Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008259.1 Hibiscus syriacus cultivar Beakdansim tig00110912_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: 2373650
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 11
Found at i:1647525 original size:18 final size:18
Alignment explanation
Indices: 1647491--1647527 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1647481 ATCTTCATCG
*
1647491 TCATCTTCATCGTCAGCT
1 TCATCTTCATCGACAGCT
*
1647509 TCATCTTCATTGACAGCT
1 TCATCTTCATCGACAGCT
1647527 T
1 T
1647528 GGTTGTCCAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.30, G:0.11, T:0.41
Consensus pattern (18 bp):
TCATCTTCATCGACAGCT
Found at i:1649729 original size:198 final size:200
Alignment explanation
Indices: 1648991--1649773 Score: 1358
Period size: 200 Copynumber: 3.9 Consensus size: 200
1648981 ATATTTAAAT
* * * * * *
1648991 TAGTATCAAAACAAAATTAAAAAGTGT-GATACATATATTACACCTATTATATTATAAAACCGGT
1 TAGTATCGACACAAAATTAAAAAGTGTCGATACATATATTACACCTAATCTCTCATAAAACCGGT
1649055 ATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCTG
66 ATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCTG
*
1649120 GGATCAACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGG
131 GGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGG
1649185 ACCAA
196 ACCAA
* *
1649190 TAGTATCGACACAAAATTAAAAAGTGTTGATACATATATTACACCTATTCTCTCATAAAACCGGT
1 TAGTATCGACACAAAATTAAAAAGTGTCGATACATATATTACACCTAATCTCTCATAAAACCGGT
*
1649255 ATACTTATATCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCTG
66 ATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCTG
* *
1649320 GGATCGACACCTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCTATTCATTCTGG
131 GGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGG
1649385 ACCAA
196 ACCAA
* *
1649390 TAGTGTCGACACAAAATTAAAAAGTGTCGTTACATATATTACACCTAATCTCTCATAAAACCGGT
1 TAGTATCGACACAAAATTAAAAAGTGTCGATACATATATTACACCTAATCTCTCATAAAACCGGT
1649455 ATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCTG
66 ATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCTG
1649520 GGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGG
131 GGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGG
1649585 A-CAA
196 ACCAA
* * * *
1649589 TAGTATCGACACAAAATTGAAAAGTGTCAATGCATAT-TATATACCTAATCTCTCATAAAA-CGG
1 TAGTATCGACACAAAATTAAAAAGTGTCGATACATATAT-TACACCTAATCTCTCATAAAACCGG
*
1649652 TATACTTATACCGGTTAGATTGAAAAACTACCTATTACATTATACTTATGGGTTTCGATGTTTCT
65 TATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCT
1649717 GGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCAT
130 GGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCAT
1649774 ATTGTAAATT
Statistics
Matches: 559, Mismatches: 23, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
198 125 0.22
199 80 0.14
200 354 0.63
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (200 bp):
TAGTATCGACACAAAATTAAAAAGTGTCGATACATATATTACACCTAATCTCTCATAAAACCGGT
ATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCTG
GGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGG
ACCAA
Found at i:1650025 original size:19 final size:19
Alignment explanation
Indices: 1650001--1650050 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
1649991 ATTACATTCA
1650001 TATACAAAATTATAAATCG
1 TATACAAAATTATAAATCG
*
1650020 TATACAAAATTATAAATCT
1 TATACAAAATTATAAATCG
1650039 TATACAAAATTA
1 TATACAAAATTA
1650051 ACCCTACATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.54, C:0.10, G:0.02, T:0.34
Consensus pattern (19 bp):
TATACAAAATTATAAATCG
Found at i:1651642 original size:33 final size:33
Alignment explanation
Indices: 1651596--1651683 Score: 133
Period size: 33 Copynumber: 2.7 Consensus size: 33
1651586 ATGACATCGA
*
1651596 CTTCCTTCC-TCCTCATTTCTTCCATCTCTTCTT
1 CTTCC-TCCTTCCTCTTTTCTTCCATCTCTTCTT
*
1651629 CTTCCTCCTTCCTCTTTTTTTCCATCTCTTCTT
1 CTTCCTCCTTCCTCTTTTCTTCCATCTCTTCTT
*
1651662 CTTCCTCCTCCCTCTTTTCTTC
1 CTTCCTCCTTCCTCTTTTCTTC
1651684 TTCATATTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
32 3 0.06
33 47 0.94
ACGTcount: A:0.03, C:0.43, G:0.00, T:0.53
Consensus pattern (33 bp):
CTTCCTCCTTCCTCTTTTCTTCCATCTCTTCTT
Found at i:1651907 original size:33 final size:33
Alignment explanation
Indices: 1651870--1651935 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
1651860 CATCTTAAGA
* *
1651870 TCACCCCTTAACACCTCAACTTCTTTCACCACT
1 TCACCCATCAACACCTCAACTTCTTTCACCACT
*
1651903 TCACCCATCAACACCTCTACTTCTTTCACCACT
1 TCACCCATCAACACCTCAACTTCTTTCACCACT
1651936 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.24, C:0.45, G:0.00, T:0.30
Consensus pattern (33 bp):
TCACCCATCAACACCTCAACTTCTTTCACCACT
Found at i:1651994 original size:21 final size:21
Alignment explanation
Indices: 1651969--1652033 Score: 112
Period size: 21 Copynumber: 3.1 Consensus size: 21
1651959 CCCCTTATGC
1651969 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
1651990 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
* *
1652011 CTATCAAGTTTCTCTTTGACT
1 CTCTCAAGTTTCTCTTCGACT
1652032 CT
1 CT
1652034 TGATTGTCTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.15, C:0.31, G:0.09, T:0.45
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:1654599 original size:181 final size:182
Alignment explanation
Indices: 1654245--1654716 Score: 750
Period size: 182 Copynumber: 2.6 Consensus size: 182
1654235 CGTACTTACG
* *
1654245 AAAGTATCGACACTTTCAATATATCCGGTAGCATTTTATCGGTTTTATCATTTTGATACCAGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAGCGTTTTATCGGTTTTATCATTTTGATACCGGTTT
1654310 TATCATATTTTTACC-GTTATATCGTTGTGGATCGATACATTTTTTTAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTTTAAAGTATCGACACTTTAT
* * * *
1654374 AGGTGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTTTCGATCCTTATA-T
131 AGGCGCTAAAACTACTTCTCTTTTAAATTAACAAAGTGTCGATCCTTATATT
*
1654425 AAAGTATCGACACTTTCAATATATCCGGTAGCGTTTTATCGGTTTCATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAGCGTTTTATCGGTTTTATCATTTTGATACCGGTTT
*
1654490 TATCATATTTTTACCTGTTATATCGTTGTGGATTGATACATTTTTTTAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTTTAAAGTATCGACACTTTAT
*
1654555 AGGCGCTAAAACTACTTCTCTTTTAAATTAACGAAGTGTCGATCCTTATATT
131 AGGCGCTAAAACTACTTCTCTTTTAAATTAACAAAGTGTCGATCCTTATATT
* * * * * * ** *
1654607 AAAGTACCGACACTTTAAATATATCCGGTACCGCTTTACCAGTTTTATCATTTCAATATCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAGCGTTTTATCGGTTTTATCATTTTGATACCGGTTT
* *
1654672 TGTCATAGTTTTACCTGTTATATCGTTGTGGATCGATACATTTTT
66 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTT
1654717 AATTTGGATC
Statistics
Matches: 268, Mismatches: 22, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
180 77 0.29
181 93 0.35
182 98 0.37
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (182 bp):
AAAGTATCGACACTTTCAATATATCCGGTAGCGTTTTATCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTTTAAAGTATCGACACTTTAT
AGGCGCTAAAACTACTTCTCTTTTAAATTAACAAAGTGTCGATCCTTATATT
Found at i:1654882 original size:11 final size:11
Alignment explanation
Indices: 1654866--1654892 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1654856 ATATATCCGA
1654866 TAACCGTATAT
1 TAACCGTATAT
1654877 TAACCGTATAT
1 TAACCGTATAT
1654888 TAACC
1 TAACC
1654893 CGTCTTTCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.37, C:0.22, G:0.07, T:0.33
Consensus pattern (11 bp):
TAACCGTATAT
Found at i:1657411 original size:2 final size:2
Alignment explanation
Indices: 1657406--1657434 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1657396 GAGAGAGGCT
1657406 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1657435 GGTTGGCCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1660494 original size:23 final size:23
Alignment explanation
Indices: 1660462--1660509 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
1660452 TATTTTCAGT
*
1660462 ATATGATTTATTTTATATCATTG
1 ATATGATTTACTTTATATCATTG
* * *
1660485 ATATGTTTTACTTTGTATTATTG
1 ATATGATTTACTTTATATCATTG
1660508 AT
1 AT
1660510 TATGCCTCAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.27, C:0.04, G:0.10, T:0.58
Consensus pattern (23 bp):
ATATGATTTACTTTATATCATTG
Found at i:1661197 original size:19 final size:19
Alignment explanation
Indices: 1661181--1661227 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
1661171 TAATTTAGTC
1661181 CTAGTTTAATTATTTAGCT
1 CTAGTTTAATTATTTAGCT
1661200 CTAGTTTAATTATTTAGCT
1 CTAGTTTAATTATTTAGCT
*
1661219 CTAGATTAA
1 CTAGTTTAA
1661228 ATCCTTTAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.49
Consensus pattern (19 bp):
CTAGTTTAATTATTTAGCT
Found at i:1667109 original size:27 final size:27
Alignment explanation
Indices: 1667053--1667109 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
1667043 GACGTGGTAG
* *
1667053 TTTCTAGAAGGTCCAGTCAGCGACAGT
1 TTTCTAGAAGATCCAGTCAGCGACACT
*
1667080 TTTCTAGAAGATCTAGTCAGCG-CACCT
1 TTTCTAGAAGATCCAGTCAGCGACA-CT
1667107 TTT
1 TTT
1667110 GGAAGATGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 2 0.08
27 24 0.92
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.32
Consensus pattern (27 bp):
TTTCTAGAAGATCCAGTCAGCGACACT
Found at i:1667996 original size:18 final size:18
Alignment explanation
Indices: 1667975--1668011 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1667965 TCCTTTATTC
*
1667975 ATTTAATCTCTTTTTACT
1 ATTTAATCTCATTTTACT
1667993 ATTTAATCTCATTTTACT
1 ATTTAATCTCATTTTACT
1668011 A
1 A
1668012 CTTTTCGCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.27, C:0.16, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTTAATCTCATTTTACT
Found at i:1674608 original size:27 final size:26
Alignment explanation
Indices: 1674555--1674608 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
1674545 GGTCTGACGT
* *
1674555 GGCAGTTTTTAGAAGGTCCAGTTAGC
1 GGCAGTTTTTAGAAGATCCAGTCAGC
*
1674581 GGCAGTTTTCTAGAAGATCTAGTCAGC
1 GGCAGTTTT-TAGAAGATCCAGTCAGC
1674608 G
1 G
1674609 CGCCTTCTAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 9 0.38
27 15 0.62
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.30
Consensus pattern (26 bp):
GGCAGTTTTTAGAAGATCCAGTCAGC
Found at i:1675505 original size:18 final size:18
Alignment explanation
Indices: 1675484--1675518 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1675474 GCCTTTATTC
*
1675484 ATTTAATCTCTTTTTACT
1 ATTTAATCTCATTTTACT
1675502 ATTTAATCTCATTTTAC
1 ATTTAATCTCATTTTAC
1675519 CAAAATCCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.17, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTTAATCTCATTTTACT
Found at i:1677259 original size:12 final size:12
Alignment explanation
Indices: 1677242--1677266 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1677232 ATATATATTT
1677242 TATATTTTTTTA
1 TATATTTTTTTA
1677254 TATATTTTTTTA
1 TATATTTTTTTA
1677266 T
1 T
1677267 TAAAAATCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TATATTTTTTTA
Found at i:1678412 original size:2 final size:2
Alignment explanation
Indices: 1678405--1678431 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1678395 ATCCTAACCC
1678405 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1678432 GAATTAGGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1682017 original size:4 final size:4
Alignment explanation
Indices: 1682008--1682033 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1681998 GCATGAGTTT
1682008 TTTC TTTC TTTC TTTC TTTC TTTC TT
1 TTTC TTTC TTTC TTTC TTTC TTTC TT
1682034 CTTCTTCTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:1682970 original size:19 final size:19
Alignment explanation
Indices: 1682933--1682978 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
1682923 TTTAAAAAGA
1682933 AAAAAT-AATAAAATAAGT
1 AAAAATAAATAAAATAAGT
*
1682951 AATAATAAATAATAAT-AGT
1 AAAAATAAATAA-AATAAGT
1682970 AAAAATAAA
1 AAAAATAAA
1682979 AAGGGGTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 5 0.21
19 16 0.67
