Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold56
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: 1793205
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 19648 characters in sequence are not A, C, G, or T
File 11 of 11
Found at i:1683460 original size:27 final size:28
Alignment explanation
Indices: 1683398--1683470 Score: 96
Period size: 27 Copynumber: 2.6 Consensus size: 28
1683388 ATAAAACCGA
*
1683398 GGTTGGAGTATCCCCTCA-GAAATAACGG
1 GGTTGGAGTATCCCC-GATGAAATAACGG
* *
1683426 GGTCGGAGTATCCCCGATG-ATTAACGG
1 GGTTGGAGTATCCCCGATGAAATAACGG
1683453 GGTTGGAGTATCCCCGAT
1 GGTTGGAGTATCCCCGAT
1683471 TGTGAAGAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
27 25 0.62
28 15 0.38
ACGTcount: A:0.23, C:0.22, G:0.32, T:0.23
Consensus pattern (28 bp):
GGTTGGAGTATCCCCGATGAAATAACGG
Found at i:1683554 original size:51 final size:52
Alignment explanation
Indices: 1683458--1683586 Score: 163
Period size: 51 Copynumber: 2.5 Consensus size: 52
1683448 AACGGGGTTG
* *
1683458 GAGTATCCCCGATTGT-GAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTA
1 GAGTATCCCCGATTGTAG-A-AAATTAGTG-TTTTTGAAAATAAAATCGGAGTTA
* *
1683512 GAGTATCCCCGATTATAGAAAATTAGTG-TTTTGAAAATAAAATCGGAGTTG
1 GAGTATCCCCGATTGTAGAAAATTAGTGTTTTTGAAAATAAAATCGGAGTTA
* *
1683563 GAATATCCCCGATTGTAGAGAATT
1 GAGTATCCCCGATTGTAGAAAATT
1683587 GAGAAACTCA
Statistics
Matches: 67, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
51 42 0.63
53 8 0.12
54 16 0.24
55 1 0.01
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.32
Consensus pattern (52 bp):
GAGTATCCCCGATTGTAGAAAATTAGTGTTTTTGAAAATAAAATCGGAGTTA
Found at i:1685962 original size:13 final size:13
Alignment explanation
Indices: 1685944--1685969 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1685934 ACAAAGATCC
1685944 ATGTATCGATACA
1 ATGTATCGATACA
1685957 ATGTATCGATACA
1 ATGTATCGATACA
1685970 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:1685965 original size:33 final size:33
Alignment explanation
Indices: 1685923--1685989 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1685913 AAAATTTCCA
***
1685923 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
1685956 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
1685989 A
1 A
1685990 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:1686049 original size:13 final size:13
Alignment explanation
Indices: 1686031--1686055 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1686021 ACAATGCTTA
1686031 TGTATCGATACAT
1 TGTATCGATACAT
1686044 TGTATCGATACA
1 TGTATCGATACA
1686056 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:1686053 original size:32 final size:32
Alignment explanation
Indices: 1686012--1686074 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
1686002 TAGCTAATTA
**
1686012 TGTATCGATACAATGCTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
1686044 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
1686075 AATTGTTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:1686076 original size:19 final size:19
Alignment explanation
Indices: 1686009--1686076 Score: 76
Period size: 19 Copynumber: 3.9 Consensus size: 19
1685999 CAGTAGCTAA
**
1686009 TTATGTATCGATACAATGC
1 TTATGTATCGATACAAAAC
1686028 TTATGTATCGATAC---A-
1 TTATGTATCGATACAAAAC
1686043 -T-TGTATCGATACAAAAC
1 TTATGTATCGATACAAAAC
1686060 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
1686077 TTGTTGAATT
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 1 0.02
18 1 0.02
19 28 0.67
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (19 bp):
TTATGTATCGATACAAAAC
Found at i:1686138 original size:21 final size:21
Alignment explanation
Indices: 1686112--1686188 Score: 111
Period size: 21 Copynumber: 3.7 Consensus size: 21
1686102 GTTGGGACCT
* *
1686112 TGTATCGATACATTTGTA-GAA
1 TGTATCGATACA-TTCTACAAA
*
1686133 TGTATCGATACATTCCACAAA
1 TGTATCGATACATTCTACAAA
1686154 TGTATCGATACATTCTACAAA
1 TGTATCGATACATTCTACAAA
1686175 TGTATCGATACATT
1 TGTATCGATACATT
1686189 TGGATAATTT
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
20 3 0.06
21 48 0.94
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (21 bp):
TGTATCGATACATTCTACAAA
Found at i:1686911 original size:42 final size:42
Alignment explanation
Indices: 1686864--1686951 Score: 115
Period size: 42 Copynumber: 2.1 Consensus size: 42
1686854 CTATTTTCCA
* *
1686864 AGGACAAAAGAAAAAGGGAAATGAAA-TATGTCCTGCTCTCTG
1 AGGACAAAAGAAAAAGGAAAAT-AAAGTATATCCTGCTCTCTG
* * *
1686906 AGGACAAAAGAAAGAGGAAAATAAAGTGTATCCTGCTCTTTG
1 AGGACAAAAGAAAAAGGAAAATAAAGTATATCCTGCTCTCTG
1686948 AGGA
1 AGGA
1686952 TTAAAAAGTG
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
41 3 0.08
42 37 0.93
ACGTcount: A:0.43, C:0.12, G:0.25, T:0.19
Consensus pattern (42 bp):
AGGACAAAAGAAAAAGGAAAATAAAGTATATCCTGCTCTCTG
Found at i:1687020 original size:55 final size:55
Alignment explanation
Indices: 1686936--1687658 Score: 869
Period size: 55 Copynumber: 12.9 Consensus size: 55
1686926 ATAAAGTGTA
* * * * *
1686936 TCCTGCTCTTTGAGGATTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
1686991 TCCTGCTCTTTGAGAATTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
1687046 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
1687101 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGTGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
*
1687156 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
1687211 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
* *
1687266 TCCTGCTCTTTGAGGACTGGAAGGCGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
* * *
1687321 TCCTGCTCTTTGGGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
1687376 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
* *
1687431 TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTATGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGTG
*
1687490 TCCCGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGG-G
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGTG
* * **
1687548 TCCCGCTCTTTGAGGACTG-AAGGTGCCACCAATTTGTGTGGGCTTTAAAAGAAAAGGCA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGTG
* ** * *
1687607 TCCCGCTCTTTGAGGACTGAAAAATGCCACCAACTCGTGTGGGCTTTAAAAG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAG
1687659 AAAAAGGCAT
Statistics
Matches: 613, Mismatches: 34, Indels: 42
0.89 0.05 0.06
Matches are distributed among these distances:
54 45 0.07
55 391 0.64
56 17 0.03
58 57 0.09
