Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007962.1 Hibiscus syriacus cultivar Beakdansim tig00110391_pilon, whole genome shotgun sequence
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: 1774241
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 8
Found at i:1551831 original size:23 final size:23
Alignment explanation
Indices: 1551805--1551859 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
1551795 TATGTTCTAT
1551805 TAATTTAATTTTAATTTAAAAAA
1 TAATTTAATTTTAATTTAAAAAA
1551828 TAATTTAATTTTAATTTAAAAAA
1 TAATTTAATTTTAATTTAAAAAA
1551851 TAATTTAAT
1 TAATTTAAT
1551860 AAATTTAATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TAATTTAATTTTAATTTAAAAAA
Found at i:1551833 original size:12 final size:12
Alignment explanation
Indices: 1551816--1551863 Score: 53
Period size: 12 Copynumber: 4.1 Consensus size: 12
1551806 AATTTAATTT
1551816 TAATTTAAAAAA
1 TAATTTAAAAAA
***
1551828 TAATTT-AATTT
1 TAATTTAAAAAA
1551839 TAATTTAAAAAA
1 TAATTTAAAAAA
*
1551851 TAATTTAATAAA
1 TAATTTAAAAAA
1551863 T
1 T
1551864 TTAATCTCTA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
11 8 0.29
12 20 0.71
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TAATTTAAAAAA
Found at i:1555489 original size:2 final size:2
Alignment explanation
Indices: 1555461--1555589 Score: 94
Period size: 2 Copynumber: 63.5 Consensus size: 2
1555451 ACACATTTAG
*
1555461 TA TA T- TA T- TA TA TA GTA TA T- TA CA TA TA TA T- TA TA GTA TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA
*
1555501 TA GTA TA GTA CA CTA TA GTA TA T- TA T- TA TA TA GTA TA TA TA TA
1 TA -TA TA -TA TA -TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA
1555544 TA TA TA TA TA TA TA T- TA TA GTA TA TA GTA TA T- TA TA TA GTA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA -TA
1555585 TA TA T
1 TA TA T
1555590 GTTGGGATTT
Statistics
Matches: 105, Mismatches: 4, Indels: 36
0.72 0.03 0.25
Matches are distributed among these distances:
1 8 0.08
2 78 0.74
3 19 0.18
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1555500 original size:12 final size:11
Alignment explanation
Indices: 1555461--1555589 Score: 106
Period size: 12 Copynumber: 11.5 Consensus size: 11
1555451 ACACATTTAG
1555461 TATAT-TATTA
1 TATATATATTA
1555471 TATAGTATATTA
1 TATA-TATATTA
*
1555483 CATATATATTA
1 TATATATATTA
*
1555494 TAGTATATAGTA
1 TA-TATATATTA
*
1555506 TAGTACACTA-TA
1 TA-TATA-TATTA
1555518 GTATAT-TATTA
1 -TATATATATTA
1555529 TATAGTATA-TA
1 TATA-TATATTA
1555540 TATATATA-TA
1 TATATATATTA
1555550 TATATATATTA
1 TATATATATTA
*
1555561 TAGTATATAGTA
1 TA-TATATATTA
*
1555573 TATTATATAGTA
1 TA-TATATATTA
1555585 TATAT
1 TATAT
1555590 GTTGGGATTT
Statistics
Matches: 102, Mismatches: 7, Indels: 19
0.80 0.05 0.15
Matches are distributed among these distances:
10 24 0.24
11 25 0.25
12 49 0.48
13 4 0.04
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (11 bp):
TATATATATTA
Found at i:1555536 original size:37 final size:31
Alignment explanation
Indices: 1555461--1555589 Score: 119
Period size: 30 Copynumber: 4.2 Consensus size: 31
1555451 ACACATTTAG
*
1555461 TATATTAT--TATATAGTATAT---TACATA
1 TATATTATAGTATATAGTATATACATATATA
1555487 TATATTATAGTATATAGTATAGTACACTATAGTA
1 TATATTATAGTATATAGTATA-TACA-TATA-TA
*
1555521 TATTATTATATAGTATATA-TATATATATATATA
1 TA-TA-T-TATAGTATATAGTATATACATATATA
*
1555554 TATATTATAGTATATAGTATAT-TATATAGTA
1 TATATTATAGTATATAGTATATACATATA-TA
1555585 TATAT
1 TATAT
1555590 GTTGGGATTT
Statistics
Matches: 88, Mismatches: 2, Indels: 21
0.79 0.02 0.19
Matches are distributed among these distances:
26 8 0.09
28 11 0.12
29 1 0.01
30 17 0.19
31 13 0.15
32 2 0.02
33 7 0.08
34 8 0.09
35 5 0.06
36 5 0.06
37 11 0.12
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (31 bp):
TATATTATAGTATATAGTATATACATATATA
Found at i:1556351 original size:24 final size:23
Alignment explanation
Indices: 1556318--1556364 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
1556308 CCAAAAACCT
1556318 GGGGGGAATCGGTTCCCCCTGGG
1 GGGGGGAATCGGTTCCCCCTGGG
* *
1556341 GGGGTGGAATCTGTTCCCTCTGGG
1 GGGG-GGAATCGGTTCCCCCTGGG
1556365 CAATCTGGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.09, C:0.23, G:0.45, T:0.23
Consensus pattern (23 bp):
GGGGGGAATCGGTTCCCCCTGGG
Found at i:1556574 original size:19 final size:20
Alignment explanation
Indices: 1556547--1556590 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
1556537 CGAATAATTT
* *
1556547 AATTGAATATATAAT-TTAA
1 AATTCAATATAAAATCTTAA
1556566 AATTCAATATAAAATCTTAA
1 AATTCAATATAAAATCTTAA
1556586 AATTC
1 AATTC
1556591 TTTAACACTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (20 bp):
AATTCAATATAAAATCTTAA
Found at i:1557753 original size:23 final size:22
Alignment explanation
Indices: 1557727--1557775 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 22
1557717 GCTTGAAAAT
*
1557727 AAAAGAAAAAAGGGAAAAACTTG
1 AAAAGAAAAAAGAG-AAAACTTG
* *
1557750 AAAAGTAAAAAGAGAAAACTTT
1 AAAAGAAAAAAGAGAAAACTTG
1557772 AAAA
1 AAAA
1557776 AAACTAGAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 11 0.48
23 12 0.52
ACGTcount: A:0.67, C:0.04, G:0.16, T:0.12
Consensus pattern (22 bp):
AAAAGAAAAAAGAGAAAACTTG
Found at i:1564636 original size:20 final size:19
Alignment explanation
Indices: 1564600--1564646 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
1564590 CTAAATCATT
*
1564600 TTTCAAAATTTCATTTTGAC
1 TTTCAAAATCTCATTTTG-C
*
1564620 TTTCAAAATCT-ATTTTTGT
1 TTTCAAAATCTCA-TTTTGC
1564639 TTTCAAAA
1 TTTCAAAA
1564647 GAAAATCGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.32, C:0.13, G:0.04, T:0.51
Consensus pattern (19 bp):
TTTCAAAATCTCATTTTGC
Found at i:1571390 original size:23 final size:22
Alignment explanation
Indices: 1571331--1571433 Score: 140
Period size: 22 Copynumber: 4.8 Consensus size: 22
1571321 ATAGGGCAAA
1571331 GGGAATCGATACCCCCTTGAAG
1 GGGAATCGATACCCCCTTGAAG
1571353 GGGAATCGATACCCCCTTGAAG
1 GGGAATCGATACCCCCTTGAAG
*
1571375 GGGAATCGATTCCCCCTTTGAAG
1 GGGAATCGATACCCCC-TTGAAG
* *
1571398 GGGAACCGATTCCCCC-T--AG
1 GGGAATCGATACCCCCTTGAAG
*
1571417 GGGAATCAATACCCCCT
1 GGGAATCGATACCCCCT
1571434 GGGGTTCTGG
Statistics
Matches: 74, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
19 15 0.20
21 1 0.01
22 37 0.50
23 21 0.28
ACGTcount: A:0.25, C:0.30, G:0.25, T:0.19
Consensus pattern (22 bp):
GGGAATCGATACCCCCTTGAAG
Found at i:1572600 original size:59 final size:58
Alignment explanation
Indices: 1572467--1572603 Score: 175
Period size: 59 Copynumber: 2.3 Consensus size: 58
1572457 ATAAGCACCG
* ** *
1572467 TAGTGCTATCCCGAATATGACACATAAGGTCGTGCCCACCATCTGTACTAGGTATCCTT
1 TAGTG-TATCCCGAATATGACACATAAGGTCGTGCCCACCATATACAATAGGTATCCTT
* ** *
1572526 AAGTACAATCTCGAATATGACACATAAGGTCGTGCCCACCATATACAATAGGTATCCTT
1 TAGT-GTATCCCGAATATGACACATAAGGTCGTGCCCACCATATACAATAGGTATCCTT
1572585 TAGTGTATTCCCGAATATG
1 TAGTGTA-TCCCGAATATG
1572604 CAGCCTGCTG
Statistics
Matches: 64, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
58 1 0.02
59 63 0.98
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (58 bp):
TAGTGTATCCCGAATATGACACATAAGGTCGTGCCCACCATATACAATAGGTATCCTT
Found at i:1573329 original size:30 final size:30
Alignment explanation
Indices: 1573295--1573358 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 30
1573285 AATCCCTCCA
* * *
1573295 TTTTCCAAAATTTACGAATTGATCTCCAAC
1 TTTTCCAAAACTTACGAAATGATCCCCAAC
*
1573325 TTTT-CAAAACTTACGAAATGATCCCCAAT
1 TTTTCCAAAACTTACGAAATGATCCCCAAC
1573354 TTTTC
1 TTTTC
1573359 TAAGACTTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 25 0.86
30 4 0.14
ACGTcount: A:0.33, C:0.23, G:0.06, T:0.38
Consensus pattern (30 bp):
TTTTCCAAAACTTACGAAATGATCCCCAAC
Found at i:1577142 original size:18 final size:18
Alignment explanation
Indices: 1577114--1577161 Score: 78
Period size: 18 Copynumber: 2.6 Consensus size: 18
1577104 ATCAAGCCAA
1577114 TTTTCCTTTCAATATTCAG
1 TTTT-CTTTCAATATTCAG
*
1577133 TTTTCTTTCAATATTCAT
1 TTTTCTTTCAATATTCAG
1577151 TTTTCTTTCAA
1 TTTTCTTTCAA
1577162 GAACACCATT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 24 0.86
19 4 0.14
ACGTcount: A:0.21, C:0.19, G:0.02, T:0.58
Consensus pattern (18 bp):
TTTTCTTTCAATATTCAG
Found at i:1578305 original size:35 final size:35
Alignment explanation
Indices: 1578256--1578325 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
1578246 CGTTACACAG
*
1578256 GGGGAATCGGTACCCCCTGGGGGGAATCTGTTCCC
1 GGGGAATCGATACCCCCTGGGGGGAATCTGTTCCC
1578291 GGGGAATCGATACCCCCTGGGGGGAATCTGTTCCC
1 GGGGAATCGATACCCCCTGGGGGGAATCTGTTCCC
1578326 TCTGGGAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.16, C:0.29, G:0.36, T:0.20
Consensus pattern (35 bp):
GGGGAATCGATACCCCCTGGGGGGAATCTGTTCCC
Found at i:1578326 original size:18 final size:18
Alignment explanation
Indices: 1578270--1578326 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 18
1578260 AATCGGTACC
1578270 CCCTGGGGGGAATCTGTT
1 CCCTGGGGGGAATCTGTT
*
1578288 CCC---GGGGAATC-GATACC
1 CCCTGGGGGGAATCTG-T--T
1578305 CCCTGGGGGGAATCTGTT
1 CCCTGGGGGGAATCTGTT
1578323 CCCT
1 CCCT
1578327 CTGGGAATTC
Statistics
Matches: 30, Mismatches: 2, Indels: 14
0.65 0.04 0.30
Matches are distributed among these distances:
14 1 0.03
15 9 0.30
17 3 0.10
18 7 0.23
20 9 0.30
21 1 0.03
ACGTcount: A:0.14, C:0.30, G:0.33, T:0.23
Consensus pattern (18 bp):
CCCTGGGGGGAATCTGTT
Found at i:1578330 original size:20 final size:20
Alignment explanation
Indices: 1578255--1578331 Score: 67
Period size: 20 Copynumber: 4.1 Consensus size: 20
1578245 TCGTTACACA
*
1578255 GGGGGAATCGGTACCCCCTG
1 GGGGGAATCTGTACCCCCTG
*
1578275 GGGGGAATCTGT--TCCC--
1 GGGGGAATCTGTACCCCCTG
1578291 -GGGGAATC-GATACCCCCTG
1 GGGGGAATCTG-TACCCCCTG
* *
1578310 GGGGGAATCTGTTCCCTCTG
1 GGGGGAATCTGTACCCCCTG
1578330 GG
1 GG
1578332 AATTCTGGTT
Statistics
Matches: 45, Mismatches: 5, Indels: 14
0.70 0.08 0.22
Matches are distributed among these distances:
14 1 0.02
15 9 0.20
17 3 0.07
18 3 0.07
20 28 0.62
21 1 0.02
ACGTcount: A:0.14, C:0.27, G:0.38, T:0.21
Consensus pattern (20 bp):
GGGGGAATCTGTACCCCCTG
Found at i:1578543 original size:19 final size:20
Alignment explanation
Indices: 1578519--1578558 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1578509 AATTTAATCG
*
1578519 AATATATAAT-TTAAAATTC
1 AATATAAAATCTTAAAATTC
1578538 AATATAAAATCTTAAAATTC
1 AATATAAAATCTTAAAATTC
1578558 A
1 A
1578559 TTAACACTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (20 bp):
AATATAAAATCTTAAAATTC
Found at i:1581836 original size:6 final size:6
Alignment explanation
Indices: 1581825--1581858 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
1581815 CAATCCATGC
1581825 TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TTTA
1 TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TTTA
1581859 TACAAGTCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTAAT
Found at i:1587207 original size:15 final size:15
Alignment explanation
Indices: 1587169--1587209 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
1587159 ATGATTAGAC
*
1587169 TTTAAAT-AAATACA
1 TTTAAATAAAATAAA
*
1587183 -TTATATAAAATAAA
1 TTTAAATAAAATAAA
1587197 TTTAAATAAAATA
1 TTTAAATAAAATA
1587210 CAATCTCATT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
13 5 0.23
14 6 0.27
15 11 0.50
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (15 bp):
TTTAAATAAAATAAA
Found at i:1589645 original size:506 final size:506
Alignment explanation