20 3 0.12
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (19 bp):
AAAAATAAATAAAATAAGT
Found at i:1683012 original size:18 final size:18
Alignment explanation
Indices: 1682991--1683033 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
1682981 GGGGTTTTTA
*
1682991 AAATAAAAGATAAGAATT
1 AAATAAAAGAAAAGAATT
*
1683009 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAAGAATT
1683027 AAATAAA
1 AAATAAA
1683034 TAATCTAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Found at i:1684807 original size:19 final size:19
Alignment explanation
Indices: 1684767--1684808 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
1684757 GTTATTTTCC
*
1684767 GATTTTTTTTTGAAACAGT
1 GATTTTTTTGTGAAACAGT
*
1684786 GATTTTTTTCGTGGAACA-T
1 GATTTTTTT-GTGAAACAGT
1684805 GATT
1 GATT
1684809 GATACAAGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.24, C:0.07, G:0.19, T:0.50
Consensus pattern (19 bp):
GATTTTTTTGTGAAACAGT
Found at i:1685973 original size:19 final size:20
Alignment explanation
Indices: 1685949--1685986 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
1685939 TGTTTAGAGA
1685949 AAAATAAAATAAA-ATAATC
1 AAAATAAAATAAATATAATC
1685968 AAAATAAAATAAATATAAT
1 AAAATAAAATAAATATAAT
1685987 GAAATTTAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (20 bp):
AAAATAAAATAAATATAATC
Found at i:1686017 original size:5 final size:5
Alignment explanation
Indices: 1686003--1686063 Score: 61
Period size: 5 Copynumber: 11.8 Consensus size: 5
1685993 TAGTTTGCTA
* * *
1686003 AAAAT AAAAT GAAAT AAAACA AAAAT AAAAAT AAAAAT AAAAT GAAAT
1 AAAAT AAAAT AAAAT AAAA-T AAAAT -AAAAT -AAAAT AAAAT AAAAT
1686051 AAAA- AAAAT AAAA
1 AAAAT AAAAT AAAA
1686064 ACAAAAATAG
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
4 4 0.09
5 28 0.60
6 15 0.32
ACGTcount: A:0.80, C:0.02, G:0.03, T:0.15
Consensus pattern (5 bp):
AAAAT
Found at i:1686027 original size:6 final size:6
Alignment explanation
Indices: 1686001--1686072 Score: 62
Period size: 6 Copynumber: 12.3 Consensus size: 6
1685991 TTTAGTTTGC
* *
1686001 TAAAAA T-AAAA T-GAAA T-AAAA CAAAAA TAAAAA TAAAAA T-AAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA
* *
1686045 TGAAATAA AAAAAA TAAAAA CAAAAA TA
1 T-AAA-AA TAAAAA TAAAAA TAAAAA TA
1686073 GAATGAAATG
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
5 17 0.31
6 30 0.56
7 5 0.09
8 2 0.04
ACGTcount: A:0.79, C:0.03, G:0.03, T:0.15
Consensus pattern (6 bp):
TAAAAA
Found at i:1686043 original size:33 final size:31
Alignment explanation
Indices: 1686001--1686081 Score: 126
Period size: 31 Copynumber: 2.5 Consensus size: 31
1685991 TTTAGTTTGC
1686001 TAAAAATAAAATGAAATAAAACAAAAATAAAAA
1 TAAAAATAAAATGAAAT-AAA-AAAAATAAAAA
1686034 TAAAAATAAAATGAAATAAAAAAAATAAAAA
1 TAAAAATAAAATGAAATAAAAAAAATAAAAA
* *
1686065 CAAAAATAGAATGAAAT
1 TAAAAATAAAATGAAAT
1686082 GGGTTGCCTC
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
31 26 0.57
32 3 0.07
33 17 0.37
ACGTcount: A:0.77, C:0.02, G:0.05, T:0.16
Consensus pattern (31 bp):
TAAAAATAAAATGAAATAAAAAAAATAAAAA
Found at i:1691744 original size:18 final size:18
Alignment explanation
Indices: 1691723--1691761 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
1691713 TTTTTAAAAG
*
1691723 AAAAGATAAGAATTAAAT
1 AAAAGAAAAGAATTAAAT
*
1691741 AAAAGAAAATAATTAAAT
1 AAAAGAAAAGAATTAAAT
1691759 AAA
1 AAA
1691762 TAATCTAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.21
Consensus pattern (18 bp):
AAAAGAAAAGAATTAAAT
Found at i:1702631 original size:19 final size:19
Alignment explanation
Indices: 1702590--1702648 Score: 75
Period size: 19 Copynumber: 3.1 Consensus size: 19
1702580 CCGTTAGACA
* *
1702590 GGGGGAAT-GGTACCCCTT
1 GGGGGAATCTGTACCCCCT
*
1702608 GGGGGGAATCTGTTCCCCCT
1 -GGGGGAATCTGTACCCCCT
1702628 GGGGGAATCTGTACCCCCT
1 GGGGGAATCTGTACCCCCT
1702647 GG
1 GG
1702649 ACAATCTGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 28 0.80
20 7 0.20
ACGTcount: A:0.14, C:0.27, G:0.37, T:0.22
Consensus pattern (19 bp):
GGGGGAATCTGTACCCCCT
Found at i:1702654 original size:18 final size:19
Alignment explanation
Indices: 1702614--1702656 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
1702604 CCTTGGGGGG
* **
1702614 AATCTGTTCCCCCTGGGGG
1 AATCTGTACCCCCTGGGAC
1702633 AATCTGTACCCCCT-GGAC
1 AATCTGTACCCCCTGGGAC
1702651 AATCTG
1 AATCTG
1702657 ATTTTTCTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.19, C:0.33, G:0.23, T:0.26
Consensus pattern (19 bp):
AATCTGTACCCCCTGGGAC
Found at i:1705983 original size:20 final size:20
Alignment explanation
Indices: 1705958--1706014 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
1705948 CATTAGACAA
* *
1705958 GGGGGAATCGGTACCCCCTG
1 GGGGGAATCTGTACCCCATG
* *
1705978 GGGGGAATCTGTTCTCCATG
1 GGGGGAATCTGTACCCCATG
1705998 GGGGGAATCTGTACCCC
1 GGGGGAATCTGTACCCC
1706015 TGGACAATAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.16, C:0.26, G:0.37, T:0.21
Consensus pattern (20 bp):
GGGGGAATCTGTACCCCATG
Found at i:1716639 original size:13 final size:13
Alignment explanation
Indices: 1716621--1716664 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
1716611 AGTAAGCTCG
1716621 ACTCGACTCGAAA
1 ACTCGACTCGAAA
** *
1716634 ACTCGACGAGCAA
1 ACTCGACTCGAAA
1716647 ACTCGACTCGAAA
1 ACTCGACTCGAAA
1716660 ACTCG
1 ACTCG
1716665 CGAGCTAAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.32, G:0.18, T:0.14
Consensus pattern (13 bp):
ACTCGACTCGAAA
Found at i:1716650 original size:26 final size:25
Alignment explanation
Indices: 1716621--1716669 Score: 89
Period size: 26 Copynumber: 1.9 Consensus size: 25
1716611 AGTAAGCTCG
1716621 ACTCGACTCGAAAACTCGACGAGCAA
1 ACTCGACTCGAAAACTCG-CGAGCAA
1716647 ACTCGACTCGAAAACTCGCGAGC
1 ACTCGACTCGAAAACTCGCGAGC
1716670 TAAAAATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 5 0.22
26 18 0.78
ACGTcount: A:0.35, C:0.33, G:0.20, T:0.12
Consensus pattern (25 bp):
ACTCGACTCGAAAACTCGCGAGCAA
Found at i:1716652 original size:31 final size:31
Alignment explanation
Indices: 1716585--1716657 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 31
1716575 TATTACTGAG
* * *
1716585 CTCGACTCGAACTCGAAAACTATAAGAGTAAG
1 CTCGACTCG-ACTCGAAAACTAGAAGAGCAAA
* *
1716617 CTCGACTCGACTCGAAAACTCGACGAGCAAA
1 CTCGACTCGACTCGAAAACTAGAAGAGCAAA
1716648 CTCGACTCGA
1 CTCGACTCGA
1716658 AAACTCGCGA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
31 27 0.75
32 9 0.25
ACGTcount: A:0.36, C:0.29, G:0.19, T:0.16
Consensus pattern (31 bp):
CTCGACTCGACTCGAAAACTAGAAGAGCAAA
Found at i:1717146 original size:33 final size:33
Alignment explanation
Indices: 1717109--1717171 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
1717099 ATTTACAACT
1717109 TCGATGACATTGTTAATTGGTTTTCA-TTAAACA
1 TCGATGACATTGTTAATT-GTTTTCACTTAAACA
1717142 TCGATGACATTGTTAATTGTTTTCACTTAA
1 TCGATGACATTGTTAATTGTTTTCACTTAA
1717172 TCTTTGTACT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 7 0.24
33 22 0.76
ACGTcount: A:0.29, C:0.13, G:0.14, T:0.44
Consensus pattern (33 bp):
TCGATGACATTGTTAATTGTTTTCACTTAAACA
Found at i:1717691 original size:33 final size:33
Alignment explanation
Indices: 1717648--1717714 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
1717638 GTTTTACTGA
*
1717648 TTCCCTTGTCTATGCCTGTCCTGTAACCAGGTT
1 TTCCCATGTCTATGCCTGTCCTGTAACCAGGTT
1717681 TTCCCATGTCTATGCCTGTCCTGTAACCAGGTT
1 TTCCCATGTCTATGCCTGTCCTGTAACCAGGTT
1717714 T
1 T
1717715 GCCAAATAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.13, C:0.30, G:0.18, T:0.39
Consensus pattern (33 bp):
TTCCCATGTCTATGCCTGTCCTGTAACCAGGTT
Found at i:1718517 original size:14 final size:14
Alignment explanation
Indices: 1718494--1718554 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 14
1718484 CAGTTTGGGA
*
1718494 GTTTATAGTTTAGG
1 GTTTAGAGTTTAGG
*
1718508 GTTTAGAGTTTATG
1 GTTTAGAGTTTAGG
* *
1718522 CTTTATG-GTTTA-A
1 GTTTA-GAGTTTAGG
*
1718535 GTTTAGGGTTTAGG
1 GTTTAGAGTTTAGG
1718549 GTTTAG
1 GTTTAG
1718555 GATTCATTAC
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
12 1 0.03
13 9 0.24
14 27 0.71
15 1 0.03
ACGTcount: A:0.20, C:0.02, G:0.30, T:0.49
Consensus pattern (14 bp):
GTTTAGAGTTTAGG
Found at i:1718545 original size:7 final size:7
Alignment explanation
Indices: 1718501--1718555 Score: 58
Period size: 7 Copynumber: 8.0 Consensus size: 7
1718491 GGAGTTTATA
1718501 GTTTAGG
1 GTTTAGG
*
1718508 GTTTAGA
1 GTTTAGG
*
1718515 GTTTATG
1 GTTTAGG
* *
1718522 CTTTATG
1 GTTTAGG
*
1718529 GTTTA-A
1 GTTTAGG
1718535 GTTTAGG
1 GTTTAGG
1718542 GTTTAGG
1 GTTTAGG
1718549 GTTTAGG
1 GTTTAGG
1718556 ATTCATTACA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
6 5 0.12
7 35 0.88
ACGTcount: A:0.18, C:0.02, G:0.33, T:0.47
Consensus pattern (7 bp):
GTTTAGG
Found at i:1718750 original size:25 final size:26
Alignment explanation
Indices: 1718705--1718759 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
1718695 AAAAATTAGT
1718705 TATTAAAAATATTATCATTAGA-AATA
1 TATTAAAAATATTATCATTAGATAA-A
* *
1718731 TATTAAATAT-TTGTCATTAGATAAA
1 TATTAAAAATATTATCATTAGATAAA
1718756 TATT
1 TATT
1718760 TTTTATTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 15 0.58
26 11 0.42
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.44
Consensus pattern (26 bp):
TATTAAAAATATTATCATTAGATAAA
Found at i:1723482 original size:6 final size:6
Alignment explanation
Indices: 1723471--1723525 Score: 58
Period size: 6 Copynumber: 9.0 Consensus size: 6
1723461 CGTTTGTTTA
* * *
1723471 ATTTTT ATTTTT ATTTTC AATTTT ATTTTT -TTGATTT ATTTTT GTTTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATT--TTT ATTTTT ATTTTT
1723520 ATTTTT
1 ATTTTT
1723526 CTTTGATTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
5 2 0.05
6 33 0.82
7 3 0.08
8 2 0.05
ACGTcount: A:0.16, C:0.02, G:0.04, T:0.78
Consensus pattern (6 bp):
ATTTTT
Found at i:1729188 original size:3 final size:3
Alignment explanation
Indices: 1729173--1729206 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
1729163 CACATATGTT
*
1729173 TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1729207 GTCTCATTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1734407 original size:31 final size:31
Alignment explanation
Indices: 1734369--1734434 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
1734359 GAGCTTATCC
1734369 CAAGGTAAGGAAAAAATTACTTTTTGATTTT
1 CAAGGTAAGGAAAAAATTACTTTTTGATTTT
** *
1734400 CAAGGTAAGGAAAATTTTTCTTTTTGATTTT
1 CAAGGTAAGGAAAAAATTACTTTTTGATTTT
1734431 CAAG
1 CAAG
1734435 CCAATTTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.35, C:0.08, G:0.17, T:0.41
Consensus pattern (31 bp):
CAAGGTAAGGAAAAAATTACTTTTTGATTTT
Found at i:1734489 original size:22 final size:22
Alignment explanation
Indices: 1734461--1734513 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
1734451 TTGGATGAAA
1734461 GCATGAAATACAAAATTGTTCT
1 GCATGAAATACAAAATTGTTCT
1734483 GCATGAAATACAAAATTGTTCT
1 GCATGAAATACAAAATTGTTCT
*
1734505 ACATGAAAT
1 GCATGAAAT
1734514 TCTCTATCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.30
Consensus pattern (22 bp):
GCATGAAATACAAAATTGTTCT
Found at i:1738269 original size:19 final size:19
Alignment explanation
Indices: 1738245--1738290 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
1738235 AAATCTAAAA
*
1738245 TAATTTAAGGATAAATTTG
1 TAATTTAACGATAAATTTG
*
1738264 TAATTTAACTATAAATTTG
1 TAATTTAACGATAAATTTG
1738283 TAATTTAA
1 TAATTTAA
1738291 TTTTCGTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.46
Consensus pattern (19 bp):
TAATTTAACGATAAATTTG
Found at i:1738980 original size:2 final size:2
Alignment explanation
Indices: 1738889--1738966 Score: 149
Period size: 2 Copynumber: 39.5 Consensus size: 2
1738879 CCATATAAAC
1738889 AT AT A- 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
1738930 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1738967 CTAACCCATA
Statistics
