation
Indices: 1287172--1287196 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1287162 ACAATACTTA
1287172 TGTATCGATACAT
1 TGTATCGATACAT
1287185 TGTATCGATACA
1 TGTATCGATACA
1287197 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1287194 original size:32 final size:32
Alignment explanation
Indices: 1287153--1287215 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1287143 TAGCTAATTA
*
1287153 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
1287185 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
1287216 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:1287341 original size:347 final size:346
Alignment explanation
Indices: 1286707--1287366 Score: 1302
Period size: 347 Copynumber: 1.9 Consensus size: 346
1286697 TACATCTGGG
1286707 TAAAATTTCCAAATGTATCGATACAAAGATCCATGTATCGATACAATGTATCGATACACAGAAAA
1 TAAAATTTCCAAATGTATCGATACAAAGATCCATGTATCGATACAATGTATCGATACACAGAAAA
1286772 ATGTATCGATACATTCCTTGGCAGTAGCTAATTATGTATCGATACAATACTTATGTATCGATACA
66 ATGTATCGATACATTCCTTGGCAGTAGCTAATTATGTATCGATACAATACTTATGTATCGATACA
1286837 TTGTATCGATACAAAACTTATGTATCGATACAAATTGTTGAATTTCAAAATTTTTGACCGTTGGG
131 TTGTATCGATACAAAACTTATGTATCGATACAAATTGTTGAATTTCAAAATTTTTGACCGTTGGG
1286902 ACCTTGTATCGATACATTCAAACAATGTATCGATACATTTGGACAAAAATGTGATTTTTTCATCC
196 ACCTTGTATCGATACATTCAAACAATGTATCGATACATTTGGACAAAAATGTGATTTTTTCATCC
*
1286967 TTTTTGCCTTGTGAACACCCTGTCTCGACTAGGAACGATGGGAAATGGATTCGGGCTTAACAAAA
261 TTTTTGCCTTGTGAACACCCTGTCTCGACTAGGAACGATGGGAAATGAATTCGGGCTTAACAAAA
1287032 AGTTAAAAAAATCTAAAAATC
326 AGTTAAAAAAATCTAAAAATC
1287053 TAAAATTTCCAAATGTATCGATACAAAGATCCATGTATCGATACAATGTATCGATACACAGAAAA
1 TAAAATTTCCAAATGTATCGATACAAAGATCCATGTATCGATACAATGTATCGATACACAGAAAA
1287118 ATGTATCGATACATTTCCTTGGCAGTAGCTAATTATGTATCGATACAATACTTATGTATCGATAC
66 ATGTATCGATACA-TTCCTTGGCAGTAGCTAATTATGTATCGATACAATACTTATGTATCGATAC
1287183 ATTGTATCGATACAAAACTTATGTATCGATACAAATTGTTGAATTTCAAAATTTTTGACCGTTGG
130 ATTGTATCGATACAAAACTTATGTATCGATACAAATTGTTGAATTTCAAAATTTTTGACCGTTGG
1287248 GACCTTGTATCGATACATTCAAACAATGTATCGATACATTTGGACAAAAATGTGATTTTTTCATC
195 GACCTTGTATCGATACATTCAAACAATGTATCGATACATTTGGACAAAAATGTGATTTTTTCATC
1287313 CTTTTTGCCTTGTGAACACCCTGTCTCGACTAGGAACGATGGGAAATGAATTCG
260 CTTTTTGCCTTGTGAACACCCTGTCTCGACTAGGAACGATGGGAAATGAATTCG
1287367 TCCCCACATA
Statistics
Matches: 312, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
346 78 0.25
347 234 0.75
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33
Consensus pattern (346 bp):
TAAAATTTCCAAATGTATCGATACAAAGATCCATGTATCGATACAATGTATCGATACACAGAAAA
ATGTATCGATACATTCCTTGGCAGTAGCTAATTATGTATCGATACAATACTTATGTATCGATACA
TTGTATCGATACAAAACTTATGTATCGATACAAATTGTTGAATTTCAAAATTTTTGACCGTTGGG
ACCTTGTATCGATACATTCAAACAATGTATCGATACATTTGGACAAAAATGTGATTTTTTCATCC
TTTTTGCCTTGTGAACACCCTGTCTCGACTAGGAACGATGGGAAATGAATTCGGGCTTAACAAAA
AGTTAAAAAAATCTAAAAATC
Found at i:1292066 original size:26 final size:25
Alignment explanation
Indices: 1292036--1292085 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 25
1292026 CTTTTCTATA
1292036 AAAAAAAACAACAACAACAAAAAAAGC
1 AAAAAAAA-AACAACAA-AAAAAAAGC
1292063 AAAAAAAAAACAACAAAAAAAAA
1 AAAAAAAAAACAACAAAAAAAAA
1292086 CGAACGAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 7 0.30
26 8 0.35
27 8 0.35
ACGTcount: A:0.84, C:0.14, G:0.02, T:0.00
Consensus pattern (25 bp):
AAAAAAAAAACAACAAAAAAAAAGC
Found at i:1292070 original size:11 final size:12
Alignment explanation
Indices: 1292048--1292111 Score: 60
Period size: 11 Copynumber: 5.2 Consensus size: 12
1292038 AAAAAACAAC
1292048 AACAACAAAAAA
1 AACAACAAAAAA
*
1292060 AGCAA-AAAAAA
1 AACAACAAAAAA
1292071 AACAACAAAAAAA
1 AACAAC-AAAAAA
*
1292084 AACGAACGAACAAA
1 AAC-AAC-AAAAAA
1292098 AA-AACAAAGAAA
1 AACAACAAA-AAA
1292110 AA
1 AA
1292112 AGAAGAATCT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
11 12 0.28
12 12 0.28
13 9 0.21
14 10 0.23
ACGTcount: A:0.80, C:0.14, G:0.06, T:0.00
Consensus pattern (12 bp):
AACAACAAAAAA
Found at i:1292074 original size:23 final size:25
Alignment explanation
Indices: 1292038--1292083 Score: 78
Period size: 23 Copynumber: 1.9 Consensus size: 25
1292028 TTTCTATAAA
1292038 AAAAAACAACAACAACAAAAAAAGC
1 AAAAAACAACAACAACAAAAAAAGC
1292063 AAAAAA-AA-AACAACAAAAAAA
1 AAAAAACAACAACAACAAAAAAA
1292084 AACGAACGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 13 0.62
24 2 0.10
25 6 0.29
ACGTcount: A:0.83, C:0.15, G:0.02, T:0.00
Consensus pattern (25 bp):
AAAAAACAACAACAACAAAAAAAGC
Found at i:1292098 original size:14 final size:13
Alignment explanation
Indices: 1292035--1292104 Score: 70
Period size: 15 Copynumber: 4.9 Consensus size: 13
1292025 TCTTTTCTAT
1292035 AAAAAAAAACAAC
1 AAAAAAAAACAAC
1292048 AACAACAAAAA-AAGC
1 AA-AA-AAAAACAA-C
1292063 AAAAAAAAAACAAC
1 -AAAAAAAAACAAC
1292077 AAAAAAAAACGAAC
1 AAAAAAAAAC-AAC
1292091 GAACAAAAAAACAA
1 -AA-AAAAAAACAA
1292105 AGAAAAAAGA
Statistics
Matches: 49, Mismatches: 0, Indels: 14
0.78 0.00 0.22
Matches are distributed among these distances:
13 12 0.24
14 13 0.27
15 14 0.29
16 10 0.20
ACGTcount: A:0.80, C:0.16, G:0.04, T:0.00
Consensus pattern (13 bp):
AAAAAAAAACAAC
Found at i:1293357 original size:55 final size:54
Alignment explanation
Indices: 1293070--1293895 Score: 825
Period size: 55 Copynumber: 14.4 Consensus size: 54
1293060 CTCCTTCCGC
*
1293070 TTTTTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 TTTTCAGTCCTCAAAGAGCAGGATGCC-TTT-C----AAAGCCCACACAAGTTGGTGGCA
** * * *
1293130 CCTTCAGTCATCAAAGAGCAGGATGTTTTTTCTTTTCAAAGCCCACATAAGTTGGTGGCA
1 TTTTCAGTCCTCAAAGAGCAGGATG------CCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
1293190 TTTTCTAGTCCTCTAAA-AGCAGGACGCCTTTTCTTTTAAAGCCCACACAATTTGGTGGCA
1 TTTTC-AGTCCTC-AAAGAGCAGGATGCC-TTTC----AAAGCCCACACAAGTTGGTGGCA
* * *
1293250 CTTTCAGTCCTCAAAGAGTAGGACGCCTTCTCCTTTCAAAGCCCACACAAGTTGGTGGCA
1 TTTTCAGTCCTCAAAGAGCAGGA-----T-GCCTTTCAAAGCCCACACAAGTTGGTGGCA
*
1293310 TTTTCCAATCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCA
1 TTTT-CAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
1293365 TTTTCCAGTCCTCAAAGAGTAGGATGCCTTTCAAAACCCACACAAGTTGGTGGCA
1 TTTT-CAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCA
1293420 TTTTCTAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
1 TTTTC-AGTCCTCAAAGAGCAGGATGC-----C-TTTCAAAGCCCACACAAGTTGGTGGCA
* * **
1293481 CCTTTCAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
1 -TTTTCAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCA
* **
1293536 TTTTCCAGTCCTTAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCA
1 TTTT-CAGTCCTCAAAGAGCAGGATGCCT-TTCAAAGCCCACACAAGTTGGTGGCA
*
1293591 CCTTTCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
1 -TTTTCAGTCCTCAAAGAGCAGGATGC-----C-TTTCAAAGCCCACACAAGTTGGTGGCA
* * * **
1293652 CCTTTCAGCCCCCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
1 -TTTTCAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCA
**
1293707 TTTTCTAGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTT-GTGGCA
1 TTTTC-AGTCCTCAAAGAGCAGGATGCCT-TTCAAAGCCCACACAAGTTGGTGGCA
* *
1293761 CCTTTT-AGTCCTCAAAGAGCAGGACGCATTTCAAAGCCCACACAAGTTGGTGGCA
1 --TTTTCAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCA
* * * * *
1293816 CCTTTCAGTCCTCAAAAAGTAGGATGCCTTTCAAAGCCCACACTAGTTTGTGGCA
1 -TTTTCAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCA
*
1293871 CTTTTTAGTCCTCAAAGAGCAGGAT
1 -TTTTCAGTCCTCAAAGAGCAGGAT
1293896 ACACTTTATT
Statistics
Matches: 662, Mismatches: 58, Indels: 97
0.81 0.07 0.12
Matches are distributed among these distances:
53 2 0.00
54 55 0.08
55 331 0.50
56 18 0.03
58 3 0.00
59 13 0.02
60 100 0.15
61 122 0.18
62 7 0.01
64 5 0.01
65 5 0.01
66 1 0.00
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (54 bp):
TTTTCAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCA
Found at i:1293476 original size:116 final size:111
Alignment explanation
Indices: 1293070--1293895 Score: 835
Period size: 116 Copynumber: 7.2 Consensus size: 111
1293060 CTCCTTCCGC
*
1293070 TTTT-TAGTCCTCAAAGAGCAGGATG-CCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCT
1 TTTTCTAGTCCTCAAAGAGCAGGATGCCCTTTT-C----AAAGCCCACACAAGTTGGTGGCACTT
* * *
1293133 TCAGTCATCAAAGAGCAGGATGTTTTTTCTTTTCAAAGCCCACATAAGTTGGTGGCA
61 TCAGTCCTCAAAGAGCAGGATG------CCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
1293190 TTTTCTAGTCCTCTAAA-AGCAGGACG-CCTTTTCTTTTAAAGCCCACACAATTTGGTGGCACTT
1 TTTTCTAGTCCTC-AAAGAGCAGGATGCCCTTTTC----AAAGCCCACACAAGTTGGTGGCACTT
* *
1293253 TCAGTCCTCAAAGAGTAGGACGCCTTCTCCTTTCAAAGCCCACACAAGTTGGTGGCA
61 TCAGTCCTCAAAGAGCAGGA-----T-GCCTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
1293310 TTTTCCAATCCTCAAAGAGCAGGATG-CC-TTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAG
1 TTTTCTAGTCCTCAAAGAGCAGGATGCCCTTTTCAAAGCCCACACAAGTTGGTGGCACTTT-CAG
* *
1293373 TCCTCAAAGAGTAGGATGCCTTTCAAAACCCACACAAGTTGGTGGCA
65 TCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCA
*
1293420 TTTTCTAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTT
1 TTTTCTAGTCCTCAAAGAGCAGGATGC----CCTTTTCAAAGCCCACACAAGTTGGTGGCA-CTT
* **
1293485 TCAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
61 TCAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
1293536 TTTTCCAGTCCTTAAAGAGCAGGA--CACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTCA
1 TTTTCTAGTCCTCAAAGAGCAGGATGC-CCTTTTCAAAGCCCACACAAGTTGGTGGCA-CTTTCA
1293598 GTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
64 GTCCTCAAAGAGCAGGATGC-----C-TTTCAAAGCCCACACAAGTTGGTGGCA
* * * *
1293652 CCTTTC-AGCCCCCAAAGAGCAGGA--CACC-TTTCAAAGCCCACACAAGTTGGTGGCATTTTCT
1 -TTTTCTAGTCCTCAAAGAGCAGGATGC-CCTTTTCAAAGCCCACACAAGTTGGTGGCACTTTC-
**
1293713 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTT-GTGGCA
63 AGTCCTCAAAGAGCAGGATGCCT-TTCAAAGCCCACACAAGTTGGTGGCA
* * *
1293761 CCTTT-TAGTCCTCAAAGAGCAGGA--CGCATTTCAAAGCCCACACAAGTTGGTGGCACCTTTCA
1 -TTTTCTAGTCCTCAAAGAGCAGGATGCCCTTTTCAAAGCCCACACAAGTTGGTGGCA-CTTTCA
* * * *