Indices: 1588606--1590119 Score: 2742
Period size: 506 Copynumber: 3.0 Consensus size: 506
1588596 CACGGATTGG
*
1588606 GCGATGTCTGTTGCTCTCTATGCAGTTATCATGTTCTTGATTCAACCGATTTTCGCACCAACAGC
1 GCGATGTCTGTTGCTCTCTATGCAGTTATCATGTTCTTGATTCAACCGATTTTCGCACCAGCAGC
* *
1588671 CTTCGCAACCTTTCAAATCGCCGCCAAAACTAGTGGAACTGCAGCTAGGGGCAGACTAATCTATG
66 CTTCGCAACCTTTCAAATCGCCGCCAAAACTAGTGGAACTGCAGCTGGGGGCAGACTAATCCATG
* * *
1588736 TCAAGTTATTAAGTAGTGAGTGGACTGGTTTCTTTTCCGGTTGTTTCCACACCCTGTCAGGGCCA
131 TCCAGTTATTAAGTAGTGCGTGGACTGGTTTCTTTTCCGGTTGTTTGCACACCCTGTCAGGGCCA
*
1588801 GACCACCTTATGGCTTTGGCTCCGCTATCGATCGGACGTACACGGATGGGAAACGCTGTTGTTGG
196 GACCACCTTATGGCTTTGGCTCCGCTATCGATCGGACGTACACGGATGGGAAGCGCTGTTGTTGG
*
1588866 AGCTCTGTGGGGTTTTGG-TATGATGCTGGTCAGGTAATCTTTGGTCTCATATTTCTACTTCTAA
261 AGCTCTGTGGGGTTTTGGCCATGATGCTGGTCAGGTAATCTTTGGTCTCATATTTCTACTTCTAA
*
1588930 AGGACAGGCTCCAAATTGAAGTCATCCGGACCTGGGGTACAAGGGTGTTGGGCTTAACATTGCTC
326 AGGACAGGCTCCAAATTGAAGTCATCCGGACCTGGGGTACAAGGGTGGTGGGCTTAACATTGCTC
1588995 GTTGTCGGAGCTATTGGTATAAGTGAAGCTTCTGAAGTTCCCGCTCCCTGCGTTGCCATAGGAAA
391 GTTGTCGGAGCTATTGGTATAAGTGAAGCTTCTGAAGTTCCCGCTCCCTGCGTTGCCATAGGAAA
* *
1589060 CATTAAGTGTGATGTTAGTGTTTACGGAACACTCGATATTGGAAAACGTAA
456 CAGTGAGTGTGATGTTAGTGTTTACGGAACACTCGATATTGGAAAACGTAA
*
1589111 GCGATGTCTGTTGCTCTCTATACAGTTATCATGTTCTTGATTCAACCGATTTTCGCACCAGCAGC
1 GCGATGTCTGTTGCTCTCTATGCAGTTATCATGTTCTTGATTCAACCGATTTTCGCACCAGCAGC
*
1589176 CTTCGCAACCTTTCAAATCACCGCCAAAACTAGTGGAACTGCAGCTGGGGGCAGACTAATCCATG
66 CTTCGCAACCTTTCAAATCGCCGCCAAAACTAGTGGAACTGCAGCTGGGGGCAGACTAATCCATG
1589241 TCCAGTTATTAAGTAGTGCGTGGACTGGTTTCTTTTCCGGTTGTTTGCACACCCTGTCAGGGCCA
131 TCCAGTTATTAAGTAGTGCGTGGACTGGTTTCTTTTCCGGTTGTTTGCACACCCTGTCAGGGCCA
*
1589306 GACCACCTTGTGGCTTTGGCTCCGCTATCGATCGGACGTACACGGATGGGAAGCGCTGTTGTTGG
196 GACCACCTTATGGCTTTGGCTCCGCTATCGATCGGACGTACACGGATGGGAAGCGCTGTTGTTGG
1589371 AGCTCTGTGGGGTTTTGGCCATGATGCTGGTCAGGTAATCTTTGGTCTCATATTTCTACTTCTAA
261 AGCTCTGTGGGGTTTTGGCCATGATGCTGGTCAGGTAATCTTTGGTCTCATATTTCTACTTCTAA
* *
1589436 AGGAAAGACTCCAAATTGAAGTCATCCGGACCTGGGGTACAAGGGTGGTGGGCTTAACATTGCTC
326 AGGACAGGCTCCAAATTGAAGTCATCCGGACCTGGGGTACAAGGGTGGTGGGCTTAACATTGCTC
*
1589501 GTTGTCGGAGCTATTGGTATAAGTGAAGCTTCTGAAGTTCCCACTCCCTGCGTTGCCATAGGAAA
391 GTTGTCGGAGCTATTGGTATAAGTGAAGCTTCTGAAGTTCCCGCTCCCTGCGTTGCCATAGGAAA
1589566 CAGTGAGTGTGATGTTAGTGTTTACGGAACACTCGATATTGGAAAACGTAA
456 CAGTGAGTGTGATGTTAGTGTTTACGGAACACTCGATATTGGAAAACGTAA
* *
1589617 GCGATGTCTGTTGCTCTCTATGCAGTTATCATATTCTTGATTCAACTGATTTTCGCACCAGCAGC
1 GCGATGTCTGTTGCTCTCTATGCAGTTATCATGTTCTTGATTCAACCGATTTTCGCACCAGCAGC
* *
1589682 CTTCGCAACCTTTCAAATCGCCGCCAAAACTAGTGGAACTGCACCTGGGGGCAGATTAATCCATG
66 CTTCGCAACCTTTCAAATCGCCGCCAAAACTAGTGGAACTGCAGCTGGGGGCAGACTAATCCATG
* *
1589747 TCCAGTTATTAAGTATTGCGTGGACTGGTTTCTTTTCCCGTTGTTTGCACACCCTGTCAGGGCCA
131 TCCAGTTATTAAGTAGTGCGTGGACTGGTTTCTTTTCCGGTTGTTTGCACACCCTGTCAGGGCCA
* *
1589812 GACCACCTTATGGCTTTGGCTTCGCTATCGATCGGACGTACACGGATGAGAAGCGCTGTTGTTGG
196 GACCACCTTATGGCTTTGGCTCCGCTATCGATCGGACGTACACGGATGGGAAGCGCTGTTGTTGG
*
1589877 AGCTCTGTGGGGGGTTTTGGCCATGATGCTGGTCAGGTAATCTTTGGTCTCATATTTCTAGTTCT
261 AGCTCTGT--GGGGTTTTGGCCATGATGCTGGTCAGGTAATCTTTGGTCTCATATTTCTACTTCT
1589942 AAAGGACAGGCTCCAAATTGAAGTCATCCGGACCTGGGGTACAAGGGTGGTGGGCTTAACATTGC
324 AAAGGACAGGCTCCAAATTGAAGTCATCCGGACCTGGGGTACAAGGGTGGTGGGCTTAACATTGC
* * *
1590007 TCGTTGTCGGAGCTATTGGTATAAATGAAGCTTCTGAAGTTCCCGCTCCCTGTGTTTCCATAGGA
389 TCGTTGTCGGAGCTATTGGTATAAGTGAAGCTTCTGAAGTTCCCGCTCCCTGCGTTGCCATAGGA
1590072 AACAGTGAGTGTGATGTTAGTGTTTACGGAACACTCGATATTGGAAAA
454 AACAGTGAGTGTGATGTTAGTGTTTACGGAACACTCGATATTGGAAAA
1590120 TGTATAAGCT
Statistics
Matches: 971, Mismatches: 35, Indels: 3
0.96 0.03 0.00
Matches are distributed among these distances:
505 268 0.28
506 477 0.49
508 226 0.23
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.30
Consensus pattern (506 bp):
GCGATGTCTGTTGCTCTCTATGCAGTTATCATGTTCTTGATTCAACCGATTTTCGCACCAGCAGC
CTTCGCAACCTTTCAAATCGCCGCCAAAACTAGTGGAACTGCAGCTGGGGGCAGACTAATCCATG
TCCAGTTATTAAGTAGTGCGTGGACTGGTTTCTTTTCCGGTTGTTTGCACACCCTGTCAGGGCCA
GACCACCTTATGGCTTTGGCTCCGCTATCGATCGGACGTACACGGATGGGAAGCGCTGTTGTTGG
AGCTCTGTGGGGTTTTGGCCATGATGCTGGTCAGGTAATCTTTGGTCTCATATTTCTACTTCTAA
AGGACAGGCTCCAAATTGAAGTCATCCGGACCTGGGGTACAAGGGTGGTGGGCTTAACATTGCTC
GTTGTCGGAGCTATTGGTATAAGTGAAGCTTCTGAAGTTCCCGCTCCCTGCGTTGCCATAGGAAA
CAGTGAGTGTGATGTTAGTGTTTACGGAACACTCGATATTGGAAAACGTAA
Found at i:1590443 original size:35 final size:35
Alignment explanation
Indices: 1590347--1590449 Score: 161
Period size: 35 Copynumber: 2.9 Consensus size: 35
1590337 AGATGAACAA
** *
1590347 TTGAATCGAAAGTGCTTATGCTTCCTCCCGTTCAC
1 TTGAATCGAAAGTGCCAATGCTTCCTTCCGTTCAC
*
1590382 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCAC
1 TTGAATCGAAAGTGCCAATGCTTCCTTCCGTTCAC
*
1590417 TTGAATCGAAAGTGCCAATGCTTCCTTTCGTTC
1 TTGAATCGAAAGTGCCAATGCTTCCTTCCGTTC
1590450 TTCTTATTCA
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 63 1.00
ACGTcount: A:0.20, C:0.27, G:0.18, T:0.34
Consensus pattern (35 bp):
TTGAATCGAAAGTGCCAATGCTTCCTTCCGTTCAC
Found at i:1600793 original size:2 final size:2
Alignment explanation
Indices: 1600788--1600831 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1600778 GTATTAAGAG
1600788 AT 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 AT
1600830 AT
1 AT
1600832 GCTTTGAGTG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1601061 original size:20 final size:19
Alignment explanation
Indices: 1601015--1601061 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
1601005 GTTTTCGCTT
*
1601015 TTAATTATTATTATGTCTA
1 TTAATTATTATAATGTCTA
1601034 TTAGATTATTTATAATTGT-TA
1 TTA-ATTA-TTATAA-TGTCTA
1601055 TTAATTA
1 TTAATTA
1601062 GTAGTTCTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 3 0.12
20 8 0.33
21 10 0.42
22 3 0.12
ACGTcount: A:0.34, C:0.02, G:0.06, T:0.57
Consensus pattern (19 bp):
TTAATTATTATAATGTCTA
Found at i:1601139 original size:5 final size:5
Alignment explanation
Indices: 1601127--1601163 Score: 67
Period size: 5 Copynumber: 7.6 Consensus size: 5
1601117 AGGTTAGTGT
1601127 TAAT- TAATA TAATA TAATA TAATA TAATA TAATA TAA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAA
1601164 ATATGTATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.12
5 28 0.88
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TAATA
Found at i:1602579 original size:13 final size:13
Alignment explanation
Indices: 1602561--1602585 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1602551 AACACACTTT
1602561 TTAAAATTATATG
1 TTAAAATTATATG
1602574 TTAAAATTATAT
1 TTAAAATTATAT
1602586 TTATCTACTT
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:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (13 bp):
TTAAAATTATATG
Found at i:1604280 original size:45 final size:46
Alignment explanation
Indices: 1604222--1604337 Score: 128
Period size: 47 Copynumber: 2.5 Consensus size: 46
1604212 GGGGCATCTT
* * * *
1604222 TTCATGCCCATTATGTACTGTTTACATTTTCCT-T-TATGACATCCA
1 TTCATACCAATTATGCACTGTTTACATTTT-ATATATATGACATCCA
* *
1604267 TTCATACCAATTATGCATTGTTGTACATTTTATATATATGACATCCT
1 TTCATACCAATTATGCACTGTT-TACATTTTATATATATGACATCCA
* *
1604314 TTCATACCACTTATGCACCGTTTA
1 TTCATACCAATTATGCACTGTTTA
1604338 TATCAAAATA
Statistics
Matches: 59, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
45 19 0.32
46 11 0.19
47 29 0.49
ACGTcount: A:0.26, C:0.22, G:0.09, T:0.43
Consensus pattern (46 bp):
TTCATACCAATTATGCACTGTTTACATTTTATATATATGACATCCA
Found at i:1604509 original size:81 final size:81
Alignment explanation
Indices: 1604358--1605586 Score: 1809
Period size: 81 Copynumber: 15.2 Consensus size: 81
1604348 CATTATAATT
* * * * * * * *
1604358 CCATTAGTCTTTTACCCAAAGGCATTTAGCCTTTCATCTAACTTGCATGACTGACACTTTTCTGC
1 CCATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGC
1604423 CAAATGCACAGCTAGG
66 CAAATGCACAGCTAGG
* * *
1604439 CAATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAATTGGCATAATTGACACCTTTATGC
1 CCATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGC
*
1604504 AAAATGCACAGCTAGG
66 CAAATGCACAGCTAGG
1604520 CCATTAATC-TTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGC
1 CCATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGC
*
1604584 CAAATGCACAGTTAGG
66 CAAATGCACAGCTAGG
* * * *
1604600 CAATTAATCTTTTACTCAAAGATATTTAACCTTTCATCTAACCT-GCATAATTGACACATTTATG
1 CCATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAA-CTGGCATAATTGACACCTTTCTG
* *
1604664 CCAAATGCACAACTATG
65 CCAAATGCACAGCTAGG
* *
1604681 CCATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAATTGGCATAATTGAAACCTTTTCTG
1 CCATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACC-TTTCTG
* *
1604746 CCAAATGCATAGCTATG
65 CCAAATGCACAGCTAGG
* *
1604763 CCATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAATTGGCATAATTGAAACCTTTTCTG
1 CCATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACC-TTTCTG
1604828 CCAAATGCACAGCTA-G
65 CCAAATGCACAGCTAGG
* * * * *
1604844 ACATTAATCTTTTACTCAAAGGTATTTATCCTTTCATGTAACTGGCATAATTGAAACCTTTTTGC
1 CCATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGC
*
1604909 CAAATGCACAACTAGG
66 CAAATGCACAGCTAGG
* *
1604925 CCATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCTTAATTGACACCTTTTTGC
1 CCATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGC
*
1604990 CAAATGCACAACTAGG
66 CAAATGCACAGCTAGG
* *
1605006 CCATTAATATTTTACTCAAAGGTATTTAACCTTTCAGT-TAACTGGAATAATTGACACCTTTCTG
1 CCATTAATCTTTTACTCAAAGGTATTTAACCTTTCA-TCTAACTGGCATAATTGACACCTTTCTG
* *
1605070 CCAAATACACAGCTAAG
65 CCAAATGCACAGCTAGG
* * * *
1605087 TCATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGAATAATTGACACATTTCAGC
1 CCATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGC
1605152 CAAATGCACAGCTAGG
66 CAAATGCACAGCTAGG
* * *
1605168 CCATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGAATAATTGACACATTTTTGC
1 CCATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGC
* *
1605233 CAAATGCACAACTAGA
66 CAAATGCACAGCTAGG
* * * * *
1605249 TCATTAATCTTTTACTCAAAGGTATTTAACATTTCATCTTACTGGAATAATTGACACATTTCTGC
1 CCATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGC
1605314 CAAATGCACAGCTAGG
66 CAAATGCACAGCTAGG
* * * * *
1605330 CCATTAATCTTTTGCTCAAAGTTATTTAACCTTTTATCTAACTGGTATAATTGATACCTTTCTGC
1 CCATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGC
1605395 CAAATGCACAGCTAGG
66 CAAATGCACAGCTAGG
* *
1605411 CCATTAATATTTTACTCAAAGGTATTTAACCTCTCATCTAACTGGCATAATTGACACCTTTCTGC
1 CCATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGC
*
1605476 CAAATGCACAACTAGG
66 CAAATGCACAGCTAGG
* * * *
1605492 CCATTAATATTTTACTCAAAGGTATTTAACCTTTCATCTAACTTGCATAATTGACACATTTATGC
1 CCATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGC
*
1605557 TAAATGCACAGCTAGG
66 CAAATGCACAGCTAGG
1605573 CCATTAATCTTTTA
1 CCATTAATCTTTTA
1605587 TTTTAGAATT
Statistics
Matches: 1049, Mismatches: 92, Indels: 14
0.91 0.08 0.01
Matches are distributed among these distances:
80 96 0.09
81 851 0.81
82 102 0.10
ACGTcount: A:0.32, C:0.22, G:0.11, T:0.35
Consensus pattern (81 bp):
CCATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGC
CAAATGCACAGCTAGG
Found at i:1605796 original size:55 final size:55
Alignment explanation
Indices: 1605672--1605898 Score: 271
Period size: 55 Copynumber: 4.1 Consensus size: 55
1605662 TTGCACATGT
* * * * *
1605672 AGTGCCAATACGGTAATTCACAAACTTATTAT-AATTTATGTGGGTTT-CACACTC
1 AGTGCCAATACGGAAATTCATAAACTTATTATGAATTTAT-TAGTTTTGCACACAC
