Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005946.1 Hibiscus syriacus cultivar Beakdansim tig00013960_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: 2465359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 11
Found at i:1508387 original size:19 final size:18
Alignment explanation
Indices: 1508301--1508387 Score: 61
Period size: 19 Copynumber: 4.6 Consensus size: 18
1508291 TTTAAAAATA
* *
1508301 ATTTTTTCTTTCATTTTT
1 ATTTTTTTTTTCATATTT
1508319 ATTATCTTTTTTTC-TA-TT
1 ATT-T-TTTTTTTCATATTT
*
1508337 ATTTTTTTATTATCATATTA
1 ATTTTTTT-TT-TCATATTT
* *
1508357 ACATTTTGTTTTCATATTT
1 A-TTTTTTTTTTCATATTT
1508376 ATTTTTGTTTTT
1 ATTTTT-TTTTT
1508388 TATCTAACAT
Statistics
Matches: 53, Mismatches: 8, Indels: 15
0.70 0.11 0.20
Matches are distributed among these distances:
16 4 0.08
17 3 0.06
18 14 0.26
19 16 0.30
20 11 0.21
21 5 0.09
ACGTcount: A:0.18, C:0.08, G:0.02, T:0.71
Consensus pattern (18 bp):
ATTTTTTTTTTCATATTT
Found at i:1511128 original size:22 final size:22
Alignment explanation
Indices: 1511093--1511134 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1511083 AAGACGCTTG
* *
1511093 AAGACGTCGGGAGATCCCAAGC
1 AAGACGCCGAGAGATCCCAAGC
1511115 AAGACGCCGAGAGATCCCAA
1 AAGACGCCGAGAGATCCCAA
1511135 ATCTACTGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.36, C:0.29, G:0.29, T:0.07
Consensus pattern (22 bp):
AAGACGCCGAGAGATCCCAAGC
Found at i:1511884 original size:26 final size:28
Alignment explanation
Indices: 1511841--1511958 Score: 138
Period size: 28 Copynumber: 4.2 Consensus size: 28
1511831 GTTACAAGAT
*
1511841 ATATGTAAAATGTT-A-AAAAAATAAGG
1 ATATATAAAATGTTAATAAAAAATAAGG
1511867 ATAT-TAAAATGTTAA-AAAAAATAAGG
1 ATATATAAAATGTTAATAAAAAATAAGG
*
1511893 ATATATATAAAATGTTAATAAAAAATTAAAG
1 --ATATATAAAATGTTAATAAAAAA-TAAGG
*
1511924 ATATA-AAAATGTTAATAAATAATTAAGG
1 ATATATAAAATGTTAATAAA-AAATAAGG
1511952 ATATATA
1 ATATATA
1511959 TGGAATAGTA
Statistics
Matches: 81, Mismatches: 3, Indels: 13
0.84 0.03 0.13
Matches are distributed among these distances:
25 9 0.11
26 16 0.20
28 27 0.33
29 19 0.23
30 6 0.07
31 4 0.05
ACGTcount: A:0.59, C:0.00, G:0.10, T:0.31
Consensus pattern (28 bp):
ATATATAAAATGTTAATAAAAAATAAGG
Found at i:1511904 original size:54 final size:59
Alignment explanation
Indices: 1511838--1511959 Score: 173
Period size: 57 Copynumber: 2.2 Consensus size: 59
1511828 GATGTTACAA
* * *
1511838 GATATATGTAAAATGTT-A-AAAAAA-TAAGGATATTAAAATGTTAA-AAA-AAATAAG
1 GATATATATAAAATGTTAATAAAAAATTAAAGATATAAAAATGTTAATAAATAAATAAG
*
1511892 GATATATATAAAATGTTAATAAAAAATTAAAGATATAAAAATGTTAATAAATAATTAAG
1 GATATATATAAAATGTTAATAAAAAATTAAAGATATAAAAATGTTAATAAATAAATAAG
1511951 GATATATAT
1 GATATATAT
1511960 GGAATAGTAT
Statistics
Matches: 59, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
54 16 0.27
55 1 0.02
56 6 0.10
57 18 0.31
58 3 0.05
59 15 0.25
ACGTcount: A:0.58, C:0.00, G:0.11, T:0.31
Consensus pattern (59 bp):
GATATATATAAAATGTTAATAAAAAATTAAAGATATAAAAATGTTAATAAATAAATAAG
Found at i:1513264 original size:6 final size:6
Alignment explanation
Indices: 1513250--1514045 Score: 1303
Period size: 6 Copynumber: 133.0 Consensus size: 6
1513240 TTTGTTTCAA
* * * * *