Matches: 75, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 74 0.99
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1742712 original size:39 final size:39
Alignment explanation
Indices: 1742667--1742751 Score: 102
Period size: 40 Copynumber: 2.2 Consensus size: 39
1742657 TGTTTTTCCA
*
1742667 TTTTTTCATGTC-TATTTTTGTTTTCT-TATCTTTTTTTC
1 TTTTTTCATGTCGAATTTTTGTTTT-TGTATCTTTTTTTC
* * *
1742705 TCTTTTTCTTTTCGAATTTTTGTTTTTGTTTCTTTTTTTC
1 T-TTTTTCATGTCGAATTTTTGTTTTTGTATCTTTTTTTC
1742745 TTTTTTC
1 TTTTTTC
1742752 GAAAATAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
38 1 0.03
39 16 0.40
40 23 0.57
ACGTcount: A:0.06, C:0.13, G:0.06, T:0.75
Consensus pattern (39 bp):
TTTTTTCATGTCGAATTTTTGTTTTTGTATCTTTTTTTC
Found at i:1757415 original size:55 final size:54
Alignment explanation
Indices: 1757332--1757440 Score: 175
Period size: 55 Copynumber: 2.0 Consensus size: 54
1757322 TAAAATTTTA
* *
1757332 GTTGTAATTTTATTGATATAATCAATTTGTTTATTTTCAAAAATTATAAAGTAC
1 GTTGTAATTTTATTGATAGAATCAATTTGTATATTTTCAAAAATTATAAAGTAC
1757386 GTTGTAATTTTTATTGATAGAAT-ATATTTGTATATTTTCAAAAATTATAAAGTAC
1 GTTGTAA-TTTTATTGATAGAATCA-ATTTGTATATTTTCAAAAATTATAAAGTAC
1757441 CCAGACATTT
Statistics
Matches: 51, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
54 8 0.16
55 43 0.84
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.48
Consensus pattern (54 bp):
GTTGTAATTTTATTGATAGAATCAATTTGTATATTTTCAAAAATTATAAAGTAC
Found at i:1757710 original size:33 final size:33
Alignment explanation
Indices: 1757673--1757739 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
1757663 ATCAAATTAG
** *
1757673 AAAATCTATAATTAGAATGTTTCGATTTATTTT
1 AAAATCTATAATTAGAATGAATCGATTTAATTT
1757706 AAAATCTATAATTAGAATGAATCGATTTAATTT
1 AAAATCTATAATTAGAATGAATCGATTTAATTT
1757739 A
1 A
1757740 CTCAAAATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.42, C:0.06, G:0.09, T:0.43
Consensus pattern (33 bp):
AAAATCTATAATTAGAATGAATCGATTTAATTT
Found at i:1784931 original size:54 final size:55
Alignment explanation
Indices: 1784868--1784976 Score: 168
Period size: 55 Copynumber: 2.0 Consensus size: 55
1784858 TAAAATTTTA
* * *
1784868 GTTGTAA-TTTTATTGATATAATCA-ATTTGTTTATTTTCAAAAATTATAAAGTAC
1 GTTGTAATTTTTATTGATAGAAT-ATATTTGTATATTTTAAAAAATTATAAAGTAC
1784922 GTTGTAATTTTTATTGATAGAATATATTTGTATATTTTAAAAAATTATAAAGTAC
1 GTTGTAATTTTTATTGATAGAATATATTTGTATATTTTAAAAAATTATAAAGTAC
1784977 CCAGACATTT
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
54 8 0.16
55 42 0.84
ACGTcount: A:0.39, C:0.04, G:0.10, T:0.48
Consensus pattern (55 bp):
GTTGTAATTTTTATTGATAGAATATATTTGTATATTTTAAAAAATTATAAAGTAC
Found at i:1785245 original size:33 final size:33
Alignment explanation
Indices: 1785208--1785274 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
1785198 ATCAAATTAG
**
1785208 AAAATCTATAATTAGAATGTTTCGATTTAATTT
1 AAAATCTATAATTAGAATGAATCGATTTAATTT
1785241 AAAATCTATAATTAGAATGAATCGATTTAATTT
1 AAAATCTATAATTAGAATGAATCGATTTAATTT
1785274 A
1 A
1785275 CTCAAAGTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.42
Consensus pattern (33 bp):
AAAATCTATAATTAGAATGAATCGATTTAATTT
Found at i:1788325 original size:16 final size:16
Alignment explanation
Indices: 1788304--1788356 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
1788294 TGCCAAAGAT
1788304 AAAATTTGATTTAGAC
1 AAAATTTGATTTAGAC
**
1788320 AAAATTTG-TGAAGA-
1 AAAATTTGATTTAGAC
*
1788334 ATAATTTTGATTTAGAC
1 A-AAATTTGATTTAGAC
1788351 AAAATT
1 AAAATT
1788357 AGATGATATG
Statistics
Matches: 28, Mismatches: 6, Indels: 6
0.70 0.15 0.15
Matches are distributed among these distances:
14 1 0.04
15 10 0.36
16 16 0.57
17 1 0.04
ACGTcount: A:0.45, C:0.04, G:0.13, T:0.38
Consensus pattern (16 bp):
AAAATTTGATTTAGAC
Found at i:1797265 original size:689 final size:689
Alignment explanation
Indices: 1795948--1797326 Score: 2284
Period size: 689 Copynumber: 2.0 Consensus size: 689
1795938 GATTAACAAG
* * *
1795948 TTGATATATATTTATCGTTGCAGTTATCGAATCGAATAATGATATCATGCATATTTTCCGAAAAC
1 TTGATATATATTTATCGTTGCAGTTATCCAATCGAACAATGATATCATGCATATTTGCCGAAAAC
* * *
1796013 GATAAAACTAGAACATGCATCTCCTATATATCGCATCAACCAAGAATTTAACCTGAATTTGAATC
66 GATAAAACTAGAACATGCATCTCCTACATATCGCATAAACCAAGAATTTAACCTGAATTCGAATC
**
1796078 ATACAAGTGGCTCTAATACCACTGTTGGGACCATCGATGCAACCACGGCACAGCAAAAACAAAAC
131 ATACAAGTGGCTCTAATACCACTGTTGGGACCATCGATGCAACCACCACACAGCAAAAACAAAAC
* * * *
1796143 TCGAAGGACTCACCAGCGGTCCAAGTACGTAAAATCGAAATCAGGAGGAAGGGATGCGAATACTT
196 TCGAAGGACTCACCAGCGATCCAAGTACATAAAATCAAAATAAGGAGGAAGGGATGCGAATACTT
* * * * *
1796208 ACAGCGGTTCCTTGAAAAACAGCAAGGACAACAACGACATCGATCGATTTGAATTGTAAGCCTTT
261 ACAACGGTTCCTTGAAAAACAACAAGGACAACAACGACATCGATCGATTTAAATCGTAAGCCTTC
1796273 ACGAAATCATGTCTCGGCCTCTACTCAGTTCACCCGATTAAGAGCAATATTTATTTTCCCCAAAA
326 ACGAAATCATGTCTCGGCCTCTACTCAGTTCACCCGATTAAGAGCAATATTTATTTTCCCCAAAA
* * *
1796338 CTGTTTTTACGAAAAACGGTTGAAGATTTTGTGTGTTCTAAAAAAACGGCTGCTAGACCTAACAC
391 CTATTTTTAAGAAAAACAGTTGAAGATTTTGTGTGTTCTAAAAAAACGGCTGCTAGACCTAACAC
* *
1796403 ATCTTTTTTATCCGAGTTACCCTAATCATTTAGAGATTTTTATTATTTAAAATTAATTAAATCTT
456 ATCTTTTATATCCAAGTTACCCTAATCATTTAGAGATTTTTATTATTTAAAATTAATTAAATCTT
*
1796468 TATTTAATTAATTGGAATTAAATATTCGGGATTATTAAAACATATGTATATCAAACATACATATA
521 TATGTAATTAATTGGAATTAAATATTCGGGATTATTAAAACATATGTATATCAAACATACATATA
* *
1796533 TTAACTCTAGATATATTTCAGTAACGTACAACAATTGTACATCCTTGCTCGTTTCAATCCAAGGG
586 TTAACTCTAGATATATTTCAGTAACGTACAACAATTGTACATCCTTGCTAGTTTCAATCCAAGGA
1796598 TGTGACCCTGTAGGTTCTTGTAACGTTAGCAGTAATTAT
651 TGTGACCCTGTAGGTTCTTGTAACGTTAGCAGTAATTAT
1796637 TTGATATATATTTATCGTTGCAGTTATCCAATCGAACAATGATATCATGCATATTTGCCGAAAAC
1 TTGATATATATTTATCGTTGCAGTTATCCAATCGAACAATGATATCATGCATATTTGCCGAAAAC
* *
1796702 GATAAAACTAGAACATGCATCTCCTACATATCGTATAAACCAAGAATTTAACTTGAATTCGAATC
66 GATAAAACTAGAACATGCATCTCCTACATATCGCATAAACCAAGAATTTAACCTGAATTCGAATC
* * * * * *
1796767 GTACAAGTGGCTCTAATACCACTGTAT-GTACCATCGGTTC-GCC-CCACACAGCAGAAACAAAA
131 ATACAAGTGGCTCTAATACCACTGT-TGGGACCATCGATGCAACCACCACACAGCAAAAACAAAA
* *
1796829 CTCGACA-GACTCACTAGCGATCCAAGTACATAAAA-CAAAAATAAGGAGGAAGGGATTCGAATA
195 CTCGA-AGGACTCACCAGCGATCCAAGTACATAAAATC-AAAATAAGGAGGAAGGGATGCGAATA
*
1796892 CTTACAACGGATTCCTTGAAAAACAACAAGGACAACAACGTCATCGATCGATTTAAATCGTAAGC
258 CTTACAACGG-TTCCTTGAAAAACAACAAGGACAACAACGACATCGATCGATTTAAATCGTAAGC
* * *
1796957 CTTCACGAAATCATGTCTCGGCCTCTACTCAGTTCACCTGATTGAGAGCAATATTTGTTTTCCCC
322 CTTCACGAAATCATGTCTCGGCCTCTACTCAGTTCACCCGATTAAGAGCAATATTTATTTTCCCC
1797022 AAAACTATTTTTAAGAAAAACAGTTGAAGATTTTGTGTGTTCTAAAAAAACGGCTGCTAGACCTA
387 AAAACTATTTTTAAGAAAAACAGTTGAAGATTTTGTGTGTTCTAAAAAAACGGCTGCTAGACCTA
*
1797087 ACACATCCTTTTATATCTAAGTTACCCTAATCATATTAGAGATTTTTATTATTTAAAATTAATTA
452 ACACAT-CTTTTATATCCAAGTTACCCTAATCAT-TTAGAGATTTTTATTATTTAAAATTAATTA
1797152 AATCTTTATGTAATTAATTGGAATTAAATATT-GGGATTATTAAAACATATGTATATCAAACATA
515 AATCTTTATGTAATTAATTGGAATTAAATATTCGGGATTATTAAAACATATGTATATCAAACATA
*
1797216 CATATATTAACTCTAGATATATTTCAGTAATGTACAACAATTGTACATCCTTGCTAGTTTCAATC
580 CATATATTAACTCTAGATATATTTCAGTAACGTACAACAATTGTACATCCTTGCTAGTTTCAATC
*
1797281 CAAGGATGTGACCCTGTAGGTTCTTGTAACGTTAGGAGTAATTAT
645 CAAGGATGTGACCCTGTAGGTTCTTGTAACGTTAGCAGTAATTAT
1797326 T
1 T
1797327 AGAACAATTC
Statistics
Matches: 642, Mismatches: 42, Indels: 12
0.92 0.06 0.02
Matches are distributed among these distances:
686 1 0.00
687 78 0.12
688 182 0.28
689 319 0.50
690 62 0.10
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (689 bp):
TTGATATATATTTATCGTTGCAGTTATCCAATCGAACAATGATATCATGCATATTTGCCGAAAAC
GATAAAACTAGAACATGCATCTCCTACATATCGCATAAACCAAGAATTTAACCTGAATTCGAATC
ATACAAGTGGCTCTAATACCACTGTTGGGACCATCGATGCAACCACCACACAGCAAAAACAAAAC
TCGAAGGACTCACCAGCGATCCAAGTACATAAAATCAAAATAAGGAGGAAGGGATGCGAATACTT
ACAACGGTTCCTTGAAAAACAACAAGGACAACAACGACATCGATCGATTTAAATCGTAAGCCTTC
ACGAAATCATGTCTCGGCCTCTACTCAGTTCACCCGATTAAGAGCAATATTTATTTTCCCCAAAA
CTATTTTTAAGAAAAACAGTTGAAGATTTTGTGTGTTCTAAAAAAACGGCTGCTAGACCTAACAC
ATCTTTTATATCCAAGTTACCCTAATCATTTAGAGATTTTTATTATTTAAAATTAATTAAATCTT
TATGTAATTAATTGGAATTAAATATTCGGGATTATTAAAACATATGTATATCAAACATACATATA
TTAACTCTAGATATATTTCAGTAACGTACAACAATTGTACATCCTTGCTAGTTTCAATCCAAGGA
TGTGACCCTGTAGGTTCTTGTAACGTTAGCAGTAATTAT
Found at i:1798309 original size:21 final size:21
Alignment explanation
Indices: 1798284--1798325 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1798274 CCGTTACACA
1798284 GGGGGAATCAGTACCCCCTGG
1 GGGGGAATCAGTACCCCCTGG
* *
1798305 GGGGGAATTAGTACCCTCTGG
1 GGGGGAATCAGTACCCCCTGG
1798326 ATATTCTGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.19, C:0.24, G:0.38, T:0.19
Consensus pattern (21 bp):
GGGGGAATCAGTACCCCCTGG
Found at i:1798608 original size:19 final size:20
Alignment explanation
Indices: 1798584--1798623 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1798574 AATTTAATCG
*
1798584 AATATATAAT-TTAAAATTC
1 AATATAAAATCTTAAAATTC
1798603 AATATAAAATCTTAAAATTC
1 AATATAAAATCTTAAAATTC
1798623 A
1 A
1798624 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:1799807 original size:19 final size:20
Alignment explanation
Indices: 1799757--1799810 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
1799747 TTTAAATCAA
* *
1799757 ATTTTTTTTTTCAAAATTTC
1 ATTTTTGTTTTCAAAATCTC
**
1799777 A-TTTTGACTTCAAAATCT-
1 ATTTTTGTTTTCAAAATCTC
1799795 ATTTTTGTTTTCAAAA
1 ATTTTTGTTTTCAAAA
1799811 GAAAATCGTT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
18 1 0.04
19 25 0.93
20 1 0.04
ACGTcount: A:0.30, C:0.11, G:0.04, T:0.56
Consensus pattern (20 bp):
ATTTTTGTTTTCAAAATCTC
Found at i:1801114 original size:21 final size:21
Alignment explanation
Indices: 1801089--1801130 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1801079 CCGTTACACA
1801089 GGGGGAATCAGTATCCC-CTGG
1 GGGGGAATCAGTA-CCCTCTGG
*
1801110 GGGGGAATTAGTACCCTCTGG
1 GGGGGAATCAGTACCCTCTGG
1801131 ATATTCTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.19, C:0.21, G:0.38, T:0.21
Consensus pattern (21 bp):
GGGGGAATCAGTACCCTCTGG
Found at i:1801412 original size:19 final size:20
Alignment explanation
Indices: 1801388--1801427 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1801378 AATTTAATCG
*
1801388 AATATATAAT-TTAAAATTC
1 AATATAAAATCTTAAAATTC
1801407 AATATAAAATCTTAAAATTC
1 AATATAAAATCTTAAAATTC
1801427 A
1 A
1801428 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:1804032 original size:74 final size:74
Alignment explanation
Indices: 1803954--1804104 Score: 293
Period size: 74 Copynumber: 2.0 Consensus size: 74
1803944 GCATAATATA
*
1803954 TATATATATATATCAATCTTAATTATACATTTTAATTCAAGTGCAATCAAATTGTACAATTATAG
1 TATATATATATATCAATCTTAATTATACATTTTAATTCAAGTACAATCAAATTGTACAATTATAG
1804019 CTCGTTTGG
66 CTCGTTTGG
1804028 TATATATATATATCAATCTTAATTATACATTTTAATTCAAGTACAATCAAATTGTACAATTATAG
1 TATATATATATATCAATCTTAATTATACATTTTAATTCAAGTACAATCAAATTGTACAATTATAG
1804093 CTCGTTTGG
66 CTCGTTTGG
1804102 TAT
1 TAT
1804105 TTGCTCATTC
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 76 1.00
ACGTcount: A:0.37, C:0.12, G:0.09, T:0.42
Consensus pattern (74 bp):
TATATATATATATCAATCTTAATTATACATTTTAATTCAAGTACAATCAAATTGTACAATTATAG
CTCGTTTGG
Found at i:1804089 original size:37 final size:37
Alignment explanation
Indices: 1803974--1804091 Score: 88
Period size: 37 Copynumber: 3.2 Consensus size: 37
1803964 TATCAATCTT
*
1803974 AATTATACATTTTAATTCAAGTGCAATCAAATTGTAC
1 AATTATACATTTTAATTCAAGTACAATCAAATTGTAC
** *
1804011 AATTATAGC-TCGTTTGGTAT-ATA-TATATATC-AATCT-T--
1 AATTATA-CAT--TTTAAT-TCA-AGTACA-ATCAAAT-TGTAC
1804048 AATTATACATTTTAATTCAAGTACAATCAAATTGTAC
1 AATTATACATTTTAATTCAAGTACAATCAAATTGTAC
1804085 AATTATA
1 AATTATA
1804092 GCTCGTTTGG
Statistics
Matches: 60, Mismatches: 7, Indels: 28
0.63 0.07 0.29
Matches are distributed among these distances:
34 6 0.10
35 12 0.20
36 1 0.02
37 23 0.38
38 1 0.02
39 11 0.18
40 6 0.10
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.41
Consensus pattern (37 bp):