* * *
1605726 ACTGCCAATATGGAAATTCATAAACTTATTATGAATTTATTAGTTTTACACACAC
1 AGTGCCAATACGGAAATTCATAAACTTATTATGAATTTATTAGTTTTGCACACAC
* * *
1605781 AGTGCCCATACGGAAATTCATAAACTTATTA-GAAGTTTCTTAGTTTTTGCACACAA
1 AGTGCCAATACGGAAATTCATAAACTTATTATGAA-TTTATTAG-TTTTGCACACAC
* * * *
1605837 AGTGCCCATACGGAAATTCATAAACTCATTATGAATTTCTTAGTTTTGCACACAT
1 AGTGCCAATACGGAAATTCATAAACTTATTATGAATTTATTAGTTTTGCACACAC
1605892 AGTGCCA
1 AGTGCCA
1605899 TTTGGTAATC
Statistics
Matches: 152, Mismatches: 16, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
54 36 0.24
55 65 0.43
56 48 0.32
57 3 0.02
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.34
Consensus pattern (55 bp):
AGTGCCAATACGGAAATTCATAAACTTATTATGAATTTATTAGTTTTGCACACAC
Found at i:1608628 original size:2 final size:2
Alignment explanation
Indices: 1608621--1608653 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1608611 CTATAAAAAC
1608621 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 T
1608654 CTGACATCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1610702 original size:81 final size:81
Alignment explanation
Indices: 1610617--1611732 Score: 1570
Period size: 81 Copynumber: 13.9 Consensus size: 81
1610607 ACCCATAGTC
* * ** * *
1610617 ATTTATCCTTTCATTTAACTTACATGATTGACACTTTTCTGCCAAATGCACAGCTAGGCCATTAA
1 ATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGCACAGCTAGGCCATTAA
*
1610682 TCTTTTACTCAAAGAT
66 TCTTTTACTCAAAGGT
* * *
1610698 ATTTAACCTTTCATCTAACTGGCATAATTGACACATTTATGCCAAATGCACAGATAGGCTATTAA
1 ATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGCACAGCTAGGCCATTAA
* *
1610763 TATTTTACTCAAAGAT
66 TCTTTTACTCAAAGGT
* * * * *
1610779 ATTTAACCCTTCATTTAACTGGTATAATTGACATC-TTTCTTCCAAATGCACAACTAGGCCATTA
1 ATTTAACCTTTCATCTAACTGGCATAATTGACA-CATTTCTGCCAAATGCACAGCTAGGCCATTA
* *
1610843 ATCTTTCACTCAAAGAT
65 ATCTTTTACTCAAAGGT
* * * * * * * *
1610860 ATTTAACCTTTTATCTAGCTGGTATAATTGACACCTTTATGCCAAATCCACAACTAGGCCACTAA
1 ATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGCACAGCTAGGCCATTAA
1610925 TCTTTTACTCAAAGGT
66 TCTTTTACTCAAAGGT
* *
1610941 ATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTACCAAATGCACAGCTAGGCCATTAA
1 ATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGCACAGCTAGGCCATTAA
1611006 TCTTTTACTCAAAGGT
66 TCTTTTACTCAAAGGT
* * *
1611022 ATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGTACAACTAGGCCATTAA
1 ATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGCACAGCTAGGCCATTAA
* *
1611087 TCTTTTAGTCAAATGT
66 TCTTTTACTCAAAGGT
* * *
1611103 ATTTAACCTTTCATCTAACTGGTATAATTGACACCTTTTTGCCAAATGCACAGCTAGGCCATTAA
1 ATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGCACAGCTAGGCCATTAA
1611168 TCTTTTACTCAAAGGT
66 TCTTTTACTCAAAGGT
* * * * *
1611184 ATTTAACATTTCATCTAACTGGCATAATTGACACTTTTCTGTCAAATGCACAACTAGGCCATTAC
1 ATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGCACAGCTAGGCCATTAA
1611249 TCTTTTACTCAAAGGT
66 TCTTTTACTCAAAGGT
* * * * *
1611265 ATTTAACCTTTTCATCTAACTGACATAATTGACACATTTCTTCCAAATGAACATCTTGGCCATTA
1 ATTTAACC-TTTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGCACAGCTAGGCCATTA
1611330 ATCTTTTACTCAAAGGT
65 ATCTTTTACTCAAAGGT
* * * * * *
1611347 ATTTAACCTTTCATCTAACAGGTATAATTGACACATTT-TCCCAATTGAACAGCTAGGTCATTAA
1 ATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGCACAGCTAGGCCATTAA
*
1611411 TCTTTTACTCAAAGAT
66 TCTTTTACTCAAAGGT
1611427 ATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGCACAGCTAGGCCATTAA
1 ATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGCACAGCTAGGCCATTAA
1611492 TCTTTTACTCAAAGGT
66 TCTTTTACTCAAAGGT
*
1611508 ATTTAACC-TT--TC--A-T---ATAATTGGCACATTTCTGCCAAATGCACAGCTAGGCCATTAA
1 ATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGCACAGCTAGGCCATTAA
1611564 TCTTTTACTCAAAGGT
66 TCTTTTACTCAAAGGT
* *
1611580 ATTTAACCTTTCATCTAACTGGCATAATTGACACATTCCTGCCAAATGCACAACTAGGCCATTAA
1 ATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGCACAGCTAGGCCATTAA
1611645 TCTTTTACTCAAAGGT
66 TCTTTTACTCAAAGGT
** * * *
1611661 AAGTAACCTTTCATCTAATTTGCATAATTGACACATTTCTACCAAATGCACAGCTAGGCCATTAA
1 ATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGCACAGCTAGGCCATTAA
*
1611726 TCGTTTA
66 TCTTTTA
1611733 TTTTAGAATT
Statistics
Matches: 929, Mismatches: 93, Indels: 26
0.89 0.09 0.02
Matches are distributed among these distances:
72 65 0.07
73 2 0.00
75 3 0.00
76 1 0.00
77 1 0.00
78 3 0.00
80 75 0.08
81 705 0.76
82 74 0.08
ACGTcount: A:0.32, C:0.22, G:0.11, T:0.35
Consensus pattern (81 bp):
ATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGCCAAATGCACAGCTAGGCCATTAA
TCTTTTACTCAAAGGT
Found at i:1612004 original size:56 final size:55
Alignment explanation
Indices: 1611877--1612043 Score: 248
Period size: 55 Copynumber: 3.0 Consensus size: 55
1611867 CCCACTACCA
* * *
1611877 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTACACACACAGTGTCC
1 ATACGGAAATTCATAAACTCATTATGAATTTCTTAGTTTTGCACACAAAGTGTCC
*
1611932 ATATGGAAATTCATAAACTCATTATGAATTTCTTAGTTTTTGCACACAAAGT-TCCC
1 ATACGGAAATTCATAAACTCATTATGAATTTCTTAG-TTTTGCACACAAAGTGT-CC
* *
1611988 ATACGGAAATTCATAAATTCATTATGAATTTCTTAGTTTTGCACACATAGTG-CC
1 ATACGGAAATTCATAAACTCATTATGAATTTCTTAGTTTTGCACACAAAGTGTCC
1612042 AT
1 AT
1612044 TTGGTAATCA
Statistics
Matches: 102, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
54 4 0.04
55 49 0.48
56 49 0.48
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.37
Consensus pattern (55 bp):
ATACGGAAATTCATAAACTCATTATGAATTTCTTAGTTTTGCACACAAAGTGTCC
Found at i:1618009 original size:2 final size:2
Alignment explanation
Indices: 1618004--1618030 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1617994 ATACAATCAT
1618004 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1618031 TATATATATC
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1626456 original size:17 final size:15
Alignment explanation
Indices: 1626416--1626467 Score: 61
Period size: 17 Copynumber: 3.3 Consensus size: 15
1626406 TTGCTTGCTT
1626416 ATAATAAAAT-AAAA
1 ATAATAAAATAAAAA
*
1626430 ATATTAAAATAAAACA
1 ATAATAAAATAAAA-A
1626446 GATAATAAAATAATAAA
1 -ATAATAAAATAA-AAA
1626463 ATAAT
1 ATAAT
1626468 TTAATTTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
14 9 0.28
15 3 0.09
16 6 0.19
17 12 0.38
18 2 0.06
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (15 bp):
ATAATAAAATAAAAA
Found at i:1626458 original size:8 final size:8
Alignment explanation
Indices: 1626416--1626467 Score: 56
Period size: 8 Copynumber: 6.6 Consensus size: 8
1626406 TTGCTTGCTT
1626416 ATAATAAA
1 ATAATAAA
1626424 AT-A-AAA
1 ATAATAAA
*
1626430 ATATTAAA
1 ATAATAAA
1626438 ATAA-AACA
1 ATAATAA-A
1626446 GATAATAAA
1 -ATAATAAA
1626455 ATAATAAA
1 ATAATAAA
1626463 ATAAT
1 ATAAT
1626468 TTAATTTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
6 5 0.14
7 3 0.08
8 22 0.59
9 5 0.14
10 2 0.05
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (8 bp):
ATAATAAA
Found at i:1627241 original size:32 final size:32
Alignment explanation
Indices: 1627200--1627271 Score: 135
Period size: 32 Copynumber: 2.2 Consensus size: 32
1627190 ATATCGCTTC
*
1627200 AGTGCCTTAGCAATCAATTTTTTATCAAAATG
1 AGTGCCTTAGCAATCAATTTGTTATCAAAATG
1627232 AGTGCCTTAGCAATCAATTTGTTATCAAAATG
1 AGTGCCTTAGCAATCAATTTGTTATCAAAATG
1627264 AGTGCCTT
1 AGTGCCTT
1627272 CATCGCTGAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (32 bp):
AGTGCCTTAGCAATCAATTTGTTATCAAAATG
Found at i:1631550 original size:40 final size:40
Alignment explanation
Indices: 1631495--1631571 Score: 145
Period size: 40 Copynumber: 1.9 Consensus size: 40
1631485 AGCTTTGAGG
*
1631495 AAGCTAGCCTGTTGTTCCTCTATAGAAAAATCATTAGAGA
1 AAGCTAGCATGTTGTTCCTCTATAGAAAAATCATTAGAGA
1631535 AAGCTAGCATGTTGTTCCTCTATAGAAAAATCATTAG
1 AAGCTAGCATGTTGTTCCTCTATAGAAAAATCATTAG
1631572 GCTCTTCAGC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (40 bp):
AAGCTAGCATGTTGTTCCTCTATAGAAAAATCATTAGAGA
Found at i:1635542 original size:18 final size:18
Alignment explanation
Indices: 1635519--1635556 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
1635509 CGTGAGGATT
1635519 GGGCAGTGGTCCAGCATG
1 GGGCAGTGGTCCAGCATG
1635537 GGGCAGTGGTCCAGCATG
1 GGGCAGTGGTCCAGCATG
1635555 GG
1 GG
1635557 CATCTGGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.16, C:0.21, G:0.47, T:0.16
Consensus pattern (18 bp):
GGGCAGTGGTCCAGCATG
Found at i:1640698 original size:24 final size:23
Alignment explanation
Indices: 1640679--1640740 Score: 106
Period size: 23 Copynumber: 2.7 Consensus size: 23
1640669 CATATGAATT
1640679 TGTCCCGAAGGACCACTATGAAA
1 TGTCCCGAAGGACCACTATGAAA
* *
1640702 TATCCCTAAGGACCACTATGAAA
1 TGTCCCGAAGGACCACTATGAAA
1640725 TGTCCCGAAGGACCAC
1 TGTCCCGAAGGACCAC
1640741 GTAGAACCCT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.34, C:0.29, G:0.19, T:0.18
Consensus pattern (23 bp):
TGTCCCGAAGGACCACTATGAAA
Found at i:1653212 original size:45 final size:45
Alignment explanation
Indices: 1653151--1653242 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
1653141 TCCTAGGCAA
1653151 AATAAGAGATAAGGGCCCTTAAAAAATAACTTAAAATTCAAGAAT
1 AATAAGAGATAAGGGCCCTTAAAAAATAACTTAAAATTCAAGAAT
1653196 AATAAGAGATAAGGGCCCTTAAAAAATAACTTAAAATTCAAGAAT
1 AATAAGAGATAAGGGCCCTTAAAAAATAACTTAAAATTCAAGAAT
1653241 AA
1 AA
1653243 ATTTTGGTAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.54, C:0.11, G:0.13, T:0.22
Consensus pattern (45 bp):
AATAAGAGATAAGGGCCCTTAAAAAATAACTTAAAATTCAAGAAT
Found at i:1661549 original size:22 final size:22
Alignment explanation
Indices: 1661517--1661562 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
1661507 TCAATACTTC
* *
1661517 AAAGTTGAAGGGCTAAATTTAT
1 AAAGTTAAAGGACTAAATTTAT
1661539 AAAGTTAAAGGACTAAATTTAT
1 AAAGTTAAAGGACTAAATTTAT
1661561 AA
1 AA
1661563 TTAAACCAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.48, C:0.04, G:0.17, T:0.30
Consensus pattern (22 bp):
AAAGTTAAAGGACTAAATTTAT
Found at i:1662038 original size:21 final size:21
Alignment explanation
Indices: 1662008--1662055 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
1661998 CGATACGCGA
*
1662008 GCGAAACGCGAATTGGAACGG
1 GCGAACCGCGAATTGGAACGG
1662029 GCGAACCGCGAATTGGAACGG
1 GCGAACCGCGAATTGGAACGG
*
1662050 ACGAAC
1 GCGAAC
1662056 TGAAACGAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.33, C:0.23, G:0.35, T:0.08
Consensus pattern (21 bp):
GCGAACCGCGAATTGGAACGG
Found at i:1666837 original size:16 final size:16
Alignment explanation
Indices: 1666818--1666869 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
1666808 TAGTGAAACC
*
1666818 GAAATCAACCAGAACT
1 GAAATTAACCAGAACT
* *
1666834 GAAATTAATCGGAACT
1 GAAATTAACCAGAACT
*
1666850 GAAATTAACCCGAACT
1 GAAATTAACCAGAACT
1666866 GAAA
1 GAAA
1666870 CCAAAATTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.48, C:0.19, G:0.15, T:0.17
Consensus pattern (16 bp):
GAAATTAACCAGAACT
Found at i:1666919 original size:16 final size:16
Alignment explanation
Indices: 1666889--1666919 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1666879 ACTCGAACTA
*
1666889 AAAGCAACCCGAACCT
1 AAAGAAACCCGAACCT
1666905 AAAGAAACCCGAACC
1 AAAGAAACCCGAACC
1666920 AAATTTTAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.35, G:0.13, T:0.03
Consensus pattern (16 bp):
AAAGAAACCCGAACCT
Found at i:1666970 original size:31 final size:32
Alignment explanation
Indices: 1666894--1666977 Score: 91
Period size: 31 Copynumber: 2.6 Consensus size: 32
1666884 AACTAAAAGC
*