1293823 GTCCTCAAAAAGTAGGATGCCTTTCAAAGCCCACACTAGTTTGTGGCA
64 GTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCA
1293871 CTTTT-TAGTCCTCAAAGAGCAGGAT
1 -TTTTCTAGTCCTCAAAGAGCAGGAT
1293896 ACACTTTATT
Statistics
Matches: 623, Mismatches: 50, Indels: 75
0.83 0.07 0.10
Matches are distributed among these distances:
108 3 0.00
109 89 0.14
110 149 0.24
111 8 0.01
114 1 0.00
115 33 0.05
116 201 0.32
117 7 0.01
119 7 0.01
120 99 0.16
121 22 0.04
122 3 0.00
125 1 0.00
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (111 bp):
TTTTCTAGTCCTCAAAGAGCAGGATGCCCTTTTCAAAGCCCACACAAGTTGGTGGCACTTTCAGT
CCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCA
Found at i:1293478 original size:171 final size:172
Alignment explanation
Indices: 1293069--1293894 Score: 1067
Period size: 171 Copynumber: 4.8 Consensus size: 172
1293059 TCTCCTTCCG
* *
1293069 CTTTTTAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTT-AAAGCCCACACAAGTTGGTGGCACC-
1 CTTTCTAGTCCTCAAAGAGCAGGATG-CTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCT
* * *
1293132 TTCAGTCATCAAAGAGCAGGATGTTTTTTCTTTTCAAAGCCCACATAAGTTGGTGGCATTTTCTA
65 TTCAGTCCTCAAAGAGCAGGATG------CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCTA
* *
1293197 GTCCTCTAAA-AGCAGGACGCCTTTTCTTTTAAAGCCCACACAATTTGGTGGCA-
124 GTCCTC-AAAGAGCAGGACACC---TC--TTAAAGCCCACACAAGTTGGTGGCAC
* * * * * *
1293250 CTTTC-AGTCCTCAAAGAGTAGGACGCCTTCTCCTTTCAAAGCCCACACAAGTTGGTGGCA-TTT
1 CTTTCTAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTT
* *
1293313 TCCAATCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTC
66 T-CAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTC
* ** *
1293378 AAAGAGTAGGATGCCT-TTCAAAACCCACACAAGTTGGTGGCA-
130 AAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCAC
*
1293420 TTTTCTAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTT
1 CTTTCTAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTT
* ** * *
1293485 TCAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTTA
66 TCAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCA
1293550 AAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCAC
131 AAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCAC
1293592 CTTTC-AGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTT
1 CTTTCTAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTT
* * **
1293656 TCAGCCCCCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCA
66 TCAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCA
1293721 AAGAGCAGGACACCTCTTAAAGCCCACACAAGTT-GTGGCAC
131 AAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCAC
* *
1293762 CTTT-TAGTCCTCAAAGAGCAGGA--C----GCATTTCAAAGCCCACACAAGTTGGTGGCACCTT
1 CTTTCTAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTT
* * * *
1293820 TCAGTCCTCAAAAAGTAGGATGCCTTTCAAAGCCCACACTAGTTTGTGGCACTTTT-TAGTCCTC
66 TCAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCTAGTCCTC
1293884 AAAGAGCAGGA
130 AAAGAGCAGGA
1293895 TACACTTTAT
Statistics
Matches: 587, Mismatches: 47, Indels: 39
0.87 0.07 0.06
Matches are distributed among these distances:
164 94 0.16
165 4 0.01
168 1 0.00
169 2 0.00
170 54 0.09
171 298 0.51
172 10 0.02
174 3 0.01
175 48 0.08
179 7 0.01
180 43 0.07
181 23 0.04
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (172 bp):
CTTTCTAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTT
TCAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCA
AAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCAC
Found at i:1293711 original size:28 final size:29
Alignment explanation
Indices: 1293625--1293822 Score: 93
Period size: 28 Copynumber: 7.2 Consensus size: 29
1293615 TGCTTTTTCT
1293625 TTTCAAAGCCCACACAAGTTGGTGGCACC
1 TTTCAAAGCCCACACAAGTTGGTGGCACC
* * **
1293654 TTTC--AGCCCCCA-AAG-AGCAGGACACC
1 TTTCAAAGCCCACACAAGTTGGTGG-CACC
*
1293680 TTTCAAAGCCCACACAAGTTGGTGGCA-T
1 TTTCAAAGCCCACACAAGTTGGTGGCACC
* * * * **
1293708 TTTC-TAGTCCTCA-AAG-AGCAGGACACC
1 TTTCAAAGCCCACACAAGTTGGTGG-CACC
1293735 TCTT-AAAGCCCACACAAGTT-GTGGCACC
1 T-TTCAAAGCCCACACAAGTTGGTGGCACC
* * * * **
1293763 TTT--TAGTCCTCA-AAG-AGCAGG-ACGC
1 TTTCAAAGCCCACACAAGTTGGTGGCAC-C
1293788 ATTTCAAAGCCCACACAAGTTGGTGGCACC
1 -TTTCAAAGCCCACACAAGTTGGTGGCACC
1293818 TTTCA
1 TTTCA
1293823 GTCCTCAAAA
Statistics
Matches: 116, Mismatches: 34, Indels: 38
0.62 0.18 0.20
Matches are distributed among these distances:
24 2 0.02
25 12 0.10
26 25 0.22
27 16 0.14
28 30 0.26
29 22 0.19
30 7 0.06
31 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.22
Consensus pattern (29 bp):
TTTCAAAGCCCACACAAGTTGGTGGCACC
Found at i:1294083 original size:40 final size:42
Alignment explanation
Indices: 1293987--1294083 Score: 101
Period size: 42 Copynumber: 2.3 Consensus size: 42
1293977 GACGTACTCT
* *
1293987 TTTTCACTTTGTCCTCAAGAAGCAGGACACTTTCCTTTTCTTC
1 TTTTC-CTTTGTCCTCAAGAAGCAAGACACTTTCCTATTCTTC
* * * *
1294030 TCTTCCTTGGTCCTCAAGGAGCAAGAC-CTATTTC-ATTC-TC
1 TTTTCCTTTGTCCTCAAGAAGCAAGACACT-TTCCTATTCTTC
1294070 TTTTCCTTTGTCCT
1 TTTTCCTTTGTCCT
1294084 TGAAAAGTGG
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
40 14 0.31
41 5 0.11
42 22 0.49
43 4 0.09
ACGTcount: A:0.16, C:0.29, G:0.12, T:0.42
Consensus pattern (42 bp):
TTTTCCTTTGTCCTCAAGAAGCAAGACACTTTCCTATTCTTC
Found at i:1294703 original size:21 final size:21
Alignment explanation
Indices: 1294656--1294713 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
1294646 CATTTTTATC
*
1294656 CAAATGTATCGATACATTTGT
1 CAAATGTATCGATACATTTGA
**
1294677 GGAATGTATCGATACATTCT-A
1 CAAATGTATCGATACATT-TGA
1294698 CAAATGTATCGATACA
1 CAAATGTATCGATACA
1294714 AGGTCCCAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 30 0.97
22 1 0.03
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.33
Consensus pattern (21 bp):
CAAATGTATCGATACATTTGA
Found at i:1294796 original size:19 final size:18
Alignment explanation
Indices: 1294745--1294834 Score: 75
Period size: 19 Copynumber: 5.1 Consensus size: 18
1294735 TTGAATTCCA
1294745 ATAA-TTTGTATCGATAC
1 ATAAGTTTGTATCGATAC
* *
1294762 ATTCAGTAAATGTATCGATAC
1 A-TAAGT--TTGTATCGATAC
1294783 ATAAGTGTTGTATCGATAC
1 ATAAGT-TTGTATCGATAC
1294802 --AA---TGTATCGATAC
1 ATAAGTTTGTATCGATAC
1294815 ATAAGTTTTGTATCGATAC
1 ATAAG-TTTGTATCGATAC
1294834 A
1 A
1294835 ATGTATCGCT
Statistics
Matches: 58, Mismatches: 5, Indels: 18
0.72 0.06 0.22
Matches are distributed among these distances:
13 11 0.19
15 2 0.03
17 3 0.05
18 2 0.03
19 24 0.41
20 4 0.07
21 12 0.21
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.37
Consensus pattern (18 bp):
ATAAGTTTGTATCGATAC
Found at i:1294809 original size:13 final size:13
Alignment explanation
Indices: 1294791--1294815 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1294781 ACATAAGTGT
1294791 TGTATCGATACAA
1 TGTATCGATACAA
1294804 TGTATCGATACA
1 TGTATCGATACA
1294816 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1294811 original size:32 final size:32
Alignment explanation
Indices: 1294770--1294842 Score: 137
Period size: 32 Copynumber: 2.3 Consensus size: 32
1294760 ACATTCAGTA
1294770 AATGTATCGATACATAAGTGTTGTATCGATAC
1 AATGTATCGATACATAAGTGTTGTATCGATAC
*
1294802 AATGTATCGATACATAAGTTTTGTATCGATAC
1 AATGTATCGATACATAAGTGTTGTATCGATAC
1294834 AATGTATCG
1 AATGTATCG
1294843 CTAGGAAGCT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (32 bp):
AATGTATCGATACATAAGTGTTGTATCGATAC
Found at i:1294930 original size:34 final size:33
Alignment explanation
Indices: 1294866--1294932 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 33
1294856 GCCAAGGAAA
* *
1294866 TGTATCAATACATTTTTCTGTGTATTGATACAT
1 TGTATCAATACATTATTCTGTGTATCGATACAT
* *
1294899 TGTATCGATACATCTATTCTTTGTATCGATACAT
1 TGTATCAATACAT-TATTCTGTGTATCGATACAT
1294933 CTAGGAAGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 12 0.41
34 17 0.59
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.46
Consensus pattern (33 bp):
TGTATCAATACATTATTCTGTGTATCGATACAT
Found at i:1297344 original size:52 final size:51
Alignment explanation
Indices: 1297278--1297577 Score: 207
Period size: 52 Copynumber: 5.7 Consensus size: 51
1297268 CAATTGTTCA
* *
1297278 TAATCAGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTT
1 TAATCGGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTTCC-T
* * * * *
1297330 TAATCGGGGGTACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCA
1 TAATCGGGGATACTCCAACCCCGGTTTTATTTCC-AAAACACCAATTTTCCT
* * * * * **
1297382 CAATCGAGGATACTCCAACCTC-G--TTATTTCATCAGGGATACTCCAA--CCCCGT
1 TAATCGGGGATACTCCAACCCCGGTTTTATTTC--CA---AAACACCAATTTTCC-T
* * * * *** *
1297434 TACCTCCGAGGGGATACTCCAACCCCAGCTTTATTTCCAAAATATTGA-TTTCCA
1 TA-AT-C--GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTTCCT
* * *
1297488 CAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACTAATTTTCCTT
1 TAATCGGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTTCC-T
*
1297540 TAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAA
1 TAATCGGGGATACTCCAACCCCGGTTTTATTTCCAAAA
1297578 AACATCAATT
Statistics
Matches: 187, Mismatches: 44, Indels: 34
0.71 0.17 0.13
Matches are distributed among these distances:
49 7 0.04
50 34 0.18
51 7 0.04
52 83 0.44
53 24 0.13
54 5 0.03
55 2 0.01
56 15 0.08
57 3 0.02
59 7 0.04
ACGTcount: A:0.29, C:0.28, G:0.12, T:0.31
Consensus pattern (51 bp):
TAATCGGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTTCCT
Found at i:1297502 original size:50 final size:51
Alignment explanation
Indices: 1297443--1297617 Score: 176
Period size: 52 Copynumber: 3.4 Consensus size: 51
1297433 TTACCTCCGA
* * * *
1297443 GGGGATACTCCAACCCCAGCTTTATTTCCAAAATATTGA-TTTCC-ACAATC
1 GGGGATACTCCAACCCC-GTTTTATTTCCAAAACACTAATTTTCCTACAATC
* **
1297493 GGGGATACTCCAACCCCGGTTTTATTTTCAAAACACTAATTTTCCTTTAATC
1 GGGGATACTCCAACCCC-GTTTTATTTCCAAAACACTAATTTTCCTACAATC
* * *
1297545 GGGGATACTCCAACCCCGATTTTATTTCCAAAAAACATCAATTTTTC-ACAACC
1 GGGGATACTCCAACCCCG-TTTTATTTCCAAAACAC-T-AATTTTCCTACAATC
* *
1297598 GAGGATACTCCAACCTCGTT
1 GGGGATACTCCAACCCCGTT
1297618 ATTTCATCGG