AATTATACATTTTAATTCAAGTACAATCAAATTGTAC
Found at i:1811097 original size:784 final size:786
Alignment explanation
Indices: 1809036--1811195 Score: 3320
Period size: 791 Copynumber: 2.8 Consensus size: 786
1809026 ACTGGATTAG
1809036 CACTCATGGCCACAACGCTCATATTATCACTCTAAATCACAAGAGTATCACTTAGAGAAATACAC
1 CACTCATGGCCACAACGCTCATATTATCACTCTAAATCACAAGAGTATCACTTAGAGAAATACAC
* *
1809101 ATGTCAGCTAAAGTGCATGCAACCAAACAACTTCAAATG-C-C-------A---C---ATA-TCA
66 ATGTCAGCTAAAGTGCACGCAGCCAAACAACTTCAAATGCCACATATGTTACTCCTTAATATTCA
* *
1809150 ACCTCTGCTGTTGATTGAGAAATCGACTGTTACCGCTTTAAGCTCCAAGCTACCATGTTCTCAAA
131 ACCTCTGTTGTTGATTGAGAAATCGACTGTTACCGCTTT-A--T-CAAGCTACCAAGTTCTCAAA
* * *
1809215 AAAATAAACGCAATATCTTGAAGTTGACCTTTTGTTATCCACGTTGTTAGCCCAATCAACATCAA
192 AAAATAAACGCAATATCTTGAAATTGACCTTTTGTCATCCACGTTGTTGGCCCAATCAACATCAA
* * *
1809280 CAAATCCAGTTACCTTTCAAATATCATAAAATACATTTGACAGTTGCCCAATGAAGTTCACATGG
257 CAAAGCCAATTACCTTTCAAATATCATAAGATACATTTGACAGTTGCCCAATGAAGTTCACATGG
* *
1809345 TTTATGCACGTACTGTGTAACCCGATTAACACTAAAAGCTATGTCATGTCTTGTATGGCTTGATA
322 TTTATGCACGTACTGTGTAACCCGATTAACACTAAAAGCTATGCCAGGTCTTGTATGGCTTGATA
* * *
1809410 GGGAAGCGGTGGCGGGTTAATGAACGTTGCTCTTGTTGAAGAATCAAACCTAGAAAGCTCTAGAC
387 GGGAAGCGATGGAGGATTAATGAACGTTGCTCTTGTTGAAGAATCAAACCTAGAAAGCTCTAGAC
1809475 TCGATGAAGAACAAAGGGGGATGAATAGTATAAGGTGGCTCCCTTATGAAGGTGAACGGTAAAGA
452 TCGATGAAGAACAAAGGGGGATGAATAGTATAAGGTGGCTCCCTTATGAAGGTGAACGGTAAAGA
* * * **
1809540 TGATGATGGTGATGATCGATTCGTGGAAAATAAATGGATGGGTGTCCTATCGAACACTCCTAGTC
517 TGATGATGGTGATGATGGATTTGTGGAAAATAGATGGATAAGTGTCCTATCGAACACTCCTAGTC
* *
1809605 GCAATGAAAAGACAAACTCGATAATATGGCTCTAACCAACCCTCCTGGTCGCAATGAAAAGGCAA
582 GCAATGAAAAGGCAAACTCGATAATATGGCTCTAACCAACCCTCCTAGTCGCAATGAAAAGGCAA
* * * *
1809670 ATTGGAGTGTGAAGATTAATCTCCCACTACAGCAAATTGTTCTACACCAGCGTTTTTAGCGGCAT
647 ATTGGAGTCTGAAGATTAATCTCCCACTACAGCAAACTATTCTACAACAGCGTTTTTAGCGGCAT
* * *
1809735 TTTGAGAGTGAACGCCACTAACTTTAAACATATAGCGGCTTTTCCATTCAAAACGCCGCAAAATA
712 TTTGAGAGTAAACACCACTAACTTTAAACATATAGCGGCATTTCCATTCAAAACGCCGCAAAATA
1809800 GTAAATTTAT
777 GTAAATTTAT
*
1809810 CACTCATGGCCACAACGCTCATATTATCACTCTAAATCACAAGAGTATCACTTAGAGAAATGCAC
1 CACTCATGGCCACAACGCTCATATTATCACTCTAAATCACAAGAGTATCACTTAGAGAAATACAC
* *
1809875 ATGTCAGCTAAAGTGCACGCAGCCAAGCAACTTCAAATGCCACATATGTTACTCCTTAATATTTA
66 ATGTCAGCTAAAGTGCACGCAGCCAAACAACTTCAAATGCCACATATGTTACTCCTTAATATTCA
* * * *
1809940 ACCTCTGTTGATGATTTAGAAATCGAATGTTACCCCTTTAAGCTCCAAGCTACCAAGTTCTCAAA
131 ACCTCTGTTGTTGATTGAGAAATCGACTGTTACCGCTTT-A--T-CAAGCTACCAAGTTCTCAAA
* *
1810005 AAAATAAACGCAATATCTTGAAATTGACCTTTTTTTCATCCTCGTTGTTGGCCCAATCAACATCA
192 AAAATAAACGCAATATCTTGAAATTGACC-TTTTGTCATCCACGTTGTTGGCCCAATCAACATCA
1810070 ACAAAGCC-ATATACCTTTCAAATATCATAAGATACATTTGACAGTTGCCCAATGAAGTTCACAT
256 ACAAAGCCAAT-TACCTTTCAAATATCATAAGATACATTTGACAGTTGCCCAATGAAGTTCACAT
* *
1810134 AGTTTATGCACGTACTGTGTAACCCGATTAACACTCAAAGCTAT-CTCAGGTCTTGTATGGCTTG
320 GGTTTATGCACGTACTGTGTAACCCGATTAACACTAAAAGCTATGC-CAGGTCTTGTATGGCTTG
* *
1810198 ATAGGGAAACGATGGCA-GATTAATGAACGTTGCTCTTTTTGAAGAATCAAACCTAGAAAGCTCT
384 ATAGGGAAGCGATGG-AGGATTAATGAACGTTGCTCTTGTTGAAGAATCAAACCTAGAAAGCTCT
* * * * *
1810262 AAACTTGATTAATAACAAAGGGGGATGAATAGTATAATGTGGCTCCCTTATGAAGGTGAACGGTA
448 AGACTCGATGAAGAACAAAGGGGGATGAATAGTATAAGGTGGCTCCCTTATGAAGGTGAACGGTA
* * * * *
1810327 AAGATGATGATGGTGATAATGGATTTGTGGAAAATAGATAGATAAGTGTGCTATTGAACTCTCCT
513 AAGATGATGATGGTGATGATGGATTTGTGGAAAATAGATGGATAAGTGTCCTATCGAACACTCCT
*
1810392 AGTCGCAATGAAAAGGCAAACTCGATAATATGGCTCTAACCAACCCTCCTAGTCGCGATGAAAAG
578 AGTCGCAATGAAAAGGCAAACTCGATAATATGGCTCTAACCAACCCTCCTAGTCGCAATGAAAAG
* *
1810457 GCAAATTGGAGTCTGAAGATTAATCTCCCACTACAGCACAACTATTCTACAACGGTGTTTTTAGC
643 GCAAATTGGAGTCTGAAGATTAATCTCCCACTACAGCA-AACTATTCTACAACAGCGTTTTTAGC
** * * *
1810522 GGTGTTTTGAGAGTAAACACCACTAAGTTTAAACATATAGTGGCATTTCCATTCAAAACGCCGCG
707 GGCATTTTGAGAGTAAACACCACTAACTTTAAACATATAGCGGCATTTCCATTCAAAACGCCGCA
1810587 AAATAGTAAATTTAT
772 AAATAGTAAATTTAT
* * * * *
1810602 CACTCATGGACACAATGCTCATATTATCACTCTAAATAAAAAGGGTATCACTTAGAGAAATACAC
1 CACTCATGGCCACAACGCTCATATTATCACTCTAAATCACAAGAGTATCACTTAGAGAAATACAC
1810667 ATGTCAGCTAAAGTGCACGCAGCCAAACAACTTCAAATGCCACATATGTTACTCCTTAATATTCA
66 ATGTCAGCTAAAGTGCACGCAGCCAAACAACTTCAAATGCCACATATGTTACTCCTTAATATTCA
* *
1810732 ACCTTTGTTGTTGATTGAGAAATTGACTGTTACCGC-TT-T-AAGCTACCAAGTTCTCAAAAAAA
131 ACCTCTGTTGTTGATTGAGAAATCGACTGTTACCGCTTTATCAAGCTACCAAGTTCTCAAAAAAA
* * *
1810794 TAAAAGCAATATCTTGAATTTGACCTTTTGTCATCCACGTTGTTGGACCAATCAACATCAACAAA
196 TAAACGCAATATCTTGAAATTGACCTTTTGTCATCCACGTTGTTGGCCCAATCAACATCAACAAA
*
1810859 GCCAATTACCTTTCAAATATCATAAGATACGTTTGACAGTTGCCCAATGAAGTTCACATGGTTTA
261 GCCAATTACCTTTCAAATATCATAAGATACATTTGACAGTTGCCCAATGAAGTTCACATGGTTTA
*
1810924 TGCATGTACTGTGTAACCCGATTAACACTAAAAGCTATGCCAGGTCTTGTATGGCTTGATAGGGA
326 TGCACGTACTGTGTAACCCGATTAACACTAAAAGCTATGCCAGGTCTTGTATGGCTTGATAGGGA
* *
1810989 AGTGATGGAGGATTAATGAACATTGCTCTTGTTGAAGAATCAAACCTAGAAAGCTCTAGACTCGA
391 AGCGATGGAGGATTAATGAACGTTGCTCTTGTTGAAGAATCAAACCTAGAAAGCTCTAGACTCGA
* * * *
1811054 TGAAGAACAAATGAGGTTGAATAGTATAAGGTGGCTACCTTATGAAGGTGAACGGTAAAGATGAT
456 TGAAGAACAAAGGGGGATGAATAGTATAAGGTGGCTCCCTTATGAAGGTGAACGGTAAAGATGAT
* * *
1811119 GATGGTGATGATGGATTTGTGGAAAATAGATGGATAAGTGTCCTATCAAACCCTCCTAGTCGCGA
521 GATGGTGATGATGGATTTGTGGAAAATAGATGGATAAGTGTCCTATCGAACACTCCTAGTCGCAA
1811184 TGAAAAGGCAAA
586 TGAAAAGGCAAA
1811196 TTGGAGTGTG
Statistics
Matches: 1259, Mismatches: 103, Indels: 38
0.90 0.07 0.03
Matches are distributed among these distances:
774 100 0.08
775 1 0.00
776 1 0.00
783 2 0.00
784 343 0.27
785 49 0.04
786 1 0.00
787 1 0.00
789 3 0.00
790 90 0.07
791 423 0.34
792 245 0.19
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.28
Consensus pattern (786 bp):
CACTCATGGCCACAACGCTCATATTATCACTCTAAATCACAAGAGTATCACTTAGAGAAATACAC
ATGTCAGCTAAAGTGCACGCAGCCAAACAACTTCAAATGCCACATATGTTACTCCTTAATATTCA
ACCTCTGTTGTTGATTGAGAAATCGACTGTTACCGCTTTATCAAGCTACCAAGTTCTCAAAAAAA
TAAACGCAATATCTTGAAATTGACCTTTTGTCATCCACGTTGTTGGCCCAATCAACATCAACAAA
GCCAATTACCTTTCAAATATCATAAGATACATTTGACAGTTGCCCAATGAAGTTCACATGGTTTA
TGCACGTACTGTGTAACCCGATTAACACTAAAAGCTATGCCAGGTCTTGTATGGCTTGATAGGGA
AGCGATGGAGGATTAATGAACGTTGCTCTTGTTGAAGAATCAAACCTAGAAAGCTCTAGACTCGA
TGAAGAACAAAGGGGGATGAATAGTATAAGGTGGCTCCCTTATGAAGGTGAACGGTAAAGATGAT
GATGGTGATGATGGATTTGTGGAAAATAGATGGATAAGTGTCCTATCGAACACTCCTAGTCGCAA
TGAAAAGGCAAACTCGATAATATGGCTCTAACCAACCCTCCTAGTCGCAATGAAAAGGCAAATTG
GAGTCTGAAGATTAATCTCCCACTACAGCAAACTATTCTACAACAGCGTTTTTAGCGGCATTTTG
AGAGTAAACACCACTAACTTTAAACATATAGCGGCATTTCCATTCAAAACGCCGCAAAATAGTAA
ATTTAT
Found at i:1811509 original size:83 final size:81
Alignment explanation
Indices: 1811306--1811511 Score: 243
Period size: 81 Copynumber: 2.5 Consensus size: 81
1811296 TGGCGTTTCA
* * * *
1811306 AAATGCTACAA-AATAGTAAATTTAGCGGCATTTTTATAAAAATGTCATAATAGGGTTCATATAT
1 AAATGCCACAACAATAGT-ACTTTAGCGGCATTTTTATACAAATGTCACAATAGGGTTCATATAT
* ** *
1811370 AGTGGTGTTTTTTCAAC
65 AGTGGCGTCGTTACAAC
* ** **
1811387 AAATGTCGTAACAATAGTACTTTAGCGGCATTTTTATACAAATGTTGCAATAGGGTTCATATATA
1 AAATGCCACAACAATAGTACTTTAGCGGCATTTTTATACAAATGTCACAATAGGGTTCATATATA
1811452 GTGGCGTCGTTACAAC
66 GTGGCGTCGTTACAAC
* *
1811468 AAATGCCACAATAGTTAAGTACTTTAGCGGCATTTTTATACAAA
1 AAATGCCACAACA-AT-AGTACTTTAGCGGCATTTTTATACAAA
1811512 CTCCACAACA
Statistics
Matches: 104, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
81 70 0.67
82 7 0.07
83 27 0.26
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.34
Consensus pattern (81 bp):
AAATGCCACAACAATAGTACTTTAGCGGCATTTTTATACAAATGTCACAATAGGGTTCATATATA
GTGGCGTCGTTACAAC
Found at i:1812057 original size:43 final size:41
Alignment explanation
Indices: 1811957--1812059 Score: 134
Period size: 41 Copynumber: 2.5 Consensus size: 41
1811947 TTTTGTTGAT
* *
1811957 ACGCCGCAATAGTCATGTACTTTAGTGGTATTTTTTAATAA
1 ACGCCGCAATAGTGATGTAATTTAGTGGTATTTTTTAATAA
* * *
1811998 ACACCGCAATAATGATGTAATTTAGTGGTCTTTTTTGTAATAA
1 ACGCCGCAATAGTGATGTAATTTAGTGGT-ATTTTT-TAATAA
*
1812041 ATGCCGCAATAGTGATGTA
1 ACGCCGCAATAGTGATGTA
1812060 CCTTAGCGGC
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
41 25 0.48
42 5 0.10
43 22 0.42
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.37
Consensus pattern (41 bp):
ACGCCGCAATAGTGATGTAATTTAGTGGTATTTTTTAATAA
Found at i:1812075 original size:43 final size:42
Alignment explanation
Indices: 1811940--1812083 Score: 143
Period size: 43 Copynumber: 3.5 Consensus size: 42
1811930 TCCGAAATTT
* *
1811940 GTGGCATTTTTGTTGAT--ACGCCGCAATAGTCATGTACTTTA
1 GTGGCATTTTT-TTAATAAACGCCGCAATAGTGATGTACTTTA
* * * *
1811981 GTGGTA-TTTTTTAATAAACACCGCAATAATGATGTAATTTA
1 GTGGCATTTTTTTAATAAACGCCGCAATAGTGATGTACTTTA
* *
1812022 GTGGTC-TTTTTTGTAATAAATGCCGCAATAGTGATGTACCTTA
1 GTGG-CATTTTTT-TAATAAACGCCGCAATAGTGATGTACTTTA
* *
1812065 GCGGCATTTTTTTGATAAA
1 GTGGCATTTTTTTAATAAA
1812084 ATGCTACAAA
Statistics
Matches: 83, Mismatches: 14, Indels: 11
0.77 0.13 0.10
Matches are distributed among these distances:
39 4 0.05
40 4 0.05
41 29 0.35
42 12 0.14
43 34 0.41
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.40
Consensus pattern (42 bp):
GTGGCATTTTTTTAATAAACGCCGCAATAGTGATGTACTTTA
Found at i:1812194 original size:41 final size:40
Alignment explanation
Indices: 1812143--1812241 Score: 144
Period size: 41 Copynumber: 2.4 Consensus size: 40
1812133 AAAGACTTAG
* * *
1812143 AATTTCGTGGCGTTTTTATTGAAACGCCACAATAATCATGT
1 AATTTAGTGGCATTTTTAAT-AAACGCCACAATAATCATGT
*
1812184 ACTTTAGTGGCATTTTTTAATAAACGCCACAATAATCATGT
1 AATTTAGTGGCA-TTTTTAATAAACGCCACAATAATCATGT
1812225 AATTTAGTGGCATTTTT
1 AATTTAGTGGCATTTTT
1812242 TTGTAATAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
40 5 0.10
41 40 0.77
42 7 0.13
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.39
Consensus pattern (40 bp):
AATTTAGTGGCATTTTTAATAAACGCCACAATAATCATGT
Found at i:1812242 original size:41 final size:42
Alignment explanation
Indices: 1812155--1812242 Score: 151
Period size: 41 Copynumber: 2.1 Consensus size: 42
1812145 TTTCGTGGCG
* *
1812155 TTTTTATTGAAACGCCACAATAATCATGTACTTTAGTGGCAT
1 TTTTTAATGAAACGCCACAATAATCATGTAATTTAGTGGCAT
1812197 TTTTTAAT-AAACGCCACAATAATCATGTAATTTAGTGGCAT
1 TTTTTAATGAAACGCCACAATAATCATGTAATTTAGTGGCAT
1812238 TTTTT
1 TTTTT
1812243 TGTAATAAAC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
41 37 0.84
42 7 0.16
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (42 bp):
TTTTTAATGAAACGCCACAATAATCATGTAATTTAGTGGCAT
Found at i:1820916 original size:17 final size:16
Alignment explanation
Indices: 1820885--1820918 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1820875 CACATGACAA
1820885 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
1820901 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
1820918 T
1 T
1820919 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:1831153 original size:17 final size:16
Alignment explanation
Indices: 1831122--1831155 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1831112 CACATGAGGA
1831122 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
1831138 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
1831155 T
1 T
1831156 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:1832221 original size:43 final size:47
Alignment explanation
Indices: 1832173--1832279 Score: 125
Period size: 50 Copynumber: 2.3 Consensus size: 47
1832163 ATAACTAATG
*
1832173 AATAAAATAATAACAAACT-AAA-CATGTTTTAACT-A-TAATTCCT
1 AATAAAATAATAACAAACTAAAATAATGTTTTAACTAACTAATTCCT
*
1832216 AATAAAATAATAA-TAACTAAAAATAATGTTTTAACTCAACCTTAATTCCT
1 AATAAAATAATAACAAACT-AAAATAATGTTTTAACT-AA-C-TAATTCCT
1832266 AATAAAATAATAAC
1 AATAAAATAATAAC
1832280 TCTAATCCTA
Statistics
Matches: 53, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
42 4 0.08
43 13 0.25
44 3 0.06
45 11 0.21
47 1 0.02
50 21 0.40
ACGTcount: A:0.53, C:0.13, G:0.02, T:0.32
Consensus pattern (47 bp):
