Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold329
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: 4121247
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 5938 characters in sequence are not A, C, G, or T
File 15 of 25
Found at i:2290825 original size:51 final size:51
Alignment explanation
Indices: 2290761--2290872 Score: 188
Period size: 51 Copynumber: 2.2 Consensus size: 51
2290751 AACGGTGTTA
* * * *
2290761 GAGTATCCTCGATTGTGAGAAATCAATATTTTAGGAATAAAGCCGGGGTTG
1 GAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAACCAGGGTTG
2290812 GAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAACCAGGGTTG
1 GAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAACCAGGGTTG
2290863 GAGTATCCCC
1 GAGTATCCCC
2290873 TCAGAAATAA
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 57 1.00
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (51 bp):
GAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAACCAGGGTTG
Found at i:2290887 original size:79 final size:79
Alignment explanation
Indices: 2290804--2291150 Score: 536
Period size: 79 Copynumber: 4.4 Consensus size: 79
2290794 GGAATAAAGC
*
2290804 CGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAACCAGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAGCCAGGGTTGGAGTAT
2290869 CCCCTCAGAAATAA
66 CCCCTCAGAAATAA
* *
2290883 CGGGGTTGAAGTATTCCCGATTGTGAGAAATCAATATTTTAGAAATAAAGCCAGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAGCCAGGGTTGGAGTAT
2290948 CCCCTCTA-AAATAA
66 CCCCTC-AGAAATAA
* * * *
2290962 CGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTAGGAATAAAGCCGGGGTTAGAGTAT
1 CGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAGCCAGGGTTGGAGTAT
*
2291027 CCCCTCGGAAATAA
66 CCCCTCAGAAATAA
* * * *
2291041 TGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTAGGAATAAAGCCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAGCCAGGGTTGGAGTAT
2291106 CCCCTC-GAAAATAA
66 CCCCTCAG-AAATAA
* *
2291120 CGGGATTGGAGTATCCCCGATTGTGAAAAAT
1 CGGGGTTGGAGTATCCCCGATTGTGAGAAAT
2291151 TGGTGTTTTT
Statistics
Matches: 249, Mismatches: 16, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
78 1 0.00
79 247 0.99
80 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (79 bp):
CGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAGCCAGGGTTGGAGTAT
CCCCTCAGAAATAA
Found at i:2290907 original size:130 final size:130
Alignment explanation
Indices: 2290674--2290951 Score: 461
Period size: 130 Copynumber: 2.1 Consensus size: 130
2290664 GCGAAAATAA
* * *
2290674 CGGGGTTGGAGTATCCCCGATTGTGAGAAATCCATATTTTAGGAATAAAACCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAACCAGGGTTGGAGTAT
* * *
2290739 CCCCTCGGAAATAACGGTGTTAGAGTATCCTCGATTGTGAGAAATCAATATTTTAGGAATAAAGC
66 CCCCTCAGAAATAACGGGGTTAGAGTATCCTCGATTGTGAGAAATCAATATTTTAGAAATAAAGC
2290804 CGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAACCAGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAACCAGGGTTGGAGTAT
2290869 CCCCTCAGAAATAACGGGGTT-GAAGTATTCC-CGATTGTGAGAAATCAATATTTTAGAAATAAA
66 CCCCTCAGAAATAACGGGGTTAG-AGTA-TCCTCGATTGTGAGAAATCAATATTTTAGAAATAAA
2290932 GC
129 GC
*
2290934 CAGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
2290952 TCTAAAATAA
Statistics
Matches: 139, Mismatches: 7, Indels: 4
0.93 0.05 0.03
Matches are distributed among these distances:
129 1 0.01
130 135 0.97
131 3 0.02
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.27
Consensus pattern (130 bp):
CGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAACCAGGGTTGGAGTAT
CCCCTCAGAAATAACGGGGTTAGAGTATCCTCGATTGTGAGAAATCAATATTTTAGAAATAAAGC
Found at i:2291009 original size:209 final size:209
Alignment explanation
Indices: 2290649--2291030 Score: 615
Period size: 209 Copynumber: 1.8 Consensus size: 209
2290639 AAAATAACGA
* *
2290649 GGTTGGAGTATCCCTGCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAGAAATCCATATTTT
1 GGTTGGAGTATCCCTGCGAAAATAACGGGGTTGAAGTATCCCCGATTGTGAGAAATCAATATTTT
* * * * * *
2290714 AGGAATAAAACCGGGGTTGGAGTATCCCCTCGGAAATAACGGTGTTAGAGTATCCTCGATTGTGA
66 AGAAATAAAACCAGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTAGAGTATCCCCGATTATGA
*
2290779 GAAATCAATATTTTAGGAATAAAGCCGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTT
131 GAAATCAATATTTTAGGAATAAAGCCGGGGTTAGAGTATCCCCGATTGTGAGAAATCAATATTTT
2290844 AGAAATAAAACCAG
196 AGAAATAAAACCAG
*
2290858 GGTTGGAGTATCCCCT-C-AGAAATAACGGGGTTGAAGTATTCCCGATTGTGAGAAATCAATATT
1 GGTTGGAGTAT-CCCTGCGA-AAATAACGGGGTTGAAGTATCCCCGATTGTGAGAAATCAATATT
* * *
2290921 TTAGAAATAAAGCCAGGGTTGGAGTATCCCCTCTAAAATAACGGGGTTGGAGTATCCCCGATTAT
64 TTAGAAATAAAACCAGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTAGAGTATCCCCGATTAT
2290986 GAGAAATCAATATTTTAGGAATAAAGCCGGGGTTAGAGTATCCCC
129 GAGAAATCAATATTTTAGGAATAAAGCCGGGGTTAGAGTATCCCC
2291031 TCGGAAATAA
Statistics
Matches: 158, Mismatches: 13, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
208 1 0.01
209 153 0.97
210 4 0.03
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (209 bp):
GGTTGGAGTATCCCTGCGAAAATAACGGGGTTGAAGTATCCCCGATTGTGAGAAATCAATATTTT
AGAAATAAAACCAGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTAGAGTATCCCCGATTATGA
GAAATCAATATTTTAGGAATAAAGCCGGGGTTAGAGTATCCCCGATTGTGAGAAATCAATATTTT
AGAAATAAAACCAG
Found at i:2293590 original size:33 final size:33
Alignment explanation
Indices: 2293553--2293620 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
2293543 ATACAATGAG
*
2293553 CAATGTATTGATACAATGCAA-AATGTATCGATA
1 CAATGTATCGATACAATG-AATAATGTATCGATA
*
2293586 CAATGTATCGATACATTGAATAATGTATCGATA
1 CAATGTATCGATACAATGAATAATGTATCGATA
2293619 CA
1 CA
2293621 TTTCCTTGGC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
32 2 0.06
33 30 0.94
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (33 bp):
CAATGTATCGATACAATGAATAATGTATCGATA
Found at i:2293592 original size:13 final size:13
Alignment explanation
Indices: 2293574--2293600 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2293564 TACAATGCAA
2293574 AATGTATCGATAC
1 AATGTATCGATAC
2293587 AATGTATCGATAC
1 AATGTATCGATAC
2293600 A
1 A
2293601 TTGAATAATG
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:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:2293622 original size:20 final size:19
Alignment explanation
Indices: 2293494--2293590 Score: 106
Period size: 20 Copynumber: 4.9 Consensus size: 19
2293484 AAAATGCCTG
* *
2293494 AATGTATCAATACATTGTAA
1 AATGTATCGATACAATG-AA
2293514 AATGTATCGATACAAT-AA
1 AATGTATCGATACAATGAA
*
2293532 GCAATGTATCGATACAATGAGC
1 --AATGTATCGATACAATGA-A
*
2293554 AATGTATTGATACAATGCAA
1 AATGTATCGATACAATG-AA
2293574 AATGTATCGATACAATG
1 AATGTATCGATACAATG
2293591 TATCGATACA
Statistics
Matches: 66, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
18 2 0.03
20 62 0.94
21 2 0.03
ACGTcount: A:0.43, C:0.12, G:0.15, T:0.29
Consensus pattern (19 bp):
AATGTATCGATACAATGAA
Found at i:2295794 original size:13 final size:13
Alignment explanation
Indices: 2295776--2295800 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2295766 CAAAGAAAGT
2295776 TATATCGATACAC
1 TATATCGATACAC
2295789 TATATCGATACA
1 TATATCGATACA
2295801 ATTTTAATGT
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:0.40, C:0.20, G:0.08, T:0.32
Consensus pattern (13 bp):
TATATCGATACAC
Found at i:2297394 original size:26 final size:28
Alignment explanation
Indices: 2297356--2297411 Score: 80
Period size: 26 Copynumber: 2.1 Consensus size: 28
2297346 TTTATAAAGT
*
2297356 GAGAGATTATTTTTGAACCAAAAAGGGA
1 GAGAGATTATTTTTGAAACAAAAAGGGA
*
2297384 GAGAGA-T-TTTTTGAAATAAAAAGGGA
1 GAGAGATTATTTTTGAAACAAAAAGGGA
2297410 GA
1 GA
2297412 TAATAAAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 19 0.73
27 1 0.04
28 6 0.23
ACGTcount: A:0.45, C:0.04, G:0.27, T:0.25
Consensus pattern (28 bp):
GAGAGATTATTTTTGAAACAAAAAGGGA
Found at i:2297891 original size:13 final size:13
Alignment explanation
Indices: 2297873--2297897 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2297863 ATTTTGCTTA
2297873 GTATCGATACATT
1 GTATCGATACATT
2297886 GTATCGATACAT
1 GTATCGATACAT
2297898 AAAACTGACA
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):
GTATCGATACATT
Found at i:2298007 original size:22 final size:22
Alignment explanation
Indices: 2297979--2298022 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2297969 CACTGTTTAG
*
2297979 CACTATTCATGTATCGATACAT
1 CACTATTCATGTATCAATACAT
2298001 CACTATTCATGTATCAATACAT
1 CACTATTCATGTATCAATACAT
2298023 GTGAATAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.23, G:0.07, T:0.36
Consensus pattern (22 bp):
CACTATTCATGTATCAATACAT
Found at i:2302358 original size:130 final size:129
Alignment explanation
Indices: 2302191--2302551 Score: 302
Period size: 130 Copynumber: 2.8 Consensus size: 129
2302181 ATTTTTGGTG
* * * ** *
2302191 AAAATCAGGGTTGGAGTATCCCTTCA-AAAATTGTAGGGTTGAAGTATCCCTTAAGATGAAAATT
1 AAAAACAGGGTTGAAGTATCCC--CACAGAATTGTAGGGTTGAAGTATCCCCGAAGATG-AAATA
* * * * *
2302255 TTGATGTTTTGAAC-TAAAAATGGGGTTAGAGTATCTCTAATAGTGAAAAATAGATATTTT-GGA
63 TCGATATTTTGAACGTAAAAACGGGGTTAGAGTATCCCAAATAGTGAAAAATAGATATTTTAGG-
2302318 AGT
127 AGT
** * * *
2302321 AAAAATGGGGTTGAAGTATCCCCACAGAATTGATAGGGTTGGAGTATCCCCGATGGTGAAATATC
1 AAAAACAGGGTTGAAGTATCCCCACAGAATTG-TAGGGTTGAAGTATCCCCGAAGATGAAATATC
* * * * *
2302386 GATATTTTGGACGTAAAAACGTGGTTGGAGTATCCCAAATGGTGAAAAATTGATATTTTAGGAGT
65 GATATTTTGAACGTAAAAACGGGGTTAGAGTATCCCAAATAGTGAAAAATAGATATTTTAGGAGT
* **** * * *
2302451 AAAAACAGGGTTGGAGTATCTTTTCAGAATTGATGGGGTT-AGAGTATCCCC-AATGGTGAAAAA
1 AAAAACAGGGTTGAAGTATCCCCACAGAATTG-TAGGGTTGA-AGTATCCCCGAA-GATGAAATA