Statistics
Matches: 104, Mismatches: 16, Indels: 8
0.81 0.12 0.06
Matches are distributed among these distances:
50 33 0.32
51 6 0.06
52 38 0.37
53 20 0.19
54 7 0.07
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.31
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGTTTTATTTCCAAAACACTAATTTTCCTACAATC
Found at i:1297662 original size:211 final size:211
Alignment explanation
Indices: 1297279--1297722 Score: 766
Period size: 211 Copynumber: 2.1 Consensus size: 211
1297269 AATTGTTCAT
* *
1297279 AATCAGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGGTACT
1 AATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGATACT
* *
1297344 CCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGGATACTCCAACCTCGTTAT
66 CCAACCCCGATTTTATTTCCAAAAACACCAATTTTTCACAACCGAGGATACTCCAACCTCGTTAT
1297409 TTCATCAGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCAGCTTTATTTCCAA
131 TTCATCAGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCAGCTTTATTTCCAA
1297474 AATATTGATTTC-CAC
196 AATATTGATTTCTCAC
*
1297489 AATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACTAATTTTCCTTTAATCGGGGATACT
1 AATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGATACT
*
1297554 CCAACCCCGATTTTATTTCCAAAAAACATCAATTTTTCACAACCGAGGATACTCCAACCTCGTTA
66 CCAACCCCGATTTTATTTCC-AAAAACACCAATTTTTCACAACCGAGGATACTCCAACCTCGTTA
* *
1297619 TTTCATC-GGGAATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGTTTTATTTCC
130 TTTCATCAGGG-ATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCAGCTTTATTTCC
*
1297683 AAAATATTGATTTCTCAT
194 AAAATATTGATTTCTCAC
*
1297701 AATTGGGGATACTCCAACCCCG
1 AATCGGGGATACTCCAACCCCG
1297723 TTATTTCCGA
Statistics
Matches: 221, Mismatches: 10, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
210 84 0.38
211 114 0.52
212 23 0.10
ACGTcount: A:0.28, C:0.29, G:0.13, T:0.30
Consensus pattern (211 bp):
AATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGATACT
CCAACCCCGATTTTATTTCCAAAAACACCAATTTTTCACAACCGAGGATACTCCAACCTCGTTAT
TTCATCAGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCAGCTTTATTTCCAA
AATATTGATTTCTCAC
Found at i:1297722 original size:79 final size:79
Alignment explanation
Indices: 1297630--1297859 Score: 248
Period size: 79 Copynumber: 2.9 Consensus size: 79
1297620 TTCATCGGGA
**
1297630 ATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGTTTTATTTCCAAAATATTGATT
1 ATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATTTCCAAAATATTGATT
** *
1297695 TCTCATAATTGGGG
66 TCTCATAACCGAGG
* * * ** *
1297709 ATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAATCCCGATTTGA-TTCCCTAATCATCGAT
1 ATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATTTCCAAAAT-ATTGAT
* *
1297773 TTTTCACAACCGAGG
65 TTCTCATAACCGAGG
* * * * * *
1297788 ATACTCCAACCCCGTTATTTTCAAGGGGACACTCCAACCCC-GTTACTATCTCCAAAATATTAAA
1 ATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTT-TTATTTCCAAAATATT-GA
1297852 TTTCTCAT
64 TTTCTCAT
1297860 CGAGACACAT
Statistics
Matches: 120, Mismatches: 27, Indels: 7
0.78 0.18 0.05
Matches are distributed among these distances:
78 9 0.08
79 98 0.82
80 13 0.11
ACGTcount: A:0.27, C:0.30, G:0.13, T:0.30
Consensus pattern (79 bp):
ATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATTTCCAAAATATTGATT
TCTCATAACCGAGG
Found at i:1299862 original size:13 final size:13
Alignment explanation
Indices: 1299806--1299867 Score: 52
Period size: 13 Copynumber: 4.4 Consensus size: 13
1299796 GAATTTAATT
1299806 TTATAATTAATTTA
1 TTATAA-TAATTTA
* *
1299820 TTATCATATTTTA
1 TTATAATAATTTA
1299833 TTATAGATAAGCATTTA
1 TTATA-AT-A--ATTTA
*
1299850 TTATAATATTTTA
1 TTATAATAATTTA
1299863 TTATA
1 TTATA
1299868 CTTGATAATT
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
13 19 0.49
14 7 0.18
15 2 0.05
16 2 0.05
17 9 0.23
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (13 bp):
TTATAATAATTTA
Found at i:1303565 original size:40 final size:40
Alignment explanation
Indices: 1303445--1303553 Score: 166
Period size: 42 Copynumber: 2.7 Consensus size: 40
1303435 ATTTTATATG
*
1303445 TAACCAAAAGAACTTGTTA-ATAGTTACCATTGTAATAATC
1 TAACCAAAATAACTTGTTAGA-AGTTACCATTGTAATAATC
*
1303485 TAACCAAAATAACTTTTGCTAGAAGTTACCATTGTAATAATC
1 TAACCAAAATAAC--TTGTTAGAAGTTACCATTGTAATAATC
1303527 TAACCAAAATAACTTGTTAGAAGTTAC
1 TAACCAAAATAACTTGTTAGAAGTTAC
1303554 ACTCATAATA
Statistics
Matches: 63, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
40 25 0.40
42 37 0.59
43 1 0.02
ACGTcount: A:0.42, C:0.16, G:0.10, T:0.32
Consensus pattern (40 bp):
TAACCAAAATAACTTGTTAGAAGTTACCATTGTAATAATC
Found at i:1313540 original size:3 final size:3
Alignment explanation
Indices: 1313532--1313566 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
1313522 TTTTCAATGT
* *
1313532 TTA TTA TTA TTA TTG TTA TTA TTA TTG TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1313567 TTTGTATTGG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1313552 original size:12 final size:12
Alignment explanation
Indices: 1313535--1313571 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
1313525 TCAATGTTTA
1313535 TTATTATTATTG
1 TTATTATTATTG
1313547 TTATTATTATTG
1 TTATTATTATTG
*
1313559 TTATTATTTTTG
1 TTATTATTATTG
1313571 T
1 T
1313572 ATTGGATGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.22, C:0.00, G:0.08, T:0.70
Consensus pattern (12 bp):
TTATTATTATTG
Found at i:1313952 original size:134 final size:135
Alignment explanation
Indices: 1313594--1314006 Score: 632
Period size: 143 Copynumber: 3.0 Consensus size: 135
1313584 AAACAACTGC
1313594 TTTGGATGTAACAGAGGAAAGTCTTAAGGTATGGGGGAGTCCTTGTGCAGTAGTAATTGTTAGAC
1 TTTGGATGTAACAGAGGAAAGTC-TAAGGTATGGGGGAGTCCTTGTGCAGTAGTAATTGTTAGAC
* *
1313659 CCAGTTGTTATATTTGAAACTCCTTCTGCTGCTACAAAAATTCAAAAATTCAAATAGTCATACAT
65 CTAGTTGTTATATTTGAAACTCCATCTGCTGCTAC----A---AAAAATTCAAATAGTCATACAT
* *
1313724 CTGCAGGGAAAAT
123 TTGCTGGGAAAAT
* *
1313737 TTTGGATGTAACAAAGGAAAGTCTTAAGTTATGGGGGAGTCCTTGTGCAGTAGTAATTGTTAGAC
1 TTTGGATGTAACAGAGGAAAGTC-TAAGGTATGGGGGAGTCCTTGTGCAGTAGTAATTGTTAGAC
*
1313802 CTAGTTGTTATATTTGAAACTCCATCTGCTGCTACAAAAAATTCAAATAGTTATACATTTGCTGG
65 CTAGTTGTTATATTTGAAACTCCATCTGCTGCTACAAAAAATTCAAATAGTCATACATTTGCTGG
1313867 GAAAAT
130 GAAAAT
* *
1313873 TTTGGATGTAACAGAGGAAAGTC-AAGGAATGGGGGAGTCGTTGTGCAGTAGTAATTGTTAGACC
1 TTTGGATGTAACAGAGGAAAGTCTAAGGTATGGGGGAGTCCTTGTGCAGTAGTAATTGTTAGACC
* *
1313937 TAGTTGTTATATTTGAAACTCCATCTGCTGCTAC-AAAAATTCAAATGGTCATACGTTTGCTGGG
66 TAGTTGTTATATTTGAAACTCCATCTGCTGCTACAAAAAATTCAAATAGTCATACATTTGCTGGG
1314001 AAAAT
131 AAAAT
1314006 T
1 T
1314007 CCCATTTTAG
Statistics
Matches: 256, Mismatches: 14, Indels: 10
0.91 0.05 0.04
Matches are distributed among these distances:
133 33 0.13
134 72 0.28
136 54 0.21
139 1 0.00
143 96 0.38
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.32
Consensus pattern (135 bp):
TTTGGATGTAACAGAGGAAAGTCTAAGGTATGGGGGAGTCCTTGTGCAGTAGTAATTGTTAGACC
TAGTTGTTATATTTGAAACTCCATCTGCTGCTACAAAAAATTCAAATAGTCATACATTTGCTGGG
AAAAT
Found at i:1317034 original size:3 final size:3
Alignment explanation
Indices: 1317026--1317051 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1317016 TTATAATTGA
1317026 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
1317052 CTACTACTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1321554 original size:21 final size:21
Alignment explanation
Indices: 1321530--1321581 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
1321520 GTTACATTTT
*
1321530 TTTCATTCAATTATTGCATTA
1 TTTCATCCAATTATTGCATTA
1321551 TTTCATCCAATTATTGCATTA
1 TTTCATCCAATTATTGCATTA
1321572 TTTCATCCAA
1 TTTCATCCAA
1321582 ATACACCTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.29, C:0.19, G:0.04, T:0.48
Consensus pattern (21 bp):
TTTCATCCAATTATTGCATTA
Found at i:1321926 original size:13 final size:13
Alignment explanation
Indices: 1321908--1321934 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1321898 ACATTATGCT
1321908 TTGTATCGATACA
1 TTGTATCGATACA
1321921 TTGTATCGATACA
1 TTGTATCGATACA
1321934 T
1 T
1321935 GAACAATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1321945 original size:20 final size:20
Alignment explanation
Indices: 1321920--1321957 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1321910 GTATCGATAC
1321920 ATTGTATCGATACATGAACA
1 ATTGTATCGATACATGAACA
1321940 ATTGTATCGATACATGAA
1 ATTGTATCGATACATGAA
1321958 ACTGGCAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (20 bp):
ATTGTATCGATACATGAACA
Found at i:1322022 original size:33 final size:32
Alignment explanation
Indices: 1321985--1322049 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 32
1321975 TACCACTGTT
1321985 TGTATCGATACATG-GCACATTGTATCGATACAA
1 TGTATCGATACATGAG-A-ATTGTATCGATACAA
1322018 TGTATCGATACATGATGAATTGTATCGATACA
1 TGTATCGATACATGA-GAATTGTATCGATACA
1322050 TTGCTTCAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 28 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.32
Consensus pattern (32 bp):
TGTATCGATACATGAGAATTGTATCGATACAA
Found at i:1322023 original size:13 final size:13
Alignment explanation
Indices: 1322005--1322029 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1321995 CATGGCACAT
1322005 TGTATCGATACAA
1 TGTATCGATACAA
1322018 TGTATCGATACA
1 TGTATCGATACA
1322030 TGATGAATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1328357 original size:21 final size:22
Alignment explanation
Indices: 1328333--1328382 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
1328323 ATCAAATCTT
* *
1328333 CTTCAAATTTCTT-ATTTTTCA
1 CTTCAAAATACTTCATTTTTCA
1328354 CTTCAAAATACTTCATTTTTCA
1 CTTCAAAATACTTCATTTTTCA
1328376 --TCAAAAT
1 CTTCAAAAT
1328383 CATCAACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 7 0.27
21 11 0.42
22 8 0.31
ACGTcount: A:0.32, C:0.20, G:0.00, T:0.48
Consensus pattern (22 bp):
CTTCAAAATACTTCATTTTTCA
Found at i:1330763 original size:13 final size:13
Alignment explanation
Indices: 1330745--1330770 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1330735 CATTATGCTC