59 78 0.13
60 25 0.04
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.28
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
Found at i:1694251 original size:17 final size:17
Alignment explanation
Indices: 1694229--1694262 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1694219 ACATCGATTC
*
1694229 TTGACTGTGGCTTCCTT
1 TTGACTGTGCCTTCCTT
*
1694246 TTGACTTTGCCTTCCTT
1 TTGACTGTGCCTTCCTT
1694263 CTTACCTCTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.06, C:0.26, G:0.18, T:0.50
Consensus pattern (17 bp):
TTGACTGTGCCTTCCTT
Found at i:1701179 original size:28 final size:28
Alignment explanation
Indices: 1701123--1701199 Score: 91
Period size: 28 Copynumber: 2.8 Consensus size: 28
1701113 GGAATAAAGC
*** *
1701123 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
1701151 CGGGGTTGGAGTGTCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
* *
1701179 CGAGGTTGGAGTATCCTCGAT
1 CGGGGTTGGAGTATCCCCGAT
1701200 TGTGAAAAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.22, C:0.19, G:0.35, T:0.23
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:1701252 original size:52 final size:51
Alignment explanation
Indices: 1701183--1701519 Score: 229
Period size: 52 Copynumber: 6.4 Consensus size: 51
1701173 AAATAACGAG
* * *
1701183 GTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATGAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGT-GTTTTGGAAATAAAATCGGA
** * * * *
1701235 GTTGGAGTATCCCCGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCAGG-
1 GTTGGAGTATCCCCGATT-GTGAAAAATTGGTGTTTTGGAAATAAAATC-GGA
* * * * *
1701287 GTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCGGG
1 GTTGGAGTATCCCCGATTGT-GAAAAATTGGTGTTTTGGAAATAAAATCGGA
* * *** * * *
1701339 GTTGGAGTATCCCC--TTG-GAAATAACGGGGTCGGAGTATCCCCGATGAT-TAA-CGGG
1 GTTGGAGTATCCCCGATTGTGAAA-AA-----TTGGTGT-T-TTGGA-AATAAAATCGGA
1701394 GTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAA-AAATTGGTG--TTTTGGAAATAAAATCGGA
* * * *
1701448 GTTAGAGTATCCCCGATTAT-AGAAAATTAGTGTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGA-AAAATTGGTGTTTTGGAAATAAAATCGGA
*
1701499 GTTGGAATATCCCCGATTGTG
1 GTTGGAGTATCCCCGATTGTG
1701520 GAGAATTGAG
Statistics
Matches: 221, Mismatches: 41, Indels: 46
0.72 0.13 0.15
Matches are distributed among these distances:
48 4 0.02
49 2 0.01
50 3 0.01
51 37 0.17
52 86 0.39
53 28 0.13
54 27 0.12
55 20 0.09
56 3 0.01
57 5 0.02
58 5 0.02
59 1 0.00
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.30
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAATCGGA
Found at i:1701306 original size:104 final size:101
Alignment explanation
Indices: 1701177--1701519 Score: 280
Period size: 104 Copynumber: 3.3 Consensus size: 101
1701167 CCGATGAAAT
* *
1701177 AACGAGGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATGAAATCGGAGTTGGAG
1 AACG-GGTTGGAGTATCCCCGATTGTGAAAAATTGGT-TTTTTGGAAATAAAATCGGAGTTGGAG
*
1701242 TATCCCCGATTAAAGGAAAATTGGCGTTTTGAAAATAA
64 TATCCCCGATTAAAGGAAAATTGGAGTTTTGAAAATAA
* * * * * *
1701280 AACCAGGGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCGGGGTTGGA
1 AA-C-GGGTTGGAGTATCCCCGATTGT-GAAAAATTGGTTTTTTGGAAATAAAATCGGAGTTGGA
* * ** * ** ** *
1701345 GTATCCCCTTGGAAATAACGG--GGTCGGAGTATCCCCGATGAT-T
63 GTATCCCC---G-ATTAAAGGAAAATTGGAGT-T--TTGAAAATAA
*
1701388 AACGGGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTAG
1 AAC-GGGTTGGAGTATCCCCGATTGTGAA-AAATT-G-GTTTTTTGGAAATAAAATCGGAGTTGG
* * *
1701453 AGTATCCCCGATTATA-GAAAATTAGTGTTTTGAAAATAA
62 AGTATCCCCGATTAAAGGAAAATTGGAGTTTTGAAAATAA
*
1701492 AATCGGAGTTGGAATATCCCCGATTGTG
1 AA-CGG-GTTGGAGTATCCCCGATTGTG
1701520 GAGAATTGAG
Statistics
Matches: 181, Mismatches: 41, Indels: 34
0.71 0.16 0.13
Matches are distributed among these distances:
103 6 0.03
104 54 0.30
105 36 0.20
106 13 0.07
107 30 0.17
108 8 0.04
109 34 0.19
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.29
Consensus pattern (101 bp):
AACGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTTTTTTGGAAATAAAATCGGAGTTGGAGTA
TCCCCGATTAAAGGAAAATTGGAGTTTTGAAAATAA
Found at i:1701366 original size:212 final size:211
Alignment explanation
Indices: 1701074--1701521 Score: 623
Period size: 212 Copynumber: 2.1 Consensus size: 211
1701064 GAAAATAACG
* * * * * *
1701074 GGGTTGGAGTATCCCCAATTAT-GAGAAATCAATATTTTGGGAATAAAGCCGGGGTTGGAGTATC
1 GGGTTGGAGTATCCCCGATTGTGGAAAAATCAATATTTTAGCAATAAAACCGGGGTTGGAGTATC
* * * *
1701138 CCCTCGGAAGTAACGGGGTTGGAGTGTCCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTGT
66 CCCTCGGAAATAACGGGGTCGGAGTATCCCCGATG-AATAACGAGGTTGGAGTATCCCCGATTGT
* * *
1701203 GAA-AAATTGGT-ATTTTTGGAAATGAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTGG
130 GAAGAAATTGGTGATTTTTGGAAATAAAATCGGAGTTAGAGTATCCCCGATTAAA-GAAAATTAG
1701266 CGTTTTGAAAATAAAACC
194 CGTTTTGAAAATAAAACC
* * *
1701284 AGGGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCGGGGTTGGAGTAT
1 -GGGTTGGAGTATCCCCGATTGTGGAAAAATCAATATTTTAGCAATAAAACCGGGGTTGGAGTAT
* * *
1701349 CCCCTTGGAAATAACGGGGTCGGAGTATCCCCGATGATTAACGGGGTTGGAGTATCCCCGATTGT
65 CCCCTCGGAAATAACGGGGTCGGAGTATCCCCGATGAATAACGAGGTTGGAGTATCCCCGATTGT
* * *
1701414 GAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTAGAGTATCCCCGATTATAGAAAATTAGT
130 GAAGAAATTGGTGATTTTTGGAAATAAAATCGGAGTTAGAGTATCCCCGATTAAAGAAAATTAGC
*
1701479 GTTTTGAAAATAAAATC
195 GTTTTGAAAATAAAACC
*
1701496 GGAGTTGGAATATCCCCGATTGTGGA
1 GG-GTTGGAGTATCCCCGATTGTGGA
1701522 GAATTGAGAA
Statistics
Matches: 209, Mismatches: 24, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
211 51 0.24
212 120 0.57
213 38 0.18
ACGTcount: A:0.30, C:0.14, G:0.28, T:0.28
Consensus pattern (211 bp):
GGGTTGGAGTATCCCCGATTGTGGAAAAATCAATATTTTAGCAATAAAACCGGGGTTGGAGTATC
CCCTCGGAAATAACGGGGTCGGAGTATCCCCGATGAATAACGAGGTTGGAGTATCCCCGATTGTG
AAGAAATTGGTGATTTTTGGAAATAAAATCGGAGTTAGAGTATCCCCGATTAAAGAAAATTAGCG
TTTTGAAAATAAAACC
Found at i:1701400 original size:27 final size:29
Alignment explanation
Indices: 1701335--1701410 Score: 104
Period size: 27 Copynumber: 2.7 Consensus size: 29
1701325 GCAATAAAAC
*
1701335 CGGGGTTGGAGTATCCCC-TTGGAAATAA
1 CGGGGTTGGAGTATCCCCGATGGAAATAA
* *
1701363 CGGGGTCGGAGTATCCCCGAT-G-ATTAA
1 CGGGGTTGGAGTATCCCCGATGGAAATAA
1701390 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
1701411 TGTGAAGAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
27 24 0.56
28 18 0.42
29 1 0.02
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (29 bp):
CGGGGTTGGAGTATCCCCGATGGAAATAA