1513250 ATACAT ATGCAT ATGCAT ATGCAT ATGCAT ATGCAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1513298 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1513346 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1513394 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1513442 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATAC--
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1513488 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1513536 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ACATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT --ATACAT ATACAT
1513586 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
* * *
1513634 ATACAT ATACAT ATACAT CTACAT CTACAT ATACAT ATACAT CTACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
* * * * * * * *
1513682 CTACAT CTACAT CTACAT CTACAT CTACAT CTACAT CTACAT CTACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
* * *
1513730 GTACAT GTACAT GTACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1513778 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1513826 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1513874 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1513922 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
* * * *
1513970 ATACAT ATACAT ATACAT ATACAT ATACAT GTACAT GTATAT GTAC--
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
* * * *
1514016 ATGCAT GTACAT GTATAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT
1514046 GTAATGTGTT
Statistics
Matches: 767, Mismatches: 17, Indels: 12
0.96 0.02 0.02
Matches are distributed among these distances:
4 6 0.01
6 755 0.98
8 6 0.01
ACGTcount: A:0.47, C:0.18, G:0.02, T:0.33
Consensus pattern (6 bp):
ATACAT
Found at i:1516028 original size:60 final size:60
Alignment explanation
Indices: 1515952--1516093 Score: 162
Period size: 60 Copynumber: 2.4 Consensus size: 60
1515942 TTTAGGGACC
*
1515952 AATGATATTCATAGTTTGGGAATGAAATTGGAATGTTCAAAAGTTTAAAGACTAATTT-A
1 AATGAGATTCATAGTTTGGGAATGAAATTGGAATGTTCAAAAGTTTAAAGACTAATTTGA
* * * * * *
1516011 GAATGAGATTCATAGTTT-TGAGATGAAATTTGAATTTTTAAATGTTTAAGGACTAATTTGA
1 -AATGAGATTCATAGTTTGGGA-ATGAAATTGGAATGTTCAAAAGTTTAAAGACTAATTTGA
** *
1516072 AATGAGGGTCATAATTTGGGAA
1 AATGAGATTCATAGTTTGGGAA
1516094 CATTTGATAA
Statistics
Matches: 68, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
59 2 0.03
60 63 0.93
61 3 0.04
ACGTcount: A:0.38, C:0.04, G:0.21, T:0.37
Consensus pattern (60 bp):
AATGAGATTCATAGTTTGGGAATGAAATTGGAATGTTCAAAAGTTTAAAGACTAATTTGA
Found at i:1516357 original size:12 final size:12
Alignment explanation
Indices: 1516340--1516376 Score: 56
Period size: 14 Copynumber: 2.9 Consensus size: 12
1516330 CAATTCTTTA
1516340 ATAAGTATATTT
1 ATAAGTATATTT
1516352 ATAAGTATATATTT
1 ATAAG--TATATTT
1516366 ATAAGTATATT
1 ATAAGTATATT
1516377 GCATTGTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 11 0.48
14 12 0.52
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (12 bp):
ATAAGTATATTT
Found at i:1516364 original size:14 final size:14
Alignment explanation
Indices: 1516345--1516375 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
1516335 CTTTAATAAG
1516345 TATATTTATAAGTA
1 TATATTTATAAGTA
1516359 TATATTTATAAGTA
1 TATATTTATAAGTA
1516373 TAT
1 TAT
1516376 TGCATTGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (14 bp):