* * * *
2302514 TCGATATTTTGGGA-TTAAAAATGGGGTTGGAGTATCCC
63 TCGATATTTT-GAACGTAAAAACGGGGTTAGAGTATCCC
2302552 CTCGAAATTG
Statistics
Matches: 189, Mismatches: 35, Indels: 14
0.79 0.15 0.06
Matches are distributed among these distances:
128 2 0.01
129 22 0.12
130 160 0.85
131 5 0.03
ACGTcount: A:0.34, C:0.10, G:0.25, T:0.30
Consensus pattern (129 bp):
AAAAACAGGGTTGAAGTATCCCCACAGAATTGTAGGGTTGAAGTATCCCCGAAGATGAAATATCG
ATATTTTGAACGTAAAAACGGGGTTAGAGTATCCCAAATAGTGAAAAATAGATATTTTAGGAGT
Found at i:2302441 original size:51 final size:51
Alignment explanation
Indices: 2302355--2302470 Score: 164
Period size: 51 Copynumber: 2.3 Consensus size: 51
2302345 CAGAATTGAT
** *
2302355 AGGGTTGGAGTATCCCCGATGGTGAAATATCGATATTTT-GGACGTAAAAAC
1 AGGGTTGGAGTATCCCAAATGGTGAAAAATCGATATTTTAGGA-GTAAAAAC
*
2302406 -GTGGTTGGAGTATCCCAAATGGTGAAAAATTGATATTTTAGGAGTAAAAAC
1 AG-GGTTGGAGTATCCCAAATGGTGAAAAATCGATATTTTAGGAGTAAAAAC
2302457 AGGGTTGGAGTATC
1 AGGGTTGGAGTATC
2302471 TTTTCAGAAT
Statistics
Matches: 58, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
50 1 0.02
51 53 0.91
52 4 0.07
ACGTcount: A:0.33, C:0.10, G:0.28, T:0.28
Consensus pattern (51 bp):
AGGGTTGGAGTATCCCAAATGGTGAAAAATCGATATTTTAGGAGTAAAAAC
Found at i:2302497 original size:79 final size:77
Alignment explanation
Indices: 2302408--2302826 Score: 391
Period size: 79 Copynumber: 5.4 Consensus size: 77
2302398 GTAAAAACGT
* * * * **
2302408 GGTTGGAGTATCCCAAATGGTGAAAAATTGATATTTTAGGAGTAAAAACAGGGTTGGAGTATCTT
1 GGTTGAAGTATCCCCAATGGTGAAAAATCGATATTTT-GGAGTAAAAACAGGGTTAGAGTATCCC
*
2302473 TTCAGAATTGATGG
65 CTC-GAATTGATGG
* ** *
2302487 GGTT-AGAGTATCCCCAATGGTGAAAAATCGATATTTTGGGATTAAAAATGGGGTTGGAGTATCC
1 GGTTGA-AGTATCCCCAATGGTGAAAAATCGATATTTT-GGAGTAAAAACAGGGTTAGAGTATCC
*
2302551 CCTCGAAATTGATAG
64 CCTCG-AATTGATGG
* * **
2302566 GGTTGAAGTATCCCCGATGGTGAAAGATCGATATTTTAAAAGT-AAAA-A--GTTAGAGTATCCC
1 GGTTGAAGTATCCCCAATGGTGAAAAATCGATATTTT-GGAGTAAAAACAGGGTTAGAGTATCCC
*
2302627 TTCGGAATTGATGG
65 CTC-GAATTGATGG
* * ** * *
2302641 GATTGAAATATTTCCAATGGTGAAAAATCGATATTTTGGAAGTAAAAATTA-GGTTAGAGTATCT
1 GGTTGAAGTATCCCCAATGGTGAAAAATCGATATTTTGG-AGTAAAAA-CAGGGTTAGAGTATCC
* *
2302705 CCTCAGAAATAATGG
64 CCTC-GAATTGATGG
* * *
2302720 GGTTGAAGTATCCTCGATGGTGAAAAATCGATATTTTGGAAGTAAAAACAGGGTTAGAGTATCCT
1 GGTTGAAGTATCCCCAATGGTGAAAAATCGATATTTTGG-AGTAAAAACAGGGTTAGAGTATCCC
* * *
2302785 CTCGAAAATAATAG
65 CTCG-AATTGATGG
* *
2302799 GGTTGGAGTATCCCCGATGGTGAAAAAT
1 GGTTGAAGTATCCCCAATGGTGAAAAAT
2302827 TCAATGCTTT
Statistics
Matches: 283, Mismatches: 46, Indels: 22
0.81 0.13 0.06
Matches are distributed among these distances:
75 56 0.20
76 5 0.02
78 8 0.03
79 213 0.75
80 1 0.00
ACGTcount: A:0.34, C:0.11, G:0.25, T:0.30
Consensus pattern (77 bp):
GGTTGAAGTATCCCCAATGGTGAAAAATCGATATTTTGGAGTAAAAACAGGGTTAGAGTATCCCC
TCGAATTGATGG
Found at i:2305262 original size:52 final size:51
Alignment explanation
Indices: 2305183--2305306 Score: 140
Period size: 52 Copynumber: 2.4 Consensus size: 51
2305173 AATAGCCTAC
* * *
2305183 ATGTATCGATACATTGAAGAATATATCAATACATTGGGGTTAAAAACCCAGA
1 ATGTATCGATACAATGAAAAATATATCAATACATTGGGGCT-AAAACCCAGA
* * * * *
2305235 ATGTATTGATACAATGAAAAATGTATCAATATATTTGGGCTAAAACTCAGA
1 ATGTATCGATACAATGAAAAATATATCAATACATTGGGGCTAAAACCCAGA
* * *
2305286 ATCTATCAATATAATGAAAAA
1 ATGTATCGATACAATGAAAAA
2305307 AAATGTACAA
Statistics
Matches: 60, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
51 26 0.43
52 34 0.57
ACGTcount: A:0.45, C:0.11, G:0.15, T:0.29
Consensus pattern (51 bp):
ATGTATCGATACAATGAAAAATATATCAATACATTGGGGCTAAAACCCAGA
Found at i:2306195 original size:2 final size:2
Alignment explanation
Indices: 2306190--2306228 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2306180 TGTGTGTGTG
2306190 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2306229 CTCATATAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2307940 original size:13 final size:11
Alignment explanation
Indices: 2307921--2307956 Score: 54
Period size: 11 Copynumber: 3.1 Consensus size: 11
2307911 GCAAAAACAA
2307921 AAAAAAAAAAG
1 AAAAAAAAAAG
2307932 AAAGCAAAAAAAG
1 AAA--AAAAAAAG
2307945 AAAAAAAAAAG
1 AAAAAAAAAAG
2307956 A
1 A
2307957 GAGTGGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 12 0.52
13 11 0.48
ACGTcount: A:0.86, C:0.03, G:0.11, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:2307948 original size:24 final size:24
Alignment explanation
Indices: 2307911--2307956 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
2307901 CTAAGCTTGG
2307911 GCAAAAACAAAAAAAAAAAAGAAA
1 GCAAAAACAAAAAAAAAAAAGAAA
2307935 GCAAAAA-AAGAAAAAAAAAAGA
1 GCAAAAACAA-AAAAAAAAAAGA
2307957 GAGTGGATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 2 0.10
24 19 0.90
ACGTcount: A:0.83, C:0.07, G:0.11, T:0.00
Consensus pattern (24 bp):
GCAAAAACAAAAAAAAAAAAGAAA
Found at i:2309032 original size:29 final size:28
Alignment explanation
Indices: 2308996--2309096 Score: 73
Period size: 29 Copynumber: 3.5 Consensus size: 28
2308986 TATTATCATG
2308996 TTTTAGGGCCATTTATGCAATTTCATATA
1 TTTTAGGGCCATTTATGCAATTTCAT-TA
* * * *
2309025 TTTTAGGGTCGTTTTTGTAATTTACCATGT-
1 TTTTAGGGCCATTTATGCAATTT--CAT-TA
* *
2309055 TTTT-GGACTATTTATGTC-ATTTCATTCA
1 TTTTAGGGCCATTTATG-CAATTTCATT-A
2309083 TTTTAGGGCCATTT
1 TTTTAGGGCCATTT
2309097 TAATAATTTC
Statistics
Matches: 53, Mismatches: 13, Indels: 12
0.68 0.17 0.15
Matches are distributed among these distances:
26 1 0.02
27 3 0.06
28 4 0.08
29 37 0.70
30 4 0.08
31 4 0.08
ACGTcount: A:0.21, C:0.13, G:0.16, T:0.50
Consensus pattern (28 bp):
TTTTAGGGCCATTTATGCAATTTCATTA
Found at i:2309104 original size:58 final size:58
Alignment explanation
Indices: 2308992--2309105 Score: 133
Period size: 58 Copynumber: 2.0 Consensus size: 58
2308982 TAAATATTAT
* * * **
2308992 CATGTTTTAGGGCCATTTATGCAATTTCATATATTTTAGGGTCGTTTTTGTAATTTAC
1 CATGTTTTAGGACCATTTATGCAATTTCATATATTTTAGGGCCATTTTAATAATTTAC
* *
2309050 CATGTTTTTGGACTATTTATGTC-ATTTCAT-TCATTTTAGGGCCATTTTAATAATTT
1 CATGTTTTAGGACCATTTATG-CAATTTCATAT-ATTTTAGGGCCATTTTAATAATTT
2309106 CTCATGATCT
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
57 1 0.02
58 45 0.96
59 1 0.02
ACGTcount: A:0.23, C:0.12, G:0.15, T:0.50
Consensus pattern (58 bp):
CATGTTTTAGGACCATTTATGCAATTTCATATATTTTAGGGCCATTTTAATAATTTAC
Found at i:2310906 original size:30 final size:30
Alignment explanation
Indices: 2310863--2310937 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
2310853 CGACAAATCA
* * * * *
2310863 GTGGCACCCTTTTCTGAAGCCCACAAGTCG
1 GTGGCATCTTTTTCTAAAGCCCACAACTCC
*
2310893 GTGGCATCTTTTTC-AAAGTCCACAACTCC
1 GTGGCATCTTTTTCTAAAGCCCACAACTCC
2310922 GTGGCACTCTTTTTCT
1 GTGGCA-TCTTTTTCT
2310938 TTTGTAAGCT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
29 17 0.46
30 20 0.54
ACGTcount: A:0.19, C:0.31, G:0.19, T:0.32
Consensus pattern (30 bp):
GTGGCATCTTTTTCTAAAGCCCACAACTCC
Found at i:2311003 original size:34 final size:36
Alignment explanation
Indices: 2310912--2311003 Score: 111
Period size: 35 Copynumber: 2.7 Consensus size: 36
2310902 TTTTCAAAGT
*
2310912 CCACAACTC-CGTGGCACTCTTTTTCTTTTGTAAGC
1 CCACAACTCTAGTGGCACTCTTTTTCTTTTGTAAGC
* *
2310947 TCACAACTCTA-TAGCACTCTTTTTCTTTT-TAAGC
1 CCACAACTCTAGTGGCACTCTTTTTCTTTTGTAAGC
* *
2310981 CCACAAGT-TAGTGGCACCCTTTT
1 CCACAACTCTAGTGGCACTCTTTT
2311004 CAAAAGCCCA
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
33 2 0.04
34 21 0.44
35 25 0.52
ACGTcount: A:0.21, C:0.29, G:0.12, T:0.38
Consensus pattern (36 bp):
CCACAACTCTAGTGGCACTCTTTTTCTTTTGTAAGC
Found at i:2311011 original size:30 final size:29
Alignment explanation
Indices: 2310977--2311100 Score: 139
Period size: 28 Copynumber: 4.3 Consensus size: 29
2310967 TTTTCTTTTT
* *
2310977 AAGCCCACAAGTTAGTGGCACCCTTTTCAA
1 AAGCCCACAAGTCAGTGGCAACC-TTTCAA
2311007 AAGCCCACAAGTCAGTGGCAACCTTT-AA
1 AAGCCCACAAGTCAGTGGCAACCTTTCAA
*
2311035 AAGCCCACAAGTCAGTAGCAACC-TTCAA
1 AAGCCCACAAGTCAGTGGCAACCTTTCAA
* * *
2311063 AAGCACACAAGT-TGAT-GCAAACCTCTCAA
1 AAGCCCACAAGTCAG-TGGC-AACCTTTCAA
2311092 AAGCCCACA
1 AAGCCCACA
2311101 TAATTTGGTG
Statistics
Matches: 83, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
27 5 0.06
28 42 0.51
29 15 0.18
30 21 0.25
ACGTcount: A:0.37, C:0.31, G:0.15, T:0.17
Consensus pattern (29 bp):
AAGCCCACAAGTCAGTGGCAACCTTTCAA
Found at i:2311278 original size:43 final size:43
Alignment explanation
Indices: 2311217--2311305 Score: 160
Period size: 43 Copynumber: 2.1 Consensus size: 43
2311207 CACCTTCATA
2311217 TTTAAGTCCAATATAGCTGACCTTGAATCAGCACATTGGCACC
1 TTTAAGTCCAATATAGCTGACCTTGAATCAGCACATTGGCACC
* *
2311260 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC
1 TTTAAGTCCAATATAGCTGACCTTGAATCAGCACATTGGCACC
2311303 TTT
1 TTT
2311306 TCCATCTTTA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (43 bp):
TTTAAGTCCAATATAGCTGACCTTGAATCAGCACATTGGCACC
Found at i:2311337 original size:52 final size:55
Alignment explanation
Indices: 2311259--2311380 Score: 169
Period size: 52 Copynumber: 2.3 Consensus size: 55
2311249 ACATTGGCAC
* * *
2311259 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CC-TTTTC-CAT
1 CTTTAAGTCCAATATAGCTAGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
* *
2311311 CTTTAAGTTCAATGTAGCTAGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTAGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
*
2311366 CTTTAAGCCCAATAT
1 CTTTAAGTCCAATAT
2311381 CGTTGGCCGT
Statistics
Matches: 59, Mismatches: 8, Indels: 3
0.84 0.11 0.04
Matches are distributed among these distances:
52 37 0.63
53 2 0.03
54 5 0.08
55 15 0.25