AATAAAATAATAACAAACTAAAATAATGTTTTAACTAACTAATTCCT
Found at i:1832555 original size:50 final size:50
Alignment explanation
Indices: 1832480--1832605 Score: 234
Period size: 50 Copynumber: 2.5 Consensus size: 50
1832470 GGAAAGATAA
*
1832480 GAGTGGATCATTTGGAAGAGTTATTACCTCTTCCTTTCCAAGGCTTGGAT
1 GAGTGGATCATTTGGAAGAGTTATTACCTCTTCCTTTCCAAGGCTTGGAC
*
1832530 GAGTGGATCATTTGGAAGAGTTATTACTTCTTCCTTTCCAAGGCTTGGAC
1 GAGTGGATCATTTGGAAGAGTTATTACCTCTTCCTTTCCAAGGCTTGGAC
1832580 GAGTGGATCATTTGGAAGAGTTATTA
1 GAGTGGATCATTTGGAAGAGTTATTA
1832606 ATCGATTGTA
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
50 74 1.00
ACGTcount: A:0.24, C:0.15, G:0.25, T:0.36
Consensus pattern (50 bp):
GAGTGGATCATTTGGAAGAGTTATTACCTCTTCCTTTCCAAGGCTTGGAC
Found at i:1836085 original size:59 final size:59
Alignment explanation
Indices: 1835993--1836113 Score: 188
Period size: 59 Copynumber: 2.1 Consensus size: 59
1835983 AATAGATAGA
** * *
1835993 TAAGTGTCCTGTCGAACCCTCCTAGTCACAATGAAAAGGCAAACTCGATAATATGGCTC
1 TAAGTGTCCAATCGAACCCTCCTAGTCACAATGAAAAGGAAAACTCGATAATATGACTC
**
1836052 TAAGTGTCCAATCGAACCCTCCTAGTTGCAATGAAAAGGAAAACTCGATAATATGACTC
1 TAAGTGTCCAATCGAACCCTCCTAGTCACAATGAAAAGGAAAACTCGATAATATGACTC
1836111 TAA
1 TAA
1836114 CCAACCCTCC
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
59 56 1.00
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (59 bp):
TAAGTGTCCAATCGAACCCTCCTAGTCACAATGAAAAGGAAAACTCGATAATATGACTC
Found at i:1841180 original size:15 final size:15
Alignment explanation
Indices: 1841162--1841191 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1841152 TAGAAAATAC
1841162 CATTGAAGAAGAGGA
1 CATTGAAGAAGAGGA
1841177 CATTGAAGAAGAGGA
1 CATTGAAGAAGAGGA
1841192 AGGGATGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.07, G:0.33, T:0.13
Consensus pattern (15 bp):
CATTGAAGAAGAGGA
Found at i:1843785 original size:109 final size:110
Alignment explanation
Indices: 1843575--1843787 Score: 383
Period size: 109 Copynumber: 1.9 Consensus size: 110
1843565 AAGACCCAAA
* *
1843575 GGACAATGGTGCAATGACAGAAACAAACTAAAGGAGGAAGCATTTAATTTTTTCAAAGAAATTTG
1 GGACAATGGTGCAATGACACAAACAAACTAAAGGAGGAAGCAGTTAATTTTTTCAAAGAAATTTG
1843640 CTCTTTTGATGTAACCTATTTGGGAGCATACCCAACTCCTAATCT
66 CTCTTTTGATGTAACCTATTTGGGAGCATACCCAACTCCTAATCT
*
1843685 GGACAATGGTGCAATGACACAAACAAACTAAAGGAGGAAGTAGTTAA-TTTTTCAAAGAAATTTG
1 GGACAATGGTGCAATGACACAAACAAACTAAAGGAGGAAGCAGTTAATTTTTTCAAAGAAATTTG
*
1843749 CTCTTTTGATGTAACCTATTTTGGAGCATACCCAACTCC
66 CTCTTTTGATGTAACCTATTTGGGAGCATACCCAACTCC
1843788 CAATTTGTTT
Statistics
Matches: 99, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
109 55 0.56
110 44 0.44
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (110 bp):
GGACAATGGTGCAATGACACAAACAAACTAAAGGAGGAAGCAGTTAATTTTTTCAAAGAAATTTG
CTCTTTTGATGTAACCTATTTGGGAGCATACCCAACTCCTAATCT
Found at i:1846611 original size:40 final size:40
Alignment explanation
Indices: 1846537--1846616 Score: 97
Period size: 40 Copynumber: 2.0 Consensus size: 40
1846527 ACGGTGTATA
* * * *
1846537 AGGTGGGCACGGCCCGACCTCAGCACTACGGTGCATTATT
1 AGGTGAGCAAGGCCCGACCTCAGCACAACGGTGCAATATT
* **
1846577 AGGTGAGCAAGGCTCGACCTCAGCACAATTGTGCAATATT
1 AGGTGAGCAAGGCCCGACCTCAGCACAACGGTGCAATATT
1846617 TGACTCCTAT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.25, C:0.26, G:0.28, T:0.21
Consensus pattern (40 bp):
AGGTGAGCAAGGCCCGACCTCAGCACAACGGTGCAATATT
Found at i:1846870 original size:20 final size:20
Alignment explanation
Indices: 1846845--1846889 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 20
1846835 TATGTGTTGC
1846845 ATTGCTTT-AATATTCGTATG
1 ATTGCTTTAAATATT-GTATG
1846865 ATTGCTTTAAATATTGTATG
1 ATTGCTTTAAATATTGTATG
1846885 ATTGC
1 ATTGC
1846890 CTCACTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 18 0.75
21 6 0.25
ACGTcount: A:0.27, C:0.09, G:0.16, T:0.49
Consensus pattern (20 bp):
ATTGCTTTAAATATTGTATG
Found at i:1848225 original size:15 final size:15
Alignment explanation
Indices: 1848192--1848244 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
1848182 CTATGAGTAC
*
1848192 ATGTTATATGTGAGA-
1 ATGTTCTATGTGA-AT
1848207 ATGTTCTATGTGAAT
1 ATGTTCTATGTGAAT
* *
1848222 ATGTGCTAAGTGAAT
1 ATGTTCTATGTGAAT
1848237 ATG-TCTAT
1 ATGTTCTAT
1848245 TAGAATAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
14 4 0.12
15 28 0.88
ACGTcount: A:0.30, C:0.06, G:0.23, T:0.42
Consensus pattern (15 bp):
ATGTTCTATGTGAAT
Found at i:1848500 original size:24 final size:24
Alignment explanation
Indices: 1848466--1848512 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1848456 AATATATGGG
* *
1848466 ACTTCGGTGCATATTCTACGTGGC
1 ACTTCGATGCAAATTCTACGTGGC
*
1848490 ACTTCGATGCAAATTCTATGTGG
1 ACTTCGATGCAAATTCTACGTGG
1848513 TAGTGGTGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.34
Consensus pattern (24 bp):
ACTTCGATGCAAATTCTACGTGGC
Found at i:1850108 original size:37 final size:37
Alignment explanation
Indices: 1850065--1850135 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
1850055 AGCATAATGT
1850065 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATACGA
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATACGA
*
1850102 TAGAGTTTTACTATGATTCAAACTCCTAAAAATA
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATA
1850136 GGATCCAAGC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.32
Consensus pattern (37 bp):
TAGAGTTTTACTAGGATTCAAACTCCTAAAAATACGA
Found at i:1850824 original size:3 final size:3
Alignment explanation
Indices: 1850811--1850860 Score: 50
Period size: 3 Copynumber: 17.3 Consensus size: 3
1850801 CTTTACTTAC
* * * *
1850811 TAT TTT TAT TAT TAG TAT TAC TAT TAT TAT TAT TAT T-C TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1850857 TAT T
1 TAT T
1850861 TCTATTTACC
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
2 3 0.08
3 34 0.92
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1850973 original size:19 final size:20
Alignment explanation
Indices: 1850949--1851035 Score: 63
Period size: 21 Copynumber: 4.2 Consensus size: 20
1850939 TACATTTGTT
1850949 TTATTTA-TTTTATTTCTTC
1 TTATTTATTTTTATTTCTTC
* *
1850968 TTATTTTATTTTTATTTGTTTA
1 TTA-TTTATTTTTATTT-CTTC
*
1850990 TTATGTATTTATTATTATCATTC
1 TTATTTATTT-TTATT-TC-TTC
*
1851013 TTTTTTCA-TTTTATTT-TTC
1 TTATTT-ATTTTTATTTCTTC
1851032 TTAT
1 TTAT
1851036 CGTATTCATT
Statistics
Matches: 53, Mismatches: 8, Indels: 14
0.71 0.11 0.19
Matches are distributed among these distances:
19 9 0.17
20 4 0.08
21 15 0.28
22 15 0.28
23 9 0.17
24 1 0.02
ACGTcount: A:0.18, C:0.07, G:0.02, T:0.72
Consensus pattern (20 bp):
TTATTTATTTTTATTTCTTC
Found at i:1855378 original size:15 final size:15
Alignment explanation
Indices: 1855354--1855387 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1855344 GAGATATGAG
*
1855354 TGTTATATGTGAAAA
1 TGTTAAATGTGAAAA
*
1855369 TGTTAAATGTGAATA
1 TGTTAAATGTGAAAA
1855384 TGTT
1 TGTT
1855388 CTATGGAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.21, T:0.44
Consensus pattern (15 bp):
TGTTAAATGTGAAAA
Found at i:1855588 original size:24 final size:24
Alignment explanation
Indices: 1855556--1855704 Score: 107
Period size: 24 Copynumber: 6.3 Consensus size: 24
1855546 TCGAGGGTTT
* *
1855556 TACGCGGTCCTTCAGGACAAATTC
1 TACGTGGTCCTTCGGGACAAATTC
1855580 TACGTGGTCCTT-GGGACAAATTC
1 TACGTGGTCCTTCGGGACAAATTC
*
1855603 TACGCT-GTCCTACGGGACAAA-TC
1 TACG-TGGTCCTTCGGGACAAATTC
* * *
1855626 TATGAGG-CACTTCGGTG-CATATTC
1 TACGTGGTC-CTTCGG-GACAAATTC
* *
1855650 TACGTGG-CACTTCGGTACATATTC
1 TACGTGGTC-CTTCGGGACAAATTC
*
1855674 TATGTGG-CACTTCGGTG-CAAATTC
1 TACGTGGTC-CTTCGG-GACAAATTC
1855698 TACGTGG
1 TACGTGG
1855705 CAGTGGTGAC
Statistics
Matches: 103, Mismatches: 14, Indels: 16
0.77 0.11 0.12
Matches are distributed among these distances:
22 1 0.01
23 33 0.32
24 69 0.67
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.30
Consensus pattern (24 bp):
TACGTGGTCCTTCGGGACAAATTC
Found at i:1855627 original size:23 final size:23
Alignment explanation
Indices: 1855556--1855624 Score: 77
Period size: 23 Copynumber: 2.9 Consensus size: 23
1855546 TCGAGGGTTT
* *
1855556 TACGCGGTCCTTCAGGACAAATTC
1 TACGCTGTCC-TCGGGACAAATTC
*
1855580 TACG-TGGTCCTTGGGACAAATTC
1 TACGCT-GTCCTCGGGACAAATTC
1855603 TACGCTGTCCTACGGGACAAAT
1 TACGCTGTCCT-CGGGACAAAT
1855625 CTATGAGGCA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
23 20 0.53
24 18 0.47
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (23 bp):
TACGCTGTCCTCGGGACAAATTC
Found at i:1855705 original size:24 final size:24
Alignment explanation
Indices: 1855573--1855706 Score: 118
Period size: 24 Copynumber: 5.7 Consensus size: 24
1855563 TCCTTCAGGA
1855573 CAAATTCTACGTGGTC-CTT-GG-G
1 CAAATTCTACGTGG-CACTTCGGTG
* *
1855595 ACAAATTCTACGCTGTC-CTACGG-G
1 -CAAATTCTACG-TGGCACTTCGGTG
* *
1855619 ACAAA-TCTATGAGGCACTTCGGTG
1 -CAAATTCTACGTGGCACTTCGGTG
* *
1855643 CATATTCTACGTGGCACTTCGGTA
1 CAAATTCTACGTGGCACTTCGGTG
* *
1855667 CATATTCTATGTGGCACTTCGGTG
1 CAAATTCTACGTGGCACTTCGGTG
1855691 CAAATTCTACGTGGCA
1 CAAATTCTACGTGGCA
1855707 GTGGTGACTG
Statistics
Matches: 92, Mismatches: 14, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
22 2 0.02
23 27 0.29
24 63 0.68
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.30
Consensus pattern (24 bp):
CAAATTCTACGTGGCACTTCGGTG
Found at i:1857182 original size:19 final size:19
Alignment explanation
Indices: 1857154--1857192 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1857144 GTGAGTGAGC
1857154 TGTTGAAGTCTATTATGAA
1 TGTTGAAGTCTATTATGAA
* *
1857173 TGTTGGAGTCTGTTATGAA
1 TGTTGAAGTCTATTATGAA
1857192 T
1 T
1857193 CTGTTATAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.05, G:0.26, T:0.44
Consensus pattern (19 bp):
TGTTGAAGTCTATTATGAA
Found at i:1866426 original size:53 final size:53
Alignment explanation
Indices: 1866300--1866427 Score: 222
Period size: 53 Copynumber: 2.4 Consensus size: 53
1866290 GCTAGGATTC
1866300 TTCTTAGGAAATGGGTTTTTATTTCAAGGAAGCAGAATCAGTGGAGAATGGCG
1 TTCTTAGGAAATGGGTTTTTATTTCAAGGAAGCAGAATCAGTGGAGAATGGCG
* *
1866353 TTCTTAGGAAATGAGG-TTTTATTTCAAGGAAGTAGAATCAGTGGTGAATGGCG
1 TTCTTAGGAAATG-GGTTTTTATTTCAAGGAAGCAGAATCAGTGGAGAATGGCG
1866406 TTCTTAGGAAATGGGTTTTTAT
1 TTCTTAGGAAATGGGTTTTTAT
1866428 GAAGCAAGAG
Statistics
Matches: 71, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
52 2 0.03
53 67 0.94
54 2 0.03
ACGTcount: A:0.29, C:0.08, G:0.29, T:0.34
Consensus pattern (53 bp):
TTCTTAGGAAATGGGTTTTTATTTCAAGGAAGCAGAATCAGTGGAGAATGGCG
Found at i:1866979 original size:82 final size:79
Alignment explanation
Indices: 1866875--1867070 Score: 232
Period size: 82 Copynumber: 2.4 Consensus size: 79
1866865 ATCGCGGTGG
* * * *
1866875 TTTTACATAAACACCACTAAAGTATGCATTTGTAG-ATGCGTTTTCACAAAAACGCCACTATATA
1 TTTTACATAAACGCCACTAAAGTACGCGTTTGTAGTA-GCATTTTCACAAAAACGCCACTATAT-
1866939 TCTAGCTATCACGACATT
64 T-TAGCTATCACGACA-T
* * * *
1866957 TTTTACATAAACGCCACTAAAGTACGTGTTTTTAGTAGCATTTTCATAAAAATGCCACTATATTT
1 TTTTACATAAACGCCACTAAAGTACGCGTTTGTAGTAGCATTTTCACAAAAACGCCACTATATTT
* ** *
1867022 GGCTATCGTGGCAT
66 AGCTATCACGACAT
*
1867036 TTTTACATAAACGCCGCTAAAGTACGCGTTTGTAG
1 TTTTACATAAACGCCACTAAAGTACGCGTTTGTAG
1867071 CGACATTTTC
Statistics
Matches: 98, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
79 33 0.34
80 10 0.10
81 1 0.01
82 53 0.54
83 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (79 bp):
TTTTACATAAACGCCACTAAAGTACGCGTTTGTAGTAGCATTTTCACAAAAACGCCACTATATTT
AGCTATCACGACAT
Found at i:1869453 original size:18 final size:17
Alignment explanation
Indices: 1869430--1869465 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
1869420 GTACTTATAT
*
1869430 TTCTATCTTTATCTGAAA
1 TTCTATCTTCATCT-AAA
1869448 TTCTATCTTCATCTAAA
1 TTCTATCTTCATCTAAA
1869465 T
1 T
1869466 CAAAAAGTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.28, C:0.19, G:0.03, T:0.50
Consensus pattern (17 bp):