Found at i:1701411 original size:107 final size:104
Alignment explanation
Indices: 1701069--1701461 Score: 310
Period size: 107 Copynumber: 3.7 Consensus size: 104
1701059 CCCTCGAAAA
* * * * * * * *
1701069 TAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGGAATAAAGCCGGGGTTGGAG
1 TAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTGGAAATAAAACCGGGGTTGGAG
* *
1701134 TATCCCCTCGGAAGTAACGGGGTTGGAGTGTCCCCGATGAAA
66 TATCCCCT-GGAAATAACGGGGTTGGAGT-TCCCCGATG-AT
* * * * * * *
1701176 TAACGAGGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATGAAATCGGAGTTGGA
1 TAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGT-GTTTTGGAAATAAAACCGGGGTTGGA
* * ** * ** **
1701241 GTATCCCC--G-ATTAAAGGAAAATTGGCGTT--TTGAAAAT
65 GTATCCCCTGGAAATAACGG--GGTTGGAGTTCCCCGATGAT
* * * *
1701278 AAAACCAGGGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCGGGGTTG
1 -TAA-CGGGGTTGGAGTATCCCCGATTGT-GAAAAATTAGTGTTTTGGAAATAAAACCGGGGTTG
*
1701343 GAGTATCCCCTTGGAAATAACGGGGTCGGAGTATCCCCGATGAT
63 GAGTATCCCC-TGGAAATAACGGGGTTGGAGT-TCCCCGATGAT
* * * *
1701387 TAACGGGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTA
1 TAACGGGGTTGGAGTATCCCCGATTGTGAA-AAATTAGTG--TTTTGGAAATAAAACCGGGGTTG
1701452 GAGTATCCCC
63 GAGTATCCCC
1701462 GATTATAGAA
Statistics
Matches: 217, Mismatches: 53, Indels: 30
0.72 0.18 0.10
Matches are distributed among these distances:
102 1 0.00
103 4 0.02
104 55 0.25
105 12 0.06
106 14 0.06
107 63 0.29
108 36 0.17
109 32 0.15
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.27
Consensus pattern (104 bp):
TAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTGGAAATAAAACCGGGGTTGGAG
TATCCCCTGGAAATAACGGGGTTGGAGTTCCCCGATGAT
Found at i:1701494 original size:51 final size:53
Alignment explanation
Indices: 1701398--1701516 Score: 154
Period size: 51 Copynumber: 2.3 Consensus size: 53
1701388 AACGGGGTTG
* * *
1701398 GAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTA
1 GAGTATCCCCGATTATGAAGAAATTAGTG-TTTTTGAAAATAAAATCGGAGTTA
*
1701452 GAGTATCCCCGATTAT--AGAAAATTAGTG-TTTTGAAAATAAAATCGGAGTTG
1 GAGTATCCCCGATTATGAAG-AAATTAGTGTTTTTGAAAATAAAATCGGAGTTA
*
1701503 GAATATCCCCGATT
1 GAGTATCCCCGATT
1701517 GTGGAGAATT
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
51 34 0.58
52 2 0.03
53 8 0.14
54 15 0.25
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.32
Consensus pattern (53 bp):
GAGTATCCCCGATTATGAAGAAATTAGTGTTTTTGAAAATAAAATCGGAGTTA
Found at i:1703988 original size:13 final size:13
Alignment explanation
Indices: 1703970--1703994 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1703960 ACAATGCTTA
1703970 TGTATCGATACAT
1 TGTATCGATACAT
1703983 TGTATCGATACA
1 TGTATCGATACA
1703995 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:1703992 original size:32 final size:32
Alignment explanation
Indices: 1703951--1704013 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
1703941 TAGCTAATTA
**
1703951 TGTATCGATACAATGCTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
1703983 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
1704014 AATTGTTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:1704015 original size:19 final size:19
Alignment explanation
Indices: 1703948--1704015 Score: 76
Period size: 19 Copynumber: 3.9 Consensus size: 19
1703938 CAGTAGCTAA
**
1703948 TTATGTATCGATACAATGC
1 TTATGTATCGATACAAAAC
1703967 TTATGTATCGATAC---A-
1 TTATGTATCGATACAAAAC
1703982 -T-TGTATCGATACAAAAC
1 TTATGTATCGATACAAAAC
1703999 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
1704016 TTGTTGAATT
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 1 0.02
18 1 0.02
19 28 0.67
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (19 bp):
TTATGTATCGATACAAAAC
Found at i:1708568 original size:8 final size:8
Alignment explanation
Indices: 1708554--1708617 Score: 53
Period size: 8 Copynumber: 7.9 Consensus size: 8
1708544 TCCTTCGTAC
1708554 CAAAAAAA
1 CAAAAAAA
*
1708562 TAAAAAAA
1 CAAAAAAA
1708570 CAAAAAAA
1 CAAAAAAA
1708578 -AAACCAAGAA
1 CAAA--AA-AA
1708588 -AAAAAAA
1 CAAAAAAA
1708595 -AGAAAAAA
1 CA-AAAAAA
*
1708603 CAAACAAA
1 CAAAAAAA
1708611 CAAAAAA
1 CAAAAAA
1708618 GAGGTCCAGA
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
7 6 0.13
8 33 0.70
9 3 0.06
10 5 0.11
ACGTcount: A:0.84, C:0.11, G:0.03, T:0.02
Consensus pattern (8 bp):
CAAAAAAA
Found at i:1708577 original size:11 final size:11
Alignment explanation
Indices: 1708563--1708617 Score: 56
Period size: 13 Copynumber: 4.5 Consensus size: 11
1708553 CCAAAAAAAT
1708563 AAAAAAACAAA
1 AAAAAAACAAA
1708574 AAAAAAACCAAGA
1 AAAAAAA-CAA-A
*
1708587 AAAAAAAAAGAA
1 AAAAAAACA-AA
1708599 AAAACAAACAAA
1 AAAA-AAACAAA
1708611 CAAAAAA
1 -AAAAAA
1708618 GAGGTCCAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
11 7 0.19
12 13 0.35
13 17 0.46
ACGTcount: A:0.85, C:0.11, G:0.04, T:0.00
Consensus pattern (11 bp):
AAAAAAACAAA
Found at i:1709896 original size:28 final size:28
Alignment explanation
Indices: 1709864--1710435 Score: 626
Period size: 28 Copynumber: 19.9 Consensus size: 28
1709854 CGTTTATCTC
* *
1709864 TTCAAAGCCCACAGGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* * * *
1709892 TTCAAAGCCCATAAATCAGTGGCATCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
1709920 TTCAAAACCCATAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
1709948 TTCAAAGCCCACAAGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
1709976 TTCAAAGCCCACAAGTCAGTGGCA-TCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
1710003 CTTCAAAAGACCACAAGTTAGTGGCATCCCT
1 -TTC-AAAGCCCACAAGTCAGTGGCA-CCCT
* *
1710034 TCCAAAGCCTACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
1710062 TTCAAAGCCCACAAGTGAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* * *
1710090 TTCAAAGCCCATAAGTCAATGGTACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
1710118 TTCAAAGCCCATAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
1710146 TTCAAAGCCCACAAGTTAGTGGCATACCCT
1 TTCAAAGCCCACAAGTCAGTGGC--ACCCT
* *
1710176 TTCAAAGCCCACACAAATCAGTGGCACTCT
1 TTCAAAG-CC-CACAAGTCAGTGGCACCCT
* * *
1710206 TCCAAAGCCTACAAGTCTGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
1710234 TTCAAAGCCCACAAGTCAGTGGCGCCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* * * * *
1710262 TTAAAAGCCAATAAGTCAGTGGTACCCC
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
1710290 TTCAAAGCCCACAAGTCAGTGGCACGCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