ACGTcount: A:0.26, C:0.25, G:0.13, T:0.36
Consensus pattern (55 bp):
CTTTAAGTCCAATATAGCTAGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
Found at i:2311394 original size:55 final size:52
Alignment explanation
Indices: 2311259--2311396 Score: 168
Period size: 52 Copynumber: 2.6 Consensus size: 52
2311249 ACATTGGCAC
* *
2311259 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACACCTTTTCCAT
* * *
2311311 CTTTAAGTTCAATGTAGCTAGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACA-CC-TTTTC-CAT
* * * *
2311366 CTTTAAGCCCAATATCGTTGGCCGTGAATCA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCA
2311397 ACATATTGGC
Statistics
Matches: 71, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
52 37 0.52
53 2 0.03
54 5 0.07
55 27 0.38
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (52 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACACCTTTTCCAT
Found at i:2312266 original size:33 final size:33
Alignment explanation
Indices: 2312224--2312288 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
2312214 TCAACGATTT
2312224 GTATCGATACATAAAGTGTTGTATCGATACAAG
1 GTATCGATACATAAAGTGTTGTATCGATACAAG
*** *
2312257 GTATCGATACATATTTTTTTGTATCGATACAA
1 GTATCGATACATAAAGTGTTGTATCGATACAA
2312289 TTCAAGCTAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (33 bp):
GTATCGATACATAAAGTGTTGTATCGATACAAG
Found at i:2312348 original size:13 final size:13
Alignment explanation
Indices: 2312330--2312354 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2312320 ATCACTTAAA
2312330 TGTATCGATACAT
1 TGTATCGATACAT
2312343 TGTATCGATACA
1 TGTATCGATACA
2312355 CAGATCTTTG
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:2312419 original size:52 final size:52
Alignment explanation
Indices: 2312363--2312491 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
2312353 CACAGATCTT
* *
2312363 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTACCCAGATGTATCGATACACTATAAAA
**
2312415 TGTATCGATACATGCAGGCAAATTTACCCAGATGTATCGATACACTATTCAA
1 TGTATCGATACATGCAGGCAAATTTACCCAGATGTATCGATACACTATAAAA
2312467 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
2312492 TCATATTTCG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTACCCAGATGTATCGATACACTATAAAA
Found at i:2315445 original size:71 final size:71
Alignment explanation
Indices: 2315327--2315468 Score: 275
Period size: 71 Copynumber: 2.0 Consensus size: 71
2315317 ACTCCAAAAT
2315327 CTCGGTCACTTCGTAGTGACCATTGAAGATCAATTAGATGGGCGATTCATCTACTGATCTTCCCC
1 CTCGGTCACTTCGTAGTGACCATTGAAGATCAATTAGATGGGCGATTCATCTACTGATCTTCCCC
2315392 CTTTAA
66 CTTTAA
*
2315398 CTCGGTCACTTCGTAGTGACCATTGAAGATCAATTAGATGGGTGATTCATCTACTGATCTTCCCC
1 CTCGGTCACTTCGTAGTGACCATTGAAGATCAATTAGATGGGCGATTCATCTACTGATCTTCCCC
2315463 CTTTAA
66 CTTTAA
2315469 TCAACACACT
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 70 1.00
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (71 bp):
CTCGGTCACTTCGTAGTGACCATTGAAGATCAATTAGATGGGCGATTCATCTACTGATCTTCCCC
CTTTAA
Found at i:2316681 original size:20 final size:20
Alignment explanation
Indices: 2316643--2316681 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2316633 TTTTAACATA
**
2316643 TTAATGAATTTCATTGCATT
1 TTAATGAATTTCACGGCATT
*
2316663 TTAATGAGTTTCACGGCAT
1 TTAATGAATTTCACGGCAT
2316682 AAAAATATTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (20 bp):
TTAATGAATTTCACGGCATT
Found at i:2319721 original size:20 final size:20
Alignment explanation
Indices: 2319696--2319747 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
2319686 ATACATTGAA
*
2319696 AATGTATCGATATATGTATG
1 AATGTATCGATATATGTATC
* *
2319716 AATGTATCGATATATTTTTC
1 AATGTATCGATATATGTATC
2319736 AATGTATCGATA
1 AATGTATCGATA
2319748 CATTCTGTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.42
Consensus pattern (20 bp):
AATGTATCGATATATGTATC
Found at i:2320713 original size:20 final size:22
Alignment explanation
Indices: 2320673--2320720 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
2320663 TAGCCTTTGA
*
2320673 CCATGCATTTTTTTACTATGTT
1 CCATGCATTTTTTAACTATGTT
2320695 CCATGCA-TTTTTAAC-ATG-T
1 CCATGCATTTTTTAACTATGTT
2320714 CCA-GCAT
1 CCATGCAT
2320721 CTCATTGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 3 0.12
19 4 0.17
20 3 0.12
21 7 0.29
22 7 0.29
ACGTcount: A:0.23, C:0.23, G:0.10, T:0.44
Consensus pattern (22 bp):
CCATGCATTTTTTAACTATGTT
Found at i:2326260 original size:20 final size:19
Alignment explanation
Indices: 2326205--2326260 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
2326195 AAAACCCTTA
*
2326205 AAAGTATCGATACATAATTC
1 AAAGTATCGATACAT-GTTC
2326225 AAAGTATCGATACATGTTGC
1 AAAGTATCGATACATGTT-C
*
2326245 AATGTATCGATACATG
1 AAAGTATCGATACATG
2326261 AAAAAGATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 2 0.06
20 31 0.94
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.30
Consensus pattern (19 bp):
AAAGTATCGATACATGTTC
Found at i:2326337 original size:13 final size:13
Alignment explanation
Indices: 2326319--2326344 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2326309 TACAGCAAGT
2326319 ATGTATCGATACA
1 ATGTATCGATACA
2326332 ATGTATCGATACA
1 ATGTATCGATACA
2326345 CAAAAAATTG
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:2328551 original size:21 final size:21
Alignment explanation
Indices: 2328518--2328562 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
2328508 TTGCAAGTTG
*
2328518 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
2328540 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
2328560 AAA
1 AAA
2328563 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:2330386 original size:15 final size:15
Alignment explanation
Indices: 2330366--2330396 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2330356 TAAAAATGTC
*
2330366 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
2330381 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
2330396 C
1 C
2330397 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:2332494 original size:13 final size:13
Alignment explanation
Indices: 2332476--2332501 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2332466 CATTTTTTCT
2332476 TTGTATCGATACA
1 TTGTATCGATACA
2332489 TTGTATCGATACA
1 TTGTATCGATACA
2332502 GGGTGATTAT
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):
TTGTATCGATACA
Found at i:2337488 original size:16 final size:17
Alignment explanation
Indices: 2337455--2337497 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
2337445 GTAATTCTTC
* *
2337455 ATATTTTAATTAATAAT
1 ATATTTAAAATAATAAT
2337472 ATATTTAAAATAA-AAT
1 ATATTTAAAATAATAAT
*
2337488 AAATTTAAAA
1 ATATTTAAAA
2337498 ACATACTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 12 0.52
17 11 0.48
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATATTTAAAATAATAAT
Found at i:2343400 original size:16 final size:16
Alignment explanation
Indices: 2343373--2343406 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
2343363 GGAAACAAGG
2343373 AAATTAAAAAGAAAGAA
1 AAATTAAAAAGAAA-AA
2343390 AAATT-AAAAGAAAAA
1 AAATTAAAAAGAAAAA
2343405 AA
1 AA
2343407 TTTTTTCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 8 0.47
17 5 0.29
ACGTcount: A:0.79, C:0.00, G:0.09, T:0.12
Consensus pattern (16 bp):
AAATTAAAAAGAAAAA
Found at i:2343778 original size:6 final size:7
Alignment explanation
Indices: 2343762--2343788 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
2343752 TCTATCCATC
2343762 TTTTTAT
1 TTTTTAT
2343769 TTTTTAT
1 TTTTTAT
2343776 TTTTTAT
1 TTTTTAT
2343783 TTTTTA
1 TTTTTA
2343789 CTCTACCTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTTAT
Found at i:2345495 original size:11 final size:11
Alignment explanation
Indices: 2345453--2345496 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
2345443 GCAGTATTTG
*
2345453 ATTTGATTTTA
1 ATTTAATTTTA
* *
2345464 GTTTAATTTTT
1 ATTTAATTTTA
2345475 ATTTAA-TTTA
1 ATTTAATTTTA
2345485 ATTTAATTTTA
1 ATTTAATTTTA
2345496 A
1 A
2345497 ATCAAATAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
10 9 0.33
11 18 0.67
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.64
Consensus pattern (11 bp):
ATTTAATTTTA
Found at i:2346378 original size:3 final size:3
Alignment explanation
Indices: 2346370--2346397 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2346360 ATATTTATAT
2346370 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2346398 ATTTAAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2347044 original size:15 final size:15
Alignment explanation
Indices: 2347024--2347071 Score: 53
Period size: 16 Copynumber: 3.2 Consensus size: 15
2347014 TTTTTGTTTT
2347024 AAAATTATTAAATAA
1 AAAATTATTAAATAA
* *
2347039 AAAATTATTATATTGA
1 AAAATTATTA-AATAA
*
2347055 TAAATTATT-AATAA
1 AAAATTATTAAATAA
2347069 AAA
1 AAA
2347072 TTAAAATATT
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
14 5 0.19
15 10 0.38
16 11 0.42
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (15 bp):
AAAATTATTAAATAA
Found at i:2347074 original size:13 final size:14
Alignment explanation
Indices: 2347024--2347071 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 14
2347014 TTTTTGTTTT
2347024 AAAATTATTAAATAA
1 AAAATTATT-AATAA
*
2347039 AAAATTATTATATTGA
1 AAAATTATTA-A-TAA
*
2347055 TAAATTATTAATAA
1 AAAATTATTAATAA
2347069 AAA
1 AAA
2347072 TTAAAATATT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
14 5 0.19
15 11 0.41
16 11 0.41
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (14 bp):
AAAATTATTAATAA
Found at i:2347080 original size:29 final size:31
Alignment explanation