TATATTTATAAGTA
Found at i:1522237 original size:24 final size:24
Alignment explanation
Indices: 1522186--1522246 Score: 79
Period size: 24 Copynumber: 2.6 Consensus size: 24
1522176 ACGAACGGAT
*
1522186 GTAAACGAACAC-AATAAACGAAC
1 GTAAACGAACACAAATAAACAAAC
* *
1522209 GTAAATGAACACAAATGAACAAAC
1 GTAAACGAACACAAATAAACAAAC
*
1522233 GTAAACAAACACAA
1 GTAAACGAACACAA
1522247 CAAATGAACA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 11 0.34
24 21 0.66
ACGTcount: A:0.59, C:0.20, G:0.11, T:0.10
Consensus pattern (24 bp):
GTAAACGAACACAAATAAACAAAC
Found at i:1522276 original size:47 final size:47
Alignment explanation
Indices: 1522168--1522276 Score: 128
Period size: 47 Copynumber: 2.3 Consensus size: 47
1522158 AATGATGAAC
** * * * *
1522168 GAACATAAACGAACGGATGTAAACGAACACAATAAACGAACGTAAAT
1 GAACATAAACGAACAAACGTAAACAAACACAACAAACGAACATAAAT
* * *
1522215 GAACACAAATGAACAAACGTAAACAAACACAACAAATGAACATAAAT
1 GAACATAAACGAACAAACGTAAACAAACACAACAAACGAACATAAAT
*
1522262 GAACGTAAACGAACA
1 GAACATAAACGAACA
1522277 TGAATGAAAA
Statistics
Matches: 50, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
47 50 1.00
ACGTcount: A:0.57, C:0.18, G:0.14, T:0.11
Consensus pattern (47 bp):
GAACATAAACGAACAAACGTAAACAAACACAACAAACGAACATAAAT
Found at i:1523437 original size:14 final size:14
Alignment explanation
Indices: 1523420--1523449 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1523410 TTCGATTATA
1523420 TTCGTTTATGTTCG
1 TTCGTTTATGTTCG
*
1523434 TTCGTTTGTGTTCG
1 TTCGTTTATGTTCG
1523448 TT
1 TT
1523450 AATAATTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.03, C:0.13, G:0.23, T:0.60
Consensus pattern (14 bp):
TTCGTTTATGTTCG
Found at i:1523578 original size:2 final size:2
Alignment explanation
Indices: 1523571--1523635 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
1523561 TTGTTTACGA
1523571 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1523613 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
1523636 GTCCCTATAT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1525196 original size:20 final size:20
Alignment explanation
Indices: 1525171--1525210 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1525161 TCTGGGCTTG
1525171 ATTATCGATACTGGATGAAC
1 ATTATCGATACTGGATGAAC
*
1525191 ATTATCGATATTGGATGAAC
1 ATTATCGATACTGGATGAAC
1525211 TGAGATGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (20 bp):
ATTATCGATACTGGATGAAC
Found at i:1528507 original size:2 final size:2
Alignment explanation
Indices: 1528500--1528525 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1528490 TTGTTTACGA
1528500 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
1528526 GAAATTTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1529575 original size:14 final size:14
Alignment explanation
Indices: 1529552--1529585 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1529542 TTTACCTTCC
*
1529552 TTCATCTTCTTCTT
1 TTCATTTTCTTCTT
*
1529566 TTCATTTTCTTTTT
1 TTCATTTTCTTCTT
1529580 TTCATT
1 TTCATT
1529586 ACCTTCTCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.09, C:0.21, G:0.00, T:0.71
Consensus pattern (14 bp):
TTCATTTTCTTCTT
Found at i:1530098 original size:20 final size:20
Alignment explanation