1710318 TTCAAAGCTCACAAG-CTAGTGGCATACCCT
1 TTCAAAGCCCACAAGTC-AGTGGC--ACCCT
* * *
1710348 TTTAAAGCCCACAAGTCGGTGGCACCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
1710376 TTCAAAGCCCACACAAGTCAGTGGCAACTCTT
1 TTCAAAG-CC-CACAAGTCAGTGGC-AC-CCT
* *
1710408 TTCAAAGCCTACACAAGTTAGTGTCACC
1 TTCAAAGCC--CACAAGTCAGTGGCACC
1710436 TTTTTTTAAA
Statistics
Matches: 461, Mismatches: 66, Indels: 32
0.82 0.12 0.06
Matches are distributed among these distances:
27 3 0.01
28 311 0.67
29 41 0.09
30 60 0.13
31 11 0.02
32 35 0.08
ACGTcount: A:0.30, C:0.31, G:0.17, T:0.22
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCACCCT
Found at i:1713649 original size:24 final size:26
Alignment explanation
Indices: 1713622--1713672 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
1713612 TCAAAAATTT
1713622 TATTTATC-A-GGGATACTCCAACCC
1 TATTTATCGAGGGGATACTCCAACCC
*
1713646 TATTTCTCTGAGGGGATACTCCAACCC
1 TATTTATC-GAGGGGATACTCCAACCC
1713673 CGTTTTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 7 0.30
26 1 0.04
27 15 0.65
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (26 bp):
TATTTATCGAGGGGATACTCCAACCC
Found at i:1715368 original size:89 final size:88
Alignment explanation
Indices: 1715243--1715619 Score: 481
Period size: 89 Copynumber: 4.3 Consensus size: 88
1715233 TCATCGTGTT
* * *
1715243 AGAAGGAATCTGATACCCACATGTATCTGTTACATCTTTCGAGTTTCAAAAAATTTATTAGGCAT
1 AGAAGGAATCTGATACCCACATGCATCTGTCACATCTTTCGAGTTTCAAGAAATTTATTAGGCAT
* *
1715308 TAGTCAAATATTTTTCGTTATATC
66 TAGTCAAATA-TTTTCGTCATGTC
* * * * *
1715332 AAAAGGAATCTGGTACCCACATGCATCTGTCACATCTTTTGGGTTCCAAGAAATTTATTAGGCAT
1 AGAAGGAATCTGATACCCACATGCATCTGTCACATCTTTCGAGTTTCAAGAAATTTATTAGGCAT
1715397 TAGTC-AATA-TTTCGTCATGTC
66 TAGTCAAATATTTTCGTCATGTC
* * * * *
1715418 AGGAGGAATTTGATACCAACATGCATCTGTCACATTTTTCGGGTTTCAAGAAATTTATTAGGCAT
1 AGAAGGAATCTGATACCCACATGCATCTGTCACATCTTTCGAGTTTCAAGAAATTTATTAGGCAT
**
1715483 TAGAT-AAATATTTTCCGTTGTGTC
66 TAG-TCAAATATTTT-CGTCATGTC
* * * * * *
1715507 AGAAGGAATTTGATATCCACATGCACCTGTCACATCTTGCGAGTTTCAACAAATTTATTAAGCAT
1 AGAAGGAATCTGATACCCACATGCATCTGTCACATCTTTCGAGTTTCAAGAAATTTATTAGGCAT
1715572 TAGTCAAATATTTTCGTCATGTC
66 TAGTCAAATATTTTCGTCATGTC
* *
1715595 AGAATGAATCTGATATCCACATGCA
1 AGAAGGAATCTGATACCCACATGCA
1715620 AAACTAATAT
Statistics
Matches: 250, Mismatches: 33, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
86 70 0.28
87 5 0.02
88 38 0.15
89 137 0.55
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (88 bp):
AGAAGGAATCTGATACCCACATGCATCTGTCACATCTTTCGAGTTTCAAGAAATTTATTAGGCAT
TAGTCAAATATTTTCGTCATGTC
Found at i:1715544 original size:175 final size:176
Alignment explanation
Indices: 1715243--1715619 Score: 499
Period size: 175 Copynumber: 2.1 Consensus size: 176
1715233 TCATCGTGTT
* *
1715243 AGAAGGAATCTGATACCCACATGTATCTGTTACATCTTTCGAGTTTCAAAAAATTTATTAGGCAT
1 AGAAGGAATCTGATA-CCACATGCATCTGTCACATCTTTCGAGTTTCAAAAAATTTATTAGGCAT
* * * **
1715308 TAGTCAAATATTTTTCGTTATATCAAAAGGAATCTGGTACCCACATGCATCTGTCACATCTTTTG
65 TAGTCAAATATTTTCCGTTATATCAAAAGGAATCTGATACCCACATGCACCTGTCACATCTTGCG
* * *
1715373 GGTTCCAAGAAATTTATTAGGCATTAGTC-AATA-TTTCGTCATGTC
130 AGTTCCAACAAATTTATTAAGCATTAGTCAAATATTTTCGTCATGTC
* * * * *
1715418 AGGAGGAATTTGATACCAACATGCATCTGTCACATTTTTCGGGTTTCAAGAAATTTATTAGGCAT
1 AGAAGGAATCTGATACC-ACATGCATCTGTCACATCTTTCGAGTTTCAAAAAATTTATTAGGCAT
* * * * *
1715483 TAGAT-AAATATTTTCCGTTGTGTCAGAAGGAATTTGATATCCACATGCACCTGTCACATCTTGC
65 TAG-TCAAATATTTTCCGTTATATCAAAAGGAATCTGATACCCACATGCACCTGTCACATCTTGC
*
1715547 GAGTTTCAACAAATTTATTAAGCATTAGTCAAATATTTTCGTCATGTC
129 GAGTTCCAACAAATTTATTAAGCATTAGTCAAATATTTTCGTCATGTC
*
1715595 AGAATGAATCTGATATCCACATGCA
1 AGAAGGAATCTGATA-CCACATGCA
1715620 AAACTAATAT
Statistics
Matches: 173, Mismatches: 24, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
174 2 0.01
175 133 0.77
176 5 0.03
177 31 0.18
178 2 0.01
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (176 bp):
AGAAGGAATCTGATACCACATGCATCTGTCACATCTTTCGAGTTTCAAAAAATTTATTAGGCATT
AGTCAAATATTTTCCGTTATATCAAAAGGAATCTGATACCCACATGCACCTGTCACATCTTGCGA
GTTCCAACAAATTTATTAAGCATTAGTCAAATATTTTCGTCATGTC
Found at i:1715644 original size:5 final size:5
Alignment explanation
Indices: 1715624--1715758 Score: 95
Period size: 5 Copynumber: 27.2 Consensus size: 5
1715614 CATGCAAAAC
1715624 TAATA TAATA -ATATA TAATA TAATA -AATA TAATA TAATA TAATA TAATA
1 TAATA TAATA TA-ATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
* *
1715673 T-ATA CTATATA TATTA TTAT- TATATA TAATA T-ATAA TAATA TAAT-
1 TAATA -TA-ATA TAATA TAATA TA-ATA TAATA TAAT-A TAATA TAATA
* * * * * *
1715718 TATATA TAGTA T-ATA TATTA TTATA TTATA TTATA TTATA T
1 TA-ATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA T
1715759 TTATATATAT
Statistics
Matches: 108, Mismatches: 9, Indels: 26
0.76 0.06 0.18
Matches are distributed among these distances:
4 16 0.15
5 80 0.74
6 9 0.08
7 3 0.03
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (5 bp):
TAATA
Found at i:1715733 original size:29 final size:29
Alignment explanation
Indices: 1715624--1715768 Score: 113
Period size: 29 Copynumber: 4.9 Consensus size: 29
1715614 CATGCAAAAC
* *
1715624 TAATATAATAATATATAATATA-ATAAATA
1 TAATATAATTATATATAATATATATATA-A
1715653 TAATATAA-TATAATATAATATATACTAT-A
1 TAATATAATTAT-ATATAATATATA-TATAA
*
1715682 T-ATATTATTAT-TAT-ATATAATATATAA
1 TAATATAATTATATATAATAT-ATATATAA
* *
1715709 TAATATAATTATATATAGTATATATATTA
1 TAATATAATTATATATAATATATATATAA
* *
1715738 TTATATTATATTATATTATATTTATATATAT
1 TAATA-TA-ATTATA-TATA-ATATATATAT
1715769 TAAAAAATGA
Statistics
Matches: 95, Mismatches: 8, Indels: 22
0.76 0.06 0.18
Matches are distributed among these distances:
26 7 0.07
27 8 0.08
28 16 0.17
29 37 0.39
30 6 0.06
31 8 0.08
32 4 0.04
33 9 0.09
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (29 bp):
TAATATAATTATATATAATATATATATAA
Found at i:1722191 original size:19 final size:20
Alignment explanation
Indices: 1722163--1722211 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1722153 ATTTCAAAGC
* *
1722163 GTATCAATACTATG-AACAT
1 GTATCGATACTAAGCAACAT
*
1722182 GTATCGATACTAAGCAATAT
1 GTATCGATACTAAGCAACAT
1722202 GTATCGATAC
1 GTATCGATAC
1722212 ATCTGGGTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 12 0.46
20 14 0.54
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.31
Consensus pattern (20 bp):
GTATCGATACTAAGCAACAT
Found at i:1723563 original size:20 final size:20
Alignment explanation