1666894 AACCCGAACCT-AAAGAAACCCGAACCAAATTTT
1 AACCCG-ACCTGAAAGCAA-CCGAACCAAATTTT
* * *
1666927 AACCCGATCTGAAAGTAACCGAACCGAA-TTT
1 AACCCGACCTGAAAGCAACCGAACCAAATTTT
*
1666958 AACCTGACCTGAAAGCAACC
1 AACCCGACCTGAAAGCAACC
1666978 TGAATAGATT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
31 20 0.45
32 12 0.27
33 12 0.27
ACGTcount: A:0.42, C:0.30, G:0.13, T:0.15
Consensus pattern (32 bp):
AACCCGACCTGAAAGCAACCGAACCAAATTTT
Found at i:1667058 original size:18 final size:17
Alignment explanation
Indices: 1667037--1667092 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 17
1667027 AATAATAAAT
1667037 TAATTTAAATAAAACTAA
1 TAATTTAAATAAAA-TAA
* *
1667055 TAATTT-ATTAAAAATAT
1 TAATTTAAAT-AAAATAA
1667072 TATATTTATAATAAAATAA
1 TA-ATTTA-AATAAAATAA
1667091 TA
1 TA
1667093 GAAAGTTTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
17 6 0.20
18 14 0.47
19 8 0.27
20 2 0.07
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (17 bp):
TAATTTAAATAAAATAA
Found at i:1667360 original size:34 final size:32
Alignment explanation
Indices: 1667313--1667376 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 32
1667303 ATGTATTATT
1667313 TTTAAAATTTAAT-AAAAATATTTCATTTATAA
1 TTTAAAATTTAATAAAAAATATTT-ATTTATAA
1667345 TTTAAGAATTTTAATAAAAAATATTTATTTAT
1 TTTAA-AA-TTTAATAAAAAATATTTATTTAT
1667377 CAAATAGTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
32 5 0.17
33 2 0.07
34 12 0.41
35 10 0.34
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (32 bp):
TTTAAAATTTAATAAAAAATATTTATTTATAA
Found at i:1667734 original size:31 final size:32
Alignment explanation
Indices: 1667684--1667769 Score: 104
Period size: 31 Copynumber: 2.7 Consensus size: 32
1667674 AAAATCAATT
* * *
1667684 GATCCAATATTGACCCGACCCGAAATAT-AACC
1 GATCCGATATTAACCCGACCCAAAAT-TCAACC
*
1667716 -ATCCGGTATTAACCCGACCCAAAATTCAACC
1 GATCCGATATTAACCCGACCCAAAATTCAACC
*
1667747 GATCTGATATTAACCCGACCCAA
1 GATCCGATATTAACCCGACCCAA
1667770 TATTGACCCG
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
30 1 0.02
31 25 0.54
32 20 0.43
ACGTcount: A:0.36, C:0.33, G:0.12, T:0.20
Consensus pattern (32 bp):
GATCCGATATTAACCCGACCCAAAATTCAACC
Found at i:1667762 original size:32 final size:31
Alignment explanation
Indices: 1667690--1667783 Score: 100
Period size: 32 Copynumber: 3.0 Consensus size: 31
1667680 AATTGATCCA
* * *
1667690 ATATTGACCCGACCCGAAATATAACC-ATCCG
1 ATATTAACCCGACCCAAAAT-TAACCGATCTG
*
1667721 GTATTAACCCGACCCAAAATTCAACCGATCTG
1 ATATTAACCCGACCCAAAATT-AACCGATCTG
* *
1667753 ATATTAACCCGACCCAATATTGACCCGATCT
1 ATATTAACCCGACCCAAAATT-AACCGATCT
1667784 AAAAATCAAC
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
30 1 0.02
31 21 0.40
32 31 0.58
ACGTcount: A:0.34, C:0.32, G:0.12, T:0.22
Consensus pattern (31 bp):
ATATTAACCCGACCCAAAATTAACCGATCTG
Found at i:1667857 original size:112 final size:113
Alignment explanation
Indices: 1667702--1667927 Score: 445
Period size: 112 Copynumber: 2.0 Consensus size: 113
1667692 ATTGACCCGA
1667702 CCCGAAATATAACCATCCGGTATTAACCCGACCCAAAATTCAACCGATCTGATATTAACCCGACC
1 CCCGAAATATAACCATCCGGTATTAACCCGACCCAAAATTCAACCGATCTGATATTAACCCGACC
1667767 CAATATTGACCCGATCTAAAAATCAACAGATCCGATA-TGATTTAAAC
66 CAATATTGACCCGATCTAAAAATCAACAGATCCGATATTGATTTAAAC
1667814 CCCGAAATATAACCATCCGGTATTAACCCGACCCAAAATTCAACCGATCTGATATTAACCCGACC
1 CCCGAAATATAACCATCCGGTATTAACCCGACCCAAAATTCAACCGATCTGATATTAACCCGACC
1667879 CAATATTGACCCGATCTAAAAATCAACAGATCCGATATTGATTTAAAC
66 CAATATTGACCCGATCTAAAAATCAACAGATCCGATATTGATTTAAAC
1667927 C
1 C
1667928 AGAAAACAAC
Statistics
Matches: 113, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
112 102 0.90
113 11 0.10
ACGTcount: A:0.38, C:0.29, G:0.11, T:0.23
Consensus pattern (113 bp):
CCCGAAATATAACCATCCGGTATTAACCCGACCCAAAATTCAACCGATCTGATATTAACCCGACC
CAATATTGACCCGATCTAAAAATCAACAGATCCGATATTGATTTAAAC
Found at i:1667875 original size:32 final size:32
Alignment explanation
Indices: 1667834--1667895 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
1667824 AACCATCCGG
1667834 TATTAACCCGACCCAAAATTCAACCGATCTGA
1 TATTAACCCGACCCAAAATTCAACCGATCTGA
* * *
1667866 TATTAACCCGACCCAATATTGACCCGATCT
1 TATTAACCCGACCCAAAATTCAACCGATCT
1667896 AAAAATCAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.34, C:0.32, G:0.10, T:0.24
Consensus pattern (32 bp):
TATTAACCCGACCCAAAATTCAACCGATCTGA
Found at i:1667960 original size:112 final size:112
Alignment explanation
Indices: 1667701--1667963 Score: 370
Period size: 112 Copynumber: 2.4 Consensus size: 112
1667691 TATTGACCCG
* ** * *
1667701 ACCC-GAAATATAACCATCCGGTATTAACCCGACCCAAAATTCAACCGATCTGATATTAACCCGA
1 ACCCAGAAATACAACCATCCAATAATAACCCAACCCAAAATTCAACCGATCTGATATTAACCCGA
1667765 CCCAATATTGACCCGATCTAAAAATCAACAGATCCGATATGATTTAA
66 CCCAATATTGACCCGATCTAAAAATCAACAGATCCGATATGATTTAA
* * ** * *
1667812 ACCCCGAAATATAACCATCCGGTATTAACCCGACCCAAAATTCAACCGATCTGATATTAACCCGA
1 ACCCAGAAATACAACCATCCAATAATAACCCAACCCAAAATTCAACCGATCTGATATTAACCCGA
1667877 CCCAATATTGACCCGATCTAAAAATCAACAGATCCGATATTGATTTAA
66 CCCAATATTGACCCGATCTAAAAATCAACAGATCCGATA-TGATTTAA
* *
1667925 A-CCAGAAA-ACAACCGATCCAATAATCACTCAACCCAAAA
1 ACCCAGAAATACAACC-ATCCAATAATAACCCAACCCAAAA
1667964 ATTGACCCGA
Statistics
Matches: 141, Mismatches: 8, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
111 9 0.06
112 123 0.87
113 9 0.06
ACGTcount: A:0.40, C:0.29, G:0.10, T:0.21
Consensus pattern (112 bp):
ACCCAGAAATACAACCATCCAATAATAACCCAACCCAAAATTCAACCGATCTGATATTAACCCGA
CCCAATATTGACCCGATCTAAAAATCAACAGATCCGATATGATTTAA
Found at i:1670783 original size:28 final size:28
Alignment explanation
Indices: 1670743--1670799 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
1670733 AGTGGAGGAT
*
1670743 GTACAAGGAATCCCTTCAGAGCCAATTC
1 GTACAAGGAATCCCTTCAGAACCAATTC
1670771 GTACAAGGAATCCCTTCAGAACCAATTC
1 GTACAAGGAATCCCTTCAGAACCAATTC
1670799 G
1 G
1670800 AACATAAGGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.21
Consensus pattern (28 bp):
GTACAAGGAATCCCTTCAGAACCAATTC
Found at i:1672925 original size:60 final size:59
Alignment explanation
Indices: 1672762--1672944 Score: 197
Period size: 60 Copynumber: 3.1 Consensus size: 59
1672752 ATGAATTTAG
* * **
1672762 GGATAAAATTAGAGTATTTAAAAGTTTAGAGATCAATTTAAAATGAGGGTCATAGTTTGA
1 GGATAAAATTAGAATATTTAAAAGTTTA-AGACCAATTTAAAATGAGTATCATAGTTTGA
* * * * * *
1672822 GAATGAAATT-GAAATATTTTAAAGTTTAAGGGCTAATTCAAAATGAGTATCATAGTTTGA
1 GGATAAAATTAG-AATATTTAAAAGTTTAA-GACCAATTTAAAATGAGTATCATAGTTTGA
* * * *
1672882 GGATAAAATTAGAATATTTAAAAGTTTAACAACCAATTTAAAATTAATATTATAGTTTGA
1 GGATAAAATTAGAATATTTAAAAGTTTAA-GACCAATTTAAAATGAGTATCATAGTTTGA
1672942 GGA
1 GGA
1672945 CATATGATGT
Statistics
Matches: 99, Mismatches: 21, Indels: 6
0.79 0.17 0.05
Matches are distributed among these distances:
59 2 0.02
60 96 0.97
61 1 0.01
ACGTcount: A:0.44, C:0.04, G:0.17, T:0.34
Consensus pattern (59 bp):
GGATAAAATTAGAATATTTAAAAGTTTAAGACCAATTTAAAATGAGTATCATAGTTTGA
Found at i:1674223 original size:22 final size:22
Alignment explanation
Indices: 1674198--1674248 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
1674188 ATTTTTAATG
1674198 AAAGTTAGAAAATAATAGGTTA
1 AAAGTTAGAAAATAATAGGTTA
*
1674220 AAAGTTATAAAATAATAGGTTA
1 AAAGTTAGAAAATAATAGGTTA
1674242 AAAGTTA
1 AAAGTTA
1674249 ATCATTGCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.55, C:0.00, G:0.16, T:0.29
Consensus pattern (22 bp):
AAAGTTAGAAAATAATAGGTTA
Found at i:1680259 original size:3 final size:3
Alignment explanation
Indices: 1680241--1680277 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
1680231 TTACTAATAG
*
1680241 TTA TTA TCA TTA -TA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1680278 TTTCATCTAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1681446 original size:2 final size:2
Alignment explanation
Indices: 1681434--1681464 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1681424 GTGACCTCAG
1681434 AT AT A- 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
1681465 CAAATATTCC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1691911 original size:16 final size:17
Alignment explanation
Indices: 1691883--1691914 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1691873 TTTATTATTT
1691883 AGAAATAATATTTTTAA
1 AGAAATAATATTTTTAA
1691900 AGAAATAA-ATTTTTA
1 AGAAATAATATTTTTA
1691915 TTGATTTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (17 bp):
AGAAATAATATTTTTAA
Found at i:1703882 original size:11 final size:11
Alignment explanation
Indices: 1703868--1703943 Score: 50
Period size: 11 Copynumber: 6.5 Consensus size: 11
1703858 ATAACTTAAT
1703868 AATAATAATAA
1 AATAATAATAA
*
1703879 AATAATCATGAA
1 AATAATAAT-AA
*
1703891 GATAATAATTTAA
1 AATAATAA--TAA
1703904 ACAT-AT-ATCAA
1 A-ATAATAAT-AA
1703915 AAGTAATAATAA
1 AA-TAATAATAA
1703927 AATAA-AATAA
1 AATAATAATAA
1703937 TAATAAT
1 -AATAAT
1703944 TAAAATGAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 19
0.69 0.05 0.26
Matches are distributed among these distances:
10 7 0.14
11 20 0.39
12 15 0.29
13 6 0.12
14 3 0.06
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (11 bp):
AATAATAATAA
Found at i:1705397 original size:2 final size:2
Alignment explanation
Indices: 1705390--1705415 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1705380 TGGGCTTGTA
1705390 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
1705416 TAATAATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1705424 original size:3 final size:3
Alignment explanation
Indices: 1705416--1705473 Score: 73
Period size: 3 Copynumber: 19.0 Consensus size: 3
1705406 ATATATATAT
* *
1705416 TAA TAA TAA TAA TAA TAA TAA TAA TAA TTAG TAA TAA TAA -ATT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TA-A TAA
1705462 TAA TAA TAA TAA
1 TAA TAA TAA TAA
1705474 AATTTAAATG
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
2 1 0.02
3 44 0.92
4 3 0.06
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1705732 original size:76 final size:76
Alignment explanation
Indices: 1705601--1706625 Score: 1793
Period size: 76 Copynumber: 13.5 Consensus size: 76
1705591 GATGGAAATG
* * * *
1705601 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTTAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1705666 CCCGAAGGCTT
66 CCCGAAGGCTT
* * * *
1705677 TTTGGAAACATCATGCACTAAAGGACTTATAGATGACCCGAATGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1705742 CCCGAAGGCTT
66 CCCGAAGGCTT
*
1705753 TTTGGAAACATCATGCACTGAAGGACTTATAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1705818 CCCGAAGGCTT
66 CCCGAAGGCTT
*
1705829 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGAT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1705894 CCCGAAGGCTT
66 CCCGAAGGCTT
*
1705905 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGAT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1705970 CCCGAAGGCTT
66 CCCGAAGGCTT
*
1705981 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGAT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1706046 CCCGAAGGCTT
66 CCCGAAGGCTT
*
1706057 TTTGGAAACATCATGCAATGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1706122 CCAC-AAGGCTT
66 CC-CGAAGGCTT
*
1706133 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1706198 CCCGAAGGCTT
66 CCCGAAGGCTT
*
1706209 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1706274 CCCGAAGGCTT
66 CCCGAAGGCTT
* *
1706285 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAACT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