Indices: 1530073--1530112 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1530063 TTTGGGTTTT
1530073 ATTATCGATACTGGATGAAC
1 ATTATCGATACTGGATGAAC
*
1530093 ATTATCGATATTGGATGAAC
1 ATTATCGATACTGGATGAAC
1530113 TAGGATGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (20 bp):
ATTATCGATACTGGATGAAC
Found at i:1542599 original size:23 final size:23
Alignment explanation
Indices: 1542569--1542617 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
1542559 TATTCCAAAC
1542569 GCCGAGATGAATTTCTCACCAGT
1 GCCGAGATGAATTTCTCACCAGT
* *
1542592 GCCGAGATGAATTTCTCGCTAGT
1 GCCGAGATGAATTTCTCACCAGT
1542615 GCC
1 GCC
1542618 TTAATGGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (23 bp):
GCCGAGATGAATTTCTCACCAGT
Found at i:1553965 original size:20 final size:20
Alignment explanation
Indices: 1553940--1553991 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1553930 TTGCACTGGG
1553940 GTATCGATACTTTGAGAGGA
1 GTATCGATACTTTGAGAGGA
*
1553960 GTATCGATACTTTGATAGGA
1 GTATCGATACTTTGAGAGGA
1553980 GTATCGATACTT
1 GTATCGATACTT
1553992 AAGGGACAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.12, G:0.25, T:0.35
Consensus pattern (20 bp):
GTATCGATACTTTGAGAGGA
Found at i:1555218 original size:2 final size:2
Alignment explanation
Indices: 1555211--1555236 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1555201 CCTCAAATTA
1555211 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
1555237 CAAGATACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1555278 original size:12 final size:12
Alignment explanation
Indices: 1555263--1555288 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1555253 TTCATACATA
1555263 CATTCAATCATG
1 CATTCAATCATG
1555275 CATTCAATCATG
1 CATTCAATCATG
1555287 CA
1 CA
1555289 CTTGTCATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.27, G:0.08, T:0.31
Consensus pattern (12 bp):
CATTCAATCATG
Found at i:1557115 original size:34 final size:34
Alignment explanation
Indices: 1557072--1557140 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
1557062 AGCTTCCTCA
*
1557072 GGTTAGGGTCTGAGTTTAAGATTTTCAGTGTCAT
1 GGTTAGGGTCTGAGTTTAAGATTTTCAGTGACAT
1557106 GGTTAGGGTCTGAGTTTAAGATTTTCAGTGACAT
1 GGTTAGGGTCTGAGTTTAAGATTTTCAGTGACAT
1557140 G
1 G
1557141 ACAAGATTAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.22, C:0.09, G:0.30, T:0.39
Consensus pattern (34 bp):
GGTTAGGGTCTGAGTTTAAGATTTTCAGTGACAT
Found at i:1565716 original size:191 final size:191
Alignment explanation
Indices: 1565386--1566152 Score: 1302
Period size: 191 Copynumber: 4.0 Consensus size: 191
1565376 CCTGTTTCTA
* *
1565386 TTTACCACATTTCTCCCTCAATGATGGTGACTTGTTTATTTATATTTGCTAGCTTTAAATGTTTA
1 TTTACCACTTTTCTCCCTCATTGATGGTGACTTGTTTATTTATATTTGCTAGCTTTAAATGTTTA
*
1565451 CGAATCTTTCAACAGATTGATGAAAACATTGCAAGGGCACTTCAACAGGAGGAAGATACACTCCC
66 CGAATCTTTCAACAGATTGATGAAAACATTGCAAGGACACTTCAACAGGAGGAAGATACACTCCC
* *
1565516 CATTACTTCTACTCGTCATCTTCGTGAGCGTCTTCAGGTGAGTAAACTTGAAATTTTTAAT
131 CAGTACTTCTACTCGTCATCTTCGTGAGTGTCTTCAGGTGAGTAAACTTGAAATTTTTAAT
1565577 TTTACCACTTTTCTCCCTCATTGATGGTGACTTGTTTATTTATATTTGCTAGCTTTAAATGTTTA
1 TTTACCACTTTTCTCCCTCATTGATGGTGACTTGTTTATTTATATTTGCTAGCTTTAAATGTTTA
* * *
1565642 CGAATCTTTAAACAGATTGATGAAAACATTGCAAGGATACTTCAACAGGAGGAAGATACAATCCC
66 CGAATCTTTCAACAGATTGATGAAAACATTGCAAGGACACTTCAACAGGAGGAAGATACACTCCC