Indices: 1723548--1723614 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
1723538 AGATGTATTA
1723548 ATACATTTTTCAATGTATCG
1 ATACATTTTTCAATGTATCG
* * *
1723568 ATACATGTATGAATGTATCG
1 ATACATTTTTCAATGTATCG
*
1723588 ATACATTCTTCAATGTATCG
1 ATACATTTTTCAATGTATCG
1723608 ATACATT
1 ATACATT
1723615 CTGTCTTTTA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (20 bp):
ATACATTTTTCAATGTATCG
Found at i:1731121 original size:13 final size:13
Alignment explanation
Indices: 1731103--1731128 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1731093 ACATTTTGGG
1731103 ATGTATCGATACA
1 ATGTATCGATACA
1731116 ATGTATCGATACA
1 ATGTATCGATACA
1731129 TATTGTGTGT
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:1731145 original size:32 final size:33
Alignment explanation
Indices: 1731081--1731148 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
1731071 CGTTACAAGC
*
1731081 CAATGTACCGATACATTTTGGGATGTATCGATA
1 CAATGTACCGATACATATTGGGATGTATCGATA
* *
1731114 CAATGTATCGATACATATTGTG-TGTATCGATA
1 CAATGTACCGATACATATTGGGATGTATCGATA
1731146 CAA
1 CAA
1731149 ACAGTTAAGG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 13 0.41
33 19 0.59
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Consensus pattern (33 bp):
CAATGTACCGATACATATTGGGATGTATCGATA
Found at i:1731247 original size:13 final size:13
Alignment explanation
Indices: 1731229--1731253 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1731219 ACATTTGGTC
1731229 ATGTATCGATACA
1 ATGTATCGATACA
1731242 ATGTATCGATAC
1 ATGTATCGATAC
1731254 TGTGCATTAT
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):
ATGTATCGATACA
Found at i:1739937 original size:33 final size:32
Alignment explanation
Indices: 1739895--1739962 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 32
1739885 CGTTTCAAGC
*
1739895 CAATGTATCGATACATTTTGGGATATATCGATA
1 CAATGTATCGATACATATTGGG-TATATCGATA
* *
1739928 CAATGTATCGATACATATTGTGTGTATCGATA
1 CAATGTATCGATACATATTGGGTATATCGATA
1739960 CAA
1 CAA
1739963 ACAATTAAGG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 12 0.38
33 20 0.62
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (32 bp):
CAATGTATCGATACATATTGGGTATATCGATA
Found at i:1740061 original size:13 final size:13
Alignment explanation
Indices: 1740043--1740067 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1740033 ACATTTGGTC
1740043 ATGTATCGATACA
1 ATGTATCGATACA
1740056 ATGTATCGATAC
1 ATGTATCGATAC
1740068 TGTGCATTAT
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):
ATGTATCGATACA
Found at i:1752788 original size:20 final size:20
Alignment explanation
Indices: 1752741--1752795 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
1752731 GTATCCATAC
**
1752741 ATTGTATCGATACAT-GTTA
1 ATTGTATCGATACATGGACA
*
1752760 ATAGTATCGATACATGGACA
1 ATTGTATCGATACATGGACA
1752780 ATTGTATCGATACATG
1 ATTGTATCGATACATG
1752796 AGATTGGCAG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.35
Consensus pattern (20 bp):
ATTGTATCGATACATGGACA
Found at i:1754597 original size:11 final size:11
Alignment explanation
Indices: 1754581--1754605 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1754571 AACACAGAAA
1754581 AAAAAAAAAAC
1 AAAAAAAAAAC
1754592 AAAAAAAAAAC
1 AAAAAAAAAAC
1754603 AAA
1 AAA
1754606 GATTTAGTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:1755570 original size:2 final size:2
Alignment explanation
Indices: 1755563--1755602 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1755553 ACCAATGGGA
1755563 AT 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 AT
1755603 TGTCACGAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1756069 original size:24 final size:22
Alignment explanation
Indices: 1756042--1756108 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 22
1756032 ATTTATACAC
1756042 TTTTTACTTAAAAAAACTCTATA
1 TTTTTACTTAAAAAAACTC-ATA
*
1756065 TTTTTTACTTGAAAAGTAAATTCATA
1 -TTTTTACTT-AAAA--AAACTCATA
1756091 -TTTTACTTAAGAAAAACT
1 TTTTTACTTAA-AAAAACT
1756109 TACGCGATAG
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
22 4 0.11
23 2 0.05
24 19 0.51
25 4 0.11
26 3 0.08
27 5 0.14
ACGTcount: A:0.42, C:0.10, G:0.04, T:0.43
Consensus pattern (22 bp):
TTTTTACTTAAAAAAACTCATA
Found at i:1756627 original size:18 final size:19
Alignment explanation
Indices: 1756601--1756639 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
1756591 TAAAATCTAT
1756601 TTTGATC-ATCTATATATA
1 TTTGATCAATCTATATATA
*
1756619 TTTGTTCATATCTATATATA
1 TTTGATCA-ATCTATATATA
1756639 T
1 T
1756640 ATATATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
20 12 0.67
ACGTcount: A:0.31, C:0.10, G:0.05, T:0.54
Consensus pattern (19 bp):
TTTGATCAATCTATATATA
Found at i:1759325 original size:12 final size:12
Alignment explanation
Indices: 1759308--1759351 Score: 70
Period size: 12 Copynumber: 3.7 Consensus size: 12
1759298 ATTTTTAAGG
*
1759308 ACATATATACAT
1 ACATATATATAT
1759320 ACATATATATAT
1 ACATATATATAT
1759332 ACATATATATAT
1 ACATATATATAT
*
1759344 ATATATAT
1 ACATATAT
1759352 CGCTCTCTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (12 bp):
ACATATATATAT
Found at i:1759327 original size:2 final size:2
Alignment explanation
Indices: 1759310--1759351 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
1759300 TTTTAAGGAC
* * *
1759310 AT AT AT AC AT AC AT AT AT AT AT AC 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 AT AT
1759352 CGCTCTCTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:1759331 original size:16 final size:16
Alignment explanation
Indices: 1759310--1759348 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
1759300 TTTTAAGGAC
1759310 ATATATACATACATAT
1 ATATATACATACATAT
*
1759326 ATATATACATATATAT
1 ATATATACATACATAT
1759342 ATATATA
1 ATATATA
1759349 TATCGCTCTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (16 bp):
ATATATACATACATAT
Found at i:1760919 original size:25 final size:27
Alignment explanation
Indices: 1760887--1760939 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
1760877 TTCAGTGCAG
*
1760887 TTTTTAAT-C-TACAAACATGTAGATT
1 TTTTTAATACATACAAACACGTAGATT
*
1760912 TTTTTAATACATATAAACACGTAGATT
1 TTTTTAATACATACAAACACGTAGATT
1760939 T
1 T
1760940 AACTAATCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 8 0.33
26 1 0.04
27 15 0.62
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.43
Consensus pattern (27 bp):
TTTTTAATACATACAAACACGTAGATT
Found at i:1761138 original size:19 final size:18