1330745 TGTATCGATACAT
1 TGTATCGATACAT
1330758 TGTATCGATACAT
1 TGTATCGATACAT
1330771 GGACAATTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1332365 original size:20 final size:20
Alignment explanation
Indices: 1332276--1332366 Score: 64
Period size: 20 Copynumber: 4.6 Consensus size: 20
1332266 ACCCTAGAAA
1332276 GTATCGATACATATCCAGA-T
1 GTATCGATACATATCCA-ATT
* *
1332296 GTATCGATACATTATGC-TTT
1 GTATCGATACA-TATCCAATT
* **
1332316 GTATCGATACAT-GCTTATT
1 GTATCGATACATATCCAATT
* *
1332335 ATATTGATACATA-CTCAATT
1 GTATCGATACATATC-CAATT
1332355 GTATCGATACAT
1 GTATCGATACAT
1332367 GAAACTGACA
Statistics
Matches: 54, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
19 14 0.26
20 36 0.67
21 4 0.07
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.38
Consensus pattern (20 bp):
GTATCGATACATATCCAATT
Found at i:1332437 original size:20 final size:20
Alignment explanation
Indices: 1332396--1332441 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
1332386 CTAAGTGAAA
* *
1332396 TGTATTAATACATGGGACAT
1 TGTATCAATACATGAGACAT
1332416 TGTATCAATACATGAAGA-AT
1 TGTATCAATACATG-AGACAT
1332436 TGTATC
1 TGTATC
1332442 GATATATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 21 0.91
21 2 0.09
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.35
Consensus pattern (20 bp):
TGTATCAATACATGAGACAT
Found at i:1336111 original size:19 final size:17
Alignment explanation
Indices: 1336086--1336215 Score: 86
Period size: 19 Copynumber: 7.9 Consensus size: 17
1336076 ATTTCAACGA
1336086 TTTGTATCGATACAGAAG
1 TTTGTATCGATACA-AAG
1336104 TGTTGTATCGATAC-AA-
1 T-TTGTATCGATACAAAG
1336120 --TGTATCGATACATAAG
1 TTTGTATCGATACA-AAG
*
1336136 TGTTGTATCGGTAC-AA-
1 T-TTGTATCGATACAAAG
1336152 --TGTATCGATACATAAG
1 TTTGTATCGATACA-AAG
*
1336168 TGTTGTATCGGTAC-AA-
1 T-TTGTATCGATACAAAG
1336184 --TGTATCGATACATAAG
1 TTTGTATCGATACA-AAG
1336200 TTTTGTATCGATACAA
1 -TTTGTATCGATACAA
1336216 TGTATCGCTA
Statistics
Matches: 89, Mismatches: 4, Indels: 38
0.68 0.03 0.29
Matches are distributed among these distances:
13 31 0.35
15 6 0.07
17 6 0.07
18 2 0.02
19 44 0.49
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.35
Consensus pattern (17 bp):
TTTGTATCGATACAAAG
Found at i:1336124 original size:32 final size:32
Alignment explanation
Indices: 1336088--1336222 Score: 234
Period size: 32 Copynumber: 4.2 Consensus size: 32
1336078 TTCAACGATT
*
1336088 TGTATCGATACAGAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
1336120 TGTATCGATACATAAGTGTTGTATCGGTACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
1336152 TGTATCGATACATAAGTGTTGTATCGGTACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
1336184 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
1336216 TGTATCG
1 TGTATCG
1336223 CTATGAAGCT
Statistics
Matches: 99, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 99 1.00
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:1336125 original size:13 final size:13
Alignment explanation
Indices: 1336107--1336195 Score: 52
Period size: 13 Copynumber: 5.9 Consensus size: 13
1336097 ACAGAAGTGT
1336107 TGTATCGATACAA
1 TGTATCGATACAA
1336120 TGTATCGATACATAA
1 TGTATCGATAC--AA
*
1336135 GTGTTGTATCGGTACAA
1 ----TGTATCGATACAA
1336152 TGTATCGATACATAA
1 TGTATCGATAC--AA
*
1336167 GTGTTGTATCGGTACAA
1 ----TGTATCGATACAA
1336184 TGTATCGATACA
1 TGTATCGATACA
1336196 TAAGTTTTGT
Statistics
Matches: 60, Mismatches: 4, Indels: 24
0.68 0.05 0.27
Matches are distributed among these distances:
13 32 0.53
15 4 0.07
17 4 0.07
19 20 0.33
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1336344 original size:52 final size:52
Alignment explanation
Indices: 1336300--1336428 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
1336290 CACTGATCTT
*
1336300 TGTATCGATACATGTAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
* * *
1336352 TGTATCGATACATACAGGCATATTTGCCTAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1336404 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
1336429 TCATATTTCG
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
Found at i:1346898 original size:61 final size:60
Alignment explanation
Indices: 1346746--1347243 Score: 295
Period size: 61 Copynumber: 8.5 Consensus size: 60
1346736 TTAATGATAA
* * * **
1346746 AAAGAGTGCCAATGTGATGATTCAAGGCGAGCGACATTGGACTTAAAGATGCA-AAGAATGAT
1 AAAG-GTGCCAATATGCTGATTCAAGGCCAGCGACATCAGACTT-AAGATG-AGAAGAATGAT
* * * * * * * * *
1346808 AAAAGTGTCAATATGTTGATTCGTA-GCCAGTGATATCGGGCTTGAAGATGAGAAGAATAAT
1 AAAGGTGCCAATATGCTGATTC-AAGGCCAGCGACATCAGACTT-AAGATGAGAAGAATGAT
* * * * * *
1346869 AAAGGTGCTAATATGCTGATTCAAGGCCAGCGATATTAGGCTTAATGATGATAAGGATGA-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATCAGACTTAA-GATGAGAAGAATGAT
* * * * * *
1346929 GAAGAATGCCAATGTGCTGATTCAAGGCCAGCGACATAAGGC-T----T-A-AA-AATAAT
1 AAAG-GTGCCAATATGCTGATTCAAGGCCAGCGACATCAGACTTAAGATGAGAAGAATGAT
* * * * *
1346982 AAACGTGCCAATATACTTATTCAAGACCAGCGATATCAGACTTAA-A-GA-AA-AA--A-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATCAGACTTAAGATGAGAAGAATGAT
* * * ** *
1347035 AGA-GTGCCAATGTGCTGATTTAAGGCCAGCGACATTGGACTTAAAGATGCGAAGAATGAT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATCAGACTT-AAGATGAGAAGAATGAT
* * * * * *
1347095 AAAGGTGTCAATATGCTGATTCAAGGCCAGCGATATCGGACTTAAAGA-AAGAAGATTTGAC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATCAGACTT-AAGATGAGAAGA-ATGAT
* * * *
1347156 AAA--TGCCAATGTGTTGATTCAAGGCCAACGACATCA-AGCTTGAAGATGAGAAAAATGAT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATCAGA-CTT-AAGATGAGAAGAATGAT
*
1347215 AAAGGTGCCAATATGTTGATTCAAGGCCA
1 AAAGGTGCCAATATGCTGATTCAAGGCCA
1347244 ACGATATTTG
Statistics
Matches: 338, Mismatches: 73, Indels: 51
0.73 0.16 0.11
Matches are distributed among these distances:
52 63 0.19
53 9 0.03
54 3 0.01
55 2 0.01
56 7 0.02
57 2 0.01
58 1 0.00
59 41 0.12
60 20 0.06
61 186 0.55
62 4 0.01
ACGTcount: A:0.38, C:0.14, G:0.24, T:0.23
Consensus pattern (60 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATCAGACTTAAGATGAGAAGAATGAT
Found at i:1347012 original size:113 final size:111
Alignment explanation
Indices: 1346867--1347429 Score: 403
Period size: 113 Copynumber: 4.9 Consensus size: 111
1346857 GAGAAGAATA
* * * *
1346867 ATAAAGGTGCTAATATGCTGATTCAAGGCCAGCGATATTAGGCTTAATGATGATAAGGATGAGAA
1 ATAAAGGTGCCAATATACTGATTCAAGGCCAGCGATATTAGACTTAAAGA-GATAA-GAT-AGAA
*
1346932 GAATGCCAATGTGCTGATTCAAGGCCAGCGACATAAGGCTT-AAAAATA
63 GAATGCCAATGTGCTGATTCAAGGCCAGCGACATAAGGCTTAAAAAATG
* * * * *
1346980 ATAAACGTGCCAATATACTTATTCAAGACCAGCGATATCAGACTT-AA-AGA-AA-A-A-AAGAG
1 ATAAAGGTGCCAATATACTGATTCAAGGCCAGCGATATTAGACTTAAAGAGATAAGATAGAAGAA
* *
1347039 TGCCAATGTGCTGATTTAAGGCCAGCGACAT-TGGACTTAAAGATGCGAAGAATG
66 TGCCAATGTGCTGATTCAAGGCCAGCGACATAAGG-CTT--A-A----AA-AATG
* * ** * * *
1347093 ATAAAGGTGTCAATATGCTGATTCAAGGCCAGCGATATCGGACTTAAAGAAAGAAGATTTGACA-
1 ATAAAGGTGCCAATATACTGATTCAAGGCCAGCGATATTAGACTTAAAGAGATAAGA-TAGA-AG
* *
1347157 AATGCCAATGTGTTGATTCAAGGCCAACGACATCAA-GCTTGAAGATGAGAAAAATG
64 AATGCCAATGTGCTGATTCAAGGCCAGCGACAT-AAGGC-T-----T-A-AAAAATG
** * * *
1347213 ATAAAGGTGCCAATATGTTGATTCAAGGCCAACGATATTTGACTTAAAAATGATAAGGATAAGAA
1 ATAAAGGTGCCAATATACTGATTCAAGGCCAGCGATATTAGACTTAAAGA-GATAA-GAT-AGAA
* * * * * *
1347278 GGATGCCAATGTACTGATTCAAGGCTAGTGACATTAGGC-TCAAAAATG
63 GAATGCCAATGTGCTGATTCAAGGCCAGCGACATAAGGCTTAAAAAATG
* ** * * *
1347326 GTAAAGGTGCCAATATACTGATTCAAGGCCAGCGATATCGGACTTAAAGACATAAGATTTGACGA
1 ATAAAGGTGCCAATATACTGATTCAAGGCCAGCGATATTAGACTTAAAGAGATAAGA-TAGAAGA
* * * * * *
1347391 GTGCCAATATGTTGATTTAAGGCCAACGACA-ATGGCTTA
65 ATGCCAATGTGCTGATTCAAGGCCAGCGACATAAGGCTTA
1347430 GAAAGGTTGC
Statistics
Matches: 352, Mismatches: 65, Indels: 68
0.73 0.13 0.14
Matches are distributed among these distances:
103 2 0.01
104 37 0.11
105 1 0.00
107 1 0.00
108 1 0.00
109 2 0.01
110 5 0.01
111 30 0.09
112 8 0.02
113 130 0.37
114 2 0.01
115 3 0.01
116 2 0.01
117 1 0.00
120 79 0.22
121 11 0.03
122 33 0.09
125 3 0.01
126 1 0.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.24
Consensus pattern (111 bp):
ATAAAGGTGCCAATATACTGATTCAAGGCCAGCGATATTAGACTTAAAGAGATAAGATAGAAGAA
TGCCAATGTGCTGATTCAAGGCCAGCGACATAAGGCTTAAAAAATG
Found at i:1347178 original size:59 final size:60
Alignment explanation
Indices: 1347037--1347311 Score: 196
Period size: 61 Copynumber: 4.5 Consensus size: 60
1347027 AGAAAAAAAG
* * ** *
1347037 AGTGCCAATGTGCTGATTTAAGGCCAGCGACATTGGACTTAAAGATGCGAAGAATGATAA
1 AGTGCCAATGTGCTGATTCAAGGCCAGCGACATCGGACTTAAAGATAAGAAGAATGACAA
* * * *
1347097 AGGTGTCAATATGCTGATTCAAGGCCAGCGATATCGGACTTAAAGA-AAGAAGATTTGACAA
1 A-GTGCCAATGTGCTGATTCAAGGCCAGCGACATCGGACTTAAAGATAAGAAGA-ATGACAA
* * * * * * *
1347158 A-TGCCAATGTGTTGATTCAAGGCCAACGACATC-AAGCTTGAAGATGAGAAAAATGATAA
1 AGTGCCAATGTGCTGATTCAAGGCCAGCGACATCGGA-CTTAAAGATAAGAAGAATGACAA
* * * * ** * * * * * *
1347217 AGGTGCCAATATGTTGATTCAAGGCCAACGATATTTGACTTAAAAATGATAAGGATAAGAA
1 A-GTGCCAATGTGCTGATTCAAGGCCAGCGACATCGGACTTAAAGATAAGAAGAATGACAA
* * * *
1347278 GGATGCCAATGTACTGATTCAAGGCTAGTGACAT
1 AG-TGCCAATGTGCTGATTCAAGGCCAGCGACAT
1347312 TAGGCTCAAA
Statistics
Matches: 168, Mismatches: 39, Indels: 15
0.76 0.18 0.07
Matches are distributed among these distances:
58 1 0.01
59 40 0.24
60 12 0.07
61 114 0.68
62 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.24, T:0.24
Consensus pattern (60 bp):
AGTGCCAATGTGCTGATTCAAGGCCAGCGACATCGGACTTAAAGATAAGAAGAATGACAA
Found at i:1347462 original size:31 final size:31
Alignment explanation
Indices: 1347427--1347876 Score: 388
Period size: 31 Copynumber: 14.1 Consensus size: 31
1347417 CGACAATGGC
1347427 TTAGAAAGGTTGCCACCGACTTGTGTGGGCT
1 TTAGAAAGGTTGCCACCGACTTGTGTGGGCT
* *
1347458 TTAGAGAAGGTTACCACCAACTTGTGTGGGCT
1 TTAGA-AAGGTTGCCACCGACTTGTGTGGGCT
* *
1347490 TTAGAAGGGTTGCCACC-AGCTTGTGTAGGCT
1 TTAGAAAGGTTGCCACCGA-CTTGTGTGGGCT
* * * *
1347521 TTAAAAAAAGAGTTGCCATCGACTTGTCTGGACT
1 TT--AGAAAG-GTTGCCACCGACTTGTGTGGGCT
*
1347555 TTGAAGAAAGCGTTTCCACC-AGCTTGTGTGGGCT