TTCTATCTTCATCTAAA
Found at i:1873651 original size:45 final size:45
Alignment explanation
Indices: 1873600--1874047 Score: 481
Period size: 45 Copynumber: 9.9 Consensus size: 45
1873590 CATGAGTGGC
* * *
1873600 ACCTTTTATACCAATAATGCACTGTTATGCATTTTCATTTATGGA
1 ACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATTTATGGA
* * * * *
1873645 ACCTTTTATGCTGATAATGTACCCTTATGCATTTTTATTTATGGC
1 ACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATTTATGGA
* ** *
1873690 ACCTTTTATGTCGATAATGCACCGTTATTTATTTTCATTTATGGC
1 ACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATTTATGGA
** * *
1873735 ACCTTTTATGCTAATAATGCACTGTTATGCATTTTCATTTAT-AA
1 ACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATTTATGGA
** * *
1873779 CACCTTTTATGCTAATAATGCACCGTTATACATTTTCATTTATGGC
1 -ACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATTTATGGA
1873825 ACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATTTAT-GA
1 ACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATTTATGGA
* * * *
1873869 CACCTTTAATGCCGATAATGCACTGTTATGAATTTTCATTTA-AGA
1 -ACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATTTATGGA
* * * * * *
1873914 CACTTTTTTATTCCAATAATGCATCGTTATTCATTTTCATTTATGGC
1 -AC-CTTTTATGCCGATAATGCACCGTTATGCATTTTCATTTATGGA
* ** *
1873961 ACATTTTATGTTGATAATGCACCGTTATGCATTTTTATTTAT-GA
1 ACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATTTATGGA
* * * *
1874005 TATCTTTTATGTCGATAATGCACCATTATGCATTTTCTTTTAT
1 -ACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATTTAT
1874048 TTTGATAACA
Statistics
Matches: 337, Mismatches: 59, Indels: 14
0.82 0.14 0.03
Matches are distributed among these distances:
44 2 0.01
45 301 0.89
46 33 0.10
47 1 0.00
ACGTcount: A:0.26, C:0.18, G:0.12, T:0.45
Consensus pattern (45 bp):
ACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATTTATGGA
Found at i:1873840 original size:135 final size:135
Alignment explanation
Indices: 1873599--1874047 Score: 587
Period size: 135 Copynumber: 3.3 Consensus size: 135
1873589 CCATGAGTGG
* * *
1873599 CACCTTTTATACCAATAATGCACTGTTATGCATTTTCATTTATGGA-ACCTTTTATGCTGATAAT
1 CACCTTTTATGCCAATAATGCACTGTTATGCATTTTCATTTAT-AACACCTTTTATGCTAATAAT
* * * * **
1873663 GTACCCTTATGCATTTTTATTTATGGCACCTTTTATGTCGATAATGCACCGTTATTTATTTTCAT
65 GCACCGTTATACATTTTCATTTATGGCACCTTTTATGTCGATAATGCACCGTTATGCATTTTCAT
*
1873728 TTATGG
130 TTATGA
*
1873734 CACCTTTTATGCTAATAATGCACTGTTATGCATTTTCATTTATAACACCTTTTATGCTAATAATG
1 CACCTTTTATGCCAATAATGCACTGTTATGCATTTTCATTTATAACACCTTTTATGCTAATAATG
*
1873799 CACCGTTATACATTTTCATTTATGGCACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATT
66 CACCGTTATACATTTTCATTTATGGCACCTTTTATGTCGATAATGCACCGTTATGCATTTTCATT
1873864 TATGA
131 TATGA
* * * * * *
1873869 CACCTTTAATGCCGATAATGCACTGTTATGAATTTTCATTTA-AGACACTTTTTTATTCCAATAA
1 CACCTTTTATGCCAATAATGCACTGTTATGCATTTTCATTTATA-ACAC-CTTTTATGCTAATAA
* * * * *
1873933 TGCATCGTTATTCATTTTCATTTATGGCACATTTTATGTTGATAATGCACCGTTATGCATTTTTA
64 TGCACCGTTATACATTTTCATTTATGGCACCTTTTATGTCGATAATGCACCGTTATGCATTTTCA
1873998 TTTATGA
129 TTTATGA
* * * * ** *
1874005 TATCTTTTATGTCGATAATGCACCATTATGCATTTTCTTTTAT
1 CACCTTTTATGCCAATAATGCACTGTTATGCATTTTCATTTAT
1874048 TTTGATAACA
Statistics
Matches: 277, Mismatches: 33, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
134 2 0.01
135 163 0.59
136 112 0.40
ACGTcount: A:0.26, C:0.18, G:0.12, T:0.45
Consensus pattern (135 bp):
CACCTTTTATGCCAATAATGCACTGTTATGCATTTTCATTTATAACACCTTTTATGCTAATAATG
CACCGTTATACATTTTCATTTATGGCACCTTTTATGTCGATAATGCACCGTTATGCATTTTCATT
TATGA
Found at i:1877005 original size:28 final size:27
Alignment explanation
Indices: 1876965--1877025 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
1876955 TATTTAAATT
* * *
1876965 AATTATAA-TTTTTTT-TGAATTATAA
1 AATTTTAATTTTTTTTATAAATTAGAA
1876990 AATATTTAATTTTTTTTATAAATTAGAA
1 AAT-TTTAATTTTTTTTATAAATTAGAA
1877018 AATTTTAA
1 AATTTTAA
1877026 AAATATTCTG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 3 0.10
26 4 0.13
27 12 0.40
28 11 0.37
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (27 bp):
AATTTTAATTTTTTTTATAAATTAGAA
Found at i:1881641 original size:45 final size:45
Alignment explanation
Indices: 1881588--1881902 Score: 420
Period size: 45 Copynumber: 7.0 Consensus size: 45
1881578 TACCAAGAGG
*
1881588 GGCACCTTTTATGCCAATAATGCACCTTTATGCATTTTCA-TTAGT
1 GGCACCTTTTATGCCGATAATGCACCTTTATGCATTTTCATTTA-T
* * * *
1881633 GACACCTTTTATGTCGATAAGGTACCGTTT-TGCATTTTCATTTAT
1 GGCACCTTTTATGCCGATAATGCACC-TTTATGCATTTTCATTTAT
1881678 GGCACCTTTTATGCCGATAATGCA-CTATTATGCATTTTCATTTAT
1 GGCACCTTTTATGCCGATAATGCACCT-TTATGCATTTTCATTTAT
* * *
1881723 GACACCTTTAATGCCGATAATGCACTTTTATGCATTTTCATTTAT
1 GGCACCTTTTATGCCGATAATGCACCTTTATGCATTTTCATTTAT
* *
1881768 GGCACTTTTTATGCCGATAATGCACCGTTATGCATTTTCATTTAT
1 GGCACCTTTTATGCCGATAATGCACCTTTATGCATTTTCATTTAT
* *
1881813 GGCACCTTTTATGTCGATAATGCACCGTTATGCATTTTCATTTAT
1 GGCACCTTTTATGCCGATAATGCACCTTTATGCATTTTCATTTAT
* ** ** *
1881858 GGTATATTTTATATCGATAATGCACCGTTATGCATTTTCATTTAT
1 GGCACCTTTTATGCCGATAATGCACCTTTATGCATTTTCATTTAT
1881903 TTTGGTAATA
Statistics
Matches: 242, Mismatches: 23, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
43 1 0.00
44 3 0.01
45 231 0.95
46 7 0.03
ACGTcount: A:0.24, C:0.19, G:0.14, T:0.43
Consensus pattern (45 bp):
GGCACCTTTTATGCCGATAATGCACCTTTATGCATTTTCATTTAT
Found at i:1881825 original size:26 final size:26
Alignment explanation
Indices: 1881747--1881825 Score: 66
Period size: 26 Copynumber: 3.3 Consensus size: 26
1881737 CGATAATGCA
1881747 CTTTTATGCATTTTCATTTATGGCAC
1 CTTTTATGCATTTTCATTTATGGCAC
* *
1881773 TTTTTATGC-----CGA-TAAT-GCAC
1 CTTTTATGCATTTTC-ATTTATGGCAC
*
1881793 C-GTTATGCATTTTCATTTATGGCAC
1 CTTTTATGCATTTTCATTTATGGCAC
1881818 CTTTTATG
1 CTTTTATG
1881826 TCGATAATGC
Statistics
Matches: 38, Mismatches: 6, Indels: 18
0.61 0.10 0.29
Matches are distributed among these distances:
19 6 0.16
20 4 0.11
21 4 0.11
22 1 0.03
23 1 0.03
24 4 0.11
25 5 0.13
26 13 0.34
ACGTcount: A:0.20, C:0.19, G:0.14, T:0.47
Consensus pattern (26 bp):
CTTTTATGCATTTTCATTTATGGCAC
Found at i:1885867 original size:16 final size:17
Alignment explanation
Indices: 1885846--1885887 Score: 68
Period size: 16 Copynumber: 2.5 Consensus size: 17
1885836 TCCAAGCGAT
*
1885846 TCCAACTCAATT-TTAC
1 TCCAACTCAATTCCTAC
1885862 TCCAACTCAATTCCTAC
1 TCCAACTCAATTCCTAC
1885879 TCCAACTCA
1 TCCAACTCA
1885888 TCATCGACGT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 12 0.50
17 12 0.50
ACGTcount: A:0.31, C:0.38, G:0.00, T:0.31
Consensus pattern (17 bp):
TCCAACTCAATTCCTAC
Found at i:1889990 original size:25 final size:24
Alignment explanation
Indices: 1889946--1889995 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 24
1889936 AGTTTTGTTT
*
1889946 ATCTTAATTTATTTTGTTTATTTA
1 ATCTTAATTTATTTTATTTATTTA
*
1889970 ATCTTTATTTCATTTTATTTATTTA
1 ATCTTAATTT-ATTTTATTTATTTA
1889995 A
1 A
1889996 ACAATTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 9 0.39
25 14 0.61
ACGTcount: A:0.26, C:0.06, G:0.02, T:0.66
Consensus pattern (24 bp):
ATCTTAATTTATTTTATTTATTTA
Found at i:1890501 original size:41 final size:42
Alignment explanation
Indices: 1890444--1890580 Score: 151
Period size: 41 Copynumber: 3.4 Consensus size: 42
1890434 AAAACGTCCC
* *
1890444 CTATGCACAAAGCAAAAAGGGGCATGCTATAAGGT-TTTCCT
1 CTATGCACAAAGCAAAAAGGGGCATGCGATAAGGTCTTACCT
*
1890485 CTATGTACAAAGCAAAAAGGGGCATGCGATAAGGTCTTACCT
1 CTATGCACAAAGCAAAAAGGGGCATGCGATAAGGTCTTACCT
* * * * * *
1890527 -TGTGCACAAAGC--AAAGGAGCATGTGGTAAGGACTTAAC-
1 CTATGCACAAAGCAAAAAGGGGCATGCGATAAGGTCTTACCT
1890565 CTATGCACAAAG-AAAA
1 CTATGCACAAAGCAAAA
1890581 GGAGCCTACA
Statistics
Matches: 81, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
39 31 0.38
40 2 0.02
41 43 0.53
42 5 0.06
ACGTcount: A:0.38, C:0.18, G:0.23, T:0.20
Consensus pattern (42 bp):
CTATGCACAAAGCAAAAAGGGGCATGCGATAAGGTCTTACCT
Found at i:1891656 original size:27 final size:26
Alignment explanation
Indices: 1891626--1891690 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 26
1891616 TGTTAGAAGA
*
1891626 TCAAGGGTATTTCGAC-CATTTTACATT
1 TCAAGGGTATTT--ACTCATTTTACAAT
**
1891653 TCAAAAGTATTTACTCATTTTACAAT
1 TCAAGGGTATTTACTCATTTTACAAT
*
1891679 TCAAGGTTATTT
1 TCAAGGGTATTT
1891691 TGGAAATTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
25 2 0.06
26 19 0.61
27 10 0.32
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.43
Consensus pattern (26 bp):
TCAAGGGTATTTACTCATTTTACAAT
Found at i:1895703 original size:21 final size:21
Alignment explanation
Indices: 1895679--1895745 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 21
1895669 CCACCACCGT
1895679 AGGGATACATACCAAGCCCAC
1 AGGGATACATACCAAGCCCAC
* * *
1895700 AGGGGTACATACCGAGCCCGC
1 AGGGATACATACCAAGCCCAC
* * * *
1895721 AGGGTTATATTCCAAGCCTAC
1 AGGGATACATACCAAGCCCAC
1895742 AGGG
1 AGGG
1895746 TTTTATGACA
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.30, C:0.28, G:0.27, T:0.15
Consensus pattern (21 bp):
AGGGATACATACCAAGCCCAC
Found at i:1896355 original size:21 final size:21
Alignment explanation
Indices: 1896312--1896356 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
1896302 ATATTACATT
* *
1896312 ACATTAGAAGCATTAACTGGA
1 ACATTAGAAGCATTAAATAGA
1896333 ACATTAGAAGCATTAAATAGA
1 ACATTAGAAGCATTAAATAGA
1896354 ACA
1 ACA
1896357 CAAGCATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.49, C:0.13, G:0.16, T:0.22
Consensus pattern (21 bp):
ACATTAGAAGCATTAAATAGA
Found at i:1896992 original size:6 final size:6
Alignment explanation
Indices: 1896983--1897023 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
1896973 GCTAAAAATA
* * *
1896983 AAATCC AAATTC AAATTC AAATTC ATATTC ATATTC AAATT
1 AAATTC AAATTC AAATTC AAATTC AAATTC AAATTC AAATT
1897024 TACATTGAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.46, C:0.17, G:0.00, T:0.37
Consensus pattern (6 bp):
AAATTC
Found at i:1898216 original size:169 final size:168
Alignment explanation
Indices: 1897922--1898859 Score: 917
Period size: 169 Copynumber: 5.5 Consensus size: 168
1897912 TAAAAATGAT
* * * * *
1897922 TCTCTGCCATGTCATATTGTCTCATCCATCAAATATATTAGGGGTTGTTGTAAATAGTTCCCCGA
1 TCTCTACCATGTCATATTATCTCATCCATCAAACATATTAGGGGTTGATGTGAATAGTTCCCCGA
* **
1897987 GTGGGAACATCATAGTTGCCTATTATTAACTGAAGAATGTAGAGAAACTCTGACGAAAAGGGAAG
66 ATGGGAACATCATAACTGCCTATTATTAACTGAAGAATGTAGAGAAACTCTGACGAAAAGGGAAG
* * *
1898052 GTGCTTCCCA-ATAGAAACGCTTTCACCTCTTTCAGAGAA
131 GTGCGTCCCACA-AGAAGCGCTTTCACCT-TTTTAGAGAA
* * * *
1898091 TCTCTACCAAGTCATATTATCTCATCTCATTAAACATATTAGGGGTTGATGTGAATAGTT-TCCT
1 TCTCTACCATGTCATATTATCTCATC-CATCAAACATATTAGGGGTTGATGTGAATAGTTCCCCG
*
1898155 AATGGGAACATCATAACTGCCTATTATTAACTGAAGAATGTAGAGAAACTCTGATGAAAAGGGAA
65 AATGGGAACATCATAACTGCCTATTATTAACTGAAGAATGTAGAGAAACTCTGACGAAAAGGGAA
* * *
1898220 GGTGCGTCCTACAAGAAGCGTTTTC-CCTTTTTTTTGAGAA
130 GGTGCGTCCCACAAGAAGCGCTTTCACC--TTTTTAGAGAA
* * * * * * *
1898260 TCTTTACCATGTCATAATGTCTTATCCCATCAAACATACTAGGGGTTCATGTTAATAGTTCCCCG
1 TCTCTACCATGTCATATTATCTCAT-CCATCAAACATATTAGGGGTTGATGTGAATAGTTCCCCG
* * * * * * * * * * *
1898325 ACTTGGAACATCATACCTTCATATTATTAACTAAAGAATGCAAAGAAACTTTGGTC-AAAAGGAA
65 AATGGGAACATCATAACTGCCTATTATTAACTGAAGAATGTAGAGAAACTCT-GACGAAAAGGGA
** * * * *
1898389 AGGCACATCCCACAAGAAGCGCTTTCACATTTTTCAAAAAA
129 AGGTGCGTCCCACAAGAAGCGCTTTCACCTTTTT-AGAGAA
** * * * * *
1898430 TCTCTGTCATGTCATACTATCTCATCACATCAAACATATTA-GGGATGACGTGAATAGCTCCTC-
1 TCTCTACCATGTCATATTATCTCATC-CATCAAACATATTAGGGGTTGATGTGAATAGTTCCCCG
** * *
1898493 AACTGGGAACATCATAGTTGCCTATTATTAACTG-AGAAATGTAGAGAAACTCTAACAAAAAGGG
65 AA-TGGGAACATCATAACTGCCTATTATTAACTGAAG-AATGTAGAGAAACTCTGACGAAAAGGG
*** * *
1898557 AAGACACGTCCCACAAGAAGCCCTTTTACCATTTTTAGAGAA
128 AAGGTGCGTCCCACAAGAAGCGCTTTCACC-TTTTTAGAGAA
* * * * * * **
1898599 TCTCTGCCATGTCATA-CAGTCCCATCCCATTAAATATATTAGGGGTTAACATGAATAGTT-CCC