*
1706350 CCAGAAGGCTT
66 CCCGAAGGCTT
*
1706361 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAACT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
* *
1706426 CCAGAAGGTTTT
66 CCCGAAGG-CTT
1706438 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
*
1706503 CCAGAAGGCTTT
66 CCCGAAGGC-TT
1706515 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1706580 CCCGAAGGCTT
66 CCCGAAGGCTT
*
1706591 TTT-GAATACATCATGCACTGAAGGGCTTACAGATG
1 TTTGGAA-ACATCATGCACTGAAGGACTTACAGATG
1706626 TAGGAAATAG
Statistics
Matches: 921, Mismatches: 23, Indels: 10
0.97 0.02 0.01
Matches are distributed among these distances:
75 4 0.00
76 767 0.83
77 150 0.16
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (76 bp):
TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTT
Found at i:1707326 original size:22 final size:22
Alignment explanation
Indices: 1707298--1707352 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
1707288 AATAAAGCTT
*
1707298 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
* *
1707320 TCATCTTTAAAAAGGGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
1707342 TCATCTTTGAA
1 TCATCTTTGAA
1707353 GAAGTAGATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:1710164 original size:115 final size:113
Alignment explanation
Indices: 1709932--1710245 Score: 425
Period size: 115 Copynumber: 2.7 Consensus size: 113
1709922 GATCATATAG
* * * *
1709932 TTCATCTTTCAATTCCAATGATTGGTTATGGGGTTCCTACCAAACCAGATCAGATAACTCAAGGA
1 TTCATCTTTCAA-TCCAATGATTGGTTTTTGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
* * * * * *
1709997 ACATTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGTAAA
65 ACACTTCAAGAAGATGCTATTGAGCCTCCTTATTTCTACCATGAGCAAA
1710046 TTCATCTTTCAA-CCAATGATTGGTTTTTTTTGGGTTCATACCAAACCAGATCAGATAACTCAAA
1 TTCATCTTTCAATCCAATGATTGG---TTTTTGGGTTCATACCAAACCAGATCAGATAACTCAAA
1710110 GAACACTTCAAGAAGATGCTATTGAGCCTCCTTATTTCTACCATGAGCAAA
63 GAACACTTCAAGAAGATGCTATTGAGCCTCCTTATTTCTACCATGAGCAAA
* * *
1710161 TTCATCTTTCAAATCCAATGATT-GATTTTGGAGTTCATACCAAATCAGATCAGATAATTCAAAG
1 TTCATCTTTC-AATCCAATGATTGGTTTTTGG-GTTCATACCAAACCAGATCAGATAACTCAAAG
* *
1710225 AACACTTCTAGAAGATACTAT
64 AACACTTCAAGAAGATGCTAT
1710246 GAGTACATTC
Statistics
Matches: 179, Mismatches: 15, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
112 11 0.06
113 6 0.03
114 61 0.34
115 89 0.50
116 3 0.02
117 9 0.05
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Consensus pattern (113 bp):
TTCATCTTTCAATCCAATGATTGGTTTTTGGGTTCATACCAAACCAGATCAGATAACTCAAAGAA
CACTTCAAGAAGATGCTATTGAGCCTCCTTATTTCTACCATGAGCAAA
Found at i:1710309 original size:92 final size:92
Alignment explanation
Indices: 1710152--1710345 Score: 282
Period size: 92 Copynumber: 2.1 Consensus size: 92
1710142 TATTTCTACC
* * *
1710152 ATGAGCAAATTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAATCAGATCAGATA
1 ATGAGCACATTCATCTTTCAAATCCAATGATTGATTCTGGAGTTCATACCAAACCAGATCAGATA
* *
1710217 ATTCAAAGAACACTTCTAGAAGATACT
66 ACTCAAAGAACACTTCCAGAAGATACT
* * * *
1710244 ATGAGTACATTCATCTTTCAAATCCAATGGTTGGTTCTGTG-GTTCATACCAAACCAGATTAGAT
1 ATGAGCACATTCATCTTTCAAATCCAATGATTGATTCTG-GAGTTCATACCAAACCAGATCAGAT
*
1710308 AACTCAAAGAACACTTCCAGAAGATGCT
65 AACTCAAAGAACACTTCCAGAAGATACT
1710336 ATGAGCACAT
1 ATGAGCACAT
1710346 GGCATTTGTT
Statistics
Matches: 90, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
92 89 0.99
93 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.29
Consensus pattern (92 bp):
ATGAGCACATTCATCTTTCAAATCCAATGATTGATTCTGGAGTTCATACCAAACCAGATCAGATA
ACTCAAAGAACACTTCCAGAAGATACT
Found at i:1716505 original size:6 final size:7
Alignment explanation
Indices: 1716485--1716514 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
1716475 TGTCTCTATT
1716485 ATTAAAA
1 ATTAAAA
1716492 ATTAAAA
1 ATTAAAA
1716499 ATTAAAA
1 ATTAAAA
1716506 ATTAAAA
1 ATTAAAA
1716513 AT
1 AT
1716515 ATATTTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (7 bp):
ATTAAAA
Found at i:1716990 original size:16 final size:18
Alignment explanation
Indices: 1716964--1717002 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
1716954 AACATATATC
1716964 AAAAGTAATAA-TAAAAT
1 AAAAGTAATAATTAAAAT
1716981 AAAA-TAATAATTAAAAT
1 AAAAGTAATAATTAAAAT
*
1716998 GAAAG
1 AAAAG
1717003 AAAACAAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (18 bp):
AAAAGTAATAATTAAAAT
Found at i:1718470 original size:3 final size:3
Alignment explanation
Indices: 1718462--1718519 Score: 57
Period size: 3 Copynumber: 19.3 Consensus size: 3
1718452 ATATATATAT
* * *
1718462 TAA TAA TAA TAA TAA TAA TAA TATT TAG TAA TAA TAA -ATT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TA-A TAA TAA
1718508 TAA TAA T-A TAA T
1 TAA TAA TAA TAA T
1718520 TTAAATGAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
2 3 0.07
3 40 0.87
4 3 0.07
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:1726239 original size:20 final size:19
Alignment explanation
Indices: 1726191--1726239 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
1726181 AACTTAAATC
*
1726191 AAAATAATTAAAATAAATAT
1 AAAATAATT-TAATAAATAT
1726211 AAAAT--TTTAATAATATAT
1 AAAATAATTTAATAA-ATAT
1726229 AAAATAATTTA
1 AAAATAATTTA
1726240 TATGATACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
17 5 0.20
18 11 0.44
20 9 0.36
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAATAATTTAATAAATAT
Found at i:1726285 original size:14 final size:14
Alignment explanation
Indices: 1726268--1726406 Score: 127
Period size: 14 Copynumber: 10.5 Consensus size: 14
1726258 ATCTATAATA
1726268 TAATATTAAAAAAT
1 TAATATTAAAAAAT
**
1726282 TAATATT---TTAT
1 TAATATTAAAAAAT
*
1726293 TTAT-TTAAAAAAT
1 TAATATTAAAAAAT
1726306 TAATATT--AAAAT
1 TAATATTAAAAAAT
* *
1726318 TAATATCTATAATA-
1 TAATAT-TAAAAAAT
1726332 TAATATTAAAAAAT
1 TAATATTAAAAAAT
1726346 TAATATT--AAAAT
1 TAATATTAAAAAAT
* *
1726358 TAATATCTATAATA-
1 TAATAT-TAAAAAAT
1726372 TAATATTAAAAAAT
1 TAATATTAAAAAAT
1726386 TAATATTAAAAAAT
1 TAATATTAAAAAAT
1726400 TAATATT
1 TAATATT
1726407 TTATTTATTT
Statistics
Matches: 101, Mismatches: 12, Indels: 24
0.74 0.09 0.18
Matches are distributed among these distances:
10 2 0.02
11 5 0.05
12 22 0.22
13 17 0.17
14 49 0.49
15 6 0.06
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (14 bp):
TAATATTAAAAAAT
Found at i:1726286 original size:64 final size:60
Alignment explanation
Indices: 1726217--1726351 Score: 148
Period size: 64 Copynumber: 2.1 Consensus size: 60
1726207 ATATAAAATT
1726217 TTAATA-A-TATATAAAATAATTTATATGATACAAAATTAAATATCTATAATATAATATTAAAAA
1 TTAATATATTATATAAAA-AA-TTA-AT-AT-CAAAATT-AATATCTATAATATAATATTAAAAA
1726280 A
60 A
* *
1726281 TTAATATTTTATTTATTTAAAAAATTAATATTAAAATTAATATCTATAATATAATATTAAAAAA
1 TTAATA---TA-TTATATAAAAAATTAATATCAAAATTAATATCTATAATATAATATTAAAAAA
1726345 TTAATAT
1 TTAATAT
1726352 TAAAATTAAT
Statistics
Matches: 63, Mismatches: 2, Indels: 15
0.79 0.03 0.19
Matches are distributed among these distances:
61 1 0.02
64 38 0.60
65 6 0.10
66 2 0.03
67 2 0.03
68 4 0.06
69 2 0.03
70 8 0.13
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (60 bp):
TTAATATATTATATAAAAAATTAATATCAAAATTAATATCTATAATATAATATTAAAAAA
Found at i:1726347 original size:40 final size:40
Alignment explanation
Indices: 1726297--1726458 Score: 221
Period size: 40 Copynumber: 4.2 Consensus size: 40
1726287 TTTTATTTAT
1726297 TTAAAAAATTAATATTAAAATTAATATCTATAATATAATA
1 TTAAAAAATTAATATTAAAATTAATATCTATAATATAATA
1726337 TTAAAAAATTAATATTAAAATTAATATCTATAATATAATA
1 TTAAAAAATTAATATTAAAATTAATATCTATAATATAATA
* *
1726377 TTAAAAAATTAATATTAAAAAATTAATAT-T-TTAT-TTAT-
1 TTAAAAAATTAATATT--AAAATTAATATCTATAATATAATA
*
1726415 TTAAAAAAATTAATATTAAAATTAAAATC-A-AATATAATA
1 TT-AAAAAATTAATATTAAAATTAATATCTATAATATAATA
1726454 -TAAAA
1 TTAAAA
1726459 TTAAATATAA
Statistics
Matches: 110, Mismatches: 5, Indels: 17
0.83 0.04 0.13
Matches are distributed among these distances:
37 16 0.15
38 6 0.05
39 17 0.15
40 59 0.54
41 1 0.01
42 11 0.10
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (40 bp):
TTAAAAAATTAATATTAAAATTAATATCTATAATATAATA
Found at i:1726390 original size:54 final size:54
Alignment explanation
Indices: 1726301--1726406 Score: 155
Period size: 54 Copynumber: 2.0 Consensus size: 54
1726291 ATTTATTTAA
* *
1726301 AAAATTAATAT-TAAAAT-TAATATCTATAATA-TAATATTAAAAAATTAATATT
1 AAAATTAATATCTAAAATATAATAT-TAAAAAATTAATATTAAAAAATTAATATT
*
1726353 AAAATTAATATCTATAATATAATATTAAAAAATTAATATTAAAAAATTAATATT
1 AAAATTAATATCTAAAATATAATATTAAAAAATTAATATTAAAAAATTAATATT
1726407 TTATTTATTT
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
52 11 0.23
53 10 0.21
54 27 0.56
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (54 bp):
AAAATTAATATCTAAAATATAATATTAAAAAATTAATATTAAAAAATTAATATT
Found at i:1726465 original size:12 final size:12
Alignment explanation
Indices: 1726420--1726470 Score: 54
Period size: 12 Copynumber: 4.3 Consensus size: 12
1726410 TTTATTTAAA
1726420 AAAATT-AATATT
1 AAAATTAAATA-T
1726432 AAAATTAAA-AT
1 AAAATTAAATAT
*
1726443 CAAA-TATAATAT
1 AAAATTA-AATAT
1726455 AAAATTAAATAT
1 AAAATTAAATAT
1726467 AAAA
1 AAAA
1726471 CCTCTTTGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
10 2 0.06
11 6 0.18
12 21 0.64
13 4 0.12
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (12 bp):
AAAATTAAATAT
Found at i:1727406 original size:14 final size:14
Alignment explanation
Indices: 1727384--1727416 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1727374 GGTTCGTGAA
*
1727384 CGTTCGGTTATGTT
1 CGTTTGGTTATGTT
1727398 CGTTTGGTTATGTT
1 CGTTTGGTTATGTT
1727412 CGTTT
1 CGTTT
1727417 ATGTTTGTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.12, G:0.27, T:0.55
Consensus pattern (14 bp):
CGTTTGGTTATGTT
Found at i:1727412 original size:24 final size:24
Alignment explanation
Indices: 1727385--1727459 Score: 80
Period size: 24 Copynumber: 3.1 Consensus size: 24
1727375 GTTCGTGAAC
* * *
1727385 GTTCGGTTATGTTCGTTTGGTTAT
1 GTTCGTTTATGTTCGTTCGATTAT
*
1727409 GTTCGTTTATGTTTGTTCGATTAT
1 GTTCGTTTATGTTCGTTCGATTAT
* *
1727433 GTTCGTTTATATTCATTC-ATTTAT
1 GTTCGTTTATGTTCGTTCGA-TTAT
1727457 GTT
1 GTT
1727460 TAACCCAATC
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
23 1 0.02
24 42 0.98
ACGTcount: A:0.13, C:0.09, G:0.20, T:0.57
Consensus pattern (24 bp):
GTTCGTTTATGTTCGTTCGATTAT
Found at i:1727425 original size:14 final size:15
Alignment explanation
Indices: 1727390--1727435 Score: 60
Period size: 14 Copynumber: 3.2 Consensus size: 15
1727380 TGAACGTTCG
*
1727390 GTTATGTTCGTTT-G
1 GTTATGTTCGTTTAT
1727404 GTTATGTTCGTTTAT
1 GTTATGTTCGTTTAT
*
1727419 GTT-TGTTCGATTAT
1 GTTATGTTCGTTTAT
1727433 GTT
1 GTT
1727436 CGTTTATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 26 0.90
15 3 0.10
ACGTcount: A:0.11, C:0.07, G:0.24, T:0.59
Consensus pattern (15 bp):
GTTATGTTCGTTTAT
Found at i:1728206 original size:16 final size:16
Alignment explanation
Indices: 1728185--1728251 Score: 102
Period size: 16 Copynumber: 4.3 Consensus size: 16
1728175 GTCTCCAACG
1728185 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
*
1728201 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
*
1728217 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
1728233 TTTATGTTCGT-TT-A
1 TTTATGTTCGTGTTCA
1728247 TTTAT
1 TTTAT
1728252 TAAATGAACG
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
14 5 0.10
15 2 0.04
16 42 0.86
ACGTcount: A:0.10, C:0.10, G:0.19, T:0.60