Indices: 2347025--2347083 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 31
2347015 TTTTGTTTTA
**
2347025 AAATTATTAAATAAAAAATTATTATATTGAT
1 AAATTATTAAATAAAAAATTAAAATATTGAT
2347056 AAATTATT-AAT-AAAAATTAAAATATTGA
1 AAATTATTAAATAAAAAATTAAAATATTGA
2347084 ATAATAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 15 0.58
30 3 0.12
31 8 0.31
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (31 bp):
AAATTATTAAATAAAAAATTAAAATATTGAT
Found at i:2347325 original size:20 final size:19
Alignment explanation
Indices: 2347282--2347328 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
2347272 ATTTAAATAA
* *
2347282 ATTAAATTTGTATATTTAT
1 ATTATATTTATATATTTAT
2347301 ATTATATTTATATATTTTAT
1 ATTATATTTATATA-TTTAT
*
2347321 TTTATATT
1 ATTATATT
2347329 AAAAATTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
ATTATATTTATATATTTAT
Found at i:2347902 original size:2 final size:2
Alignment explanation
Indices: 2347890--2347921 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2347880 TTGGGACACT
2347890 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2347922 TGGAATATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2348093 original size:34 final size:33
Alignment explanation
Indices: 2348024--2348108 Score: 86
Period size: 34 Copynumber: 2.6 Consensus size: 33
2348014 TTTAAAAAAT
* * *
2348024 TAAAATAAAAATTAAATTAATATGATAAATTTTA
1 TAAAATAAAAATT-AATTAAGATCATAAATATTA
2348058 TAAAATAAAAATTAATTAAGA-CATAACATAATTA
1 TAAAATAAAAATTAATTAAGATCATAA-AT-ATTA
*
2348092 TAACA-AAAAA-TAATTAA
1 TAAAATAAAAATTAATTAA
2348109 AATACGATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
32 11 0.24
33 14 0.31
34 20 0.44
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (33 bp):
TAAAATAAAAATTAATTAAGATCATAAATATTA
Found at i:2348417 original size:23 final size:23
Alignment explanation
Indices: 2348391--2348466 Score: 84
Period size: 23 Copynumber: 3.2 Consensus size: 23
2348381 TGTATTAAAT
2348391 TAAAAAATAA-TACAAATATAATA
1 TAAAAAATAATTA-AAATATAATA
2348414 TAAAAAATAATTAAAATATAATA
1 TAAAAAATAATTAAAATATAATA
* *
2348437 TAAATAAAATTTATTAAAAAAT-ATA
1 T-AA-AAAA-TAATTAAAATATAATA
2348462 TAAAA
1 TAAAA
2348467 TAAATCATAT
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
23 23 0.49
24 6 0.13
25 8 0.17
26 10 0.21
ACGTcount: A:0.68, C:0.01, G:0.00, T:0.30
Consensus pattern (23 bp):
TAAAAAATAATTAAAATATAATA
Found at i:2348444 original size:16 final size:16
Alignment explanation
Indices: 2348373--2348471 Score: 53
Period size: 16 Copynumber: 6.1 Consensus size: 16
2348363 GGTAAACTAT
*
2348373 ATAAAATAT-GTATTAA
1 ATAAAATATAATA-TAA
* *
2348389 ATTAAAAAATAATACAA
1 A-TAAAATATAATATAA
* *
2348406 ATATAATATAAAAAATAA
1 ATA-AA-ATATAATATAA
*
2348424 TTAAAATATAATATAA
1 ATAAAATATAATATAA
*
2348440 ATAAAAT-TTAT-TAA
1 ATAAAATATAATATAA
*
2348454 A-AAATATATAAAATAA
1 ATAAA-ATATAATATAA
2348470 AT
1 AT
2348472 CATATAAAAT
Statistics
Matches: 61, Mismatches: 14, Indels: 15
0.68 0.16 0.17
Matches are distributed among these distances:
13 3 0.05
14 6 0.10
15 5 0.08
16 22 0.36
17 14 0.23
18 11 0.18
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32
Consensus pattern (16 bp):
ATAAAATATAATATAA
Found at i:2348465 original size:11 final size:11
Alignment explanation
Indices: 2348391--2348491 Score: 53
Period size: 11 Copynumber: 8.5 Consensus size: 11
2348381 TGTATTAAAT
2348391 TAAAAAATA-A
1 TAAAAAATATA
*
2348401 TACAAATATAATA
1 TA-AAAAAT-ATA
2348414 TAAAAAATA-A
1 TAAAAAATATA
*
2348424 TTAAAATATAATA
1 -TAAAAAAT-ATA
*
2348437 TAAATAAAATTTA
1 T-AA-AAAATATA
2348450 TTAAAAAATATA
1 -TAAAAAATATA
2348462 TAAAATAAATCATA
1 T-AAA-AAAT-ATA
**
2348476 TAAAATTTATA
1 TAAAAAATATA
2348487 TAAAA
1 TAAAA
2348492 TTAAAATACT
Statistics
Matches: 71, Mismatches: 8, Indels: 23
0.70 0.08 0.23
Matches are distributed among these distances:
10 3 0.04
11 22 0.31
12 20 0.28
13 17 0.24
14 9 0.13
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (11 bp):
TAAAAAATATA
Found at i:2348466 original size:37 final size:36
Alignment explanation
Indices: 2348411--2348491 Score: 105
Period size: 37 Copynumber: 2.2 Consensus size: 36
2348401 TACAAATATA
2348411 ATATAAAAAATAATTAAAATATAAT-ATAAATAAAATTT
1 ATATAAAAAATAATTAAAATA-AATCAT--ATAAAATTT
2348449 AT-TAAAAAAT-ATATAAAATAAATCATATAAAATTT
1 ATATAAAAAATAAT-TAAAATAAATCATATAAAATTT
2348484 ATATAAAA
1 ATATAAAA
2348492 TTAAAATACT
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
35 11 0.28
36 10 0.25
37 17 0.43
38 2 0.05
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.33
Consensus pattern (36 bp):
ATATAAAAAATAATTAAAATAAATCATATAAAATTT
Found at i:2348478 original size:14 final size:13
Alignment explanation
Indices: 2348365--2348481 Score: 50
Period size: 12 Copynumber: 9.1 Consensus size: 13
2348355 ATAATCATGG
2348365 TAAACTATATAAAA
1 TAAA-TATATAAAA
** *
2348379 TATGTAT-TAAAT
1 TAAATATATAAAA
* *
2348391 TAAA-AAATAATA
1 TAAATATATAAAA
*
2348403 CAAATATAATATAAA
1 TAAATAT-ATA-AAA
2348418 -AAATA-ATTAAAA
1 TAAATATA-TAAAA
*
2348430 TATA-ATAT-AAA
1 TAAATATATAAAA
* *
2348441 TAAAATTTATTAAA
1 T-AAATATATAAAA
2348455 -AAATATATAAAA
1 TAAATATATAAAA
2348467 TAAATCATATAAAA
1 TAAAT-ATATAAAA
2348481 T
1 T
2348482 TTATATAAAA
Statistics
Matches: 75, Mismatches: 16, Indels: 24
0.65 0.14 0.21
Matches are distributed among these distances:
11 5 0.07
12 30 0.40
13 16 0.21
14 22 0.29
15 2 0.03
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.32
Consensus pattern (13 bp):
TAAATATATAAAA
Found at i:2348710 original size:11 final size:11
Alignment explanation
Indices: 2348694--2348736 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
2348684 GCTCTTATCT
2348694 CTTTTTTTTTC
1 CTTTTTTTTTC
*
2348705 CTTTTTTCTT-
1 CTTTTTTTTTC
*
2348715 CTTTTTTTTTT
1 CTTTTTTTTTC
*
2348726 CTTTTCTTTTC
1 CTTTTTTTTTC
2348737 TTTCTTTCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
10 9 0.33
11 18 0.67
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (11 bp):
CTTTTTTTTTC
Found at i:2348717 original size:21 final size:21
Alignment explanation
Indices: 2348693--2348739 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
2348683 TGCTCTTATC
2348693 TCTTTTTTTTTCCTTTT-TTCT
1 TCTTTTTTTTTCCTTTTCTT-T
*
2348714 TCTTTTTTTTTTCTTTTCTTT
1 TCTTTTTTTTTCCTTTTCTTT
2348735 TCTTT
1 TCTTT
2348740 CTTTCATCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 22 0.92
22 2 0.08
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (21 bp):
TCTTTTTTTTTCCTTTTCTTT
Found at i:2348725 original size:14 final size:14
Alignment explanation
Indices: 2348706--2348743 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
2348696 TTTTTTTTCC
2348706 TTTTTTCTTCTT-TT
1 TTTTTTCTT-TTCTT
2348720 TTTTTTCTTTTCTT
1 TTTTTTCTTTTCTT
*
2348734 TTCTTTCTTT
1 TTTTTTCTTT
2348744 CATCAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 2 0.09
14 20 0.91
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTTTTCTTTTCTT
Found at i:2348737 original size:140 final size:137
Alignment explanation
Indices: 2348531--2348806 Score: 353
Period size: 136 Copynumber: 2.0 Consensus size: 137
2348521 AAGTCCAAGC
* * *
2348531 ACAAACACAAATTGTTCTTTCCTTTTCTTTTTTTCGTTTCCTCTCTTTTTCCTTTTCTGTTCTTT
1 ACAAACACAAATTGCTCTTTCCTCTTCTTTTTTTCCTTTCCTCTCTTTTTCCTTTTCTGTTC--T
**
2348596 CTTTCTTTCTTTCATCAAATTAAAAAA-AAAAACTTTAAAATACCTAAACTAACCCTTCACAAAT
64 -TTTCTTTCTTTCATCAAA-TAAAAAAGAAAAAAATTAAAATACCTAAACTAACCCTTCACAAAT
*
2348660 CTTAATTTCAA
127 CCTAATTTCAA
* ** * *
2348671 ACAAATACAAATTGCTCTTAT-CTCTT-TTTTTTTCCTTTTTTCTTCTTTTT-TTTTTCTTTTCT
1 ACAAACACAAATTGCTCTT-TCCTCTTCTTTTTTTCCTTTCCTC-TCTTTTTCCTTTTCTGTTCT
* *
2348733 TTTCTTTCTTTCATCAAATAAAAAAGAAAAAAATTCAAATACCTAAGCTAACCCTTCACAAATCC
64 TTTCTTTCTTTCATCAAATAAAAAAGAAAAAAATTAAAATACCTAAACTAACCCTTCACAAATCC
2348798 TAATTTCAA
129 TAATTTCAA
2348807 TGTTGAGTTG
Statistics
Matches: 120, Mismatches: 13, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
135 7 0.06
136 61 0.51
137 1 0.01
139 22 0.18
140 28 0.23
141 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.02, T:0.46
Consensus pattern (137 bp):
ACAAACACAAATTGCTCTTTCCTCTTCTTTTTTTCCTTTCCTCTCTTTTTCCTTTTCTGTTCTTT
TCTTTCTTTCATCAAATAAAAAAGAAAAAAATTAAAATACCTAAACTAACCCTTCACAAATCCTA
ATTTCAA
Found at i:2349591 original size:21 final size:22
Alignment explanation
Indices: 2349553--2349593 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
2349543 ATAATAAAAA
*
2349553 TTTAATTAATTTTAAAATTATT
1 TTTAATTAATTGTAAAATTATT
2349575 TTTAATT-ATTGTAAAATTA
1 TTTAATTAATTGTAAAATTA
2349594 AATTCTGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
TTTAATTAATTGTAAAATTATT
Found at i:2349653 original size:37 final size:35
Alignment explanation
Indices: 2349607--2349676 Score: 86
Period size: 37 Copynumber: 1.9 Consensus size: 35
2349597 TCTGATTAAG
*
2349607 TTATATTTAATTTAAGTAAATATTAAATATTTAAAAC
1 TTATATTTAATTCAAGTAAATATT-AAT-TTTAAAAC
* * *
2349644 TTATCTTTAATTCAATTATATATTAATTTTAAA
1 TTATATTTAATTCAAGTAAATATTAATTTTAAA
2349677 TTATTTTTGC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 6 0.21
36 3 0.10
37 20 0.69
ACGTcount: A:0.44, C:0.04, G:0.01, T:0.50
Consensus pattern (35 bp):
TTATATTTAATTCAAGTAAATATTAATTTTAAAAC
Found at i:2349931 original size:21 final size:22
Alignment explanation
Indices: 2349893--2349933 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
2349883 ATAATAAAAA
*
2349893 TTTAATTAATTTTAAAATTATT
1 TTTAATTAATTGTAAAATTATT
2349915 TTTAATT-ATTGTAAAATTA
1 TTTAATTAATTGTAAAATTA
2349934 AATTCTGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
TTTAATTAATTGTAAAATTATT
Found at i:2349993 original size:37 final size:35
Alignment explanation