1 TCTCTACCATGTCATATTA-TCTCAT-CCATCAAACATATTAGGGGTTGATGTGAATAGTTCCCC
* * * *
1898662 AAACTGGGAACATCATTACTGCCTATTATTAACTGGAGAATGCAGAGAAACTCTGACGAAAAGGG
64 GAA-TGGGAACATCATAACTGCCTATTATTAACTGAAGAATGTAGAGAAACTCTGACGAAAAGGG
* *
1898727 AAGGTGCGTCTCACAAGAAG-GACTTTTACCTTTTTAGAGAA
128 AAGGTGCGTCCCACAAGAAGCG-CTTTCACCTTTTTAGAGAA
* * * ** *
1898768 TCTCTACCATGTCACATTGTCTAATCCATCAAACATATTATTGGTTGTTGTGAATAGTTCCCCGA
1 TCTCTACCATGTCATATTATCTCATCCATCAAACATATTAGGGGTTGATGTGAATAGTTCCCCGA
* *
1898833 TTGGGAACATCATTTA-TGCCTATTATT
66 ATGGGAACATCA-TAACTGCCTATTATT
1898860 TAATCAGGAA
Statistics
Matches: 625, Mismatches: 121, Indels: 47
0.79 0.15 0.06
Matches are distributed among these distances:
168 55 0.09
169 327 0.52
170 239 0.38
171 4 0.01
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (168 bp):
TCTCTACCATGTCATATTATCTCATCCATCAAACATATTAGGGGTTGATGTGAATAGTTCCCCGA
ATGGGAACATCATAACTGCCTATTATTAACTGAAGAATGTAGAGAAACTCTGACGAAAAGGGAAG
GTGCGTCCCACAAGAAGCGCTTTCACCTTTTTAGAGAA
Found at i:1898744 original size:339 final size:335
Alignment explanation
Indices: 1897922--1898807 Score: 991
Period size: 339 Copynumber: 2.6 Consensus size: 335
1897912 TAAAAATGAT
* **
1897922 TCTCTGCCATGTCATATTGTCTCAT-CCATCAAATATATTAGGGGTTGTTGTAAATAGTTCCCCG
1 TCTCTGCCATGTCATA-AGTCTCATCCCATCAAATATATTAGGGGTTCATG--AATAGTTCCCCG
* ** *
1897986 AGTGGGAACATCATAGTTGCCTATTATTAACTGAAGAATGTAGAGAAACTCTGACGAAAAGGGAA
63 ACTGGGAACATCATACCTGCCTATTATTAACTGAAGAATGCAGAGAAACTCTGACGAAAAGGGAA
* * * *
1898051 GGTGCTTCCCA-ATAGAAACGCTTTCACCTCTTTCAGAGAATCTCTACCAAGTCATATTATCTCA
128 GGTGCATCCCACA-AGAAGCGCTTTCACCTTTTTCAGAGAATCTCTACCATGTCATATTATCTCA
* * * *
1898115 TCTCATTAAACATATTAGGGGTTGATGTGAATAGTTTCCTAATGGGAACATCATAACTGCCTATT
192 TC-CATCAAACATATTAGGGGATGACGTGAATAGTCTCCTAATGGGAACATCATAACTGCCTATT
* ** *** * * *
1898180 ATTAACTGAAGAATGTAGAGAAACTCTGATGAAAAGGGAAGGTGCGTCCTACAAGAAGCGTTTTC
256 ATTAACTGAAGAATGTAGAGAAACTCTAACAAAAAGGGAAGACACGTCCCACAAGAAGCCTTTTA
* *
1898245 CCTTTTTTTTGAGAA
321 CCTATTTTTAGAGAA
* * * * *
1898260 TCTTTACCATGTCATAATGTCTTATCCCATCAAACATACTAGGGGTTCATGTTAATAGTTCCCCG
1 TCTCTGCCATGTCATAA-GTCTCATCCCATCAAATATATTAGGGGTTCATG--AATAGTTCCCCG
* * * * * * * *
1898325 ACTTGGAACATCATACCTTCATATTATTAACTAAAGAATGCAAAGAAACTTTGGTC-AAAAGGAA
63 ACTGGGAACATCATACCTGCCTATTATTAACTGAAGAATGCAGAGAAACTCT-GACGAAAAGGGA
** * * * ** *
1898389 AGGCACATCCCACAAGAAGCGCTTTCACATTTTTCAAAAAATCTCTGTCATGTCATACTATCTCA
127 AGGTGCATCCCACAAGAAGCGCTTTCACCTTTTTCAGAGAATCTCTACCATGTCATATTATCTCA
**
1898454 TCACATCAAACATATTA-GGGATGACGTGAATAG-CTCCTCAACTGGGAACATCATAGTTGCCTA
192 TC-CATCAAACATATTAGGGGATGACGTGAATAGTCTCCT-AA-TGGGAACATCATAACTGCCTA
1898517 TTATTAACTG-AGAAATGTAGAGAAACTCTAACAAAAAGGGAAGACACGTCCCACAAGAAGCCCT
254 TTATTAACTGAAG-AATGTAGAGAAACTCTAACAAAAAGGGAAGACACGTCCCACAAGAAG-CCT
1898581 TTTACC-ATTTTTAGAGAA
317 TTTACCTATTTTTAGAGAA
* * **
1898599 TCTCTGCCATGTCATACAGTCCCATCCCATTAAATATATTAGGGGTTAACATGAATAGTTCCCAA
1 TCTCTGCCATGTCATA-AGTCTCATCCCATCAAATATATTAGGGGTT--CATGAATAGTTCCCCG
*
1898664 ACTGGGAACATCATTA-CTGCCTATTATTAACTGGAGAATGCAGAGAAACTCTGACGAAAAGGGA
63 ACTGGGAACATCA-TACCTGCCTATTATTAACTGAAGAATGCAGAGAAACTCTGACGAAAAGGGA
* * * * * *
1898728 AGGTGCGTCTCACAAGAAG-GACTTTTACCTTTTT-AGAGAATCTCTACCATGTCACATTGTCTA
127 AGGTGCATCCCACAAGAAGCG-CTTTCACCTTTTTCAGAGAATCTCTACCATGTCATATTATCTC
1898791 ATCCATCAAACATATTA
191 ATCCATCAAACATATTA
1898808 TTGGTTGTTG
Statistics
Matches: 451, Mismatches: 83, Indels: 29
0.80 0.15 0.05
Matches are distributed among these distances:
337 18 0.04
338 65 0.14
339 351 0.78
340 13 0.03
341 4 0.01
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.29
Consensus pattern (335 bp):
TCTCTGCCATGTCATAAGTCTCATCCCATCAAATATATTAGGGGTTCATGAATAGTTCCCCGACT
GGGAACATCATACCTGCCTATTATTAACTGAAGAATGCAGAGAAACTCTGACGAAAAGGGAAGGT
GCATCCCACAAGAAGCGCTTTCACCTTTTTCAGAGAATCTCTACCATGTCATATTATCTCATCCA
TCAAACATATTAGGGGATGACGTGAATAGTCTCCTAATGGGAACATCATAACTGCCTATTATTAA
CTGAAGAATGTAGAGAAACTCTAACAAAAAGGGAAGACACGTCCCACAAGAAGCCTTTTACCTAT
TTTTAGAGAA
Found at i:1901271 original size:54 final size:54
Alignment explanation
Indices: 1901212--1901319 Score: 189
Period size: 54 Copynumber: 2.0 Consensus size: 54
1901202 TTAGCAGATC
1901212 TACATAAAAAAGTTGCAACATCAAATGGTATATTGGTAACGAATTTTTCTTGCA
1 TACATAAAAAAGTTGCAACATCAAATGGTATATTGGTAACGAATTTTTCTTGCA
* * *
1901266 TACATAAAAAAGTTGCAGCATCAAATGGTATGTTGGTAATGAATTTTTCTTGCA
1 TACATAAAAAAGTTGCAACATCAAATGGTATATTGGTAACGAATTTTTCTTGCA
1901320 CCTGTGAATT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (54 bp):
TACATAAAAAAGTTGCAACATCAAATGGTATATTGGTAACGAATTTTTCTTGCA
Found at i:1901879 original size:25 final size:25
Alignment explanation
Indices: 1901792--1901925 Score: 100
Period size: 25 Copynumber: 5.3 Consensus size: 25
1901782 TATGTAATTG
*
1901792 TATTTTCTAATATTTCAACGTATG-
1 TATTTTCTAATATTTCAATGTATGT
* *
1901816 -CTTTTCTGATATTTCAATGTAATTGCAT
1 TATTTTCTAATATTTCAATGT-A-TG--T
*
1901844 T-TTTT-TGATATTTCAATGTATGT
1 TATTTTCTAATATTTCAATGTATGT
* *
1901867 TCTTTTCTAATATTTCTATGTAAT-T
1 TATTTTCTAATATTTCAATGT-ATGT
*
1901892 GTATTTTCTAATATCTC-ATGTATGT
1 -TATTTTCTAATATTTCAATGTATGT
1901917 GTATTTTCT
1 -TATTTTCT
1901926 TTTTTTTTTT
Statistics
Matches: 92, Mismatches: 7, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
23 19 0.21
24 7 0.08
25 31 0.34
26 17 0.18
27 14 0.15
28 4 0.04
ACGTcount: A:0.24, C:0.11, G:0.10, T:0.55
Consensus pattern (25 bp):
TATTTTCTAATATTTCAATGTATGT
Found at i:1901882 original size:52 final size:50
Alignment explanation
Indices: 1901783--1901905 Score: 160
Period size: 52 Copynumber: 2.5 Consensus size: 50
1901773 ACCATTACTT
*
1901783 ATGTAATTGTA-TTTTCTAATATTTCAACGTATGCTTTTCTGATATTTCA
1 ATGTAATTGTATTTTTCTAATATTTCAACGTATGCTTTTCTAATATTTCA
* * * * *
1901832 ATGTAATTGCATTTTTTTGATATTTCAATGTATGTTCTTTTCTAATATTTCT
1 ATGTAATTGTATTTTTCTAATATTTCAACGTATG--CTTTTCTAATATTTCA
1901884 ATGTAATTGTA-TTTTCTAATAT
1 ATGTAATTGTATTTTTCTAATAT
1901906 CTCATGTATG
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
49 10 0.16
50 19 0.31
51 9 0.15
52 24 0.39
ACGTcount: A:0.26, C:0.10, G:0.10, T:0.54
Consensus pattern (50 bp):
ATGTAATTGTATTTTTCTAATATTTCAACGTATGCTTTTCTAATATTTCA
Found at i:1902299 original size:25 final size:25
Alignment explanation
Indices: 1902271--1902347 Score: 100
Period size: 25 Copynumber: 3.1 Consensus size: 25
1902261 TAAAAAAATC
* *
1902271 AACCTTAAATTGCTTTAACCTAAAA
1 AACCTTAAACTACTTTAACCTAAAA
*
1902296 AACCCTAAACTACTTTAACCTAAAA
1 AACCTTAAACTACTTTAACCTAAAA
* * *
1902321 AACCTTAAACCAATTCAACCTAAAA
1 AACCTTAAACTACTTTAACCTAAAA
1902346 AA
1 AA
1902348 ATTTAAAACC
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 45 1.00
ACGTcount: A:0.49, C:0.25, G:0.01, T:0.25
Consensus pattern (25 bp):
AACCTTAAACTACTTTAACCTAAAA
Found at i:1903810 original size:2 final size:2
Alignment explanation
Indices: 1903803--1903840 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1903793 TAAATCAATA
1903803 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
1903841 GACTCGTATC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1904441 original size:23 final size:22
Alignment explanation
Indices: 1904399--1904442 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
1904389 TCTCTTTTTA
*
1904399 CCATTGTATACTTGCTTATGAG
1 CCATTGTATACTTGCCTATGAG
1904421 CCATATGTATCACTT-CCTATGA
1 CCAT-TGTAT-ACTTGCCTATGA
1904443 ATCACATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 4 0.21
23 11 0.58
24 4 0.21
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.39
Consensus pattern (22 bp):
CCATTGTATACTTGCCTATGAG
Found at i:1904747 original size:21 final size:19
Alignment explanation
Indices: 1904723--1904768 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
1904713 TTGGAAATTA
*
1904723 ATTAAGAAAATATTTTTAAAT
1 ATTAA-AAAATAATTTT-AAT
*
1904744 ATTAAAATATAATTTTAAT
1 ATTAAAAAATAATTTTAAT
1904763 ATTAAA
1 ATTAAA
1904769 TATGATTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 9 0.39
20 9 0.39
21 5 0.22
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
ATTAAAAAATAATTTTAAT
Found at i:1904750 original size:18 final size:18
Alignment explanation
Indices: 1904729--1904782 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 18
1904719 ATTAATTAAG
1904729 AAAATATTTTTAAATATT
1 AAAATATTTTTAAATATT
1904747 AAAATATAATTTT-AATATT
1 AAAATAT--TTTTAAATATT
1904766 AAATATGATTTTATAAA
1 AAA-AT-ATTTT-TAAA
1904783 GGTTTATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
18 7 0.23
19 12 0.40
20 7 0.23
21 4 0.13
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (18 bp):
AAAATATTTTTAAATATT
Found at i:1904765 original size:19 final size:18
Alignment explanation
Indices: 1904736--1904778 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
1904726 AAGAAAATAT
1904736 TTTTAAATATTAAAATATAA
1 TTTT-AATATT-AAATATAA
*
1904756 TTTTAATATTAAATATGA
1 TTTTAATATTAAATATAA
1904774 TTTTA
1 TTTTA
1904779 TAAAGGTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 12 0.55
19 6 0.27
20 4 0.18
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (18 bp):
TTTTAATATTAAATATAA
Found at i:1911740 original size:3 final size:3
Alignment explanation
Indices: 1911686--1911727 Score: 57
Period size: 3 Copynumber: 13.3 Consensus size: 3
1911676 ATATCGTTAA
*
1911686 TAT TAT TAT AAT TAT TAAT TAT TAAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT T-AT TAT T-AT TAT TAT TAT TAT TAT T
1911728 TAGTTTTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 29 0.83
4 6 0.17
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:1911740 original size:20 final size:20
Alignment explanation
Indices: 1911682--1911727 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
1911672 GGAGATATCG
*
1911682 TTAA-TATT-ATTATAATTA
1 TTAATTATTAATTATTATTA
1911700 TTAATTATTAATTATTATTA
1 TTAATTATTAATTATTATTA
1911720 TT-ATTATT
1 TTAATTATT
1911728 TAGTTTTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 4 0.16
19 10 0.40
20 11 0.44
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TTAATTATTAATTATTATTA
Found at i:1911833 original size:6 final size:6
Alignment explanation
Indices: 1911742--1911830 Score: 142
Period size: 6 Copynumber: 14.8 Consensus size: 6
1911732 TTTTATTATA
* *
1911742 TTCATA TTCATA TTCATG TTCATG TTCATG TTCATG TTCATG TTCATG
1 TTCATG TTCATG TTCATG TTCATG TTCATG TTCATG TTCATG TTCATG
* *
1911790 TTCATG TTCATG TTCATG TTCATG TTCATA TTCATA TTCAT
1 TTCATG TTCATG TTCATG TTCATG TTCATG TTCATG TTCAT
1911831 ATTTATTTAT
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 81 1.00
ACGTcount: A:0.21, C:0.17, G:0.11, T:0.51
Consensus pattern (6 bp):
TTCATG
Found at i:1913884 original size:16 final size:16
Alignment explanation
Indices: 1913863--1913893 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1913853 CAAAGAATGT
1913863 TTTTATTGTTATTTAA
1 TTTTATTGTTATTTAA
1913879 TTTTATTGTTATTTA
1 TTTTATTGTTATTTA
1913894 TGCATTTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (16 bp):
TTTTATTGTTATTTAA
Found at i:1918336 original size:18 final size:18
Alignment explanation
Indices: 1918313--1918351 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
1918303 GTTAAATGCC
1918313 CCAACTTTATGAATAGAT
1 CCAACTTTATGAATAGAT
1918331 CCAACTTTATGAATAGAT
1 CCAACTTTATGAATAGAT
1918349 CCA
1 CCA
1918352 GCTAGTCCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (18 bp):
CCAACTTTATGAATAGAT
Found at i:1920855 original size:242 final size:242
Alignment explanation
Indices: 1920276--1921417 Score: 1359
Period size: 242 Copynumber: 4.8 Consensus size: 242
1920266 ATGGATGTCT
* * * * *
1920276 TTCGGGCCATCTATAAGACCTTTGGGC-ATATGTTTTCACATGATTTTT--AAAAAATGAGAAAA
1 TTCGGGCCATCCATAAGACCTTCGGGCAAGATATTTTCACATGATTTTTAAAAAAAATGAGAAAG
* * *
1920338 TGATTTCCAAAGTTTCTCATTTAAATCTTTTCTGAAAATTGATTTTTTTTAAAAGTAAAAAAACA
66 TGATTTCCAAAGTTTCTCATTTAAATCTTTTCTGAAAATTGATTTTTTTGAAAAGTAAGAAAACG
* * ** *