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:1728224 original size:32 final size:32
Alignment explanation
Indices: 1728183--1728243 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
1728173 GGGTCTCCAA
1728183 CGTTTATGTTCGTGTTCATTTATGTTCGTGTT
1 CGTTTATGTTCGTGTTCATTTATGTTCGTGTT
*
1728215 CGTTTATGTTCGTGTTCGTTTATGTTCGT
1 CGTTTATGTTCGTGTTCATTTATGTTCGT
1728244 TTATTTATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.08, C:0.13, G:0.23, T:0.56
Consensus pattern (32 bp):
CGTTTATGTTCGTGTTCATTTATGTTCGTGTT
Found at i:1728334 original size:16 final size:16
Alignment explanation
Indices: 1728313--1728345 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1728303 AAAAAAATTT
1728313 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1728329 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1728345 T
1 T
1728346 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:1729114 original size:2 final size:2
Alignment explanation
Indices: 1729107--1729166 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
1729097 TGACAAATAA
1729107 AT 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 AT
1729149 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
1729167 GACTAACACA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1730653 original size:130 final size:129
Alignment explanation
Indices: 1730420--1730767 Score: 393
Period size: 130 Copynumber: 2.7 Consensus size: 129
1730410 TATTAATATA
* * *
1730420 TTACCGTGTACATTGTTAATTTACATATTACTTTAAAGTAATAGGTTTCAAAATTATAAGAATCG
1 TTACCGTGTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTATAAGTATCG
* * * *
1730485 ATACTTATATGACA---GCATCGATACTTGTACATTTACGCCTATTTTCATTATA-TCGGTAGAA
66 ATACTT-TAT-ACATGTGTATCGATACTTGTACATTTACGCCTATTATCACTATACT-GATAG--
1730546 ACGT
126 ACGT
* * *
1730550 TTACCGTGTACATTGTTAATTTACCTATTACTTTAAAGCAGTAGGTTTCGAAATTCA-ACGTATC
1 TTACCGTGTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATT-ATAAGTATC
** *
1730614 GATACTTTATACATGTGTATCGATACTTG-ATGTTTACGCCTATTATCACTATACTGATAGACTT
65 GATACTTTATACATGTGTATCGATACTTGTACATTTACGCCTATTATCACTATACTGATAGACGT
* * * * * * * * *
1730678 TTGCCGTTTTCATTGTAAATTAATCTATTACATTACAGTAATAGGTTTCGACATTATAAGTATCG
1 TTACCGTGTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTATAAGTATCG
*
1730743 ATACTTTATATATGTGTATCGATAC
66 ATACTTTATACATGTGTATCGATAC
1730768 ATTTTGCATG
Statistics
Matches: 186, Mismatches: 26, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
127 1 0.01
128 81 0.44
129 3 0.02
130 87 0.47
131 14 0.08
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (129 bp):
TTACCGTGTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTATAAGTATCG
ATACTTTATACATGTGTATCGATACTTGTACATTTACGCCTATTATCACTATACTGATAGACGT
Found at i:1730930 original size:179 final size:178
Alignment explanation
Indices: 1730630--1730996 Score: 466
Period size: 179 Copynumber: 2.1 Consensus size: 178
1730620 TTATACATGT
* * * *
1730630 GTATCGATACTTGATGTTTACGCCTATTATCACTATACTGATAGACTTTTGCCGTTTTCATTGTA
1 GTATCGATACTTGATATTTACGCCTATTATCAATATACTGATAGACTTTTACCGTTTACATTGTA
* * * *
1730695 AATTAATCTATTACATTACAGTAATAGGTTTCGACATTATAAGTATCGATACTTTATATATGTGT
66 AATTAATCTATAACATTACAGTAATAGGTTTCGAAATTACAAGTATCGATACTTTATACATGTGT
* * * *
1730760 ATCGATACATTTTGCATGCAAATTGTTTGAGAAGCATACTGAAATAATA
131 ATCAATACACTTTGCATGCAAATT-ATTGAGAAGCATACTGAAATAAAA
* * * * *
1730809 GTATCGATACTTGGTATTTACTCCTATTATCAATATGCTGGTAGTCTTTTACCGTTTACATTGTA
1 GTATCGATACTTGATATTTACGCCTATTATCAATATACTGATAGACTTTTACCGTTTACATTGTA
* * * * * **
1730874 AATTTA-CATATAACTTTACAGTAATCGGTTTTGAAATTCCGTGTATCGATACTTTATACATGTG
66 AATTAATC-TATAACATTACAGTAATAGGTTTCGAAATTACAAGTATCGATACTTTATACATGTG
* * *
1730938 TATCAATACACTTTGCTTGTAAATTATTGAGAAGCATACTGAACTAAAA
130 TATCAATACACTTTGCATGCAAATTATTGAGAAGCATACTGAAATAAAA
1730987 GTATCGATAC
1 GTATCGATAC
1730997 ATATATATAA
Statistics
Matches: 160, Mismatches: 27, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
178 32 0.20
179 128 0.80
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (178 bp):
GTATCGATACTTGATATTTACGCCTATTATCAATATACTGATAGACTTTTACCGTTTACATTGTA
AATTAATCTATAACATTACAGTAATAGGTTTCGAAATTACAAGTATCGATACTTTATACATGTGT
ATCAATACACTTTGCATGCAAATTATTGAGAAGCATACTGAAATAAAA
Found at i:1731145 original size:21 final size:21
Alignment explanation
Indices: 1731115--1731155 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1731105 GAAATTCCAA
*
1731115 GTATCGATACTTTGTACATGT
1 GTATCAATACTTTGTACATGT
*
1731136 GTATCAATACTTTGTGCATG
1 GTATCAATACTTTGTACATG
1731156 CAAAATGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.41
Consensus pattern (21 bp):
GTATCAATACTTTGTACATGT
Found at i:1731317 original size:179 final size:179
Alignment explanation
Indices: 1731013--1731363 Score: 454
Period size: 179 Copynumber: 2.0 Consensus size: 179
1731003 ATAATATATA
* *
1731013 GATACTTTATGTTTACGCCTATTATCATTAAATCGGAAAACTTTTACCGTCTACATTGTAAATTT
1 GATACTTGATGTTTACACCTATTATCATTAAATCGGAAAACTTTTACCGTCTACATTGTAAATTT
* * * * * *
1731078 ACGTATTATTTTATAGTAATAAGTATTGAAATTCCAAGTATCGATACTTTGTACATGTGTATCAA
66 ACCTATTACTTTAAAGAAATAAGTATTGAAATTACAAGTATCGATACTTTATACATGTGTATCAA
*
1731143 TACTTTGTGCATGCAAAATGTTTGATAAGAAAACTGGAATAAAAGTATC
131 TACTTTGTGCATGCAAAATATTTGATAAGAAAACTGGAATAAAAGTATC
* * * *
1731192 GATACTTGATGTTTACACCTATTATCATTAAA-CTGATAGATTTTTACCGTTTACATTGTAAATT
1 GATACTTGATGTTTACACCTATTATCATTAAATCGGA-AAACTTTTACCGTCTACATTGTAAATT
* * * *
1731256 TACCTATTACTTTAAAGAAATAGGT-TTCGAATTTATAAGTATCGATACTTTATATATGTGTATC
65 TACCTATTACTTTAAAGAAATAAGTATT-GAAATTACAAGTATCGATACTTTATACATGTGTATC
* * * * * * *
1731320 GATACTTTTTGCGTGCCAATTATTTGATATGAACACTGGAATAA
129 AATACTTTGTGCATGCAAAATATTTGATAAGAAAACTGGAATAA
1731364 CAATATTGAT
Statistics
Matches: 146, Mismatches: 24, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
178 5 0.03
179 141 0.97
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.40
Consensus pattern (179 bp):
GATACTTGATGTTTACACCTATTATCATTAAATCGGAAAACTTTTACCGTCTACATTGTAAATTT
ACCTATTACTTTAAAGAAATAAGTATTGAAATTACAAGTATCGATACTTTATACATGTGTATCAA
TACTTTGTGCATGCAAAATATTTGATAAGAAAACTGGAATAAAAGTATC
Found at i:1731343 original size:378 final size:380
Alignment explanation
Indices: 1730630--1731424 Score: 903
Period size: 378 Copynumber: 2.1 Consensus size: 380
1730620 TTATACATGT
* * * * * * *
1730630 GTATC-GATACTTGATGTTTACGCCTATTATCACTATACTGATAGACTTTTGCCGTTTTCATTGT
1 GTATCAGATACTTTATGTTTACGCCTATTATCACTAAACGGATAAACTTTTACCGTCTACATTGT
* * * *
1730694 AAATTAATCTATTACATTACAGTAATAGGTTTCGACATTATAAGTATCGATACTTTATATATGTG
66 AAATTAATCTATTACATTACAGTAATAAGTTTCGAAATTACAAGTATCGATACTTTATACATGTG
* * * * * *
1730759 TATCGATACATTTTGCATGCAAATTGTTTGAGAAGCATACTGAAATAATAGTATCGATACTTGGT
131 TATCAATACATTTTGCATGCAAAATGTTTGAGAAGAAAACTGAAATAAAAGTATCGATACTTGAT
* ** *
1730824 ATTTACTCCTATTATCAATATGCTGGTAGTCTTTTACCGTTTACATTGTAAATTTACATATAACT
196 ATTTACACCTATTATCAATAAACTGATAGTCTTTTACCGTTTACATTGTAAATTTACATATAACT
* * * * * **
1730889 TTACAGTAATCGGTTTTGAAATTCCGTGTATCGATACTTTATACATGTGTATCAATACACTTTGC
261 TTAAAGAAATAGGTTTCGAAATTACAAGTATCGATACTTTATACATGTGTATCAATACACTTTGC
* * * *
1730954 TTGTAAATTA-TTGAGAAGCATACT-GAACTAA-AAGTATCGATACATATAT-ATAA
326 GTGCAAATTATTTGAGAAGAACACTGGAA-TAACAA-TATCGATACATATATAATAA
* *
1731007 -TATATAGATACTTTATGTTTACGCCTATTATCATTAAATCGGA-AAACTTTTACCGTCTACATT
1 GTAT-CAGATACTTTATGTTTACGCCTATTATCACTAAA-CGGATAAACTTTTACCGTCTACATT
* ** * * *
1731070 GTAAATTTA-CGTATTATTTTATAGTAATAAGTATT-GAAATTCCAAGTATCGATACTTTGTACA
64 GTAAATTAATC-TATTACATTACAGTAATAAGT-TTCGAAATTACAAGTATCGATACTTTATACA
* *
1731133 TGTGTATCAATAC-TTTGTGCATGCAAAATGTTTGATAAGAAAACTGGAATAAAAGTATCGATAC
127 TGTGTATCAATACATTT-TGCATGCAAAATGTTTGAGAAGAAAACTGAAATAAAAGTATCGATAC
* * *
1731197 TTGATGTTTACACCTATTATCATTAAACTGATAGAT-TTTTACCGTTTACATTGTAAATTTACCT
191 TTGATATTTACACCTATTATCAATAAACTGATAG-TCTTTTACCGTTTACATTGTAAATTTACAT
* * * * * *
1731261 ATTACTTTAAAGAAATAGGTTTCGAATTTATAAGTATCGATACTTTATATATGTGTATCGATACT
255 ATAACTTTAAAGAAATAGGTTTCGAAATTACAAGTATCGATACTTTATACATGTGTATCAATACA
* * * * * *
1731326 TTTTGCGTGCCAATTATTTGATATGAACACTGGAATAACAATATTGATACCTATATAATAA
320 CTTTGCGTGCAAATTATTTGAGAAGAACACTGGAATAACAATATCGATACATATATAATAA
* *
1731387 GTATCA-ATACTTTATGTTTACACCTATTATCAGTAAAC
1 GTATCAGATACTTTATGTTTACGCCTATTATCACTAAAC
1731425 CAATAGATTT
Statistics
Matches: 346, Mismatches: 60, Indels: 23
0.81 0.14 0.05
Matches are distributed among these distances:
376 3 0.01
377 4 0.01
378 265 0.77
379 61 0.18
380 10 0.03
381 3 0.01
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.39
Consensus pattern (380 bp):
GTATCAGATACTTTATGTTTACGCCTATTATCACTAAACGGATAAACTTTTACCGTCTACATTGT
AAATTAATCTATTACATTACAGTAATAAGTTTCGAAATTACAAGTATCGATACTTTATACATGTG
TATCAATACATTTTGCATGCAAAATGTTTGAGAAGAAAACTGAAATAAAAGTATCGATACTTGAT
ATTTACACCTATTATCAATAAACTGATAGTCTTTTACCGTTTACATTGTAAATTTACATATAACT
TTAAAGAAATAGGTTTCGAAATTACAAGTATCGATACTTTATACATGTGTATCAATACACTTTGC
GTGCAAATTATTTGAGAAGAACACTGGAATAACAATATCGATACATATATAATAA
Found at i:1735078 original size:14 final size:14
Alignment explanation
Indices: 1735059--1735086 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1735049 ATGGCAGTGA
1735059 AGTTGTAATGGATT
1 AGTTGTAATGGATT
1735073 AGTTGTAATGGATT
1 AGTTGTAATGGATT
1735087 CACCCTTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.43
Consensus pattern (14 bp):
AGTTGTAATGGATT
Found at i:1735380 original size:2 final size:2
Alignment explanation
Indices: 1735373--1735462 Score: 180
Period size: 2 Copynumber: 45.0 Consensus size: 2
1735363 TAGATTCTAG
1735373 AT 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 AT
1735415 AT 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 AT
1735457 AT AT AT
1 AT AT AT
1735463 CTTCCCCATT
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 88 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1735793 original size:18 final size:18
Alignment explanation
Indices: 1735772--1735806 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1735762 GATCAGAATC
1735772 CCTTACTTGAGAAGAAGA
1 CCTTACTTGAGAAGAAGA
**
1735790 CCTTGGTTGAGAAGAAG
1 CCTTACTTGAGAAGAAG
1735807 GTTTTGCATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.14, G:0.29, T:0.23
Consensus pattern (18 bp):
CCTTACTTGAGAAGAAGA
Found at i:1736338 original size:21 final size:21
Alignment explanation
Indices: 1736308--1736368 Score: 104
Period size: 21 Copynumber: 2.9 Consensus size: 21
1736298 TGGTGTTGTT
* *
1736308 TATATCAAAAGTATCGATATC
1 TATATAAAAAGTATTGATATC
1736329 TATATAAAAAGTATTGATATC
1 TATATAAAAAGTATTGATATC
1736350 TATATAAAAAGTATTGATA
1 TATATAAAAAGTATTGATA
1736369 CTTTATGTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.48, C:0.07, G:0.10, T:0.36
Consensus pattern (21 bp):
TATATAAAAAGTATTGATATC
Found at i:1736680 original size:201 final size:201
Alignment explanation
Indices: 1736335--1736953 Score: 890
Period size: 200 Copynumber: 3.1 Consensus size: 201
1736325 TATCTATATA
* * *
1736335 AAAAGTATTGATA-TCTATATAAAAAGTATTGATACTTTATGTTTACGCCTATTATCATTAAACC
1 AAAAGTATCGATACT-TATATAAAAAGTATCGATACTTGATGTTTACGCCTATTATCATTAAACC
* * * *
1736399 GGAAGATTTTTACCGTTTACATTGTAAATTTACCTATTACTTCAAAGATATAGGTTTCGAAATTA
65 GGTAGATTTTTACCGTTTACATTGTAAATTTACCTATTTCTTTAAAGAAATAGGTTTCGAAATTA
*
1736464 TAAGTATCGATACTTGTTATACGTGTATC-AGTACTTTTTTGCA-TGCAAATTGTTTGAGATGCA
130 TAAGTATCGATACTTGTTATACGTGTATCGA-TACTTTTTTG-AGTGCAAATTGTTTGAGATTCA
1736527 TACTGGAAT
193 TACTGGAAT
* * **