*
1565707 CAGTACTTCTACTCTTCATCTTCGTGAGTGTCTTCAGGTGAGTAAACTTGAAATTTTTAAT
131 CAGTACTTCTACTCGTCATCTTCGTGAGTGTCTTCAGGTGAGTAAACTTGAAATTTTTAAT
*
1565768 TTTATCACTTTTCTCCCTCATTGATGGTGACTTGTTTATTTATATTTGCTAGCTTTAAATGTTTA
1 TTTACCACTTTTCTCCCTCATTGATGGTGACTTGTTTATTTATATTTGCTAGCTTTAAATGTTTA
* * * * *
1565833 CGAATCTTTCTACAGAATGATGAAATCATTGCAAAGACACTTCAACAGGAGGAAGATACACTTCC
66 CGAATCTTTCAACAGATTGATGAAAACATTGCAAGGACACTTCAACAGGAGGAAGATACACTCCC
* *
1565898 CAGTATTTCTACTCGTCATCTTCGTGAGTGTCTTCAGGTGAGAAAACTTGAAATTTTTAAT
131 CAGTACTTCTACTCGTCATCTTCGTGAGTGTCTTCAGGTGAGTAAACTTGAAATTTTTAAT
* *
1565959 TCTACCACTTTTCTCCCTCATTGATGGTTACTTGTTTATTTATATTTGCTAGCTTTAAATGTTTA
1 TTTACCACTTTTCTCCCTCATTGATGGTGACTTGTTTATTTATATTTGCTAGCTTTAAATGTTTA
* *
1566024 CGAATCTTTCAACAGATTGAAGAAATCATTGCAATGG-CACTTCAACAGGAGGAAGATACACTCC
66 CGAATCTTTCAACAGATTGATGAAAACATTGCAA-GGACACTTCAACAGGAGGAAGATACACTCC
* * *
1566088 CCAGTACTTCTACTCATCACCTTCGTGAGTATCTTCAGGTGAGTAAACTTGAAATTTTTAAT
130 CCAGTACTTCTACTCGTCATCTTCGTGAGTGTCTTCAGGTGAGTAAACTTGAAATTTTTAAT
1566150 TTT
1 TTT
1566153 TTATTGTTTT
Statistics
Matches: 540, Mismatches: 35, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
191 539 1.00
192 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.37
Consensus pattern (191 bp):
TTTACCACTTTTCTCCCTCATTGATGGTGACTTGTTTATTTATATTTGCTAGCTTTAAATGTTTA
CGAATCTTTCAACAGATTGATGAAAACATTGCAAGGACACTTCAACAGGAGGAAGATACACTCCC
CAGTACTTCTACTCGTCATCTTCGTGAGTGTCTTCAGGTGAGTAAACTTGAAATTTTTAAT
Found at i:1578427 original size:166 final size:166
Alignment explanation
Indices: 1578148--1578478 Score: 511
Period size: 166 Copynumber: 2.0 Consensus size: 166
1578138 TTTTCCTTGC
* *
1578148 TTTTCCTTTTTGAATTTGTGCAAGTTACTCCTGTTGTATCATTCTTTGCTTCTTATGCAGAGAGG
1 TTTTCCTTTTTGAATTTGTGCAAGTTACTACTGTTATATCATTCTTTGCTTCTTATGCAGAGAGG
* * * *
1578213 CTCAGCAAGGCAGTCTCGTACTCGGTCTCCATTGCGGACTTTTCAGAATACTTCAAATAGGAGAG
66 CTCAGCAAGGCAGTCTCGTACTCGGTCCCCATTGCGAACTTCTCAGAATACTTCAAATAGAAGAG
** * *
1578278 GTGTACGGACTCATTTTTGTACTTCTTCTAGAGTGA
131 GTACACGGACTCATTTTTCTACTTATTCTAGAGTGA
*
1578314 TTTTCC-TTTTGAATTTGTGCAAGTTACTACTGTTTATATTATTCTTTGCTTCTTATGCAGAGAG
1 TTTTCCTTTTTGAATTTGTGCAAGTTACTACTG-TTATATCATTCTTTGCTTCTTATGCAGAGAG
*
1578378 GCTCAGCAAGGCAGTCTCGTGCTCGGTCCCCATTGCGAACTTCTCAGAATACTTCAAATAGAAGA
65 GCTCAGCAAGGCAGTCTCGTACTCGGTCCCCATTGCGAACTTCTCAGAATACTTCAAATAGAAGA
** *
1578443 GGTACACGGGTTCGTTTTTCTACTTATTCTAGAGTG
130 GGTACACGGACTCATTTTTCTACTTATTCTAGAGTG
1578479 TCGCGGTCAA
Statistics
Matches: 149, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
165 25 0.17
166 124 0.83
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.38
Consensus pattern (166 bp):
TTTTCCTTTTTGAATTTGTGCAAGTTACTACTGTTATATCATTCTTTGCTTCTTATGCAGAGAGG
CTCAGCAAGGCAGTCTCGTACTCGGTCCCCATTGCGAACTTCTCAGAATACTTCAAATAGAAGAG
GTACACGGACTCATTTTTCTACTTATTCTAGAGTGA
Found at i:1581162 original size:15 final size:14
Alignment explanation
Indices: 1581142--1581180 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
1581132 AAATTTATAT
1581142 TATATTAATATTAAA
1 TATATTAAT-TTAAA
*
1581157 TATATTAATGTAAA
1 TATATTAATTTAAA
1581171 -ATATTAATTT
1 TATATTAATTT
1581181 TAAAAGATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 9 0.41
14 4 0.18
15 9 0.41