1920403 ATTTCCAAAATATCTTACGTAGTAAGTCCTTCGTCCCATCAATAAGTCTTTCGAGTATGATGCTT
131 ATTTCCAAAATTTCTTACTTAGTAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGCTT
* * * *
1920468 AAATCCTTTGGGTCATCTATAA-TCTTTTCGAGGAAGATGAAAAGTCC
196 AAATCCTTCGGGTCATCTATAAGCCTTTT-GAGTAAGATGATAAGTCC
* * * *
1920515 TTCGGG-----C---A-ACCTTTGGACAGGATATTTTCACATGATTTTTAAAAAAAAATCAGAAA
1 TTCGGGCCATCCATAAGACCTTCGGGCAAGATATTTTCACATGATTTTT-AAAAAAAATGAGAAA
* * *
1920571 ATGATTTCCAAAGTTTCTCTTTTAAATCATTTCTGAAAATTGATTTTTTTGAAAAGTAAGAAAAC
65 GTGATTTCCAAAGTTTCTCATTTAAATCTTTTCTGAAAATTGATTTTTTTGAAAAGTAAGAAAAC
* *
1920636 GATTTCCAAAATTTCTTACTTAATAAGTCCTTTGGGCCAT-AATAAGTCTTTCGAGCATGATGCT
130 GATTTCCAAAATTTCTTACTTAGTAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGCT
** * *
1920700 TAAATCCTTATGGTCATTTATAAGCCTTTTGCGTAAGATGATAAGTCC
195 TAAATCCTTCGGGTCATCTATAAGCCTTTTGAGTAAGATGATAAGTCC
* * *
1920748 TTCGGGTCATCCATAAGACCTTCGGGCAAGATGTTTTCACATTATTTTTGAAAAAAAATGAGAAA
1 TTCGGGCCATCCATAAGACCTTCGGGCAAGATATTTTCACATGATTTTT-AAAAAAAATGAGAAA
*
1920813 GTGATTTCCAAAATTTCTCATTTAAATCTTTTCTGAAAATTGA--TTTTTGAAAAGTAAGAAAAC
65 GTGATTTCCAAAGTTTCTCATTTAAATCTTTTCTGAAAATTGATTTTTTTGAAAAGTAAGAAAAC
* * * * * * *
1920876 TATTTCAAAAAACTT-TT-CTT-GTAAGTCCTTTGGGTCATCAATAAGTCTTTTGAGCGTGATGC
130 GATTTC-CAAAATTTCTTACTTAGTAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGC
* * *
1920938 TTAAATCCTTCGGGCCATCTATAAGCCTTTCGAGTAAGATGATAAGTCT
194 TTAAATCCTTCGGGTCATCTATAAGCCTTTTGAGTAAGATGATAAGTCC
* * *
1920987 TTCGGGCCATACATAAGACCTTCGAGCATGATA--TT----TGATTTTTGAAAACAAAAATGAGA
1 TTCGGGCCATCCATAAGACCTTCGGGCAAGATATTTTCACATGATTTTT--AAA-AAAAATGAGA
*
1921046 AAGTGATTTCCAAAATTTCTCATTTAAATCTTTTCTGAAAATTGA--TTTTTGAAAAGTAAGAAA
63 AAGTGATTTCCAAAGTTTCTCATTTAAATCTTTTCTGAAAATTGATTTTTTTGAAAAGTAAGAAA
* * * *
1921109 ATGATTTCCAAAGTTTCTTACTTAGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGTTG
128 ACGATTTCCAAAATTTCTTACTTAGTAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATG
** * *
1921174 CCCAAAATCCTTCGGGTCATCTATAAGCCTTTTGAGCAAGCTGATAAGTCC
193 -CTTAAATCCTTCGGGTCATCTATAAGCCTTTTGAGTAAGATGATAAGTCC
* * * * *
1921225 TTCAGACCATCCATAAGACGTTCGGGCAAGATATTTTCACATGA-TTTTCAAATAAATGAGAAAG
1 TTCGGGCCATCCATAAGACCTTCGGGCAAGATATTTTCACATGATTTTTAAAAAAAATGAGAAAG
** * *
1921289 CAATTTCCAAAGTTTCTCATTTAAATCTTTTCTGAAAATTGATTTTTTTGAAAAATAAGAAAATG
66 TGATTTCCAAAGTTTCTCATTTAAATCTTTTCTGAAAATTGATTTTTTTGAAAAGTAAGAAAACG
* ** * ** * *
1921354 ATTTTCAATGTTTCTTACTCAGTAAGTCCTTCCTGCCATCAGTAAGTCTTTCGAGCATAATGCT
131 ATTTCCAAAATTTCTTACTTAGTAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGCT
1921418 CAAGTCGAGG
Statistics
Matches: 778, Mismatches: 95, Indels: 58
0.84 0.10 0.06
Matches are distributed among these distances:
230 9 0.01
231 19 0.02
233 71 0.09
234 119 0.15
235 81 0.10
236 3 0.00
237 37 0.05
238 87 0.11
239 100 0.13
240 80 0.10
241 10 0.01
242 155 0.20
243 4 0.01
244 3 0.00
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (242 bp):
TTCGGGCCATCCATAAGACCTTCGGGCAAGATATTTTCACATGATTTTTAAAAAAAATGAGAAAG
TGATTTCCAAAGTTTCTCATTTAAATCTTTTCTGAAAATTGATTTTTTTGAAAAGTAAGAAAACG
ATTTCCAAAATTTCTTACTTAGTAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGCTT
AAATCCTTCGGGTCATCTATAAGCCTTTTGAGTAAGATGATAAGTCC
Found at i:1921240 original size:477 final size:472
Alignment explanation
Indices: 1920282--1921417 Score: 1367
Period size: 477 Copynumber: 2.4 Consensus size: 472
1920272 GTCTTTCGGG
* * * *
1920282 CCATCTATAAGACCTTTGGGC-ATATGTTTTCACATGATTTTT-AAAAAATGAGAAAATGATTTC
1 CCATCCATAAGACCTTCGGGCAAGATGTTTTCACATGATTTTTAAAAAAATGAGAAAGTGATTTC
* *
1920345 CAAAGTTTCTCATTTAAATCTTTTCTGAAAATTGATTTTTTTTAAAAGTAAAAAAACAATTTCCA
66 CAAAGTTTCTCATTTAAATCTTTTCTGAAAATTGA-TTTTTTGAAAAGTAAGAAAACAATTTCCA
* * *
1920410 AAATATCTTACGTAGTAAGTCCTTCGTCCCATCAATAAGTCTTTCGAGTATGATGCTTAAATCCT
130 AAAAATCTTACGTAGTAAGTCCTTCGGCCCATCAATAAGTCTTTCGAGCATGATGCTTAAATCCT
* * * * * ** * *
1920475 TTGGGTCATCTATAATCTTTTCGAGGAAGATGAAAAGTCCTTCGGGCAACCTTTGGACAGGATAT
195 TCGGGCCATCTATAAGCCTTTCGAGGAAGATGAAAAGTCCTTCGGGCAACCATAAGACACGACAT
** * *
1920540 TTTCACATGATTTTTAAAAAAAAATCAGAAAATGATTTCCAAAGTTTCTCTTTTAAATCATTTCT
260 GATCACATGATTTTTAAAAAAAAATCAGAAAATGATTTCCAAAATTTCTCATTTAAATCATTTCT
*
1920605 GAAAATTGATTTTTTTGAAAAGTAAGAAAACGATTTCCAAAATTTCTTACTTAATAAGTCCTTTG
325 GAAAATTGA-TTTTTTGAAAAGTAAGAAAACGATTTCCAAAATTTCTTACTTAATAAGTCCTTCG
** * * * *
1920670 GGCCATAATAAGTCTTTCGAGCATGATGCTTAAATCCTTATGGTCATTTATAAGCCTTTTGCGTA
389 GGCCATAATAAGTCTTTCGAGCATGATGCCAAAATCCTTAGGGTCATCTATAAGCCTTTTGAGCA
* *
1920735 AGATGATAAGTCCTTCGGG
454 AGATGATAAGTCCTTCAGA
* *
1920754 TCATCCATAAGACCTTCGGGCAAGATGTTTTCACATTATTTTTGAAAAAAAATGAGAAAGTGATT
1 CCATCCATAAGACCTTCGGGCAAGATGTTTTCACATGATTTTT--AAAAAAATGAGAAAGTGATT
* *
1920819 TCCAAAATTTCTCATTTAAATCTTTTCTGAAAATTGA-TTTTTGAAAAGTAAGAAAACTATTT-C
64 TCCAAAGTTTCTCATTTAAATCTTTTCTGAAAATTGATTTTTTGAAAAGTAAGAAAACAATTTCC
* * * ** * *
1920882 AAAAAA-CTTTTC-TTGTAAGTCCTTTGGGTCATCAATAAGTCTTTTGAGCGTGATGCTTAAATC
129 AAAAAATC-TTACGTAGTAAGTCCTTCGGCCCATCAATAAGTCTTTCGAGCATGATGCTTAAATC
* * * *
1920945 CTTCGGGCCATCTATAAGCCTTTCGAGTAAGATGATAAGTCTTTCGGGCCATA-CATAAGACCTT
193 CTTCGGGCCATCTATAAGCCTTTCGAGGAAGATGAAAAGTCCTTCGGG-CA-ACCATAAGA-C-A
** * *
1921009 CGAGCATGAT-ATTTGATTTTTGAAAACAAAAATGAGAAAGTGATTTCCAAAATTTCTCATTTAA
254 CGA-CATGATCACATGATTTTT-AAAA-AAAAATCAGAAAATGATTTCCAAAATTTCTCATTTAA
* * * *
1921073 ATCTTTTCTGAAAATTGA-TTTTTGAAAAGTAAGAAAATGATTTCCAAAGTTTCTTACTTAGTAA
316 ATCATTTCTGAAAATTGATTTTTTGAAAAGTAAGAAAACGATTTCCAAAATTTCTTACTTAATAA
* * *
1921137 GTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGTTGCCCAAAATCCTTCGGGTCATCTATAAGC
381 GTCCTTCGGGCCAT-AATAAGTCTTTCGAGCATGATG-CCAAAATCCTTAGGGTCATCTATAAGC
*
1921202 CTTTTGAGCAAGCTGATAAGTCCTTCAGA
444 CTTTTGAGCAAGATGATAAGTCCTTCAGA
* * * * **
1921231 CCATCCATAAGACGTTCGGGCAAGATATTTTCACATGATTTTCAAATAAATGAGAAAGCAATTTC
1 CCATCCATAAGACCTTCGGGCAAGATGTTTTCACATGATTTTTAAAAAAATGAGAAAGTGATTTC
* ** *
1921296 CAAAGTTTCTCATTTAAATCTTTTCTGAAAATTGATTTTTTTGAAAAATAAGAAAATGATTTTCA
66 CAAAGTTTCTCATTTAAATCTTTTCTGAAAATTGA-TTTTTTGAAAAGTAAGAAAACAATTTCCA
**** * * *
1921361 ATGTTTCTTAC-TCAGTAAGTCCTTCCTG-CCATCAGTAAGTCTTTCGAGCATAATGCT
130 AAAAATCTTACGT-AGTAAGTCCTT-CGGCCCATCAATAAGTCTTTCGAGCATGATGCT
1921418 CAAGTCGAGG
Statistics
Matches: 561, Mismatches: 83, Indels: 33
0.83 0.12 0.05
Matches are distributed among these distances:
472 103 0.18
473 34 0.06
474 24 0.04
475 120 0.21
476 81 0.14
477 156 0.28
478 7 0.01
479 35 0.06
480 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (472 bp):
CCATCCATAAGACCTTCGGGCAAGATGTTTTCACATGATTTTTAAAAAAATGAGAAAGTGATTTC
CAAAGTTTCTCATTTAAATCTTTTCTGAAAATTGATTTTTTGAAAAGTAAGAAAACAATTTCCAA
AAAATCTTACGTAGTAAGTCCTTCGGCCCATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTT
CGGGCCATCTATAAGCCTTTCGAGGAAGATGAAAAGTCCTTCGGGCAACCATAAGACACGACATG
ATCACATGATTTTTAAAAAAAAATCAGAAAATGATTTCCAAAATTTCTCATTTAAATCATTTCTG
AAAATTGATTTTTTGAAAAGTAAGAAAACGATTTCCAAAATTTCTTACTTAATAAGTCCTTCGGG
CCATAATAAGTCTTTCGAGCATGATGCCAAAATCCTTAGGGTCATCTATAAGCCTTTTGAGCAAG
ATGATAAGTCCTTCAGA
Found at i:1921892 original size:131 final size:130
Alignment explanation
Indices: 1921610--1922030 Score: 352
Period size: 131 Copynumber: 3.2 Consensus size: 130
1921600 ATTCTACCTT
* * * * *
1921610 GATTCAATCTTCCCTGAAGAGTAGTGAAATGAATCAATGTTTCCAAATCTGATCTACCCTGAAGA
1 GATTCTATC-TCCCTAAAGAGTAGTGGAATGAGTCAATGTTTCCATATCTGATCTACCCTGAAGA
** * * * * * * * *
1921675 GCAG-ATAAGCAAAACCCTATTTTTTAGATTTTATCTTCCCTGAATAGCATTGGAATAAATCTTC
65 GCAGCGGAA-CATAACCC-CTTTTTCAGATTTGATCTTCCCTGAAAAGCATTAGAACAAATCTGC
1921739 CAT-
128 C-TC
* * * * * * *
1921742 GATTC-ATTCTACTTGAAGAGTAATGGAATGAGTCAATGTTTCCATATCTGATTTACCCTAAAAA
1 GATTCTA-TCTCCCTAAAGAGTAGTGGAATGAGTCAATGTTTCCATATCTGATCTACCCTGAAGA
* * *
1921806 GTAGCGGATCATAACCCCTTATTTCAGATTTGATCTTCCCTGAAAAGCAGTAGAACAAATCTGCC
65 GCAGCGGAACATAACCCCTT-TTTCAGATTTGATCTTCCCTGAAAAGCATTAGAACAAATCTGCC
1921871 TC
129 TC
** *
1921873 GATTCTATCTCCCTAAAGAGTAGT-GAAGTG-GATCAACATTTCC-TGATCTGATCTACCTTGAA
1 GATTCTATCTCCCTAAAGAGTAGTGGAA-TGAG-TCAATGTTTCCAT-ATCTGATCTACCCTGAA
* * * * *
1921935 GAGCAGCGGAACATATCCCCCCTTTTCCAGATTTGATCTTTCCTGAGAAA-AATTAGAACAAATT
63 GAGCAGCGGAACATA--ACCCCTTTTTCAGATTTGATCTTCCCTGA-AAAGCATTAGAACAAATC
1921999 TGCCTC
125 TGCCTC
* *
1922005 GATTTTGATCTACCCTAAAAAGTAGT
1 GATTCT-ATCT-CCCTAAAGAGTAGT
1922031 ATAGTGAATC
Statistics
Matches: 234, Mismatches: 42, Indels: 24
0.78 0.14 0.08
Matches are distributed among these distances:
130 8 0.03
131 149 0.64
132 51 0.22
133 13 0.06
134 13 0.06
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.32
Consensus pattern (130 bp):
GATTCTATCTCCCTAAAGAGTAGTGGAATGAGTCAATGTTTCCATATCTGATCTACCCTGAAGAG
CAGCGGAACATAACCCCTTTTTCAGATTTGATCTTCCCTGAAAAGCATTAGAACAAATCTGCCTC
Found at i:1922251 original size:25 final size:25
Alignment explanation
Indices: 1922223--1922270 Score: 64
Period size: 24 Copynumber: 1.9 Consensus size: 25
1922213 TAATTATTAG
1922223 TTTTTATTATTGT-TTTTTT-TTTATA
1 TTTTTA-TATT-TATTTTTTATTTATA
1922248 TTTTTATATTTATTTTTTATTTA
1 TTTTTATATTTATTTTTTATTTA
1922271 CTTTACAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 1 0.05
24 10 0.48
25 10 0.48
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (25 bp):
TTTTTATATTTATTTTTTATTTATA
Found at i:1927398 original size:29 final size:28
Alignment explanation
Indices: 1927344--1927553 Score: 171
Period size: 29 Copynumber: 7.4 Consensus size: 28
1927334 TACTTTTTAA
*
1927344 AAATTA-AATTAAAGGATAAACCTTTTTGT
1 AAATTACAA-TAAA-GACAAACCTTTTTGT
* *
1927373 -AATTATAATAAATGACAAACCTTTTTTT
1 AAATTACAATAAA-GACAAACCTTTTTGT
*
1927401 AAATTATAATAAATGA-AAACC-TTTTGT
1 AAATTACAATAAA-GACAAACCTTTTTGT
* *
1927428 AAATTACAATAAA-ATAAACCTTATTGT
1 AAATTACAATAAAGACAAACCTTTTTGT
*
1927455 AAATTAAAATAAAGGAC-AACACTTTTTGT
1 AAATTACAATAAA-GACAAAC-CTTTTTGT
* *
1927484 AAATTACAACAAAGAACAAACCTTTTTAT
1 AAATTACAATAAAG-ACAAACCTTTTTGT
* * * * * *
1927513 AAATCATAATAAAAATCAAAACTTCTTAT
1 AAATTACAATAAAGA-CAAACCTTTTTGT
1927542 AAATTACAATAA
1 AAATTACAATAA
1927554 TGATATATAT
Statistics
Matches: 151, Mismatches: 20, Indels: 20
0.79 0.10 0.10
Matches are distributed among these distances:
25 1 0.01
26 5 0.03
27 34 0.23
28 32 0.21
29 76 0.50
30 3 0.02
ACGTcount: A:0.50, C:0.11, G:0.05, T:0.34
Consensus pattern (28 bp):
AAATTACAATAAAGACAAACCTTTTTGT
Found at i:1927525 original size:112 final size:112
Alignment explanation
Indices: 1927344--1927553 Score: 275
Period size: 112 Copynumber: 1.9 Consensus size: 112
1927334 TACTTTTTAA
* * * * * *
1927344 AAATTAAATTAAAGGATAAACCTTTTTGTAATTATAATAAATGACAAACCTTTTTTTAAATTATA
1 AAATTAAAATAAAGGACAAACCTTTTTGTAATTACAACAAATGACAAACCTTTTTATAAATCATA
* *
1927409 AT-AAATGAAAACCTT-TTGTAAATTACAATAAAATAAACCTTATTGT
66 ATAAAATCAAAA-CTTCTTATAAATTACAATAAAATAAACCTTATTGT
1927455 AAATTAAAATAAAGGAC-AACACTTTTTGTAAATTACAACAAA-GAACAAACCTTTTTATAAATC
1 AAATTAAAATAAAGGACAAAC-CTTTTTGT-AATTACAACAAATG-ACAAACCTTTTTATAAATC
1927518 ATAATAAAAATCAAAACTTCTTATAAATTACAATAA
63 ATAAT-AAAATCAAAACTTCTTATAAATTACAATAA
1927554 TGATATATAT
Statistics
Matches: 85, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
110 3 0.04
111 24 0.28
112 32 0.38
113 3 0.04
114 23 0.27
ACGTcount: A:0.50, C:0.11, G:0.05, T:0.34
Consensus pattern (112 bp):
AAATTAAAATAAAGGACAAACCTTTTTGTAATTACAACAAATGACAAACCTTTTTATAAATCATA
ATAAAATCAAAACTTCTTATAAATTACAATAAAATAAACCTTATTGT
Found at i:1928007 original size:35 final size:35
Alignment explanation
Indices: 1927957--1928027 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
1927947 AACGATCACT
**
1927957 GATGATTAATGATTAATAGTTAAAAATAGTTAACA
1 GATGATTAACAATTAATAGTTAAAAATAGTTAACA
*
1927992 GATGATTAACAATTAATAGTTAACAATAGTTAACA
1 GATGATTAACAATTAATAGTTAAAAATAGTTAACA
1928027 G
1 G
1928028 TTAACAATGG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.48, C:0.06, G:0.14, T:0.32
Consensus pattern (35 bp):
GATGATTAACAATTAATAGTTAAAAATAGTTAACA
Done.