1736536 AAAAGTATCGATACTTATATAAAAAATATCGATACTTGATGTTTACGCCTATTATCATTCAGTCG
1 AAAAGTATCGATACTTATATAAAAAGTATCGATACTTGATGTTTACGCCTATTATCATTAAACCG
* * * * *
1736601 GTAGATTTTTACAGATTACATTGTAAATTTACCTATTTCTTTTAAGAAATAGGTTTCAAAACTAT
66 GTAGATTTTTACCGTTTACATTGTAAATTTACCTATTTCTTTAAAGAAATAGGTTTCGAAATTAT
*
1736666 AAGTATCGATACTTGTTATACGTGTATCGATA-TATTTTT-AGTGCAAAATGTTTGAGATTCATA
131 AAGTATCGATACTTGTTATACGTGTATCGATACT-TTTTTGAGTGCAAATTGTTTGAGATTCATA
1736729 CTGGAAT
195 CTGGAAT
* * * * *
1736736 AAAAGTATTGATACTTATGTAAAAAGTATCGATACTTGATATTTATGCCTATTATCATTTAACCG
1 AAAAGTATCGATACTTATATAAAAAGTATCGATACTTGATGTTTACGCCTATTATCATTAAACCG
* *
1736801 ATAGATTTTTACCGTTTACATTGTAAATTTACCTATTTCTTTAAAGAAATAGGTTTCGAATTTAT
66 GTAGATTTTTACCGTTTACATTGTAAATTTACCTATTTCTTTAAAGAAATAGGTTTCGAAATTAT
* * *
1736866 ATGTATCGATACTAGTTATACGTGTATCGATAC-TTTTTGAGTGCAAATTGTTTGAGATTCATAT
131 AAGTATCGATACTTGTTATACGTGTATCGATACTTTTTTGAGTGCAAATTGTTTGAGATTCATAC
1736930 TGGAAT
196 TGGAAT
1736936 ATATAAGTATCGATACTT
1 A-A-AAGTATCGATACTT
1736954 GATGTTTGCA
Statistics
Matches: 372, Mismatches: 38, Indels: 15
0.88 0.09 0.04
Matches are distributed among these distances:
199 6 0.02
200 203 0.55
201 148 0.40
202 15 0.04
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (201 bp):
AAAAGTATCGATACTTATATAAAAAGTATCGATACTTGATGTTTACGCCTATTATCATTAAACCG
GTAGATTTTTACCGTTTACATTGTAAATTTACCTATTTCTTTAAAGAAATAGGTTTCGAAATTAT
AAGTATCGATACTTGTTATACGTGTATCGATACTTTTTTGAGTGCAAATTGTTTGAGATTCATAC
TGGAAT
Found at i:1737164 original size:120 final size:120
Alignment explanation
Indices: 1736938--1737157 Score: 359
Period size: 120 Copynumber: 1.8 Consensus size: 120
1736928 ATTGGAATAT
* *
1736938 ATAAGTATCGATACTTGATGTTTGCACCTATTATCATTCAACCGGTAAATTTTTACCATTTACAT
1 ATAAGTATCGATACTTGATGTTTACACCTATTATCATTAAACCGGTAAATTTTTACCATTTACAT
** *
1737003 TGTAAATTTGTCTATTTCTTTAAAGAAATAGGTTTCAAAATTATAAGCACTGATA
66 TGTAAATTTACCTATTACTTTAAAGAAATAGGTTTCAAAATTATAAGCACTGATA
* * *
1737058 ATAAGTATCGATACTTGATGTTTACGCTTATTATCATTAAATCGGTAAATTTTTACCATTTACAT
1 ATAAGTATCGATACTTGATGTTTACACCTATTATCATTAAACCGGTAAATTTTTACCATTTACAT
*
1737123 TGTAAATTTACCTATTACTTTAAAGTAATAGGTTT
66 TGTAAATTTACCTATTACTTTAAAGAAATAGGTTT
1737158 TGAAATTCAA
Statistics
Matches: 91, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
120 91 1.00
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.42
Consensus pattern (120 bp):
ATAAGTATCGATACTTGATGTTTACACCTATTATCATTAAACCGGTAAATTTTTACCATTTACAT
TGTAAATTTACCTATTACTTTAAAGAAATAGGTTTCAAAATTATAAGCACTGATA
Found at i:1739373 original size:282 final size:279
Alignment explanation
Indices: 1738546--1739376 Score: 1421
Period size: 279 Copynumber: 3.0 Consensus size: 279
1738536 GTGCTGAATT
* * *
1738546 TTTTTTTACAAACCATGATGAATAAATCACCTCTTTCAGTTGTCACCGATGGGGATAGGACAATA
1 TTTTTTTACAAGCCATGATGAATAAATCACCTCTTTCAGTTGTCACCGATGGGGATAGGGCAATG
1738611 CAGAGGTCTATCAAATTATTATCCCTTTTGCTAAGCACATATTATGTTGGCATCTTTCTCGTAAT
66 CAGAGGTCTATCAAATTATTATCCCTTTTGCTAAGCACATATTATGTTGGCATCTTTCTCGTAAT
1738676 GCACAAGCTAACATTGATGACCGTAAATTTACAACATTTTCTATATGCATAGATTCCTGGTGAAC
131 GCACAAGCTAACATTGATGACCGTAAATTTACAACATTTTCTATATGCATAGATTCCTGGTGAAC
1738741 AACAGAAGAATTTGATATTCAATGGCGTTCAATTGTTTCAGAAATCAATGTCAAAAAGCATCCAT
196 AACAGAAGAATTTGATATTCAATGGCGTTCAATTGTTTCAGAAATCAATGTCAAAAAGCATCCAT
1738806 GGGTGATTGAAAATAGAAA
261 GGGTGATTGAAAATAGAAA
1738825 TTTTTTTACAAGCCATGATGAATAAATCACCTCTTTCAGTTGTCACCGATGGGGATAGGGCAATG
1 TTTTTTTACAAGCCATGATGAATAAATCACCTCTTTCAGTTGTCACCGATGGGGATAGGGCAATG
1738890 CAGAGGTCTATCAAATTATTATCCCTTTTGCTAAGCACATATTATGTTGGCATCTTTCTCGTAAT
66 CAGAGGTCTATCAAATTATTATCCCTTTTGCTAAGCACATATTATGTTGGCATCTTTCTCGTAAT
* * *
1738955 GCACAAGCTAATATTGATGACCGTAAATTTACAACATTTTCTATATGCATAGATTCCTGGTGGAT
131 GCACAAGCTAACATTGATGACCGTAAATTTACAACATTTTCTATATGCATAGATTCCTGGTGAAC
* * *
1739020 AATAGAAGAATTTGATATTCAATGGCATTCAATTATTTCAGAAATCAATGTCAAAAAGCATCCAT
196 AACAGAAGAATTTGATATTCAATGGCGTTCAATTGTTTCAGAAATCAATGTCAAAAAGCATCCAT
*
1739085 GGGTGATTGAGAAT-GAAA
261 GGGTGATTGAAAATAGAAA
*
1739103 TATTTTTTACAAGCCATGATGAATAAATCACCTCTTTCAGTTGTCACCGATGAGGATAGGGCAAT
1 T-TTTTTTACAAGCCATGATGAATAAATCACCTCTTTCAGTTGTCACCGATGGGGATAGGGCAAT
* *
1739168 GCAGAGGTCTATCAAATTATTATCCCTTTTGCTAAGAACATATTATGTTCTTGGCAACTTTCTCG
65 GCAGAGGTCTATCAAATTATTATCCCTTTTGCTAAGCACATATTATG---TTGGCATCTTTCTCG
* * * * * *
1739233 TAATGCACAAGCTAACATGGGTGACCGTAAATTTACAACATTTTCTACATGCATGGCTTCTTGGT
127 TAATGCACAAGCTAACATTGATGACCGTAAATTTACAACATTTTCTATATGCATAGATTCCTGGT
* * *
1739298 GAACAACAAAAGAATTTGATATTCAATGGCGTTCAATTGTTTCAGAATTCAATGTCGAAAAGCAT
192 GAACAACAGAAGAATTTGATATTCAATGGCGTTCAATTGTTTCAGAAATCAATGTCAAAAAGCAT
1739363 CCATGGGTGATTGA
257 CCATGGGTGATTGA
1739377 TAAGGGAAAT
Statistics
Matches: 520, Mismatches: 28, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
278 5 0.01
279 372 0.72
282 143 0.28
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (279 bp):
TTTTTTTACAAGCCATGATGAATAAATCACCTCTTTCAGTTGTCACCGATGGGGATAGGGCAATG
CAGAGGTCTATCAAATTATTATCCCTTTTGCTAAGCACATATTATGTTGGCATCTTTCTCGTAAT
GCACAAGCTAACATTGATGACCGTAAATTTACAACATTTTCTATATGCATAGATTCCTGGTGAAC
AACAGAAGAATTTGATATTCAATGGCGTTCAATTGTTTCAGAAATCAATGTCAAAAAGCATCCAT
GGGTGATTGAAAATAGAAA
Found at i:1745747 original size:46 final size:46
Alignment explanation
Indices: 1745674--1745798 Score: 162
Period size: 46 Copynumber: 2.7 Consensus size: 46
1745664 ATGAGTGACA
* * * *
1745674 CCTTTTATGCCG-TTAATACACCGTTATGTATTTTCATTTGTGGCAT
1 CCTTTCATGCCGATT-ATACACCGTTATGCATTTTCAATTATGGCAT
*
1745720 TCTTTCATGCCGATTATACACCGTTATGCATTTTCAATTATGGCAT
1 CCTTTCATGCCGATTATACACCGTTATGCATTTTCAATTATGGCAT
* * *
1745766 CCTTTCATGTCGATAATGCACCGTTATGCATTT
1 CCTTTCATGCCGATTATACACCGTTATGCATTT
1745799 AACATTCATT
Statistics
Matches: 69, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
46 67 0.97
47 2 0.03
ACGTcount: A:0.22, C:0.22, G:0.14, T:0.42
Consensus pattern (46 bp):
CCTTTCATGCCGATTATACACCGTTATGCATTTTCAATTATGGCAT
Found at i:1745895 original size:98 final size:98
Alignment explanation
Indices: 1745780--1746097 Score: 426
Period size: 98 Copynumber: 3.2 Consensus size: 98
1745770 TCATGTCGAT
* *
1745780 AATGCACCGTTATGCATTTAACATT-CATTAGTGGCACCTTTCTGCCGAAAATGCACCATTTGTC
1 AATGCACCGTTAGGCATTTAAC-TTGCATTAGTGGCACCTTTCTGCCAAAAATGCACCATTTGTC
* *
1745844 ATCTAACTAGCATTAGTGGTACCTTCCTACCAAA
65 ATCTAACTTGCATTAGTGGTACCTTTCTACCAAA
* ** * *
1745878 AATGCACCGTTAGGCATTTAACTTGCAGTAGTGGCATATTTTTGCAAAAAATGCACCATTTGTCA
1 AATGCACCGTTAGGCATTTAACTTGCATTAGTGGCACCTTTCTGCCAAAAATGCACCATTTGTCA
*
1745943 TCTAACTTG-ATTTAGTGATACCTTTCTACCAAA
66 TCTAACTTGCA-TTAGTGGTACCTTTCTACCAAA
* * * * * * *
1745976 AATGTATCGTTAGGTATTTAACTTGCATTATTGGTACCTTTCTGCCAAAAATACA-TAGTTTGTC
1 AATGCACCGTTAGGCATTTAACTTGCATTAGTGGCACCTTTCTGCCAAAAATGCACCA-TTTGTC
1746040 ATCTAACTTGCATTAGTGGTACCTTTCTACCAAA
65 ATCTAACTTGCATTAGTGGTACCTTTCTACCAAA
*
1746074 AATCCACCGTTAGGCATTTAACTT
1 AATGCACCGTTAGGCATTTAACTT
1746098 TTATTTTAGA
Statistics
Matches: 189, Mismatches: 27, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
97 4 0.02
98 184 0.97
99 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.35
Consensus pattern (98 bp):
AATGCACCGTTAGGCATTTAACTTGCATTAGTGGCACCTTTCTGCCAAAAATGCACCATTTGTCA
TCTAACTTGCATTAGTGGTACCTTTCTACCAAA
Found at i:1746096 original size:49 final size:49
Alignment explanation
Indices: 1745780--1746097 Score: 298
Period size: 49 Copynumber: 6.5 Consensus size: 49
1745770 TCATGTCGAT
* * * *
1745780 AATGCACCGTTATGCATTTAACATT-CATTAGTGGCACCTTTCTGCCGAA
1 AATGCACCGTTAGGCATTTAAC-TTGCATTAGTGGTACCTTTCTACCAAA
* * * * * *
1745829 AATGCACCATTTGTCATCTAACTAGCATTAGTGGTACCTTCCTACCAAA
1 AATGCACCGTTAGGCATTTAACTTGCATTAGTGGTACCTTTCTACCAAA
* * ** * * *
1745878 AATGCACCGTTAGGCATTTAACTTGCAGTAGTGGCATATTTTTGCAAAA
1 AATGCACCGTTAGGCATTTAACTTGCATTAGTGGTACCTTTCTACCAAA
* * * * *
1745927 AATGCACCATTTGTCATCTAACTTG-ATTTAGTGATACCTTTCTACCAAA
1 AATGCACCGTTAGGCATTTAACTTGCA-TTAGTGGTACCTTTCTACCAAA
* * * * *
1745976 AATGTATCGTTAGGTATTTAACTTGCATTATTGGTACCTTTCTGCCAAA
1 AATGCACCGTTAGGCATTTAACTTGCATTAGTGGTACCTTTCTACCAAA
* ** * * *
1746025 AATACATAGTTTGTCATCTAACTTGCATTAGTGGTACCTTTCTACCAAA
1 AATGCACCGTTAGGCATTTAACTTGCATTAGTGGTACCTTTCTACCAAA
*
1746074 AATCCACCGTTAGGCATTTAACTT
1 AATGCACCGTTAGGCATTTAACTT
1746098 TTATTTTAGA
Statistics
Matches: 206, Mismatches: 60, Indels: 6
0.76 0.22 0.02
Matches are distributed among these distances:
48 2 0.01
49 203 0.99
50 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.35
Consensus pattern (49 bp):
AATGCACCGTTAGGCATTTAACTTGCATTAGTGGTACCTTTCTACCAAA
Found at i:1749807 original size:26 final size:24
Alignment explanation
Indices: 1749753--1749805 Score: 61
Period size: 27 Copynumber: 2.1 Consensus size: 24
1749743 TAAGTCTATA
*
1749753 AAACTTAAACATTTATTCTCAAAT
1 AAACTTAAACATTTATTCACAAAT
*
1749777 AAACTTATAATCATTTGATTCACTAAT
1 AAACTTA-AA-CATTT-ATTCACAAAT
1749804 AA
1 AA
1749806 CTCAACTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 7 0.29
25 2 0.08
26 5 0.21
27 10 0.42
ACGTcount: A:0.45, C:0.15, G:0.02, T:0.38
Consensus pattern (24 bp):
AAACTTAAACATTTATTCACAAAT
Found at i:1751283 original size:98 final size:98
Alignment explanation
Indices: 1751158--1751774 Score: 968
Period size: 98 Copynumber: 6.3 Consensus size: 98
1751148 TCATGCTGAT
* * * *
1751158 AATGAACCGTTATGCATTTAACATGCATTAGTGGCACCTTTCTGTCAAAAATGCACCATTTGTCA
1 AATGCACCGTTAGGCATTTAACTTGCATTAGTGGCACCTTTCTGCCAAAAATGCACCATTTGTCA
1751223 TCTAACTTGCATTAGTGGTACCTTTCTACCAAA
66 TCTAACTTGCATTAGTGGTACCTTTCTACCAAA
* * * * *
1751256 AATGCACCGTCAGGCATTTAACTTGCATTAGTGGCACCTTTTTTTGCAAAAAAAGCACAATTTGT
1 AATGCACCGTTAGGCATTTAACTTGCATTAGTGGCACC--TTTCTGCCAAAAATGCACCATTTGT
1751321 CATCTAACTTGCATTAGTGGTACCTTTCTACC-AA
64 CATCTAACTTGCATTAGTGGTACCTTTCTACCAAA
** *
1751355 AATGCACCGTTAGGCATTTAACTTGCATTAGTGGCATATTTCTGCCAAAAATGCACCATTTGTTA
1 AATGCACCGTTAGGCATTTAACTTGCATTAGTGGCACCTTTCTGCCAAAAATGCACCATTTGTCA
* * *
1751420 TCTAACTTGCATTAGTGGTACATTTATACCGAA
66 TCTAACTTGCATTAGTGGTACCTTTCTACCAAA
1751453 AATGCACCGTTAGGCATTTAACTTGCATTAGTGGCACCTTTCTGCCAAAAATGCACCATTTGTCA
1 AATGCACCGTTAGGCATTTAACTTGCATTAGTGGCACCTTTCTGCCAAAAATGCACCATTTGTCA
*
1751518 TCTAACTTGCATTAGTGGAACCTTTCTACCAAA
66 TCTAACTTGCATTAGTGGTACCTTTCTACCAAA
* * *
1751551 AATGCATCGTTAGGCATTTAACTTGCATTAGTGGCACCTTTCTGCAAAAAATGAACCATTTGTCA
1 AATGCACCGTTAGGCATTTAACTTGCATTAGTGGCACCTTTCTGCCAAAAATGCACCATTTGTCA
* *
1751616 CCTAACTTGCATTAGTGGTACCTTTCTA-AAAA
66 TCTAACTTGCATTAGTGGTACCTTTCTACCAAA
* * * *
1751648 AATGCACGGTTATGCATTTAATTTGCATTAGTGGCACCTTTTTGCCAAAAATGCACCATTTGTCA
1 AATGCACCGTTAGGCATTTAACTTGCATTAGTGGCACCTTTCTGCCAAAAATGCACCATTTGTCA
1751713 TCTAACTTGCATTAGTGGTACCTTTCTACCAAA
66 TCTAACTTGCATTAGTGGTACCTTTCTACCAAA
*
1751746 AATGCACCGTTAGGCATTTAACTTTCATT
1 AATGCACCGTTAGGCATTTAACTTGCATT
1751775 TTAGAGCAGT
Statistics
Matches: 470, Mismatches: 45, Indels: 8
0.90 0.09 0.02
Matches are distributed among these distances:
97 138 0.29
98 243 0.52
99 37 0.08
100 52 0.11
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (98 bp):
AATGCACCGTTAGGCATTTAACTTGCATTAGTGGCACCTTTCTGCCAAAAATGCACCATTTGTCA
TCTAACTTGCATTAGTGGTACCTTTCTACCAAA
Found at i:1751667 original size:195 final size:195
Alignment explanation
Indices: 1751158--1751774 Score: 968
Period size: 195 Copynumber: 3.1 Consensus size: 195
1751148 TCATGCTGAT
* * *
1751158 AATGAACCGTTATGCATTTAACATGCATTAGTGGCACCTTTCTGTCAAAAATGCACCATTTGTCA
1 AATGCACCGTTAGGCATTTAACTTGCATTAGTGGCACCTTTCTG-CAAAAATGCACCATTTGTCA
*