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (14 bp):
TATATTAATTTAAA
Found at i:1581174 original size:13 final size:15
Alignment explanation
Indices: 1581142--1581178 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
1581132 AAATTTATAT
*
1581142 TATATTAATATTAAA
1 TATATTAATAGTAAA
1581157 TATATTAAT-GTAAA
1 TATATTAATAGTAAA
1581171 -ATATTAAT
1 TATATTAAT
1581179 TTTAAAAGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 8 0.38
14 4 0.19
15 9 0.43
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (15 bp):
TATATTAATAGTAAA
Found at i:1582273 original size:23 final size:23
Alignment explanation
Indices: 1582241--1582303 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
1582231 CTGAATGATT
*
1582241 CAGTGCTGACTGATTCAGCAAAA
1 CAGTGTTGACTGATTCAGCAAAA
*
1582264 CAGTGTTGACTAATTCAGCAAAA
1 CAGTGTTGACTGATTCAGCAAAA
*
1582287 CAGTGTTGAATGATTCA
1 CAGTGTTGACTGATTCA
1582304 TCACAGAAGT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.27
Consensus pattern (23 bp):
CAGTGTTGACTGATTCAGCAAAA
Found at i:1582331 original size:27 final size:27
Alignment explanation
Indices: 1582293--1582412 Score: 177
Period size: 27 Copynumber: 4.4 Consensus size: 27
1582283 AAAACAGTGT
* *
1582293 TGAATGATTCATCACAGAAGTACATCC
1 TGAATGATTCAGCACAGAAGTACATTC
* *
1582320 TGAATGATTCATCACAGAAGTACATTA
1 TGAATGATTCAGCACAGAAGTACATTC
*
1582347 TGAATGATTCAGCACATAAGTACATTC
1 TGAATGATTCAGCACAGAAGTACATTC
* *
1582374 TGAATGATTCAGCACATAAGTATATTC
1 TGAATGATTCAGCACAGAAGTACATTC
1582401 TGAATGATTCAG
1 TGAATGATTCAG
1582413 AGTCATTATC
Statistics
Matches: 87, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 87 1.00
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.30
Consensus pattern (27 bp):
TGAATGATTCAGCACAGAAGTACATTC
Found at i:1584749 original size:2 final size:2
Alignment explanation
Indices: 1584736--1584770 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1584726 CATGATCTAA
*
1584736 AT AT AA 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 A
1584771 GGAAGATATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1597701 original size:14 final size:14
Alignment explanation
Indices: 1597677--1597715 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
1597667 TCTGTCTATA
*
1597677 TTGCAGAGATTT-T
1 TTGCAGGGATTTAT
1597690 TATGCAGGGATTTAT
1 T-TGCAGGGATTTAT
1597705 TTGCAGGGATT
1 TTGCAGGGATT
1597716 ACTTCCCATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 1 0.04
14 20 0.87
15 2 0.09
ACGTcount: A:0.23, C:0.08, G:0.28, T:0.41
Consensus pattern (14 bp):
TTGCAGGGATTTAT
Found at i:1599395 original size:16 final size:16
Alignment explanation
Indices: 1599374--1599404 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1599364 TTGTAAAAAT
*
1599374 AAATATTTAAATTTAA
1 AAATATTAAAATTTAA
1599390 AAATATTAAAATTTA
1 AAATATTAAAATTTA
1599405 TTAAAATTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AAATATTAAAATTTAA
Found at i:1600849 original size:23 final size:23
Alignment explanation
Indices: 1600823--1600867 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1600813 CTGAAAGATC
* * *
1600823 CAGTGTTGACTGATTCAGCAAAA
1 CAGTGCTGAATGATTAAGCAAAA
1600846 CAGTGCTGAATGATTAAGCAAA
1 CAGTGCTGAATGATTAAGCAAA
1600868 GAAGTACATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (23 bp):