Alignment explanation
Indices: 1761078--1761138 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 18
1761068 ATTAGTCTTG
1761078 TTTTTAAAAG-AATCTA-T
1 TTTTTAAAAGAAAT-TATT
*
1761095 TTTTTAAAAAAAGATTAATT
1 TTTTTAAAAGAA-ATT-ATT
*
1761115 ATTTTAAAAGAAATTGATT
1 TTTTTAAAAGAAATT-ATT
1761134 TTTTT
1 TTTTT
1761139 GTGTGAAAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
17 9 0.26
18 2 0.06
19 13 0.37
20 11 0.31
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.49
Consensus pattern (18 bp):
TTTTTAAAAGAAATTATT
Found at i:1763859 original size:24 final size:24
Alignment explanation
Indices: 1763803--1763861 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 24
1763793 TTTATTATAT
1763803 AATAATAAATTTATTTATATATTAA
1 AATAA-AAATTTATTTATATATTAA
* * *
1763828 ATTAAAAAATTATTTTATATTTTAA
1 AATAAAAATTTA-TTTATATATTAA
1763853 AATAAAAAT
1 AATAAAAAT
1763862 CAAATTAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
24 6 0.21
25 22 0.79
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
AATAAAAATTTATTTATATATTAA
Found at i:1764119 original size:34 final size:34
Alignment explanation
Indices: 1764050--1764132 Score: 91
Period size: 34 Copynumber: 2.4 Consensus size: 34
1764040 TTTTATTTTT
*
1764050 TAGT-TATTTTTAAGTAATTTTATATATATATATA
1 TAGTATATTTTTAA-TAATTTTATATACATATATA
*
1764084 TA-TATATTTTTAATAATTCTTATTTAACATA-ATA
1 TAGTATATTTTTAATAATT-TTATAT-ACATATATA
*
1764118 TAGTATAATTTTAAT
1 TAGTATATTTTTAAT
1764133 TCATTCTTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
33 6 0.14
34 21 0.50
35 15 0.36
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (34 bp):
TAGTATATTTTTAATAATTTTATATACATATATA
Found at i:1764313 original size:21 final size:21
Alignment explanation
Indices: 1764285--1764337 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
1764275 TATTAATTTT
1764285 TAAT-TTTAATTATA-CTATTA
1 TAATATTTAATTATATC-ATTA
*
1764305 TAATATTTAATTTTATCATTA
1 TAATATTTAATTATATCATTA
*
1764326 TAATAATTAATT
1 TAATATTTAATT
1764338 TCGTAGTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 4 0.14
21 24 0.83
22 1 0.03
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.55
Consensus pattern (21 bp):
TAATATTTAATTATATCATTA
Found at i:1766340 original size:21 final size:21
Alignment explanation
Indices: 1766316--1766357 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1766306 ATAATAATTT
1766316 TAAATAAAAATTTTT-ATTAAA
1 TAAAT-AAAATTTTTAATTAAA
*
1766337 TAAATAATATTTTTAATTAAA
1 TAAATAAAATTTTTAATTAAA
1766358 GTGATTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TAAATAAAATTTTTAATTAAA
Found at i:1766352 original size:17 final size:17
Alignment explanation
Indices: 1766306--1766357 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
1766296 AAGACTTTTT
*
1766306 ATAATAATTTTAAATAA
1 ATAATATTTTTAAATAA
*
1766323 A-AATTTTTATTAAATAA
1 ATAATATTT-TTAAATAA
*
1766340 ATAATATTTTTAATTAA
1 ATAATATTTTTAAATAA
1766357 A
1 A
1766358 GTGATTAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
16 5 0.17
17 18 0.62
18 6 0.21
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATAATATTTTTAAATAA
Found at i:1766539 original size:38 final size:38
Alignment explanation
Indices: 1766488--1766563 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
1766478 TTAGACTCGA
1766488 GACGTGAATCGTGGCTTTCAATTACTTTTCTTTTTTTT
1 GACGTGAATCGTGGCTTTCAATTACTTTTCTTTTTTTT
1766526 GACGTGAATCGTGGCTTTCAATTACTTTTCTTTTTTTT
1 GACGTGAATCGTGGCTTTCAATTACTTTTCTTTTTTTT
1766564 CTTTTGTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.53
Consensus pattern (38 bp):
GACGTGAATCGTGGCTTTCAATTACTTTTCTTTTTTTT
Found at i:1766575 original size:13 final size:13
Alignment explanation
Indices: 1766550--1766586 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1766540 CTTTCAATTA
1766550 CTTTTCTTTTTTTT
1 CTTTTC-TTTTTTT
*
1766564 CTTTTGTTTTTTT
1 CTTTTCTTTTTTT
1766577 CTTTTCTTTT
1 CTTTTCTTTT
1766587 CAAATGGCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 16 0.76
14 5 0.24
ACGTcount: A:0.00, C:0.14, G:0.03, T:0.84
Consensus pattern (13 bp):
CTTTTCTTTTTTT
Found at i:1767032 original size:47 final size:46
Alignment explanation
Indices: 1766947--1767040 Score: 134
Period size: 47 Copynumber: 2.0 Consensus size: 46
1766937 CTTATAAATT
* *
1766947 TTGTCATGATTAGAAAGTATCCGTTAATATTTAAGTTTGGAAGAAA
1 TTGTCATGATTAGAAAGTATCAGTTAATACTTAAGTTTGGAAGAAA
** *
1766993 TTGTCATGATTAGAAAGGTATCAGTTTTTGCTTAAGTTTGGAAGAAA
1 TTGTCATGATTAGAAA-GTATCAGTTAATACTTAAGTTTGGAAGAAA
1767040 T
1 T
1767041 GTGTAGATAA
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
46 16 0.38
47 26 0.62
ACGTcount: A:0.34, C:0.06, G:0.21, T:0.38
Consensus pattern (46 bp):
TTGTCATGATTAGAAAGTATCAGTTAATACTTAAGTTTGGAAGAAA
Found at i:1767170 original size:11 final size:11
Alignment explanation
Indices: 1767150--1767187 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
1767140 GTTTATTTTA
1767150 TAATTTAAAA-
1 TAATTTAAAAT
1767160 TAATATTAAAAAT
1 TAAT-TT-AAAAT
1767173 TAATTTAAAAT
1 TAATTTAAAAT
1767184 TAAT
1 TAAT
1767188 ATTTATAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 4 0.16
11 11 0.44
12 6 0.24
13 4 0.16
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
TAATTTAAAAT
Found at i:1767337 original size:20 final size:21
Alignment explanation
Indices: 1767307--1767352 Score: 85
Period size: 20 Copynumber: 2.2 Consensus size: 21
1767297 GCTATTCACA
1767307 TAAACAAAAGATTTGTGAGAT
1 TAAACAAAAGATTTGTGAGAT
1767328 TAAA-AAAAGATTTGTGAGAT
1 TAAACAAAAGATTTGTGAGAT
1767348 TAAAC
1 TAAAC
1767353 TTTTTTTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 20 0.83
21 4 0.17
ACGTcount: A:0.50, C:0.04, G:0.17, T:0.28
Consensus pattern (21 bp):
TAAACAAAAGATTTGTGAGAT
Found at i:1768522 original size:2 final size:2
Alignment explanation
Indices: 1768477--1768503 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1768467 AAAAAGTTAC
1768477 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
1768504 AACACATATA
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:1769075 original size:16 final size:15
Alignment explanation
Indices: 1769056--1769085 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1769046 ATTAATAAGT
1769056 TAAATCTAACATAATC
1 TAAATCTAA-ATAATC
1769072 TAAATCTAAATAAT
1 TAAATCTAAATAAT
1769086 TTGAGTATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.33
Consensus pattern (15 bp):
TAAATCTAAATAATC
Found at i:1770059 original size:2 final size:2
Alignment explanation