1 TT--AGAAAG-GTTGCCACCGA-CTTGTGTGGGCT
* *
1347589 TTAGAGAAGATTGCCACCGACTTGTATGGGCT
1 TTAGA-AAGGTTGCCACCGACTTGTGTGGGCT
* * * *
1347621 TTAGAAGGGTTGCCAGC-AGCTTATGTAGGCT
1 TTAGAAAGGTTGCCACCGA-CTTGTGTGGGCT
* * ** *
1347652 TTGGAGAAGGTTGTCACTAACTTATGTGGGCT
1 TTAGA-AAGGTTGCCACCGACTTGTGTGGGCT
** * *
1347684 TTAGAGGGGTTGCCATC-AGCTTGTGTAGGCT
1 TTAGAAAGGTTGCCACCGA-CTTGTGTGGGCT
* *
1347715 TTA-AAGGGGTTACCACCGACTTGTGTGGGCT
1 TTAGAA-AGGTTGCCACCGACTTGTGTGGGCT
* * *
1347746 TTTGAAAGGGTGCCACCAACTTGTGTGGGCT
1 TTAGAAAGGTTGCCACCGACTTGTGTGGGCT
* * *
1347777 TTGAGGAGAGGTTGCCACCAACTTATGTGGGCT
1 TT-A-GAAAGGTTGCCACCGACTTGTGTGGGCT
* *
1347810 TTAGAAGAGGTTGCCACCGGCTTGTATGGGCT
1 TTAGAA-AGGTTGCCACCGACTTGTGTGGGCT
1347842 TTAGAGAAGGGTTGCCACCGACTTGTGTGGGCT
1 TTAGA-AA-GGTTGCCACCGACTTGTGTGGGCT
1347875 TT
1 TT
1347877 TGAGAGGAAA
Statistics
Matches: 337, Mismatches: 61, Indels: 40
0.77 0.14 0.09
Matches are distributed among these distances:
30 4 0.01
31 117 0.35
32 109 0.32
33 62 0.18
34 44 0.13
35 1 0.00
ACGTcount: A:0.21, C:0.18, G:0.31, T:0.30
Consensus pattern (31 bp):
TTAGAAAGGTTGCCACCGACTTGTGTGGGCT
Found at i:1347659 original size:63 final size:63
Alignment explanation
Indices: 1347427--1347876 Score: 476
Period size: 63 Copynumber: 7.0 Consensus size: 63
1347417 CGACAATGGC
* * *
1347427 TTAGAAAGGTTGCCACC-GACTTGTGTGGGCTTTAGAGAAGGTTACCACCAACTTGTGTGGGCT
1 TTAGAAGGGTTGCCACCAG-CTTGTGTGGGCTTTAGAGAAGGTTGCCACCGACTTGTGTGGGCT
* * * * * *
1347490 TTAGAAGGGTTGCCACCAGCTTGTGTAGGCTTTAAAAAAAGAGTTGCCATCGACTTGTCTGGACT
1 TTAGAAGGGTTGCCACCAGCTTGTGTGGGCTTT-AGAGAAG-GTTGCCACCGACTTGTGTGGGCT
* * * *
1347555 TTGAAGAAAGCGTTTCCACCAGCTTGTGTGGGCTTTAGAGAAGATTGCCACCGACTTGTATGGGC
1 TT--AG-AAGGGTTGCCACCAGCTTGTGTGGGCTTTAGAGAAGGTTGCCACCGACTTGTGTGGGC
1347620 T
63 T
* * * * * ** *
1347621 TTAGAAGGGTTGCCAGCAGCTTATGTAGGCTTTGGAGAAGGTTGTCACTAACTTATGTGGGCT
1 TTAGAAGGGTTGCCACCAGCTTGTGTGGGCTTTAGAGAAGGTTGCCACCGACTTGTGTGGGCT
* * * * * *
1347684 TTAGAGGGGTTGCCATCAGCTTGTGTAGGCTTTAAAG-GGGTTACCACCGACTTGTGTGGGCT
1 TTAGAAGGGTTGCCACCAGCTTGTGTGGGCTTTAGAGAAGGTTGCCACCGACTTGTGTGGGCT
* * * *
1347746 TTTGAAAGGG-TGCCACCAACTTGTGTGGGCTTT-GAGGAGAGGTTGCCACCAACTTATGTGGGC
1 TTAG-AAGGGTTGCCACCAGCTTGTGTGGGCTTTAGA-GA-AGGTTGCCACCGACTTGTGTGGGC
1347809 T
63 T
* *
1347810 TTAGAAGAGGTTGCCACCGGCTTGTATGGGCTTTAGAGAAGGGTTGCCACCGACTTGTGTGGGCT
1 TTAGAAG-GGTTGCCACCAGCTTGTGTGGGCTTTAGAGAA-GGTTGCCACCGACTTGTGTGGGCT
1347875 TT
1 TT
1347877 TGAGAGGAAA
Statistics
Matches: 316, Mismatches: 57, Indels: 26
0.79 0.14 0.07
Matches are distributed among these distances:
61 1 0.00
62 43 0.14
63 115 0.36
64 35 0.11
65 66 0.21
66 23 0.07
67 7 0.02
68 26 0.08
ACGTcount: A:0.21, C:0.18, G:0.31, T:0.30
Consensus pattern (63 bp):
TTAGAAGGGTTGCCACCAGCTTGTGTGGGCTTTAGAGAAGGTTGCCACCGACTTGTGTGGGCT
Found at i:1347991 original size:32 final size:32
Alignment explanation
Indices: 1347920--1348016 Score: 119
Period size: 33 Copynumber: 3.1 Consensus size: 32
1347910 TGTGTGGGCT
*
1347920 TTGAAGAAAAAAGATGCCACTAGGTCATGGAC
1 TTGAAGAAAAAAGATGCCACTAAGTCATGGAC
*
1347952 TTGGAAGAAAAAATATGCCACTAAGTCATGGAC
1 TT-GAAGAAAAAAGATGCCACTAAGTCATGGAC
* *
1347985 TTGAAG--AAGAGATGCCACTGAA-TCGTGGAC
1 TTGAAGAAAAAAGATGCCACT-AAGTCATGGAC
1348015 TT
1 TT
1348017 TGGAAAGGGT
Statistics
Matches: 58, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
30 20 0.34
31 2 0.03
32 6 0.10
33 30 0.52
ACGTcount: A:0.38, C:0.15, G:0.25, T:0.22
Consensus pattern (32 bp):
TTGAAGAAAAAAGATGCCACTAAGTCATGGAC
Found at i:1348822 original size:26 final size:28
Alignment explanation
Indices: 1348764--1348822 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
1348754 GACTTGCTTG
**
1348764 ACAAGAAATGTGATACAGTTTAATTTTTA
1 ACAAGAAATGTGATA-AGTTTAATTTCCA
*
1348793 ACAAGAAATGTGAT-GGTTT-ATTTCCA
1 ACAAGAAATGTGATAAGTTTAATTTCCA
1348819 ACAA
1 ACAA
1348823 AATGGTTTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 9 0.33
27 4 0.15
29 14 0.52
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (28 bp):
ACAAGAAATGTGATAAGTTTAATTTCCA
Found at i:1349325 original size:52 final size:51
Alignment explanation
Indices: 1349269--1349379 Score: 118
Period size: 52 Copynumber: 2.2 Consensus size: 51
1349259 ATTCATGTCC
* * *
1349269 TTGTTTTTCGATTTTTATTGTTC-TTTT-TTTTTTATTTTGCTTTTGTACTTTT
1 TTGTTTTTCGATTCTT-TT-TTCATTTTCTTTGTGATTTTGCTTTTG-ACTTTT
*** *
1349321 TTGTTTTTTTCTTCTTTTTTCATTTTCTTTGTGCTTTTGCTTTTGACTTTT
1 TTGTTTTTCGATTCTTTTTTCATTTTCTTTGTGATTTTGCTTTTGACTTTT
1349372 TTGTTTTT
1 TTGTTTTT
1349380 TTGAAGGGAA
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
50 3 0.06
51 20 0.40
52 27 0.54
ACGTcount: A:0.05, C:0.10, G:0.10, T:0.75
Consensus pattern (51 bp):
TTGTTTTTCGATTCTTTTTTCATTTTCTTTGTGATTTTGCTTTTGACTTTT
Found at i:1351171 original size:79 final size:78
Alignment explanation
Indices: 1351053--1351278 Score: 231
Period size: 79 Copynumber: 2.9 Consensus size: 78
1351043 CGAGAAATTT
* * *
1351053 AATATTTTGGAGATAATAA-CAGGGTTGGAGTATCCCCTTGAAAATAATAGGGTTGGAGTATCCC
1 AATATTTAGGAAATAA-AACCAGGGTTGGAGTATCCCCTTGGAAATAA-AGGGTTGGAGTATCCC
* *
1351117 CGGTTGTGAAAAATC
64 CGATTATGAAAAATC
* * * *
1351132 GATGA-TTAGGAAATAAAATCAGGATTGGAGTATCCCCTTGGAAATAACGAGGTTGGAGTATCCC
1 AAT-ATTTAGGAAATAAAACCAGGGTTGGAGTATCCCCTTGGAAATAAAG-GGTTGGAGTATCCC
* *
1351196 CAATTATGAGAAATC
64 CGATTATGAAAAATC
* * * * ** *
1351211 AATATTTTGGAAATAAAGCCGGGGTTGGAGTATCCCCTCGGAGGTAACGGGGTTGGAGTATCCCC
1 AATATTTAGGAAATAAAACCAGGGTTGGAGTATCCCCTTGGAAATAA-AGGGTTGGAGTATCCCC
1351276 GAT
65 GAT
1351279 GAAATAACGA
Statistics
Matches: 121, Mismatches: 21, Indels: 10
0.80 0.14 0.07
Matches are distributed among these distances:
78 4 0.03
79 115 0.95
80 2 0.02
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.27
Consensus pattern (78 bp):
AATATTTAGGAAATAAAACCAGGGTTGGAGTATCCCCTTGGAAATAAAGGGTTGGAGTATCCCCG
ATTATGAAAAATC
Found at i:1351273 original size:107 final size:108
Alignment explanation
Indices: 1351156--1351355 Score: 269
Period size: 107 Copynumber: 1.9 Consensus size: 108
1351146 AAAATCAGGA
* *
1351156 TTGGAGTATCCCC-TTGGAAATAACGAGGTTGGAGTATCCCCAATTATGAGAAATCAAT-ATTTT
1 TTGGAGTATCCCCGAT-GAAATAACGAGGTTGGAGTATCCCCAATTATGAAAAATCAATGATTTT
* *
1351219 GGAAATAAAGCCGGGGTTGGAGTATCCCCTCGGAGGTAACGGGG
65 GGAAATAAAACCGGAGTTGGAGTATCCCCTCGGAGGTAACGGGG
* * * *** *
1351263 TTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTGTGAAAAATTGGTGTTTTTG
1 TTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCCCAATTATGAAAAATCAATGATTTTG
*
1351328 GAAATAAAATCGGAGTTGGAGTATCCCC
66 GAAATAAAACCGGAGTTGGAGTATCCCC
1351356 GATTAAAGGA
Statistics
Matches: 79, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
107 48 0.61
108 31 0.39
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (108 bp):
TTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCCCAATTATGAAAAATCAATGATTTTG
GAAATAAAACCGGAGTTGGAGTATCCCCTCGGAGGTAACGGGG
Found at i:1351286 original size:28 final size:28
Alignment explanation
Indices: 1351230--1351306 Score: 91
Period size: 28 Copynumber: 2.8 Consensus size: 28
1351220 GAAATAAAGC
*** **
1351230 CGGGGTTGGAGTATCCCCTCGGAGGTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
1351258 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
* *
1351286 CGAGGTTGGAGTATCCTCGAT
1 CGGGGTTGGAGTATCCCCGAT
1351307 TGTGAAAAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.22, C:0.19, G:0.35, T:0.23
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:1351359 original size:52 final size:51
Alignment explanation
Indices: 1351290--1351461 Score: 173
Period size: 52 Copynumber: 3.3 Consensus size: 51
1351280 AAATAACGAG
* * * * *
1351290 GTTGGAGTATCCTCGATTGTGAAAAATTGGTGTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAAATTAGTG-TTTTGAAAATAAAACCGGA
* * *
1351342 GTTGGAGTATCCCCGATTAAAGGAAAATTAGTGTTTTGAAAATAAAACCGGG
1 GTTGGAGTATCCCCGATT-ATGAAAAATTAGTGTTTTGAAAATAAAACCGGA
* * * * ** * * *
1351394 GTTGGAGTATCCCCGATTATGAGAAATCAATATTTTGGGAATAAAGCTGGG
1 GTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGAAAATAAAACCGGA
1351445 GTTGGAGTATCCCCGAT
1 GTTGGAGTATCCCCGAT
1351462 GAGATAACAA
Statistics
Matches: 101, Mismatches: 18, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
51 40 0.40
52 51 0.50
53 10 0.10
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.30
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGAAAATAAAACCGGA
Found at i:1351449 original size:51 final size:52
Alignment explanation
Indices: 1351323--1351461 Score: 156
Period size: 51 Copynumber: 2.7 Consensus size: 52
1351313 AAATTGGTGT
* * * * * *
1351323 TTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTAGTG
1 TTTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTAAAGGAAAATCAATA
*
1351375 TTTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATT--ATGAGAAATCAATA
1 TTTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTAAAGGA-AAATCAATA
** * *
1351426 TTTTGGGAATAAAGCTGGGGTTGGAGTATCCCCGAT
1 TTTTGAAAATAAAACCGGGGTTGGAGTATCCCCGAT
1351462 GAGATAACAA
Statistics
Matches: 75, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
50 3 0.04
51 38 0.51
52 34 0.45
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (52 bp):
TTTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTAAAGGAAAATCAATA
Found at i:1351477 original size:183 final size:183
Alignment explanation
Indices: 1351259--1351598 Score: 617
Period size: 183 Copynumber: 1.9 Consensus size: 183
1351249 CGGAGGTAAC
* * *
1351259 GGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTGTGAAAAATTGGTGTT
1 GGGGTTGGAGTATCCCCGATGAAATAACAAGGTTGGAGTATCCTCGATCGGGAAAAATTGGTGTT
1351324 TTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTAGTGTTTTGAAAATAAAA
66 TTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTAGTGTTTTGAAAATAAAA
1351389 CCGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTGGGAATAAAGCT
131 CCGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTGGGAATAAAGCT
*
1351442 GGGGTTGGAGTATCCCCGATGAGATAACAAGGTTGGAGTATCCTCGATCGGGAAAAATTGGTGTT