CAGTGCTGAATGATTAAGCAAAA
Found at i:1600965 original size:15 final size:15
Alignment explanation
Indices: 1600929--1600982 Score: 72
Period size: 15 Copynumber: 3.5 Consensus size: 15
1600919 AGAGCCTCTG
**
1600929 AATCATTCAACATTT
1 AATCATTCAACGCTT
1600944 GAATCATTCAACGCTT
1 -AATCATTCAACGCTT
*
1600960 AATCATTCAGCGCTT
1 AATCATTCAACGCTT
1600975 AATCATTC
1 AATCATTC
1600983 TGAAGTAAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
15 22 0.63
16 13 0.37
ACGTcount: A:0.33, C:0.24, G:0.07, T:0.35
Consensus pattern (15 bp):
AATCATTCAACGCTT
Found at i:1630232 original size:36 final size:36
Alignment explanation
Indices: 1630181--1630349 Score: 293
Period size: 36 Copynumber: 4.7 Consensus size: 36
1630171 CAAAAGTTTG
* * *
1630181 TTCCGATTCAAGTCGAACGGAGGGAAGCATCTGCTC
1 TTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCAC
* *
1630217 TTCTGATTCAAGTCGAACGGAGGGAAGCATCGGCAC
1 TTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCAC
1630253 TTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCAC
1 TTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCAC
1630289 TTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCAC
1 TTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCAC
1630325 TTCCGATTCAAGTCGAACGGAAGGA
1 TTCCGATTCAAGTCGAACGGAAGGA
1630350 TGTGTCTTAC
Statistics
Matches: 128, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 128 1.00
ACGTcount: A:0.29, C:0.24, G:0.28, T:0.19
Consensus pattern (36 bp):
TTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCAC
Found at i:1634327 original size:31 final size:31
Alignment explanation
Indices: 1634284--1634389 Score: 113
Period size: 31 Copynumber: 3.4 Consensus size: 31
1634274 CAATTGAAAG
* *
1634284 TTTAGGTATTAAAATGGACCAAAATTAATAC
1 TTTAAGTATTAAAATGGACCAAAATTAATAA
* * *
1634315 TTTAAGTATTAAAATGAACCAAAATGAAAAA
1 TTTAAGTATTAAAATGGACCAAAATTAATAA
* * * * * *
1634346 TTTAAGTACTAAAATTGACTAAAACTGATAG
1 TTTAAGTATTAAAATGGACCAAAATTAATAA
1634377 TTTAAGTATTAAA
1 TTTAAGTATTAAA
1634390 TGTATAATTA
Statistics
Matches: 60, Mismatches: 15, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 60 1.00
ACGTcount: A:0.49, C:0.08, G:0.11, T:0.32
Consensus pattern (31 bp):
TTTAAGTATTAAAATGGACCAAAATTAATAA
Found at i:1635031 original size:26 final size:30
Alignment explanation
Indices: 1634969--1635036 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 30
1634959 CGATAATGAG
*
1634969 CTTAACGAGCAACGAGTCGAGCAACAAGTTTT
1 CTTAACGAGCAACGAGACGAGCAACAA--TTT
1635001 CTTAACGAGC-ACGAGACGAGCAA-AA-TT
1 CTTAACGAGCAACGAGACGAGCAACAATTT
1635028 -TTAACGAGC
1 CTTAACGAGC
1635037 TTAAAGAACA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
26 9 0.26
27 2 0.06
30 2 0.06
31 12 0.34
32 10 0.29
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.19
Consensus pattern (30 bp):
CTTAACGAGCAACGAGACGAGCAACAATTT
Found at i:1635673 original size:21 final size:21
Alignment explanation
Indices: 1635649--1635690 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1635639 TAACAAAAAA
1635649 ATTAAATA-ATATATATTAAAT
1 ATTAAATATATAT-TATTAAAT
1635670 ATTAAATATATATTATTAAAT
1 ATTAAATATATATTATTAAAT
1635691 TCAGTCAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
ATTAAATATATATTATTAAAT
Found at i:1636217 original size:31 final size:31