Indices: 1770048--1770085 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1770038 TTTCCTGTTC
1770048 TA TA -A 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
1770086 TCTTTCATGT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1770779 original size:2 final size:2
Alignment explanation
Indices: 1770772--1770803 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1770762 AAAGCAATCA
1770772 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
1770804 TACATAGATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1771102 original size:2 final size:2
Alignment explanation
Indices: 1771095--1771123 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1771085 TTTAAGGGTG
1771095 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 T
1771124 TTTGGGGGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1772653 original size:21 final size:20
Alignment explanation
Indices: 1772620--1772679 Score: 93
Period size: 20 Copynumber: 3.0 Consensus size: 20
1772610 AAAATATACA
*
1772620 TAAAAATAATTTTTCAATTT
1 TAAAAATAATTTTTTAATTT
1772640 TAAAAATAATTTTTTAATTT
1 TAAAAATAATTTTTTAATTT
* *
1772660 TAAAAATTATTTTTGAATTT
1 TAAAAATAATTTTTTAATTT
1772680 AAGAACTTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (20 bp):
TAAAAATAATTTTTTAATTT
Found at i:1774607 original size:2 final size:2
Alignment explanation
Indices: 1774600--1774628 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1774590 TATGTTTATG
1774600 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 T
1774629 TTTTATTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1775948 original size:77 final size:77
Alignment explanation
Indices: 1775815--1776037 Score: 270
Period size: 77 Copynumber: 2.8 Consensus size: 77
1775805 CAAACCCCTT
* * * *
1775815 TATTTCTGAGAGGATACTCTAACCCCGGTTCCATTTTCAAAATATCGATTTTTCACCATTGAGGA
1 TATTTCTGAGGGGATACTCTAACCCC-GTTTCATTTT-TAAATATCGATTTTTCACCATCGAGGA
**
1775880 TACTCCAACTCTGC
64 TACTCCAACTCCAC
1775894 TATTT-TGGAGGGGATA-TCTAACCCCAGTTTCATTTTTAAATATCGATTTTTCACCATCGAGGA
1 TATTTCT-GAGGGGATACTCTAACCCC-GTTTCATTTTTAAATATCGATTTTTCACCATCGAGGA
*
1775957 TACTCCAACTCCAT
64 TACTCCAACTCCAC
* * * * *
1775971 TATTTCTGAGGGGATACTCCAACCTCGGTTCTATTTTTAAAATATTGATTTTTCACCATCGGGGA
1 TATTTCTGAGGGGATACTCTAACCCCGTTTC-ATTTTT-AAATATCGATTTTTCACCATCGAGGA
1776036 TA
64 TA
1776038 TTCTAATCCC
Statistics
Matches: 126, Mismatches: 13, Indels: 10
0.85 0.09 0.07
Matches are distributed among these distances:
77 54 0.43
78 33 0.26
79 39 0.31
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.36
Consensus pattern (77 bp):
TATTTCTGAGGGGATACTCTAACCCCGTTTCATTTTTAAATATCGATTTTTCACCATCGAGGATA
CTCCAACTCCAC
Found at i:1776053 original size:79 final size:79
Alignment explanation
Indices: 1775773--1776061 Score: 311
Period size: 79 Copynumber: 3.7 Consensus size: 79
1775763 TTTTATTTCC
* * * * * * *
1775773 AAAATAT-GATTTTCTTCACCATCGAAGACATTCAAACCCCTTTATTTCTGAGAGGATACTCTAA
1 AAAATATCGA-TTT-TTCACCATCGAGGATACTCCAACTCCGTTATTTCTGAGGGGATACTCTAA
* *
1775837 CCCCGGTTCCATTTTC
64 CCCCGGTTCTATTTTT
* * *
1775853 AAAATATCGATTTTTCACCATTGAGGATACTCCAACTCTGCTATTT-TGGAGGGGATA-TCTAAC
1 AAAATATCGATTTTTCACCATCGAGGATACTCCAACTCCGTTATTTCT-GAGGGGATACTCTAAC
*
1775916 CCCAGTT-TCATTTTT
65 CCCGGTTCT-ATTTTT
* *
1775931 -AAATATCGATTTTTCACCATCGAGGATACTCCAACTCCATTATTTCTGAGGGGATACTCCAACC
1 AAAATATCGATTTTTCACCATCGAGGATACTCCAACTCCGTTATTTCTGAGGGGATACTCTAACC
*
1775995 TCGGTTCTATTTTT
66 CCGGTTCTATTTTT
* * * *
1776009 AAAATATTGATTTTTCACCATCGGGGATATTCTAA-TCCCGTTATTTCTGAGGG
1 AAAATATCGATTTTTCACCATCGAGGATACTCCAACT-CCGTTATTTCTGAGGG
1776062 TATCGTAATG
Statistics
Matches: 176, Mismatches: 25, Indels: 17
0.81 0.11 0.08
Matches are distributed among these distances:
77 50 0.28
78 36 0.20
79 78 0.44
80 10 0.06
81 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (79 bp):
AAAATATCGATTTTTCACCATCGAGGATACTCCAACTCCGTTATTTCTGAGGGGATACTCTAACC
CCGGTTCTATTTTT
Found at i:1777363 original size:20 final size:20
Alignment explanation
Indices: 1777335--1777409 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 20
1777325 TTTTACCTTG
1777335 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
1777355 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
1777375 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
*
1777395 ATGTATTGATACATT
1 ATGTATCGATACATT
1777410 ATGTCTTTTT
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1777406 original size:40 final size:39
Alignment explanation
Indices: 1777335--1777412 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
1777325 TTTTACCTTG
* *
1777335 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* * *
1777375 ATGTATCGATATATTCTACAATGTATTGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
1777413 TCTTTTTACC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.41
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:1778363 original size:22 final size:23
Alignment explanation
Indices: 1778323--1778379 Score: 98
Period size: 22 Copynumber: 2.5 Consensus size: 23
1778313 AGCCTTTGAC
1778323 CATGCATTTTTTTTGATTATGTTT
1 CATGCA-TTTTTTTGATTATGTTT
1778347 CATGCATTTTTTT-ATTATGTTT
1 CATGCATTTTTTTGATTATGTTT
1778369 CATGCATTTTT
1 CATGCATTTTT
1778380 AACATGTCCA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 20 0.61
23 7 0.21
24 6 0.18
ACGTcount: A:0.18, C:0.11, G:0.11, T:0.61
Consensus pattern (23 bp):
CATGCATTTTTTTGATTATGTTT
Found at i:1778386 original size:20 final size:21
Alignment explanation
Indices: 1778341--1778386 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
1778331 TTTTTTGATT
**
1778341 ATGTTTCATGCATTTTTTTATT
1 ATGTTTCATGCA-TTTTTTAAC
1778363 ATGTTTCATGCA-TTTTTAAC
1 ATGTTTCATGCATTTTTTAAC
1778383 ATGT
1 ATGT
1778387 CCAGCATCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 10 0.45
22 12 0.55
ACGTcount: A:0.22, C:0.11, G:0.11, T:0.57
Consensus pattern (21 bp):
ATGTTTCATGCATTTTTTAAC
Found at i:1779861 original size:55 final size:55
Alignment explanation
Indices: 1779775--1780521 Score: 960
Period size: 55 Copynumber: 13.3 Consensus size: 55
1779765 ATCCTTCTTA
* * *
1779775 TTGAGGAGT-AAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCCTGCTCT
1 TTGAGGACTGAAAAA-TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCT
**
1779830 TTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTGTCCTGCTCT
1 TTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAA-AGGTGTCCTGCTCT
* ** * ** *