1 GGGGTTGGAGTATCCCCGATGAAATAACAAGGTTGGAGTATCCTCGATCGGGAAAAATTGGTGTT
* *
1351507 TTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAACTTGGTGTTTTGAAAATAAAA
66 TTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTAGTGTTTTGAAAATAAAA
*
1351572 TCGGGGTTGGAGTATCCCCGATTATGA
131 CCGGGGTTGGAGTATCCCCGATTATGA
1351599 ACAATTGAGA
Statistics
Matches: 150, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
183 150 1.00
ACGTcount: A:0.31, C:0.12, G:0.28, T:0.29
Consensus pattern (183 bp):
GGGGTTGGAGTATCCCCGATGAAATAACAAGGTTGGAGTATCCTCGATCGGGAAAAATTGGTGTT
TTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTAGTGTTTTGAAAATAAAA
CCGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTGGGAATAAAGCT
Found at i:1352394 original size:19 final size:19
Alignment explanation
Indices: 1352370--1352409 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
1352360 AACGTCCATA
1352370 ATCGAGAAGGGGAGGTAAC
1 ATCGAGAAGGGGAGGTAAC
1352389 ATCGAGAAGGGGAGGTAAC
1 ATCGAGAAGGGGAGGTAAC
1352408 AT
1 AT
1352410 GGGCATCACG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.38, C:0.10, G:0.40, T:0.12
Consensus pattern (19 bp):
ATCGAGAAGGGGAGGTAAC
Found at i:1357623 original size:13 final size:13
Alignment explanation
Indices: 1357605--1357630 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1357595 CAATTTTTTG
1357605 TGTATCGATACAT
1 TGTATCGATACAT
1357618 TGTATCGATACAT
1 TGTATCGATACAT
1357631 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1357642 original size:32 final size:33
Alignment explanation
Indices: 1357585--1357648 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
1357575 TACAAGCCAA
**
1357585 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
1357618 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
1357649 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:1360128 original size:55 final size:55
Alignment explanation
Indices: 1359998--1361290 Score: 1338
Period size: 55 Copynumber: 22.5 Consensus size: 55
1359988 GCACCTCTTT
1359998 TGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTCAAAGCCCACACAAGTTGG
1 TGGCACTTTTCAGTCCTCAAAGAGCAGGACG-C----C-TTTCAAAGCCCACACAAGTTGG
*
1360059 TGGCACCTTTCAGTCCTCAAAGAGCAAGG-CGCCTTTCAAAGCCCACACAAGTTGG
1 TGGCACTTTTCAGTCCTCAAAGAGC-AGGACGCCTTTCAAAGCCCACACAAGTTGG
* * * * * * * *
1360114 TGGCA-TTTTCCAGTCCTCAAAAAGAATGATGCCTTTTAAAGCCCACATAAGTCGA
1 TGGCACTTTT-CAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGG
*
1360169 TGGCA-TTTTCCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGG
1 TGGCACTTTT-CAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGG
* * *
1360224 TGGCACTTCTCAATCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGG
1 TGGCACTTTTCAGTCCTCAAAGAGCAGGACGCC-TTT-C----AAAGCCCACACAAGTTGG
* *
1360285 TGGCACCTTTT-AGTCCTCAAAGAACAGGACACCTTTTTCCCTTTCAAAGCCCACACAAGTTGG
1 TGGCA-CTTTTCAGTCCTCAAAGAGCAGG--A-C-----GCCTTTCAAAGCCCACACAAGTTGG
* * * *
1360348 TGGCACCTTTCAGTCTTCAAAGAGCAGGACGCCTTTTAAAGTCCACACAAGTTGG
1 TGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGG
* * *
1360403 TGGCACCTTTCAGTCCTCAAAGAGCAAGATGCCTTTTCAAAGCCCACACAAGTTGG
1 TGGCACTTTTCAGTCCTCAAAGAGCAGGACGCC-TTTCAAAGCCCACACAAGTTGG
* * *
1360459 TGGCACCTTTCAGTCCTCAAAAAGCAGGACACCTTTCAAAGCCCACACAAGTTGG
1 TGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGG
* * *
1360514 TGGCA-TTTTCCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACATAAGTCGG
1 TGGCACTTTT-CAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGG
* *
1360569 TGGCA-TTTTCCAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACGAGTTGG
1 TGGCACTTTT-CAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGG
* *
1360624 TGGCACTTCTCAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGG
1 TGGCACTTTTCAGTCCTCAAAGAGCAGGACGCC-TTT-C----AAAGCCCACACAAGTTGG
*
1360685 TGGCACCTTTT-AGTCCTCAAAGAGCAGGACACCTTTTTCCCTTTCAAAGCCCACACAAGTTGG
1 TGGCA-CTTTTCAGTCCTCAAAGAGCAGG--A-C-----GCCTTTCAAAGCCCACACAAGTTGG
* * * *
1360748 TGGCACCTTTCAGTCCTCAAAGAGCAGGATG-CTTTTAAAGCCCACACGAGTTGG
1 TGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGG
* * *
1360802 TGGCA-TTTTCCAGTCCTCAAAGAGCAGGATGCCTTTTAAAGCTCACACAAGTTGG
1 TGGCACTTTT-CAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGG
*
1360857 TGGCACCTTTT-AGTCCTCAAAGAGCAGGACGTCTTTCCTTTGTAAAGCCCACACAAGTTGG
1 TGGCA-CTTTTCAGTCCTCAAAGAGCAGGACG-----CCTTT-CAAAGCCCACACAAGTTGG
* * *
1360918 TTGCACCTTCCAGTCCTCAAA-AGCAGGACGCCTTTCCCTTTCAAAGCCCACACAAGTTGG
1 TGGCACTTTTCAGTCCTCAAAGAGCAGGACG------CCTTTCAAAGCCCACACAAGTTGG
* *
1360978 TGGCA-TTTTCCAATCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGG
1 TGGCACTTTT-CAGTCCTCAAAGAGCAGGACGC-----C-TTTCAAAGCCCACACAAGTTGG
*
1361039 TGGCA-TTTTCTAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGG
1 TGGCACTTTTC-AGTCCTCAAAGAGCAGGACGC-----C-TTTCAAAGCCCACACAAGTTGG
* * * *
1361100 TGGCACCTTTCAATCCCCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGG
1 TGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGG
*
1361155 TGGCA-TTTTCCAGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGG
1 TGGCACTTTT-CAGTCCTCAAAGAGCAGGACGCCT-TTCAAAGCCCACACAAGTTGG
* *
1361210 TGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGG
1 TGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGG
*
1361265 TGGCACTTTTTAGTCCTCAAAGAGCA
1 TGGCACTTTTCAGTCCTCAAAGAGCA
1361291 CGATGCACTT
Statistics
Matches: 1072, Mismatches: 95, Indels: 136
0.82 0.07 0.10
Matches are distributed among these distances:
53 3 0.00
54 60 0.06
55 512 0.48
56 68 0.06
57 6 0.01
59 2 0.00
60 53 0.05
61 253 0.24
62 23 0.02
63 80 0.07
67 2 0.00
68 6 0.01
69 4 0.00
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (55 bp):
TGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGG
Found at i:1360775 original size:400 final size:399
Alignment explanation
Indices: 1359998--1361290 Score: 1844
Period size: 400 Copynumber: 3.2 Consensus size: 399
1359988 GCACCTCTTT
*
1359998 TGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTCAAAGCCCACACAAGTTGGTGGC
1 TGGCACCTTTCAGTCCTCAAAGAGCAGGACG-C----CTTTTCAAAGCCCACACAAGTTGGTGGC
*
1360063 ACCTTTCAGTCCTCAAAGAGCAAGG-CGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAG
61 ACCTTTCAGTCCTCAAAGAGC-AGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAG
* * * *
1360127 TCCTCAAAAAGAATGATGCCTTTTAAAGCCCACATAAGTCGATGGCATTTTCCAGTCCTCAAAGA
125 TCCTC-AAAAGCAGGACGCCTTTTAAAGCCCACATAAGTCGGTGGCATTTTCCAGTCCTCAAAGA
* *
1360192 GCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCACTTCTCAATCCTCAAAGAGCAGGATGCC
189 GCAGGATGCCTTTCAAAGCCCACACGAGTTGGTGGCACTTCTCAGTCCTCAAAGAGCAGGATGCC
*
1360257 TTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAACAGGACACCTTTT
254 TTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACACCTTTT
*
1360322 TCCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCTTCAAAGAGCAGGACGCCTTTTAA
319 TCCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTAA
*
1360387 AGTCCACACAAGTTGG
384 AGCCCACACAAGTTGG
* *
1360403 TGGCACCTTTCAGTCCTCAAAGAGCAAGATGCCTTTTCAAAGCCCACACAAGTTGGTGGCACCTT
1 TGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCAAAGCCCACACAAGTTGGTGGCACCTT
*
1360468 TCAGTCCTCAAAAAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCA
66 TCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCA
1360533 AAGAGCAGGACGCCTTTTAAAGCCCACATAAGTCGGTGGCATTTTCCAGTCCTCAAAGAGCAGGA
131 AA-AGCAGGACGCCTTTTAAAGCCCACATAAGTCGGTGGCATTTTCCAGTCCTCAAAGAGCAGGA
1360598 TGCCTTTCAAAGCCCACACGAGTTGGTGGCACTTCTCAGTCCTCAAAGAGCAGGATGCCTTTTCC
195 TGCCTTTCAAAGCCCACACGAGTTGGTGGCACTTCTCAGTCCTCAAAGAGCAGGATGCCTTTTCC
1360663 TTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACACCTTTTTCCCTT
260 TTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACACCTTTTTCCCTT
*
1360728 TCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGATG-CTTTTAAAGCCCA
325 TCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCA
*
1360792 CACGAGTTGG
390 CACAAGTTGG
* * *
1360802 TGGCA-TTTTCCAGTCCTCAAAGAGCAGGATGCCTTTT-AAAGCTCACACAAGTTGGTGGCACCT
1 TGGCACCTTT-CAGTCCTCAAAGAGCAGGACGCCTTTTCAAAGCCCACACAAGTTGGTGGCACCT
* * * * **
1360865 TTTAGTCCTCAAAGAGCAGGACGTCTTTCCTTTGTAAAGCCCACACAAGTTGGTTGCACCTTCCA
65 TTCAGTCCTCAAAGAGCAGGA---C--ACCTTT-CAAAGCCCACACAAGTTGGTGGCATTTTCCA
* * *
1360930 GTCCTCAAAAGCAGGACGCCTTTCCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAATCCT
124 GTCCTCAAAAGCAGGACGCC--T---TTT-AAAGCCCACATAAGTCGGTGGCATTTTCCAGTCCT
* *
1360995 CAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCTAGTCCTCAA
183 CAAAGAGCAGGATGC-----C-TTTCAAAGCCCACACGAGTTGGTGGCACTTCTC-AGTCCTCAA
* * * *
1361059 AGAGCAGGATG-CTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAATCCCCAAAGA
241 AGAGCAGGATGCCTTTTCCTTTT-AAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGA
*
1361123 GCAGGACA--------CCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAG
305 GCAGGACACCTTTTTCCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAG
* *
1361179 CAGGACACCTCTTAAAGCCCACACAAGTTGG
369 CAGGACGCCTTTTAAAGCCCACACAAGTTGG
* *
1361210 TGGCACCTTTCAGTCCTCAAAGAGCAGGACGCC-TTTCAAAGCCCACACGAGTTGGTGGCACTTT
1 TGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCAAAGCCCACACAAGTTGGTGGCACCTT
*
1361274 TTAGTCCTCAAAGAGCA
66 TCAGTCCTCAAAGAGCA
1361291 CGATGCACTT
Statistics
Matches: 816, Mismatches: 45, Indels: 51
0.89 0.05 0.06
Matches are distributed among these distances:
398 47 0.06
399 58 0.07
400 325 0.40
401 1 0.00
403 16 0.02
404 37 0.05
405 29 0.04
406 3 0.00
407 51 0.06
408 92 0.11
409 50 0.06
414 15 0.02
415 92 0.11
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (399 bp):
TGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCAAAGCCCACACAAGTTGGTGGCACCTT
TCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCA
AAAGCAGGACGCCTTTTAAAGCCCACATAAGTCGGTGGCATTTTCCAGTCCTCAAAGAGCAGGAT
GCCTTTCAAAGCCCACACGAGTTGGTGGCACTTCTCAGTCCTCAAAGAGCAGGATGCCTTTTCCT
TTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACACCTTTTTCCCTTT
CAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCAC
ACAAGTTGG
Found at i:1362052 original size:19 final size:19
Alignment explanation
Indices: 1362028--1362089 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
1362018 TTTTGAATTT
1362028 CAAACAGTTTGTATCGATA
1 CAAACAGTTTGTATCGATA
**
1362047 CAAACAGAAAATGTATCGATA
1 CAAACAG--TTTGTATCGATA
*
1362068 CATA-AGTATTGTATCGATA
1 CAAACAGT-TTGTATCGATA
1362087 CAA
1 CAA
1362090 TGTATCGATA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
19 19 0.56
20 2 0.06
21 13 0.38
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.27
Consensus pattern (19 bp):
CAAACAGTTTGTATCGATA
Found at i:1362095 original size:13 final size:13
Alignment explanation
Indices: 1362077--1362101 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1362067 ACATAAGTAT
1362077 TGTATCGATACAA
1 TGTATCGATACAA
1362090 TGTATCGATACA
1 TGTATCGATACA
1362102 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1362097 original size:32 final size:32
Alignment explanation
Indices: 1362056--1362128 Score: 137
Period size: 32 Copynumber: 2.3 Consensus size: 32
1362046 ACAAACAGAA
1362056 AATGTATCGATACATAAGTATTGTATCGATAC
1 AATGTATCGATACATAAGTATTGTATCGATAC
*
1362088 AATGTATCGATACATAAGTTTTGTATCGATAC
1 AATGTATCGATACATAAGTATTGTATCGATAC
1362120 AATGTATCG
1 AATGTATCG
1362129 CTACGAAGCT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (32 bp):
AATGTATCGATACATAAGTATTGTATCGATAC
Found at i:1362114 original size:19 final size:18
Alignment explanation
Indices: 1362058--1362120 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
1362048 AAACAGAAAA
1362058 TGTATCGATACATAAGTAT
1 TGTATCGATACATAAGT-T
1362077 TGTATCGATAC--AA---
1 TGTATCGATACATAAGTT
1362090 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAG-TT
1362109 TGTATCGATACA
1 TGTATCGATACA
1362121 ATGTATCGCT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
15 2 0.05
17 2 0.05
19 23 0.61
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (18 bp):
TGTATCGATACATAAGTT
Found at i:1362171 original size:21 final size:21
Alignment explanation
Indices: 1362145--1362186 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1362135 AGCTACTGCC
1362145 AAGGAAATGTATCGATACATT
1 AAGGAAATGTATCGATACATT
1362166 AAGGAAATGTATCGATACATT
1 AAGGAAATGTATCGATACATT
1362187 GTATCGATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.10, G:0.19, T:0.29
Consensus pattern (21 bp):
AAGGAAATGTATCGATACATT
Found at i:1362191 original size:13 final size:13
Alignment explanation
Indices: 1362173--1362198 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1362163 ATTAAGGAAA
1362173 TGTATCGATACAT
1 TGTATCGATACAT
1362186 TGTATCGATACAT
1 TGTATCGATACAT
1362199 CGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1364769 original size:79 final size:79
Alignment explanation
Indices: 1364672--1364891 Score: 239
Period size: 78 Copynumber: 2.8 Consensus size: 79
1364662 ATTTCATCGA
* ** *
1364672 GGATACTCTAACCCCGTTACCTCCAAGGGGATACTCCAACCCCGGCTTTATTTCCAAAATATTGA
1 GGATACTCCAACCCCGTTATTTCCAAGGGGATACTCCAACCCCGGTTTTATTTCCAAAATATTGA
* **
1364737 TTTCTCATAATTGG
66 TTTCTCACAACCGG
* * * * *
1364751 GGATACTCCAACCTCGTTATTTCCAA-GGGATACTCCAATCCCGATTTTATTTCC-TAATCATCG
1 GGATACTCCAACCCCGTTATTTCCAAGGGGATACTCCAACCCCGGTTTTATTTCCAAAAT-ATTG
* *
1364814 ATTTTTCACAACCGT
65 ATTTCTCACAACCGG
* * * *
1364829 GAATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAACCTC-GTTATTATCTCCAAAATATT
1 GGATACTCCAACCCCGTTATTTCCAAGGGGATACTCCAACCCCGGTT-TTATTTCCAAAATATT
1364892 AAATTTTTCG
Statistics
Matches: 114, Mismatches: 23, Indels: 8
0.79 0.16 0.06
Matches are distributed among these distances:
77 3 0.03
78 63 0.55
79 45 0.39
80 3 0.03
ACGTcount: A:0.27, C:0.28, G:0.13, T:0.32
Consensus pattern (79 bp):
GGATACTCCAACCCCGTTATTTCCAAGGGGATACTCCAACCCCGGTTTTATTTCCAAAATATTGA
TTTCTCACAACCGG
Found at i:1375465 original size:79 final size:78
Alignment explanation
Indices: 1375368--1375561 Score: 228
Period size: 79 Copynumber: 2.4 Consensus size: 78
1375358 GGGTTGGAGC
* ** * *
1375368 ATCCCCTTGAAAATAACGGGGTTGGAGTATCCCCGGTTGTGAAAAATCGATGA-TTAGGAAATAA
1 ATCCCCTCG-AAATAACGGGGTTGGAGTATCCCCGAATATGAAAAATCAAT-ATTTAGGAAATAA
1375432 AATCGGGATTAGAGT
64 AATCGGGATTAGAGT
** * *
1375447 ATCCCCTCAGAAATAACGGGGTTGGAGTATCCCTAAATATGAGAAATCAATATTTTGGAAATAAA
1 ATCCCCTC-GAAATAACGGGGTTGGAGTATCCCCGAATATGAAAAATCAATATTTAGGAAATAAA
* * *
1375512 GTCGGGGTTGGAGT
65 ATCGGGATTAGAGT
*
1375526 ATCCCCTCGAACGTAACGGGGTTGGAGTATCCCCGA
1 ATCCCCTCGAA-ATAACGGGGTTGGAGTATCCCCGA
1375562 TGAAATAACG
Statistics
Matches: 97, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
78 4 0.04
79 92 0.95
80 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.25
Consensus pattern (78 bp):
ATCCCCTCGAAATAACGGGGTTGGAGTATCCCCGAATATGAAAAATCAATATTTAGGAAATAAAA
TCGGGATTAGAGT
Found at i:1375554 original size:28 final size:27
Alignment explanation
Indices: 1375514--1375585 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 27
1375504 GAAATAAAGT
*
1375514 CGGGGTTGGAGTATCCCC-TCGAACGTAA
1 CGGGGTTGGAGTATCCCCAT-GAA-ATAA
1375542 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCC-ATGAAATAA
*
1375570 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
1375586 TCGGTTGTGA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
28 36 0.90
29 3 0.08
30 1 0.03
ACGTcount: A:0.24, C:0.21, G:0.33, T:0.22
Consensus pattern (27 bp):
CGGGGTTGGAGTATCCCCATGAAATAA
Found at i:1375568 original size:107 final size:108
Alignment explanation
Indices: 1375443--1375639 Score: 256
Period size: 107 Copynumber: 1.8 Consensus size: 108
1375433 ATCGGGATTA
* *
1375443 GAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCC-CTAAATATGAGAAATCAAT-ATTTTGGA
1 GAGTATCCCCTCAGAAATAACGAGGTTGGAGTATCCTC-AAATATGAAAAATCAATGATTTTGGA
*
1375506 AATAAAGTCGGGGTTGGAGTATCCCCTCGAACGTAACGGGGTTG
65 AATAAAGTCGAGGTTGGAGTATCCCCTCGAACGTAACGGGGTTG
* *** * ** *
1375550 GAGTATCCCC-GATGAAATAACGAGGTTGGAGTATCCTCGGTTGTGAAAAATTGATGTTTTTGGA
1 GAGTATCCCCTCA-GAAATAACGAGGTTGGAGTATCCTCAAATATGAAAAATCAATGATTTTGGA
1375614 AATAAAGTCGAGGTTGGAGTATCCCC
65 AATAAAGTCGAGGTTGGAGTATCCCC
1375640 GATTAAAGGA
Statistics
Matches: 76, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
106 1 0.01
107 42 0.55
108 33 0.43
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.27
Consensus pattern (108 bp):
GAGTATCCCCTCAGAAATAACGAGGTTGGAGTATCCTCAAATATGAAAAATCAATGATTTTGGAA
ATAAAGTCGAGGTTGGAGTATCCCCTCGAACGTAACGGGGTTG
Found at i:1385497 original size:79 final size:79
Alignment explanation
Indices: 1385340--1385561 Score: 252
Period size: 79 Copynumber: 2.8 Consensus size: 79
1385330 CGAGAAATTT
* * * *
1385340 AATATTTTGGAGATAATAAC-GGGGTTGGAGTATCCCCTTGAAAATAACGGGGTTGGAGTATCCC
1 AATATTTAGGAAATAA-AACAGGGATTGGAGTATCCCCTTGGAAATAACGGGGTTGGAGTATCCC
** *
1385404 CGGTTGTGAAAAATC
65 CAATTATGAAAAATC
* *
1385419 GATGA-TTAGGAAATAAAATAGGGATTGGAGTATCCCCTTGGAAATAACGGGGTTGGAGTATCCC
1 AAT-ATTTAGGAAATAAAACAGGGATTGGAGTATCCCCTTGGAAATAACGGGGTTGGAGTATCCC
*
1385483 CAATTATGAGAAATC
65 CAATTATGAAAAATC
* * * * * **
1385498 AATATTTTGGAAATAAAGCCGGGGTTGGAGTAT-CCCTCGGAGGTAACGGGGTTGGAGTATCCCC
1 AATATTTAGGAAATAAAACAGGGATTGGAGTATCCCCTTGGAAATAACGGGGTTGGAGTATCCCC
1385562 GATGAAATAA
Statistics
Matches: 121, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
78 31 0.26
79 89 0.74
80 1 0.01
ACGTcount: A:0.31, C:0.14, G:0.29, T:0.26
Consensus pattern (79 bp):
AATATTTAGGAAATAAAACAGGGATTGGAGTATCCCCTTGGAAATAACGGGGTTGGAGTATCCCC
AATTATGAAAAATC
Found at i:1385555 original size:27 final size:27
Alignment explanation
Indices: 1385517--1385587 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 27
1385507 GAAATAAAGC
**
1385517 CGGGGTTGGAGTATCCCTCG-GAGGTAA
1 CGGGGTTGGAGTATCCC-CGAGAAATAA
1385544 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGA-GAAATAA
*
1385572 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
1385588 TCGATTGTGA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
26 2 0.05
27 17 0.44
28 20 0.51
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (27 bp):
CGGGGTTGGAGTATCCCCGAGAAATAA
Found at i:1385645 original size:52 final size:52
Alignment explanation
Indices: 1385575--1385962 Score: 279
Period size: 52 Copynumber: 7.5 Consensus size: 52
1385565 GAAATAACGA
* * *
1385575 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTGTTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTTGGAAATAAAACCGG
* * * * *
1385627 AGTTGGAGTATCCCCGATTAAAGGAAAATTAGTG-TTTTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT-ATGAAAAATTGGTGTTTTTGGAAATAAAACCGG
* * * *
1385679 GGTTGGAGTATCCCCGATTGTGGAAAATTAGTG-TTTTAGAAATAAAACCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTTGGAAATAAAACCGG
* *** * * *
1385730 GGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTAGG-AATAAAGCCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTTGGAAATAAAACCGG
* * * *** * * * * * * *
1385781 GGTTGGAGTATCCCCTCA-GAGGTAACGGGGTTGGAGTATTCTCGATGAGATAA-CGA
1 GGTTGGAGTATCCCC-GATTATG-AA--AAATTGGTGT-TTTTGGA-AATAAAACCGG
** * *
1385837 GGTTGGAGTAT--CCGATCGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTTGGAAATAAAACCGG
* * * * *
1385887 AGTTGGAGTATCCCCGATTAAAGGAAAATTGGTG-TTTTGAAAATAAAATCGG
1 GGTTGGAGTATCCCCGATT-ATGAAAAATTGGTGTTTTTGGAAATAAAACCGG
1385939 GGTTGGAGTATCCCCGATTATGAA
1 GGTTGGAGTATCCCCGATTATGAA
1385963 CAACTGAGAA
Statistics
Matches: 255, Mismatches: 67, Indels: 29
0.73 0.19 0.08
Matches are distributed among these distances:
49 4 0.02
50 17 0.07
51 90 0.35
52 97 0.38
53 23 0.09
54 5 0.02
55 3 0.01
56 13 0.05
57 3 0.01
ACGTcount: A:0.32, C:0.12, G:0.28, T:0.29
Consensus pattern (52 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTTGGAAATAAAACCGG
Found at i:1385725 original size:51 final size:51
Alignment explanation
Indices: 1385575--1385795 Score: 266
Period size: 51 Copynumber: 4.3 Consensus size: 51
1385565 GAAATAACGA
* * * * * *
1385575 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTGTTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGGAAAATTAGTG-TTTTAGAAATAAAACCGG