Indices: 2349947--2350016 Score: 86
Period size: 37 Copynumber: 1.9 Consensus size: 35
2349937 TCTGATTAAG
*
2349947 TTATATTTAATTTAAGTAAATATTAAATATTTAAAAC
1 TTATATTTAATTCAAGTAAATATT-AAT-TTTAAAAC
* * *
2349984 TTATCTTTAATTCAATTATATATTAATTTTAAA
1 TTATATTTAATTCAAGTAAATATTAATTTTAAA
2350017 TTATTTTTGC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 6 0.21
36 3 0.10
37 20 0.69
ACGTcount: A:0.44, C:0.04, G:0.01, T:0.50
Consensus pattern (35 bp):
TTATATTTAATTCAAGTAAATATTAATTTTAAAAC
Found at i:2350260 original size:2 final size:2
Alignment explanation
Indices: 2350255--2350279 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2350245 GTAAAAAAAC
2350255 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2350280 AAACTATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2350332 original size:340 final size:340
Alignment explanation
Indices: 2349543--2350223 Score: 1060
Period size: 340 Copynumber: 2.0 Consensus size: 340
2349533 TAATTACAAA
* ** ** * * *
2349543 ATAATAAAAATTTAATTAATTTTAAAATTATTTTTAATTATTGTAAAATTAAATTCTGATTAAGT
1 ATAATAAAAATTGAATTAATTTTAAAAAAACATATAATTATTATAAAATTAAATACTGATTAAGT
* * * * * *
2349608 TATATTTAATTTAAGTAAATATTAAATATTTAAAACTTATCTTTAATTCAATTATATATTAATTT
66 CAAATGTAATCTAAGTAAATATTAAATAATCAAAACTTATCTTTAATTCAATTATATATTAATTT
2349673 TAAATTATTTTTGCTTAAAATAATTTGAAAAGTTTTTAATGGTAAAAAAGTTGATTAAAATAAAA
131 TAAATTATTTTTGCTTAAAATAATTTGAAAAGTTTTTAATGGTAAAAAAGTTGATTAAAATAAAA
* *
2349738 AAAATAATGCTAAATAATATAAAAGAGAAGAAAAAAAATGAAATGTGAATTCAGAGAGCTTAACT
196 AAAATAATGCTAAATAATATAAAAAAGAAGAAAAAAAATGAAATATGAATTCAGAGAGCTTAACT
*
2349803 TTTTTATTCATATAACTACTCTTAAGAGGTTATATTTAGTAAGTCTGTAATTCTAATGCAAATAT
261 TTTTTATTCATATAACTACTCTTAAGAGGTTATATTTAATAAGTCTGTAATTCTAATGCAAATAT
2349868 TTACAATTCCATTTC
326 TTACAATTCCATTTC
* ** ** * * *
2349883 ATAATAAAAATTTAATTAATTTTAAAATTATTTTTAATTATTGTAAAATTAAATTCTGATTAAGT
1 ATAATAAAAATTGAATTAATTTTAAAAAAACATATAATTATTATAAAATTAAATACTGATTAAGT
* * * * * *
2349948 TATATTTAATTTAAGTAAATATTAAATATTTAAAACTTATCTTTAATTCAATTATATATTAATTT
66 CAAATGTAATCTAAGTAAATATTAAATAATCAAAACTTATCTTTAATTCAATTATATATTAATTT
2350013 TAAATTATTTTTGCTTAAAATAATTTGAAAAGTTTTTAATGGTAAAAAAGTTGATTAAAAT-AAA
131 TAAATTATTTTTGCTTAAAATAATTTGAAAAGTTTTTAATGGTAAAAAAGTTGATTAAAATAAAA
2350077 AAAATAATGCTAAATAATATAAAAAAGAAG-AAAAAAATGAAATATGAATTCAGAGAGCTTAACT
196 AAAATAATGCTAAATAATATAAAAAAGAAGAAAAAAAATGAAATATGAATTCAGAGAGCTTAACT
2350141 TTTTTATTCATATAACTACTCTTAAGAGGTTATATTTAATAAGTCTGTAATTCTAATGCAAATAT
261 TTTTTATTCATATAACTACTCTTAAGAGGTTATATTTAATAAGTCTGTAATTCTAATGCAAATAT
*
2350206 TTACAATTCCTTTTC
326 TTACAATTCCATTTC
2350221 ATA
1 ATA
2350224 TCTTAGGTTG
Statistics
Matches: 337, Mismatches: 4, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
338 114 0.34
339 32 0.09
340 191 0.57
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.41
Consensus pattern (340 bp):
ATAATAAAAATTGAATTAATTTTAAAAAAACATATAATTATTATAAAATTAAATACTGATTAAGT
CAAATGTAATCTAAGTAAATATTAAATAATCAAAACTTATCTTTAATTCAATTATATATTAATTT
TAAATTATTTTTGCTTAAAATAATTTGAAAAGTTTTTAATGGTAAAAAAGTTGATTAAAATAAAA
AAAATAATGCTAAATAATATAAAAAAGAAGAAAAAAAATGAAATATGAATTCAGAGAGCTTAACT
TTTTTATTCATATAACTACTCTTAAGAGGTTATATTTAATAAGTCTGTAATTCTAATGCAAATAT
TTACAATTCCATTTC
Found at i:2350927 original size:22 final size:23
Alignment explanation
Indices: 2350888--2350932 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
2350878 GATAAAAAAA
2350888 ATAATAAAATAAATAAATAATTT
1 ATAATAAAATAAATAAATAATTT
2350911 ATAA-AAAATTAAA-AAATAATTT
1 ATAATAAAA-TAAATAAATAATTT
2350933 TTTATTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (23 bp):
ATAATAAAATAAATAAATAATTT
Found at i:2351974 original size:37 final size:36
Alignment explanation
Indices: 2351928--2352027 Score: 98
Period size: 36 Copynumber: 2.7 Consensus size: 36
2351918 TATATCCAAA
*
2351928 AAATAATTTAATTATTTTATA-TTAATATTTTAA-AATAT
1 AAAT-ATTT-ATTATTTTAAATTTAAT-TTTTAATAAT-T
*
2351966 AAATATTTATAATTTTAAATTTAATTTTTAATAATT
1 AAATATTTATTATTTTAAATTTAATTTTTAATAATT
*
2352002 ATAATATTT-TTATTTTTAATTATAAT
1 A-AATATTTATTATTTTAAATT-TAAT
2352028 CTCATATATA
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
36 27 0.50
37 23 0.43
38 4 0.07
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (36 bp):
AAATATTTATTATTTTAAATTTAATTTTTAATAATT
Found at i:2351999 original size:22 final size:22
Alignment explanation
Indices: 2351949--2352021 Score: 60
Period size: 22 Copynumber: 3.2 Consensus size: 22
2351939 TTATTTTATA
* *
2351949 TTAAT-ATTTTAAAATATAAATAT
1 TTAATAATTTT-AAAT-TTAATTT
2351972 TT-ATAATTTTAAATTTAATTT
1 TTAATAATTTTAAATTTAATTT
* *
2351993 TTAATAATTATAATATTTTTATTT
1 TTAATAATTTTAA-A-TTTAATTT
2352017 TTAAT
1 TTAAT
2352022 TATAATCTCA
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
21 7 0.17
22 15 0.36
23 8 0.19
24 12 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TTAATAATTTTAAATTTAATTT
Found at i:2353096 original size:1 final size:1
Alignment explanation
Indices: 2353049--2353083 Score: 52
Period size: 1 Copynumber: 35.0 Consensus size: 1
2353039 TCATTTTCTG
* *
2353049 AAAAAAAAAAAAAAAAAAAAACAAAAACAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2353084 GCTTGAGGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.94, C:0.06, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:2353238 original size:16 final size:16
Alignment explanation
Indices: 2353217--2353274 Score: 91
Period size: 16 Copynumber: 3.7 Consensus size: 16
2353207 GTTAAATTAT
2353217 TTAATTTAAATTTAAA
1 TTAATTTAAATTTAAA
2353233 TTAATTTAAATTTAAA
1 TTAATTTAAATTTAAA
* *
2353249 ATAA-TAAAATTTAAA
1 TTAATTTAAATTTAAA
2353264 TTAATTTAAAT
1 TTAATTTAAAT
2353275 AATTAGTTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
15 13 0.35
16 24 0.65
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TTAATTTAAATTTAAA
Found at i:2353275 original size:21 final size:21
Alignment explanation
Indices: 2353215--2353276 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
2353205 TTGTTAAATT
* *
2353215 ATTTAATTTAAATTTAAAT-TA
1 ATTTAAATT-AATTTAAATAAA
**
2353236 ATTTAAATTTAAAAT-AATAAA
1 ATTTAAA-TTAATTTAAATAAA
2353257 ATTTAAATTAATTTAAATAA
1 ATTTAAATTAATTTAAATAA
2353277 TTAGTTTAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
20 8 0.25
21 22 0.69
22 2 0.06
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
ATTTAAATTAATTTAAATAAA
Found at i:2354472 original size:16 final size:16
Alignment explanation
Indices: 2354451--2354510 Score: 75
Period size: 16 Copynumber: 3.8 Consensus size: 16
2354441 CTTAAAGGAC
2354451 ATAAATTTAAAATAAA
1 ATAAATTTAAAATAAA
*
2354467 ATAAATTTAAAATAAT
1 ATAAATTTAAAATAAA
* *
2354483 TTAAATATAAAATAAA
1 ATAAATTTAAAATAAA
* *
2354499 TTAAATCTAAAA
1 ATAAATTTAAAA
2354511 ATAATTTTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (16 bp):
ATAAATTTAAAATAAA
Found at i:2354477 original size:11 final size:11
Alignment explanation
Indices: 2354463--2354523 Score: 54
Period size: 11 Copynumber: 5.5 Consensus size: 11
2354453 AAATTTAAAA
2354463 TAAAATAAATT
1 TAAAATAAATT
2354474 TAAAAT-AATT
1 TAAAATAAATT
*
2354484 TAAATATAAA-A
1 TAAA-ATAAATT
*
2354495 TAAATTAAATCT
1 TAAAATAAAT-T
* *
2354507 AAAAATAATTT
1 TAAAATAAATT
2354518 TAAAAT
1 TAAAAT
2354524 TTAAATTAAC
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
10 12 0.31
11 18 0.46
12 9 0.23
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (11 bp):
TAAAATAAATT
Found at i:2354488 original size:32 final size:34
Alignment explanation
Indices: 2354452--2354528 Score: 104
Period size: 32 Copynumber: 2.3 Consensus size: 34
2354442 TTAAAGGACA
*
2354452 TAAATTTAAAATAAAATAAAT-TTAAAATAA-TT
1 TAAATTTAAAATAAAATAAATCTAAAAATAATTT
* *
2354484 TAAATATAAAATAAATTAAATCTAAAAATAATTT
1 TAAATTTAAAATAAAATAAATCTAAAAATAATTT
2354518 TAAAATTTAAA
1 T-AAATTTAAA
2354529 TTAACCCGAC
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
32 19 0.50
33 8 0.21
34 3 0.08
35 8 0.21
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.36
Consensus pattern (34 bp):
TAAATTTAAAATAAAATAAATCTAAAAATAATTT
Found at i:2355028 original size:2 final size:2
Alignment explanation
Indices: 2355021--2355056 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
2355011 TGAAATCAAG
* *
2355021 CT CT CT CT CT CT CT CT CT TT CT CT CT CT CT AT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2355057 TTGTAGAGCT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.03, C:0.44, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:2356228 original size:2 final size:2
Alignment explanation
Indices: 2356211--2356243 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
2356201 TTCCATATGC
*
2356211 AT AT A- AT AT AT CT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2356244 GCAGATGTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2359269 original size:53 final size:51
Alignment explanation
Indices: 2359212--2359327 Score: 128
Period size: 51 Copynumber: 2.2 Consensus size: 51
2359202 TAAGTTAATA
**
2359212 ATATTTTTTTTAAAATATATTAAAATAT-AATTAAT-TAAATATTATTTTTAAAT
1 ATATTTTTAATAAAA-ATATTAAAATATAAATTAATATAAA-A-T-TTTTTAAAT
* * * *
2359265 ATATTTTAAATAAAAATATTACAATTTAAATTAGTATAAAATTTTTTAAAT
1 ATATTTTTAATAAAAATATTAAAATATAAATTAATATAAAATTTTTTAAAT
2359316 ATATTTTTAATA
1 ATATTTTTAATA
2359328 TATTACAATT
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
51 20 0.37
52 11 0.20
53 19 0.35
54 4 0.07
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (51 bp):
ATATTTTTAATAAAAATATTAAAATATAAATTAATATAAAATTTTTTAAAT
Found at i:2359342 original size:47 final size:49
Alignment explanation
Indices: 2359211--2359366 Score: 140