1779885 TTGGGGACTGAAAGGTGCCACCAACTTGTGTGAGCTTTGAAAAGAAAAAGCATCCTGTTCT
1 TTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTG-AAAG-----GTGTCCTGCTCT
* * *
1779946 TTAAGGACTGAAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCT
1 TTGAGGACTG-AAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCT
*
1780002 TTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCT
1 TTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCT
* ** * **
1780057 TTGGGGACTGAAAGGTGCCACCAACCTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCT
1 TTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTG-AAAG-----GTGTCCTGCTCT
* *
1780118 TTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCT
1 TTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCT
* *
1780173 TTGAGGACTG-GAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTTCTCT
1 TTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCT
** **
1780227 TTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCT
1 TTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTG-AAAG-----GTGTCCTGCTCT
* *
1780288 TTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCT
1 TTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCT
*
1780343 TTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCT
1 TTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCT
*
1780398 TTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCATTGAAAGGTGTCCTGCTCT
1 TTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCT
*
1780453 TTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCT
1 TTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCT
*
1780508 TTGGGGACTGAAAA
1 TTGAGGACTGAAAA
1780522 GCGGAAGGAG
Statistics
Matches: 607, Mismatches: 62, Indels: 46
0.85 0.09 0.06
Matches are distributed among these distances:
54 52 0.09
55 380 0.63
56 31 0.05
57 2 0.00
60 8 0.01
61 110 0.18
62 24 0.04
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (55 bp):
TTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCT
Found at i:1779900 original size:26 final size:26
Alignment explanation
Indices: 1779812--1779901 Score: 67
Period size: 26 Copynumber: 3.3 Consensus size: 26
1779802 GTGTGGGCTT
* *
1779812 TGAAAGGCGTCCTGCTCTTTGAGGAC
1 TGAAAGGTGTCCTGCTCTTTGGGGAC
** *
1779838 TGAAAGGTG-CCACCAACTTGTGTGGG-C
1 TGAAAGGTGTCCTGC-TCTT-TG-GGGAC
*
1779865 TTTAAGAGGTGTCCTGCTCTTTGGGGAC
1 -TGAA-AGGTGTCCTGCTCTTTGGGGAC
1779893 TGAAAGGTG
1 TGAAAGGTG
1779902 CCACCAACTT
Statistics
Matches: 47, Mismatches: 10, Indels: 14
0.66 0.14 0.20
Matches are distributed among these distances:
25 3 0.06
26 16 0.34
27 9 0.19
28 8 0.17
29 8 0.17
30 3 0.06
ACGTcount: A:0.20, C:0.19, G:0.33, T:0.28
Consensus pattern (26 bp):
TGAAAGGTGTCCTGCTCTTTGGGGAC
Found at i:1780259 original size:170 final size:171
Alignment explanation
Indices: 1779775--1780521 Score: 1185
Period size: 170 Copynumber: 4.4 Consensus size: 171
1779765 ATCCTTCTTA
* * *
1779775 TTGAGGAGT-AAAAAGTGCCACCAA-CTCGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGAC
1 TTGAGGACTGAAAAA-TGCCACCAACCT-GTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGAGGAC
* *
1779838 T-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTGTCCTGCTCTTTGGGGACTGAAAGGT
64 TGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTGTCCTGCTCTTTGAGGACTGAAAGGT
* *
1779901 GCCACCAACTTGTGTGAGCTTTGAAAAGAAAAAGCATCCTGTTCT
127 GCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCT
*
1779946 TTAAGGACTGAAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGAGGACT
1 TTGAGGACTG-AAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGAGGACT
*
1780011 GGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGGGGACTGAAAGGTGCC
65 GGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGAAAGGTGCC
*
1780076 ACCAACCTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCT
130 ACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCT
1780118 TTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGAGGACTG
1 TTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGAGGACTG
*
1780183 G-AAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTTCTCTTTGAGGACTGAAAGGTGCCA
66 GAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGAAAGGTGCCA
1780247 CCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCT
131 CCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCT
1780288 TTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGAGGACTG
1 TTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGAGGACTG
**
1780353 GAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGAAAAATGCCA
66 GAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGAAAGGTGCCA
* **
1780418 CCAACTTGTGTGGGCATTG-AAAG-----GTGTCCTGCTCT
131 CCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCT
* * * *
1780453 TTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGGGGACT-
1 TTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGAGGACTG
1780517 GAAAA
66 GAAAA
1780522 GCGGAAGGAG
Statistics
Matches: 548, Mismatches: 22, Indels: 19
0.93 0.04 0.03
Matches are distributed among these distances:
164 5 0.01
165 70 0.13
170 171 0.31
171 141 0.26
172 148 0.27
173 13 0.02
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (171 bp):
TTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGAGGACTG
GAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGAAAGGTGCCA
CCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCT
Found at i:1781527 original size:10 final size:9
Alignment explanation
Indices: 1781499--1781549 Score: 50
Period size: 10 Copynumber: 5.6 Consensus size: 9
1781489 CTTTTCTCTC
*
1781499 TTTTTCTTT
1 TTTTTGTTT
*
1781508 GTTTTG-TT
1 TTTTTGTTT
1781516 TTTTTGTTT
1 TTTTTGTTT
*
1781525 TTTTTCCTTT
1 TTTTT-GTTT
1781535 TTTTTGCTTT
1 TTTTTG-TTT
1781545 TTTTT
1 TTTTT
1781550 TGAAGAGAAG
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
8 7 0.21
9 11 0.32
10 16 0.47
ACGTcount: A:0.00, C:0.08, G:0.08, T:0.84
Consensus pattern (9 bp):
TTTTTGTTT
Found at i:1781551 original size:11 final size:10
Alignment explanation
Indices: 1781514--1781549 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
1781504 CTTTGTTTTG
1781514 TTTTTTTG-T
1 TTTTTTTGCT
*
1781523 TTTTTTTCCT
1 TTTTTTTGCT
1781533 TTTTTTTGCT
1 TTTTTTTGCT
1781543 TTTTTTT
1 TTTTTTT
1781550 TGAAGAGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
9 7 0.29
10 17 0.71
ACGTcount: A:0.00, C:0.08, G:0.06, T:0.86
Consensus pattern (10 bp):
TTTTTTTGCT
Done.