* *
1385627 AGTTGGAGTATCCCCGATTAAAGGAAAATTAGTGTTTT-GAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT-ATGGAAAATTAGTGTTTTAG-AAATAAAACCGG
*
1385679 GGTTGGAGTATCCCCGATTGTGGAAAATTAGTGTTTTAGAAATAAAACCGG
1 GGTTGGAGTATCCCCGATTATGGAAAATTAGTGTTTTAGAAATAAAACCGG
* * * * *
1385730 GGTTGGAGTATCCCCGATTAT-GAGAAATCAATATTTTAGGAATAAAGCCGG
1 GGTTGGAGTATCCCCGATTATGGA-AAATTAGTGTTTTAGAAATAAAACCGG
1385781 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
1385796 TCAGAGGTAA
Statistics
Matches: 149, Mismatches: 16, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
50 2 0.01
51 86 0.58
52 51 0.34
53 10 0.07
ACGTcount: A:0.32, C:0.12, G:0.27, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGGAAAATTAGTGTTTTAGAAATAAAACCGG
Found at i:1385818 original size:28 final size:30
Alignment explanation
Indices: 1385778--1385849 Score: 89
Period size: 28 Copynumber: 2.5 Consensus size: 30
1385768 GGAATAAAGC
*
1385778 CGGGGTTGGAGTATCCCCTC-A-GAGGTAA
1 CGGGGTTGGAGTATCCCCTCGATGAGATAA
*
1385806 CGGGGTTGGAGTAT--TCTCGATGAGATAA
1 CGGGGTTGGAGTATCCCCTCGATGAGATAA
*
1385834 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
1385850 GATCGTGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
26 3 0.08
27 1 0.03
28 33 0.89
ACGTcount: A:0.22, C:0.17, G:0.36, T:0.25
Consensus pattern (30 bp):
CGGGGTTGGAGTATCCCCTCGATGAGATAA
Found at i:1385928 original size:260 final size:261
Alignment explanation
Indices: 1385466--1385957 Score: 864
Period size: 260 Copynumber: 1.9 Consensus size: 261
1385456 TTGGAAATAA
1385466 CGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTAT
* *
1385531 CCCTCGGAGGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTGT
66 CCCTCAGAGGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGATCGT
*
1385596 GAAAAATTGGTGTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTAGTG
131 GAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTAGTG
1385661 TTTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTGTGGAAAATTAGTGTTTTAGAAATAAAA
196 TTTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTGTGGAAAATTAGTGTTTTAGAAATAAAA
1385726 C
261 C
*
1385727 CGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTAGG-AATAAAGCCGGGGTTGGAGTA
1 CGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTT-GGAAATAAAGCCGGGGTTGGAGTA
* * *
1385791 TCCCCTCAGAGGTAACGGGGTTGGAGTATTCTCGATGAGATAACGAGGTTGGAGTAT-C-CGATC
65 T-CCCTCAGAGGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGATC
*
1385854 GTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTGG
129 GTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTAG
*
1385919 TGTTTTGAAAATAAAATCGGGGTTGGAGTATCCCCGATT
194 TGTTTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATT
1385958 ATGAACAACT
Statistics
Matches: 220, Mismatches: 9, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
260 105 0.48
261 62 0.28
262 53 0.24
ACGTcount: A:0.31, C:0.13, G:0.28, T:0.28
Consensus pattern (261 bp):
CGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTAT
CCCTCAGAGGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGATCGT
GAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTAGTG
TTTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTGTGGAAAATTAGTGTTTTAGAAATAAAA
C
Found at i:1388327 original size:21 final size:21
Alignment explanation
Indices: 1388301--1388357 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
1388291 GTAAACTTCC
1388301 TAGATGTATCGATACAAAGAA
1 TAGATGTATCGATACAAAGAA
*
1388322 TAGATGTATCGATACACAGAA
1 TAGATGTATCGATACAAAGAA
*
1388343 -AAATGTATCGATACA
1 TAGATGTATCGATACA
1388358 TTTCCTTGGC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
20 14 0.41
21 20 0.59
ACGTcount: A:0.46, C:0.12, G:0.18, T:0.25
Consensus pattern (21 bp):
TAGATGTATCGATACAAAGAA
Found at i:1405710 original size:16 final size:16
Alignment explanation
Indices: 1405668--1405717 Score: 73
Period size: 16 Copynumber: 3.1 Consensus size: 16
1405658 CAAATTCAAT
*
1405668 ATAATTTAAACTTAAA
1 ATAATTTAAATTTAAA
*
1405684 ATGATTTAAATTTAAA
1 ATAATTTAAATTTAAA
*
1405700 ATAATTTAAATTCAAA
1 ATAATTTAAATTTAAA
1405716 AT
1 AT
1405718 TAATCTAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (16 bp):
ATAATTTAAATTTAAA
Found at i:1411139 original size:19 final size:20
Alignment explanation
Indices: 1411095--1411147 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 20
1411085 CTACCAGTTT
**
1411095 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGAA
*
1411115 CATGTATGGATACAA-TGAA
1 CATGTATCGATACAATTGAA
1411134 CATGTATCGATACA
1 CATGTATCGATACA
1411148 TTGCATCGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:1413563 original size:22 final size:21
Alignment explanation
Indices: 1413528--1413577 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
1413518 TTTGTTGATG
*
1413528 ATTTTG-A-TGAAAAATGAAGT
1 ATTTTGAAGTGAAAAAT-AAGA
1413548 ATTTTGAAGTGAAAAATAAGA
1 ATTTTGAAGTGAAAAATAAGA
*
1413569 AATTTGAAG
1 ATTTTGAAG
1413578 AAGATTTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 6 0.23
21 12 0.46
22 8 0.31
ACGTcount: A:0.48, C:0.00, G:0.20, T:0.32
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAATAAGA
Found at i:1413574 original size:21 final size:22
Alignment explanation
Indices: 1413535--1413577 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1413525 ATGATTTTGA
* *
1413535 TGAAAAATGAAGTATTTTGAAG
1 TGAAAAATGAAGAAATTTGAAG
1413557 TGAAAAAT-AAGAAATTTGAAG
1 TGAAAAATGAAGAAATTTGAAG
1413578 AAGATTTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.51, C:0.00, G:0.21, T:0.28
Consensus pattern (22 bp):
TGAAAAATGAAGAAATTTGAAG
Found at i:1419877 original size:43 final size:43
Alignment explanation
Indices: 1419816--1419915 Score: 191
Period size: 43 Copynumber: 2.3 Consensus size: 43
1419806 GTTTGAAGCA
1419816 ATGTATCGATACAAATAGTGGTAGGGTAACTACTGCCAGTTTC
1 ATGTATCGATACAAATAGTGGTAGGGTAACTACTGCCAGTTTC
*
1419859 ATGTATCGATATAAATAGTGGTAGGGTAACTACTGCCAGTTTC
1 ATGTATCGATACAAATAGTGGTAGGGTAACTACTGCCAGTTTC
1419902 ATGTATCGATACAA
1 ATGTATCGATACAA
1419916 TTGTCCATGT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 55 1.00
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.31
Consensus pattern (43 bp):
ATGTATCGATACAAATAGTGGTAGGGTAACTACTGCCAGTTTC
Found at i:1419926 original size:20 final size:19
Alignment explanation
Indices: 1419901--1419973 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 19
1419891 CTGCCAGTTT
**
1419901 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAA
1419921 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
* *
1419940 CATGTATCGAAACAAAGCATA
1 CATGTATCGATACAATG-A-A
1419961 -ATGTATCGATACA
1 CATGTATCGATACA
1419974 TCTAGGTGTG
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
19 17 0.37
20 28 0.61
21 1 0.02
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.27
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:1420283 original size:13 final size:13
Alignment explanation
Indices: 1420265--1420291 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1420255 TCCTAACACT
1420265 TTGTATCGATACA
1 TTGTATCGATACA
1420278 TTGTATCGATACA
1 TTGTATCGATACA
1420291 T
1 T
1420292 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1420321 original size:20 final size:19
Alignment explanation
Indices: 1420275--1420331 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 19
1420265 TTGTATCGAT
*
1420275 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGC
*
1420294 TCATTGTATCGATACATGC
1 ACATTGTATCGATACATGC
1420313 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
1420332 AAACTGACAG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 18 0.53
20 16 0.47
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.35
Consensus pattern (19 bp):
ACATTGTATCGATACATGC
Found at i:1422614 original size:20 final size:20
Alignment explanation
Indices: 1422598--1422642 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
1422588 CTTAGAAAGG
1422598 GAAAA-GAAGAATTAGAAAA
1 GAAAATGAAGAATTAGAAAA
1422617 GAAAATGAAGAATTAGAAAA
1 GAAAATGAAGAATTAGAAAA
1422637 GAAAAT
1 GAAAAT
1422643 AATTGAATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.67, C:0.00, G:0.20, T:0.13
Consensus pattern (20 bp):
GAAAATGAAGAATTAGAAAA
Found at i:1427730 original size:13 final size:13
Alignment explanation
Indices: 1427708--1427766 Score: 58
Period size: 13 Copynumber: 4.9 Consensus size: 13
1427698 CAAAGATCAG
1427708 TGTATCGATACAA
1 TGTATCGATACAA
*
1427721 TGTATTGATAC-A
1 TGTATCGATACAA
1427733 T-T-T-GAGT--AA
1 TGTATCGA-TACAA
1427742 TGTATCGATACAA
1 TGTATCGATACAA
1427755 TGTATCGATACA
1 TGTATCGATACA
1427767 TTTACATTTG
Statistics
Matches: 38, Mismatches: 1, Indels: 14
0.72 0.02 0.26
Matches are distributed among these distances:
9 4 0.11
10 3 0.08
11 3 0.08
12 4 0.11
13 24 0.63
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1427832 original size:13 final size:13
Alignment explanation
Indices: 1427814--1427871 Score: 53
Period size: 13 Copynumber: 3.9 Consensus size: 13
1427804 CAAAAAAATA
1427814 TGTATCGATACAT
1 TGTATCGATACAT
1427827 TGTATCGATACAACACTTT
1 TGTATCGAT---ACA---T
1427846 ATGTATCGATACAT
1 -TGTATCGATACAT
1427860 TGTATCGATACA
1 TGTATCGATACA
1427872 ACACTTTATG
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
16 3 0.08
17 3 0.08
19 1 0.03
20 9 0.24
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1427834 original size:33 final size:33
Alignment explanation
Indices: 1427792--1427891 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
1427782 AGTAGCTTAA
* ***
1427792 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAACACTTTATGTATCGATAC
1427825 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAACACTTTATGTATCGATAC
1427858 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAACACTTTATGTATCGATAC
1427891 A
1 A
1427892 AATCGTTGAA
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 63 1.00
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAACACTTTATGTATCGATAC
Done.