Period size: 47 Copynumber: 3.1 Consensus size: 49
2359201 TTAAGTTAAT
* * * * * *
2359211 AATATTTTTTTTAAAATATATTAAAATAT-AATTAATTAAATATTATTTTTA
1 AATATATTTTATAAAA-ATATTACAATTTAAATTAGTAAAATA-T-TTTTTA
2359262 AATATATTTTAAATAAAAATATTACAATTTAAATTAGTATAAA-ATTTTTTA
1 AATATATTTT--ATAAAAATATTACAATTTAAATTAGTA-AAATATTTTTTA
* *
2359313 AATATATTTT-T-AATATATTACAATTTAAATTTGTAAAATATTGTTTTCA
1 AATATATTTTATAAAAATATTACAATTTAAATTAGTAAAATATT-TTTT-A
2359362 AATAT
1 AATAT
2359367 GAAGTATAAT
Statistics
Matches: 90, Mismatches: 8, Indels: 16
0.79 0.07 0.14
Matches are distributed among these distances:
46 3 0.03
47 25 0.28
48 5 0.06
49 6 0.07
51 25 0.28
52 11 0.12
53 12 0.13
54 3 0.03
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (49 bp):
AATATATTTTATAAAAATATTACAATTTAAATTAGTAAAATATTTTTTA
Found at i:2361402 original size:26 final size:25
Alignment explanation
Indices: 2361373--2361435 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 25
2361363 TTATTTTAAT
2361373 TAAAATTAGTATTTTTTAT-AAATAAA
1 TAAAATTA-TATTTTTTATCAAA-AAA
* *
2361399 TAAAATAATA-ATTTTATCAAAAAA
1 TAAAATTATATTTTTTATCAAAAAA
2361423 T-AAATTATATTTT
1 TAAAATTATATTTT
2361436 ACACTTGTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
23 7 0.23
24 12 0.39
25 5 0.16
26 7 0.23
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (25 bp):
TAAAATTATATTTTTTATCAAAAAA
Found at i:2364464 original size:38 final size:38
Alignment explanation
Indices: 2364413--2364507 Score: 127
Period size: 38 Copynumber: 2.5 Consensus size: 38
2364403 GTTACTGTTT
*
2364413 AGAATAGTAGTTTTTATTTCAAACCATGCCATTAATTG
1 AGAATAGTAGTTTTTATTTCAAACCATGCCATCAATTG
* * ** * *
2364451 AGAATACTAGTTTTTGTTTTGAACCATGCCATCACTTT
1 AGAATAGTAGTTTTTATTTCAAACCATGCCATCAATTG
2364489 AGAATAGTAGTTTTTATTT
1 AGAATAGTAGTTTTTATTT
2364508 TAACTTATAC
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 48 1.00
ACGTcount: A:0.31, C:0.13, G:0.14, T:0.43
Consensus pattern (38 bp):
AGAATAGTAGTTTTTATTTCAAACCATGCCATCAATTG
Found at i:2364648 original size:16 final size:17
Alignment explanation
Indices: 2364604--2364649 Score: 60
Period size: 16 Copynumber: 2.7 Consensus size: 17
2364594 TTGTTATTTG
2364604 ATAAATGTAATTTTGAAA
1 ATAAATG-AATTTTGAAA
2364622 ATAATAT-AATTTT-AAA
1 ATAA-ATGAATTTTGAAA
2364638 ATAAATGAATTT
1 ATAAATGAATTT
2364650 ATTGAATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 2 0.08
16 12 0.46
17 6 0.23
18 4 0.15
19 2 0.08
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (17 bp):
ATAAATGAATTTTGAAA
Found at i:2368839 original size:47 final size:47
Alignment explanation
Indices: 2368752--2368849 Score: 117
Period size: 47 Copynumber: 2.1 Consensus size: 47
2368742 CAAATATTGC
* * * * *
2368752 TATGCCAAGTAGTGTTATTACTAAGAAGCATTGTAGCCAAAGAGTGA
1 TATGCCAAGTAATGGTATTACTAAGAAGCACTCTAGCCAAAAAGTGA
* *
2368799 TATGCCAAGTAATGGTATTGCTAAGAAGCACCTCTA-CCAAAAAGTGT
1 TATGCCAAGTAATGGTATTACTAAGAAGCA-CTCTAGCCAAAAAGTGA
2368846 TATG
1 TATG
2368850 TAGCATTAGT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
47 40 0.93
48 3 0.07
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (47 bp):
TATGCCAAGTAATGGTATTACTAAGAAGCACTCTAGCCAAAAAGTGA
Found at i:2370274 original size:2 final size:2
Alignment explanation
Indices: 2370267--2370294 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2370257 CTCCCCTATT
2370267 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2370295 CTCACGAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2374541 original size:79 final size:77
Alignment explanation
Indices: 2374345--2374704 Score: 366
Period size: 79 Copynumber: 4.6 Consensus size: 77
2374335 TCATTAATAT
* * * * *
2374345 TTTTATTTCTAAAATA-TCGATTTTTTGCCATCGGGGAAACTCTAAGCCCGTTATTTTCGAGAGG
1 TTTTATTTCTAAAACACT-GATTTTCTACCATCGGGGATACTCTAACCCCGTTATTTTCGAG-GG
*
2374409 ATATTCCAACCCTG
64 ATACTCCAACCCTG
* * * * * *
2374423 GTTTATTTCTAAAACACCGATTTTCCACCATTGGAGATACTCTAACCTCGTTATTTTCGAAGGGA
1 TTTTATTTCTAAAACACTGATTTTCTACCATCGGGGATACTCTAACCCCGTTATTTTCG-AGGGA
*
2374488 TACTCCAACCCCAG
65 TACTCCAA-CCCTG
* * *
2374502 TTTTATTTCTAAAACACTGATTTTCTACCATCAGGGATACTTTAACCCCCTTATTTTCGAGGGGA
1 TTTTATTTCTAAAACACTGATTTTCTACCATCGGGGATACTCTAACCCCGTTATTTTCGA-GGGA
** *
2374567 TACTTTAACCTTG
65 TACTCCAACCCTG
* * * *
2374580 ATTTTATTTCTAAAACACCGATTTTATCACCATCGGGGATATTCCAACCCCGTTATTTTCGAGGG
1 -TTTTATTTCTAAAACACTGATTTTCT-ACCATCGGGGATACTCTAACCCCGTTATTTTCGAGGG
* * *
2374645 AATTCTTCAACCTTGG
64 -ATACTCCAACCCT-G
* *
2374661 TTTTATTT-TAAAACACTAATTTTCTACTATC-GGGATACTCTAAC
1 TTTTATTTCTAAAACACTGATTTTCTACCATCGGGGATACTCTAAC
2374705 TCTATTTTCA
Statistics
Matches: 233, Mismatches: 41, Indels: 17
0.80 0.14 0.06
Matches are distributed among these distances:
77 11 0.05
78 66 0.28
79 107 0.46
80 48 0.21
81 1 0.00
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.37
Consensus pattern (77 bp):
TTTTATTTCTAAAACACTGATTTTCTACCATCGGGGATACTCTAACCCCGTTATTTTCGAGGGAT
ACTCCAACCCTG
Found at i:2374728 original size:158 final size:157
Alignment explanation
Indices: 2374345--2374704 Score: 363
Period size: 157 Copynumber: 2.3 Consensus size: 157
2374335 TCATTAATAT
* * * * * * * * *
2374345 TTTTATTTCTAAAATA-TCGATTTTTTGCCATCGGGGAAACTCTAAGCCCGTTATTTTCGAGAGG
1 TTTTATTTCTAAAACACT-AATTTTCTACCATCAGGGATACTCTAA-CCCCTTATTTTCCAAAGG
* * * * * *
2374409 ATA-TTCCAACCCTG-GTTTATTTCTAAAACACCGATTTTCCACCATTGGAGATACTCTAACCTC
64 ATACTT-TAACCTTGATTTTATTTCTAAAACACCGATTTTCCACCATCGGAGATACTCCAACCCC
2374472 GTTATTTTCGAAGGGATACTCCAACCCCAG
128 GTTATTTTCGAAGGGATACTCCAACCCCAG
* * * **
2374502 TTTTATTTCTAAAACACTGATTTTCTACCATCAGGGATACTTTAACCCCCTTATTTTCGAGGGGA
1 TTTTATTTCTAAAACACTAATTTTCTACCATCAGGGATACTCTAA-CCCCTTATTTTCCAAAGGA
* * *
2374567 TACTTTAACCTTGATTTTATTTCTAAAACACCGATTTTATCACCATCGGGGATATTCCAACCCCG
65 TACTTTAACCTTGATTTTATTTCTAAAACACCGATTTT-CCACCATCGGAGATACTCCAACCCCG
* * ***
2374632 TTATTTTCG-AGGGAATTCTTCAACCTTGG
129 TTATTTTCGAAGGG-ATACTCCAACCCCAG
*
2374661 TTTTATTT-TAAAACACTAATTTTCTACTATC-GGGATACTCTAAC
1 TTTTATTTCTAAAACACTAATTTTCTACCATCAGGGATACTCTAAC
2374705 TCTATTTTCA
Statistics
Matches: 172, Mismatches: 26, Indels: 11
0.82 0.12 0.05
Matches are distributed among these distances:
156 1 0.01
157 73 0.42
158 51 0.30
159 47 0.27
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.37
Consensus pattern (157 bp):
TTTTATTTCTAAAACACTAATTTTCTACCATCAGGGATACTCTAACCCCTTATTTTCCAAAGGAT
ACTTTAACCTTGATTTTATTTCTAAAACACCGATTTTCCACCATCGGAGATACTCCAACCCCGTT
ATTTTCGAAGGGATACTCCAACCCCAG
Found at i:2374845 original size:51 final size:51
Alignment explanation
Indices: 2374749--2374865 Score: 175
Period size: 51 Copynumber: 2.3 Consensus size: 51
2374739 TGTTTTCGAA
2374749 AGGATACTCTAA-CCCAATTTTATTTTTAAAATATCGACTTTTCACCATCG
1 AGGATACTCTAACCCCAATTTTATTTTTAAAATATCGACTTTTCACCATCG
* * *
2374799 AGGATACTCCAACCCCATTTTTATTTTTAAAATATTGA-TTTCTCACCATCG
1 AGGATACTCTAACCCCAATTTTATTTTTAAAATATCGACTTT-TCACCATCG
*
2374850 GGGATACTCTAACCCC
1 AGGATACTCTAACCCC
2374866 GTTGTTTTCG
Statistics
Matches: 60, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
50 14 0.23
51 46 0.77
ACGTcount: A:0.30, C:0.25, G:0.09, T:0.36
Consensus pattern (51 bp):
AGGATACTCTAACCCCAATTTTATTTTTAAAATATCGACTTTTCACCATCG
Found at i:2380970 original size:20 final size:20
Alignment explanation
Indices: 2380927--2380976 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
2380917 GTTTGGGACA
* *
2380927 ATGTATCGATACAATTCTTT
1 ATGTATCGATACAATTCGTC
2380947 ATGTATCGATACAATGT-GTC
1 ATGTATCGATACAAT-TCGTC
2380967 ATGTATCGAT
1 ATGTATCGAT
2380977 GCAAACAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 26 0.96
21 1 0.04
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACAATTCGTC
Found at i:2381613 original size:19 final size:20
Alignment explanation
Indices: 2381586--2381623 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
2381576 GAACAAATAT
2381586 CAAAGTTTC-TCTTAAAGCA
1 CAAAGTTTCGTCTTAAAGCA
* *
2381605 CAAATTTTCGTTTTAAAGC
1 CAAAGTTTCGTCTTAAAGC
2381624 TTTCATTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.37
Consensus pattern (20 bp):
CAAAGTTTCGTCTTAAAGCA
Found at i:2383622 original size:15 final size:16
Alignment explanation
Indices: 2383592--2383622 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2383582 CAACATTTCC
2383592 TCTATTAAAAACTTTT
1 TCTATTAAAAACTTTT
2383608 TCTATTAAAAA-TTTT
1 TCTATTAAAAACTTTT
2383623 GAAAGCTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.52
Consensus pattern (16 bp):
TCTATTAAAAACTTTT
Found at i:2386751 original size:9 final size:9
Alignment explanation
Indices: 2386712--2386749 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
2386702 CGAGTCAACT
2386712 TCATCATTA
1 TCATCATTA
*
2386721 TCATCATCA
1 TCATCATTA
2386730 TCATCATTA
1 TCATCATTA
*
2386739 TCTTCATTA
1 TCATCATTA
2386748 TC
1 TC
2386750 TTTGATGGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.29, C:0.26, G:0.00, T:0.45
Consensus pattern (9 bp):
TCATCATTA
Found at i:2388365 original size:20 final size:20
Alignment explanation
Indices: 2388340--2388393 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 20
2388330 ATTTGGGACA
2388340 ATGTATCGATACAAT-T-CTTC
1 ATGTATCGATACAATGTGC--C
2388360 ATGTATCGATACAATGTGCC
1 ATGTATCGATACAATGTGCC
2388380 ATGTATCGATACAA
1 ATGTATCGATACAA
2388394 ACAGTGGTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 30 0.94
21 1 0.03
22 1 0.03
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACAATGTGCC
Found at i:2389349 original size:161 final size:161
Alignment explanation
Indices: 2389083--2389405 Score: 556
Period size: 161 Copynumber: 2.0 Consensus size: 161