1751223 TCTAACTTGCATTAGTGGTACCTTTCTACCAAAAATGCACCGTCAGGCATTTAACTTGCATTAGT
65 TCTAACTTGCATTAGTGGTACCTTTCTACCAAAAATGCACCGTTAGGCATTTAACTTGCATTAGT
* * *
1751288 GGCACCTTTTTTTGCAAAAAAAGCACAATTTGTCATCTAACTTGCATTAGTGGTACCTTTCTACC
130 GGCACC--TTTTTGCCAAAAATGCACCATTTGTCATCTAACTTGCATTAGTGGTACCTTTCTACC
1751353 -AA
193 AAA
** *
1751355 AATGCACCGTTAGGCATTTAACTTGCATTAGTGGCATATTTCTGCCAAAAATGCACCATTTGTTA
1 AATGCACCGTTAGGCATTTAACTTGCATTAGTGGCACCTTTCTG-CAAAAATGCACCATTTGTCA
* * *
1751420 TCTAACTTGCATTAGTGGTACATTTATACCGAAAATGCACCGTTAGGCATTTAACTTGCATTAGT
65 TCTAACTTGCATTAGTGGTACCTTTCTACCAAAAATGCACCGTTAGGCATTTAACTTGCATTAGT
* *
1751485 GGCACCTTTCTGCCAAAAATGCACCATTTGTCATCTAACTTGCATTAGTGGAACCTTTCTACCAA
130 GGCACCTTTTTGCCAAAAATGCACCATTTGTCATCTAACTTGCATTAGTGGTACCTTTCTACCAA
1751550 A
195 A
* *
1751551 AATGCATCGTTAGGCATTTAACTTGCATTAGTGGCACCTTTCTGCAAAAAATGAACCATTTGTCA
1 AATGCACCGTTAGGCATTTAACTTGCATTAGTGGCACCTTTCTGC-AAAAATGCACCATTTGTCA
* * * * *
1751616 CCTAACTTGCATTAGTGGTACCTTTCTA-AAAAAATGCACGGTTATGCATTTAATTTGCATTAGT
65 TCTAACTTGCATTAGTGGTACCTTTCTACCAAAAATGCACCGTTAGGCATTTAACTTGCATTAGT
1751680 GGCACCTTTTTGCCAAAAATGCACCATTTGTCATCTAACTTGCATTAGTGGTACCTTTCTACCAA
130 GGCACCTTTTTGCCAAAAATGCACCATTTGTCATCTAACTTGCATTAGTGGTACCTTTCTACCAA
1751745 A
195 A
*
1751746 AATGCACCGTTAGGCATTTAACTTTCATT
1 AATGCACCGTTAGGCATTTAACTTGCATT
1751775 TTAGAGCAGT
Statistics
Matches: 385, Mismatches: 33, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
195 175 0.45
196 85 0.22
197 125 0.32
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (195 bp):
AATGCACCGTTAGGCATTTAACTTGCATTAGTGGCACCTTTCTGCAAAAATGCACCATTTGTCAT
CTAACTTGCATTAGTGGTACCTTTCTACCAAAAATGCACCGTTAGGCATTTAACTTGCATTAGTG
GCACCTTTTTGCCAAAAATGCACCATTTGTCATCTAACTTGCATTAGTGGTACCTTTCTACCAAA
Found at i:1751768 original size:49 final size:49
Alignment explanation
Indices: 1751158--1751774 Score: 653
Period size: 49 Copynumber: 12.6 Consensus size: 49
1751148 TCATGCTGAT
* * * **
1751158 AATGAACCGTTATGCATTTAACATGCATTAGTGGCACCTTTCTGTCAAA
1 AATGCACCGTTAGGCATTTAACTTGCATTAGTGGCACCTTTCTACCAAA
* * * * *
1751207 AATGCACCATTTGTCATCTAACTTGCATTAGTGGTACCTTTCTACCAAA
1 AATGCACCGTTAGGCATTTAACTTGCATTAGTGGCACCTTTCTACCAAA
* * * *
1751256 AATGCACCGTCAGGCATTTAACTTGCATTAGTGGCACCTTTTTTTGCAAAA
1 AATGCACCGTTAGGCATTTAACTTGCATTAGTGGCACC--TTTCTACCAAA
* ** * * * *
1751307 AAAGCACAATTTGTCATCTAACTTGCATTAGTGGTACCTTTCTACC-AA
1 AATGCACCGTTAGGCATTTAACTTGCATTAGTGGCACCTTTCTACCAAA
** *
1751355 AATGCACCGTTAGGCATTTAACTTGCATTAGTGGCATATTTCTGCCAAA
1 AATGCACCGTTAGGCATTTAACTTGCATTAGTGGCACCTTTCTACCAAA
* * ** * * * * *
1751404 AATGCACCATTTGTTATCTAACTTGCATTAGTGGTACATTTATACCGAA
1 AATGCACCGTTAGGCATTTAACTTGCATTAGTGGCACCTTTCTACCAAA
*
1751453 AATGCACCGTTAGGCATTTAACTTGCATTAGTGGCACCTTTCTGCCAAA
1 AATGCACCGTTAGGCATTTAACTTGCATTAGTGGCACCTTTCTACCAAA
* * * * *
1751502 AATGCACCATTTGTCATCTAACTTGCATTAGTGGAACCTTTCTACCAAA
1 AATGCACCGTTAGGCATTTAACTTGCATTAGTGGCACCTTTCTACCAAA
* * *
1751551 AATGCATCGTTAGGCATTTAACTTGCATTAGTGGCACCTTTCTGCAAAA
1 AATGCACCGTTAGGCATTTAACTTGCATTAGTGGCACCTTTCTACCAAA
* * * * ** * *
1751600 AATGAACCATTTGTCACCTAACTTGCATTAGTGGTACCTTTCTA-AAAA
1 AATGCACCGTTAGGCATTTAACTTGCATTAGTGGCACCTTTCTACCAAA
* * * * *
1751648 AATGCACGGTTATGCATTTAATTTGCATTAGTGGCACCTTTTTGCCAAA
1 AATGCACCGTTAGGCATTTAACTTGCATTAGTGGCACCTTTCTACCAAA
* * * * *
1751697 AATGCACCATTTGTCATCTAACTTGCATTAGTGGTACCTTTCTACCAAA
1 AATGCACCGTTAGGCATTTAACTTGCATTAGTGGCACCTTTCTACCAAA
*
1751746 AATGCACCGTTAGGCATTTAACTTTCATT
1 AATGCACCGTTAGGCATTTAACTTGCATT
1751775 TTAGAGCAGT
Statistics
Matches: 453, Mismatches: 111, Indels: 8
0.79 0.19 0.01
Matches are distributed among these distances:
48 74 0.16
49 341 0.75
51 38 0.08
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (49 bp):
AATGCACCGTTAGGCATTTAACTTGCATTAGTGGCACCTTTCTACCAAA
Found at i:1754764 original size:2 final size:2
Alignment explanation
Indices: 1754759--1754805 Score: 66
Period size: 2 Copynumber: 25.5 Consensus size: 2
1754749 TAATTATTTA
1754759 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A- AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1754798 AT A- AT AT A
1 AT AT AT AT A
1754806 ATAATAAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
1 4 0.10
2 37 0.90
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1762746 original size:15 final size:15
Alignment explanation
Indices: 1762726--1762754 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1762716 AGTACATGTA
1762726 TGTGTAAGATTGATG
1 TGTGTAAGATTGATG
1762741 TGTGTAAGATTGAT
1 TGTGTAAGATTGAT
1762755 ATGGGAGGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.31, T:0.41
Consensus pattern (15 bp):
TGTGTAAGATTGATG
Found at i:1764542 original size:22 final size:22
Alignment explanation
Indices: 1764517--1764558 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
1764507 TCGTTGTCTA
1764517 AATTTTTTTTATTCATCCATGT
1 AATTTTTTTTATTCATCCATGT
1764539 AATTTTTTTTATTCATCCAT
1 AATTTTTTTTATTCATCCAT
1764559 ATATCTAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.24, C:0.14, G:0.02, T:0.60
Consensus pattern (22 bp):
AATTTTTTTTATTCATCCATGT
Found at i:1764916 original size:23 final size:23
Alignment explanation
Indices: 1764826--1764908 Score: 130
Period size: 23 Copynumber: 3.6 Consensus size: 23
1764816 ATTATTATAT
1764826 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
1764849 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* * *
1764872 GGCACTAAGGTGCAATTCTATGT
1 GGCACTACGGTGCAATTCTACGC
*
1764895 GGCACTTCGGTGCA
1 GGCACTACGGTGCA
1764909 TTTATATGAG
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 55 1.00
ACGTcount: A:0.22, C:0.27, G:0.28, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:1765893 original size:16 final size:16
Alignment explanation
Indices: 1765872--1765939 Score: 109
Period size: 16 Copynumber: 4.2 Consensus size: 16
1765862 ACCAAAGATG
*
1765872 TCAACTTTTCCAACTT
1 TCAACTTTGCCAACTT
1765888 TCAACTTTGCCAACTT
1 TCAACTTTGCCAACTT
*
1765904 TCAATTTTGCCAACTT
1 TCAACTTTGCCAACTT
*
1765920 TCTACTTTGCCAACTT
1 TCAACTTTGCCAACTT
1765936 TCAA
1 TCAA
1765940 GTCAAACATA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.25, C:0.29, G:0.04, T:0.41
Consensus pattern (16 bp):
TCAACTTTGCCAACTT
Found at i:1770659 original size:9 final size:7
Alignment explanation
Indices: 1770643--1770710 Score: 55
Period size: 9 Copynumber: 8.6 Consensus size: 7
1770633 ACCAAAGATG
1770643 TCAACTT
1 TCAACTT
1770650 TGCGAACTT
1 T-C-AACTT
*
1770659 TCAATTTT
1 TCAA-CTT
1770667 TCCAACTT
1 T-CAACTT
1770675 TCAACTT
1 TCAACTT
1770682 TGCCAACTT
1 T--CAACTT
1770691 TCAACTT
1 TCAACTT
1770698 TGCCAACTT
1 T--CAACTT
1770707 TCAA
1 TCAA
1770711 GCCAAACATA
Statistics
Matches: 51, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
7 20 0.39
8 8 0.16
9 23 0.45
ACGTcount: A:0.26, C:0.28, G:0.06, T:0.40
Consensus pattern (7 bp):
TCAACTT
Found at i:1770673 original size:16 final size:16
Alignment explanation
Indices: 1770643--1770710 Score: 109
Period size: 16 Copynumber: 4.2 Consensus size: 16
1770633 ACCAAAGATG
*
1770643 TCAACTTTGCGAACTT
1 TCAACTTTGCCAACTT
* *
1770659 TCAATTTTTCCAACTT
1 TCAACTTTGCCAACTT
1770675 TCAACTTTGCCAACTT
1 TCAACTTTGCCAACTT
1770691 TCAACTTTGCCAACTT
1 TCAACTTTGCCAACTT
1770707 TCAA
1 TCAA
1770711 GCCAAACATA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.26, C:0.28, G:0.06, T:0.40
Consensus pattern (16 bp):
TCAACTTTGCCAACTT
Found at i:1772489 original size:20 final size:20
Alignment explanation
Indices: 1772464--1772719 Score: 212
Period size: 20 Copynumber: 12.7 Consensus size: 20
1772454 GATTTTCCAG
** *
1772464 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATCCGTA
* *
1772484 AATCGCAACGCGATTCTG-A
1 AATCGCAACGCGAATCCGTA
* * *
1772503 CTATCGCAACGAGTATCCGTAA
1 -AATCGCAACGCGAATCCGT-A
*
1772525 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
**
1772545 AATCGCAACGAC-AATAAGTAA
1 AATCGCAACG-CGAATCCGT-A
*
1772566 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
* *
1772586 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATCCGTA
* * * *
1772606 AATCACAACACGTATCTGTA
1 AATCGCAACGCGAATCCGTA
* *
1772626 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATCCGTA
* * *
1772646 ATTCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
*
1772666 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATCCGT-A
*
1772687 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
1772707 AATCGCAACGCGA
1 AATCGCAACGCGA
1772720 TCGATAATTC
Statistics
Matches: 185, Mismatches: 42, Indels: 18
0.76 0.17 0.07
Matches are distributed among these distances:
19 1 0.01
20 133 0.72
21 50 0.27
22 1 0.01
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAATCCGTA
Found at i:1772550 original size:41 final size:41
Alignment explanation
Indices: 1772464--1772716 Score: 327
Period size: 41 Copynumber: 6.2 Consensus size: 41
1772454 GATTTTCCAG
* * *
1772464 AATCGCAACGCGAATATG-AAAATCGCAACGCG-ATTC-TGA
1 AATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGT-A
* * *
1772503 CTATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCCGTA
1 -AATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTA
* *
1772545 AATCGCAACGACAATAAGTAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTA
* * *
1772586 AATCGCAACGAGAATACGT-AAATCACAACACGTATCTGTA
1 AATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTA
* *
1772626 AATCGCAACGAGAATACGT-AATTCGCAATGCGTATCCGTA
1 AATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTA
*
1772666 AATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTA
1772707 AATCGCAACG
1 AATCGCAACG
1772717 CGATCGATAA
Statistics
Matches: 185, Mismatches: 24, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
40 84 0.45
41 96 0.52
42 4 0.02
43 1 0.01
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (41 bp):
AATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTA
Found at i:1772822 original size:21 final size:21
Alignment explanation
Indices: 1772793--1772832 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1772783 GACTATCGCA
*
1772793 TTGCGATTTCCCAAATTCGTG
1 TTGCAATTTCCCAAATTCGTG
* *
1772814 TTGCAATTTTCCTAATTCG
1 TTGCAATTTCCCAAATTCG
1772833 CAATGCGAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.20, C:0.23, G:0.15, T:0.42
Consensus pattern (21 bp):
TTGCAATTTCCCAAATTCGTG
Found at i:1772855 original size:20 final size:20
Alignment explanation
Indices: 1772830--1772955 Score: 175
Period size: 20 Copynumber: 6.3 Consensus size: 20
1772820 TTTTCCTAAT
1772830 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
1772850 TCGCAACGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * *
1772870 TCGCAATGCGATTAGGTGAA
1 TCGCAATGCGAATACGTAAA
*
1772890 TCGCAATGCAAATACGTAAA
1 TCGCAATGCGAATACGTAAA
1772910 TCGCAATGCGAAT-CTGTAAA
1 TCGCAATGCGAATAC-GTAAA
1772930 TCGCAATGCGAAT-CTGTAAA
1 TCGCAATGCGAATAC-GTAAA
1772950 TCGCAA
1 TCGCAA
1772956 CGAGATTCTG
Statistics
Matches: 95, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
19 1 0.01
20 94 0.99
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:1773844 original size:24 final size:24
Alignment explanation
Indices: 1773817--1773870 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1773807 GTATTCAAAA
1773817 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
1773841 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
1773865 TTTGAT
1 TTTGAT
1773871 AATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Done.