2389073 TTTTTGATAA
2389083 AAAATGGATTTTAAAATATAACTGATAATTTAAATAAAAGGACTAAATTAATTTTTTTTAGTGTT
1 AAAATGGATTTTAAAATATAACTGATAATTTAAATAAAAGGACTAAATTAATTTTTTTTAGTGTT
* ** **
2389148 TGGGCCTTGATCTGACCCTAATGAGATCCATATTTGACTTAAAAATCCATCAAAGTGTTGATTGA
66 TGGGCCTTGATCCGACCCTAATGAGATCCATACATGACTTAAAAATCCATCAAAGCATTGATTGA
*
2389213 GCCTTTCAGACCCATTCAAAGGCATTCAAAC
131 GCCTATCAGACCCATTCAAAGGCATTCAAAC
* * *
2389244 AAAATGGATTTTAAAATATAACTGATAATTTAAATAAAAGGACTAAATTGATTTTTTTTTGTTTT
1 AAAATGGATTTTAAAATATAACTGATAATTTAAATAAAAGGACTAAATTAATTTTTTTTAGTGTT
*
2389309 TGGGCCTTGATCCGACCTTAATGAGATCCATACATGACTTAAAAATCCATCAAAGCATTGATTGA
66 TGGGCCTTGATCCGACCCTAATGAGATCCATACATGACTTAAAAATCCATCAAAGCATTGATTGA
2389374 GCCTATCAGACCCATTCAAAGGCATTCAAAC
131 GCCTATCAGACCCATTCAAAGGCATTCAAAC
2389405 A
1 A
2389406 CCTTGAAAAG
Statistics
Matches: 152, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
161 152 1.00
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.33
Consensus pattern (161 bp):
AAAATGGATTTTAAAATATAACTGATAATTTAAATAAAAGGACTAAATTAATTTTTTTTAGTGTT
TGGGCCTTGATCCGACCCTAATGAGATCCATACATGACTTAAAAATCCATCAAAGCATTGATTGA
GCCTATCAGACCCATTCAAAGGCATTCAAAC
Found at i:2390924 original size:10 final size:10
Alignment explanation
Indices: 2390909--2390942 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
2390899 AAACCTCAAA
2390909 TTTTCTTAAG
1 TTTTCTTAAG
2390919 TTTTCTTAAG
1 TTTTCTTAAG
* *
2390929 GTTTCTTAGG
1 TTTTCTTAAG
2390939 TTTT
1 TTTT
2390943 TTTGGTCTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.15, C:0.09, G:0.15, T:0.62
Consensus pattern (10 bp):
TTTTCTTAAG
Found at i:2392463 original size:20 final size:20
Alignment explanation
Indices: 2392418--2392469 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
2392408 GTAGCCAAAC
**
2392418 TTGTATCGATACACAAAGTA
1 TTGTATCGATACACAAAAAA
2392438 -TGTATCGATACACAAAAAA
1 TTGTATCGATACACAAAAAA
2392457 TTGTATCGATACA
1 TTGTATCGATACA
2392470 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.29
Consensus pattern (20 bp):
TTGTATCGATACACAAAAAA
Found at i:2392532 original size:20 final size:21
Alignment explanation
Indices: 2392503--2392541 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
2392493 GCTATATTTT
2392503 AAAATATGTATCGATACATCA
1 AAAATATGTATCGATACATCA
2392524 AAAAT-TGTATCGATACAT
1 AAAATATGTATCGATACAT
2392542 TCACACGGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.46, C:0.13, G:0.10, T:0.31
Consensus pattern (21 bp):
AAAATATGTATCGATACATCA
Found at i:2394704 original size:21 final size:21
Alignment explanation
Indices: 2394671--2394720 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
2394661 TTGCAAGTTG
*
2394671 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
2394693 AAATAATG-AGTTAGCTAAGAA
1 AAATAAAGAAGTTAGCTAAG-A
2394714 AAATAAA
1 AAATAAA
2394721 AACTTGCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 16 0.67
22 7 0.29
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:2398813 original size:32 final size:33
Alignment explanation
Indices: 2398770--2398833 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
2398760 TAGCCAAACT
* **
2398770 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCAATACACAAAAAATTGTATCGATACAA
2398802 TGTATCAATACACAAAAAATTGTATCGATACA
1 TGTATCAATACACAAAAAATTGTATCGATACA
2398834 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.28
Consensus pattern (33 bp):
TGTATCAATACACAAAAAATTGTATCGATACAA
Found at i:2398896 original size:20 final size:21
Alignment explanation
Indices: 2398867--2398905 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
2398857 GCTATATTTT
2398867 AAAATATGTATCGATACATCA
1 AAAATATGTATCGATACATCA
2398888 AAAAT-TGTATCGATACAT
1 AAAATATGTATCGATACAT
2398906 TCACACGGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.46, C:0.13, G:0.10, T:0.31
Consensus pattern (21 bp):
AAAATATGTATCGATACATCA
Found at i:2402006 original size:28 final size:28
Alignment explanation
Indices: 2401925--2402006 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
2401915 TTTTGGAGAT
*
2401925 AATAACGAGGTTGGAGTGTTCCCTCG--GA
1 AATAACGAGGTTGGAGT-AT-CCTCGATGA
* * *
2401953 AGTAACGGGGTTGGAGTATCCCCGATGA
1 AATAACGAGGTTGGAGTATCCTCGATGA
2401981 AATAACGAGGTTGGAGTATCCTCGAT
1 AATAACGAGGTTGGAGTATCCTCGAT
2402007 TGTGAAAAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
26 4 0.09
27 1 0.02
28 40 0.89
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (28 bp):
AATAACGAGGTTGGAGTATCCTCGATGA
Found at i:2402149 original size:51 final size:51
Alignment explanation
Indices: 2401989--2402159 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
2401979 GAAATAACGA
* * *
2401989 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGAAAATAAAATCGG
** * * * * *
2402041 AATTGGAGTATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT--ATGAAAAATTGGTATTTTGAAAATAAAATCGG
* * *
2402094 GGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
2402145 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
2402160 TCAGAAATAA
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 39 0.40
52 16 0.16
53 32 0.33
54 10 0.10
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
Found at i:2402205 original size:27 final size:28
Alignment explanation
Indices: 2402142--2402217 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
2402132 AAAATAAAGT
*
2402142 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
*
2402170 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
2402197 CGGGGTTGGAGTGTCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
2402218 TGTGAAGAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:2404700 original size:13 final size:13
Alignment explanation
Indices: 2404682--2404707 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2404672 ACAAAGATCC
2404682 ATGTATCGATACA
1 ATGTATCGATACA
2404695 ATGTATCGATACA
1 ATGTATCGATACA
2404708 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:2404703 original size:33 final size:33
Alignment explanation
Indices: 2404661--2404727 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2404651 AAAATTTCCA
***
2404661 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
2404694 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
2404727 A
1 A
2404728 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:2404771 original size:19 final size:18
Alignment explanation
Indices: 2404747--2404814 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
2404737 CAGTAGCTAA
2404747 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
2404766 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
2404781 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
2404798 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
2404815 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:2404787 original size:13 final size:13
Alignment explanation
Indices: 2404769--2404793 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2404759 ACAATACTTA
2404769 TGTATCGATACAT
1 TGTATCGATACAT
2404782 TGTATCGATACA
1 TGTATCGATACA
2404794 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:2404791 original size:32 final size:32
Alignment explanation
Indices: 2404750--2404812 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
2404740 TAGCTAATTA
*
2404750 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
2404782 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
2404813 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:2404894 original size:21 final size:21
Alignment explanation
Indices: 2404870--2404926 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
2404860 CATTTGTAGG
2404870 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
2404891 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
2404912 ATGTATCGATACATT
1 ATGTATCGATACATT
2404927 TATTTATTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:2406763 original size:345 final size:345
Alignment explanation
Indices: 2406126--2406823 Score: 1360
Period size: 345 Copynumber: 2.0 Consensus size: 345
2406116 CCATTCCTTT
*
2406126 TCTTTTATATCCACAGAACAAACCTCTTCATGTAGTACACCAAGAATAGAATCTGGTATAACTTC
1 TCTTTCATATCCACAGAACAAACCTCTTCATGTAGTACACCAAGAATAGAATCTGGTATAACTTC
2406191 ATCATATTGAAATAACTAGTATGTTAGCAAATCTAATAATGTTTTAGACTTTATAACCTTTTGTT
66 ATCATATTGAAATAACTAGTATGTTAGCAAATCTAATAATGTTTTAGACTTTATAACCTTTTGTT
2406256 AAGCAGCTAATGTCAAACTCTCCTAATAGCAAAAGCCATTTTGCTATCCTCCCTAATATTGTTGG
131 AAGCAGCTAATGTCAAACTCTCCTAATAGCAAAAGCCATTTTGCTATCCTCCCTAATATTGTTGG
*
2406321 CTTGGAAAGAAATTACTTAATCGGATTAAACTTAGTCATTACCATGAGTTTTTGAGCTAGAAAGT
196 CTTGGAAAGAAATTACTTAATCAGATTAAACTTAGTCATTACCATGAGTTTTTGAGCTAGAAAGT
2406386 TGTGATCGAGATTTTGAATAGCAAACACCAATGTAAGATAGTACTTCTGCATTAAAAGATAATTC
261 TGTGATCGAGATTTTGAATAGCAAACACCAATGTAAGATAGTACTTCTGCATTAAAAGATAATTC
2406451 ACCTCACTACCATGCAAACA
326 ACCTCACTACCATGCAAACA
2406471 TCTTTCATATCCACAGAACAAACCTCTTCATGTAGTACACCAAGAATAGAATCTGGTATAACTTC
1 TCTTTCATATCCACAGAACAAACCTCTTCATGTAGTACACCAAGAATAGAATCTGGTATAACTTC
*
2406536 ATCATATTGAAATAAGTAGTATGTTAGCAAATCTAATAATGTTTTAGACTTTATAACCTTTTGTT
66 ATCATATTGAAATAACTAGTATGTTAGCAAATCTAATAATGTTTTAGACTTTATAACCTTTTGTT
2406601 AAGCAGCTAATGTCAAACTCTCCTAATAGCAAAAGCCATTTTGCTATCCTCCCTAATATTGTTGG
131 AAGCAGCTAATGTCAAACTCTCCTAATAGCAAAAGCCATTTTGCTATCCTCCCTAATATTGTTGG
2406666 CTTGGAAAGAAATTACTTAATCAGATTAAACTTAGTCATTACCATGAGTTTTTGAGCTAGAAAGT
196 CTTGGAAAGAAATTACTTAATCAGATTAAACTTAGTCATTACCATGAGTTTTTGAGCTAGAAAGT
2406731 TGTGATCGAGATTTTGAATAGCAAACACCAATGTAAGATAGTACTTCTGCATTAAAAGATAATTC
261 TGTGATCGAGATTTTGAATAGCAAACACCAATGTAAGATAGTACTTCTGCATTAAAAGATAATTC
2406796 ACCTCACTACCATGCAAACA
326 ACCTCACTACCATGCAAACA
2406816 TCTATTCA
1 TCT-TTCA
2406824 AATAGTTCAT
Statistics
Matches: 349, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
345 345 0.99
346 4 0.01
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.33
Consensus pattern (345 bp):
TCTTTCATATCCACAGAACAAACCTCTTCATGTAGTACACCAAGAATAGAATCTGGTATAACTTC
ATCATATTGAAATAACTAGTATGTTAGCAAATCTAATAATGTTTTAGACTTTATAACCTTTTGTT
AAGCAGCTAATGTCAAACTCTCCTAATAGCAAAAGCCATTTTGCTATCCTCCCTAATATTGTTGG
CTTGGAAAGAAATTACTTAATCAGATTAAACTTAGTCATTACCATGAGTTTTTGAGCTAGAAAGT
TGTGATCGAGATTTTGAATAGCAAACACCAATGTAAGATAGTACTTCTGCATTAAAAGATAATTC
ACCTCACTACCATGCAAACA
Found at i:2409600 original size:155 final size:154
Alignment explanation
Indices: 2408956--2409641 Score: 406
Period size: 153 Copynumber: 4.5 Consensus size: 154
2408946 TTTAATATAG
* * ** ** *
2408956 AATTACCAAAATACCTTT-GTGGTATACCTTCGA-TATAAAAATGCCCCGATAACTCC-AAAAGC
1 AATTACCAAAATGCCTTTAG-GGTATACATTCGACT-TAAAAATATCCTAATAAC-CCTAAAAGA
* * * *
2409018 CTTGAAAATAATCAT-AGAAAGGTGAACATATCCTAAATGCACACATTT-ACATAAAAGCAT-CT
63 CTTAAAAATAATCATAAG-AAGGTGAACCTATCCTAAATGCACACCTTTGGCATAAAAGCATCCT
* * *
2409080 AGGTGATTATATTAGACTC-GATTATAAAA
127 A-GTGACTATATCAGACTCAGTTTA-AAAA
* * * * * * ** * *** * *
2409109 AATTATCAAAATACCCTTAGGG-ACTATC-TT-TATTTTGAAAGCATCCCAGCGACCCTACAGGA
1 AATTACCAAAATGCCTTTAGGGTA-TA-CATTCGA-CTTAAAAATATCCTAATAACCCTAAAAGA
* ** * *
2409171 CTTAAAGATAATCATAA-AAGAGAAAATCTATCCTAAATACACACCTTTGGCAT-AAAGCAT-CT
63 CTTAAAAATAATCATAAGAAG-GTGAACCTATCCTAAATGCACACCTTTGGCATAAAAGCATCCT
* *
2409233 CGGTGACTATATC-GAACTCAGTTTTAAAA
127 -AGTGACTATATCAG-ACTCAGTTTAAAAA
* * *
2409262 AATTATCAAAATGCCTTTAGGATATAGC-TTCGACTTAAAAATGTCCTAATAACCCTAAAAGACT
1 AATTACCAAAATGCCTTTAGGGTATA-CATTCGACTTAAAAATATCCTAATAACCCTAAAAGACT
* * * *
2409326 TGAAAATAATCATAAGAAGGTGAACTTATCCTAAATGCACACCTTTGGTATAAAAGCA-CCTTGA
65 TAAAAATAATCATAAGAAGGTGAACCTATCCTAAATGCACACCTTTGGCATAAAAGCATCCTAG-
* * * **
2409390 TGACCACATCAGACTTAGTTTTAGGAA
129 TGACTATATCAGACTCAG-TTTAAAAA
* * * ** * * * * * * * *
2409417 AATTACTAAAATGCCCTAAAAG-ACTACATTTGTCTTGAATATATTCTGATAACCTTAAAGGA-T
1 AATTACCAAAATGCCTTTAGGGTA-TACATTCGACTTAAAAATATCCTAATAACCCTAAAAGACT
* *
2409480 TAAAAAATGATCATAA-AAGGGTGAACCTATCCTAAATGCATA-CTTTGGCATAAAAGCATCCTA
65 T-AAAAATAATCATAAGAA-GGTGAACCTATCCTAAATGCACACCTTTGGCATAAAAGCATCCTA
*
2409543 GTGACTATATCAGACTCAATTCTAAAAAA
128 GTGACTATATCAGACTCAGTT-T-AAAAA
* * * * ** * *
2409572 AATTACCAAAATGCCTTTGGGGTATACATTCGACAT-GAAATATCCTGATGGCCCTAAAATACTA
1 AATTACCAAAATGCCTTTAGGGTATACATTCGACTTAAAAATATCCTAATAACCCTAAAAGACTT
2409636 AAAAAT
66 AAAAAT
2409642 GATATTTTTA
Statistics
Matches: 398, Mismatches: 106, Indels: 57
0.71 0.19 0.10
Matches are distributed among these distances:
152 8 0.02
153 180 0.45
154 95 0.24
155 114 0.29
156 1 0.00
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.28
Consensus pattern (154 bp):
AATTACCAAAATGCCTTTAGGGTATACATTCGACTTAAAAATATCCTAATAACCCTAAAAGACTT
AAAAATAATCATAAGAAGGTGAACCTATCCTAAATGCACACCTTTGGCATAAAAGCATCCTAGTG
ACTATATCAGACTCAGTTTAAAAA
Found at i:2410242 original size:166 final size:164
Alignment explanation
Indices: 2410045--2410344 Score: 397
Period size: 166 Copynumber: 1.8 Consensus size: 164
2410035 TAAAACACAA
* ** *
2410045 AATTAAACATCAAATATATCAAAATTAATACAAAAATTGGATCCAAAAGCCACAAAAAAGGTTTA
1 AATTAAACATCAAATATATCAAAACTAATACAAAAATCAGATCCAAAAGCCACAAAAAA-GATTA
* *
2410110 -GCCAATCACCTTTGACCTTGAAACAAATTTTTTTAATATTTACAAATAAA-CTCTTCAACATTT
65 GGCCAATCACCTTTGACCTAG-AACAAA-TTTTTTAATATTTACAAATAAACCTC-TAAACATTT
2410173 TAAATTTGGAAATTGATCTTTACATAATTGAAACTTAG
127 TAAATTTGGAAATTGATCTTTACATAATTGAAACTTAG
* * * * *
2410211 AATTAAACATCCAATATATCAAAACTAATACAAAAATCATATCCAAAAGTCATAAGAAAGATTAG
1 AATTAAACATCAAATATATCAAAACTAATACAAAAATCAGATCCAAAAGCCACAAAAAAGATTAG
** * * * *
2410276 GCCAATTTCCTTTGGCCTAGAACAAATTTTTTAATGTTTACAAATAAGCCTCTAAACATTTTAGA
66 GCCAATCACCTTTGACCTAGAACAAATTTTTTAATATTTACAAATAAACCTCTAAACATTTTAAA
2410341 TTTG
131 TTTG
2410345 CAAAAAGGCT
Statistics
Matches: 115, Mismatches: 17, Indels: 6
0.83 0.12 0.04
Matches are distributed among these distances:
164 35 0.30
165 13 0.11
166 67 0.58
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (164 bp):
AATTAAACATCAAATATATCAAAACTAATACAAAAATCAGATCCAAAAGCCACAAAAAAGATTAG
GCCAATCACCTTTGACCTAGAACAAATTTTTTAATATTTACAAATAAACCTCTAAACATTTTAAA
TTTGGAAATTGATCTTTACATAATTGAAACTTAG
Found at i:2418291 original size:19 final size:20
Alignment explanation
Indices: 2418267--2418307 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
2418257 CTCCATCAAT
*
2418267 TACTTTTATTGTCAAA-AAA
1 TACTTTTAATGTCAAATAAA
*
2418286 TACTTTTAATGTTAAATAAA
1 TACTTTTAATGTCAAATAAA
2418306 TA
1 TA
2418308 ATAAATATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (20 bp):
TACTTTTAATGTCAAATAAA
Found at i:2418464 original size:10 final size:9
Alignment explanation
Indices: 2418449--2418477 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
2418439 AAAAATTCAA
2418449 TTTTTTTCT
1 TTTTTTTCT
2418458 TTTTTTTCT
1 TTTTTTTCT
2418467 TTTTTTT-T
1 TTTTTTTCT
2418475 TTT
1 TTT
2418478 ACACGTTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 4 0.20
9 16 0.80
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:2420056 original size:40 final size:39
Alignment explanation
Indices: 2420008--2420089 Score: 114
Period size: 40 Copynumber: 2.1 Consensus size: 39
2419998 TAATCCACTT
*
2420008 ATTAATATTTAAATATTATTT-AATTTATTTATTTA-AAAA
1 ATTAATATTTAAATATT-TTTAAATTTA-TAATTTATAAAA
2420047 ATTATATATTTAAATATTTTTAAATTTATAATTTATAAAA
1 ATTA-ATATTTAAATATTTTTAAATTTATAATTTATAAAA
2420087 ATT
1 ATT
2420090 TATTAATAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
39 13 0.33
40 26 0.67
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (39 bp):
ATTAATATTTAAATATTTTTAAATTTATAATTTATAAAA
Found at i:2420960 original size:11 final size:11
Alignment explanation
Indices: 2420944--2421030 Score: 63
Period size: 11 Copynumber: 7.8 Consensus size: 11
2420934 CAATGAATTG
2420944 ATATTATATTT
1 ATATTATATTT
*
2420955 ATATTATTTTT
1 ATATTATATTT
*
2420966 ATATTATAATT
1 ATATTATATTT
2420977 ATATTCATA-TT
1 ATATT-ATATTT
**
2420988 ATTATATATATAA
1 A-TAT-TATATTT
*
2421001 ATTTTAATATTT
1 ATATT-ATATTT
2421013 -TATTA-ATTT
1 ATATTATATTT
*
2421022 TTATTATAT
1 ATATTATAT
2421031 AAATTTTGAT
Statistics
Matches: 60, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
9 4 0.07
10 6 0.10
11 33 0.55
12 15 0.25
13 2 0.03
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (11 bp):
ATATTATATTT
Found at i:2420977 original size:17 final size:18
Alignment explanation
Indices: 2420947--2420998 Score: 56
Period size: 17 Copynumber: 3.0 Consensus size: 18
2420937 TGAATTGATA
*
2420947 TTATATT-TATATTATTT
1 TTATATTATATATTATAT
2420964 TTATATTATA-ATTATAT
1 TTATATTATATATTATAT
*
2420981 TCATATTAT-TATATATAT
1 TTATATTATATAT-TATAT
2420999 AAATTTTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
17 23 0.77
18 7 0.23
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (18 bp):
TTATATTATATATTATAT
Found at i:2421035 original size:15 final size:15
Alignment explanation
Indices: 2420989--2421037 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
2420979 ATTCATATTA
2420989 TTATATATATAAATTT
1 TTAT-TATATAAATTT
* *
2421005 TAATATTTTATTAATTT
1 T--TATTATATAAATTT
2421022 TTATTATATAAATTT
1 TTATTATATAAATTT
2421037 T
1 T
2421038 GATATATTCA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
15 13 0.48
16 1 0.04
17 10 0.37
18 3 0.11
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TTATTATATAAATTT
Found at i:2422112 original size:32 final size:32
Alignment explanation
Indices: 2422072--2422138 Score: 125
Period size: 32 Copynumber: 2.1 Consensus size: 32
2422062 CATTAAACAG
*
2422072 CCAACCAACAACACCAACAATAGCAACCACCA
1 CCAACCAACAACACCAACAATAGCAACAACCA
2422104 CCAACCAACAACACCAACAATAGCAACAACCA
1 CCAACCAACAACACCAACAATAGCAACAACCA
2422136 CCA
1 CCA
2422139 TTACTTATAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.51, C:0.43, G:0.03, T:0.03
Consensus pattern (32 bp):
CCAACCAACAACACCAACAATAGCAACAACCA
Found at i:2422353 original size:23 final size:24
Alignment explanation
Indices: 2422327--2422374 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
2422317 TGACAAATCT
2422327 ACTAAAAC-ATAAAAAATAA-TAAA
1 ACTAAAACTATAAAAAA-AAGTAAA
*
2422350 ACTAAAACTTTAAAAAAAAGTAAA
1 ACTAAAACTATAAAAAAAAGTAAA
2422374 A
1 A
2422375 TCTTGTTAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 10 0.45
24 12 0.55
ACGTcount: A:0.71, C:0.08, G:0.02, T:0.19
Consensus pattern (24 bp):
ACTAAAACTATAAAAAAAAGTAAA
Found at i:2424279 original size:2 final size:2
Alignment explanation
Indices: 2424272--2424309 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2424262 GAGAAGCTAC
2424272 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2424310 CTTTGACATG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2424356 original size:2 final size:2
Alignment explanation
Indices: 2424349--2424375 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2424339 AAAGAGTGTA
2424349 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
2424376 ATAGGAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2425920 original size:18 final size:19
Alignment explanation
Indices: 2425897--2425932 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
2425887 TACGTGAGTG
2425897 AAATTATATTTAA-AAAAA
1 AAATTATATTTAAGAAAAA
*
2425915 AAATTATGTTTAAGAAAA
1 AAATTATATTTAAGAAAA
2425933 TTAAAGGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (19 bp):
AAATTATATTTAAGAAAAA
Done.