Alignment explanation
Indices: 1636177--1636248 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
1636167 AAATAGTCCT
* *
1636177 TAACGTTATTGATTCATTCGATTTTAGTCTC
1 TAACATTATTAATTCATTCGATTTTAGTCTC
*
1636208 TAACATTATTAATTCGTTCGATTTTAGTCTC
1 TAACATTATTAATTCATTCGATTTTAGTCTC
1636239 TCAACCATTA
1 T-AA-CATTA
1636249 ACTCTCGTTC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
31 29 0.81
32 2 0.06
33 5 0.14
ACGTcount: A:0.26, C:0.18, G:0.10, T:0.46
Consensus pattern (31 bp):
TAACATTATTAATTCATTCGATTTTAGTCTC
Found at i:1636264 original size:32 final size:30
Alignment explanation
Indices: 1636188--1636273 Score: 84
Period size: 31 Copynumber: 2.8 Consensus size: 30
1636178 AACGTTATTG
* *
1636188 ATTCATTCGATTTTAGTCTCTAACATTATTA
1 ATTCGTTCAATTTTAGTCTCTAACATTA-TA
*
1636219 ATTCGTTCGATTTTAGTCTCTCAACCATTA-A
1 ATTCGTTCAATTTTAGTCTCT-AA-CATTATA
* *
1636250 CTCTCGTTCAATTTTAGTCCCTAA
1 AT-TCGTTCAATTTTAGTCTCTAA
1636274 GCCATGTTAG
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
31 24 0.50
32 19 0.40
33 5 0.10
ACGTcount: A:0.26, C:0.22, G:0.08, T:0.44
Consensus pattern (30 bp):
ATTCGTTCAATTTTAGTCTCTAACATTATA
Found at i:1637196 original size:113 final size:113
Alignment explanation
Indices: 1636998--1638014 Score: 1917
Period size: 113 Copynumber: 9.0 Consensus size: 113
1636988 CATATGAGCT
* * *
1636998 GCAAGGGTATTCTCGATTCTTGATGATCAAATTGCTTTTAATATGTCTCGGAAATCATGGTTGTT
1 GCAAGGGTATTCTGGATTCTTGATGATCAAATTGCTTTTAACATGTCTAGGAAATCATGGTTGTT
*
1637063 CTTGTGAGAACTAGATTATCTGTCCAATTGCTTATCTTATAAGGACCG
66 CTTGTGAGAACTATATTATCTGTCCAATTGCTTATCTTATAAGGACCG
* * *
1637111 GCAAGGGTATTCTCGATTCTTGATGATCAAATTGCTTTTAATATGTCTCGGAAATCATGGTTGTT
1 GCAAGGGTATTCTGGATTCTTGATGATCAAATTGCTTTTAACATGTCTAGGAAATCATGGTTGTT
*
1637176 CTTGTGAGAACTAGATTATCTGTCCAATTGCTTATCTTATAAGGACCG
66 CTTGTGAGAACTATATTATCTGTCCAATTGCTTATCTTATAAGGACCG
*
1637224 GCAAGGGTATTCTCGATTCTTGATGATCAAATTGCTTTTAACATGTCTAGGAAATCATGGTTGTT
1 GCAAGGGTATTCTGGATTCTTGATGATCAAATTGCTTTTAACATGTCTAGGAAATCATGGTTGTT
1637289 CTTGTGAGAACTATATTATCTGTCCAATTGCTTATCTTATAAGGACCG
66 CTTGTGAGAACTATATTATCTGTCCAATTGCTTATCTTATAAGGACCG
1637337 GCAAGGGTATTCTGGATTCTTGATGATCAAATTGCTTTTAACATGTCTAGGAAATCATGGTTGTT
1 GCAAGGGTATTCTGGATTCTTGATGATCAAATTGCTTTTAACATGTCTAGGAAATCATGGTTGTT
*
1637402 CTTGTGAGAACTAGATTATCTGTCCAATTGCTTATCTTATAAGGACCG
66 CTTGTGAGAACTATATTATCTGTCCAATTGCTTATCTTATAAGGACCG
1637450 GCAAGGGTATTCTGGATTCTTGATGATCAAATTGCTTTTAACATGTCTAGGAAATCATGGTTGTT
1 GCAAGGGTATTCTGGATTCTTGATGATCAAATTGCTTTTAACATGTCTAGGAAATCATGGTTGTT
*
1637515 CTTGTGAGAACTAGATTATCTGTCCAATTGCTTATCTTATAAGGACCG
66 CTTGTGAGAACTATATTATCTGTCCAATTGCTTATCTTATAAGGACCG
1637563 GCAAGGGTATTCTGGATTCTTGATGATCAAATTGCTTTTAACATGTCTAGGAAATCATGGTTGTT
1 GCAAGGGTATTCTGGATTCTTGATGATCAAATTGCTTTTAACATGTCTAGGAAATCATGGTTGTT
1637628 CTTGTGAGAACTATATTATCTGTCCAATTGCTTATCTTATAAGGACCG
66 CTTGTGAGAACTATATTATCTGTCCAATTGCTTATCTTATAAGGACCG
1637676 GCAAGGGTATTCTGGATTCTTGATGATCAAATTGCTTTTAACATGTCTAGGAAATCATGGTTGTT
1 GCAAGGGTATTCTGGATTCTTGATGATCAAATTGCTTTTAACATGTCTAGGAAATCATGGTTGTT
1637741 CTTGTGAGAACTATATTATCTGTCCAATTGCTTATCTTATAAGGACCG
66 CTTGTGAGAACTATATTATCTGTCCAATTGCTTATCTTATAAGGACCG
1637789 GCAAGGGTATTCTGGATTCTTGATGATCAAATTGCTTTTAACATGTCTAGGAAATCATGGTTGTT
1 GCAAGGGTATTCTGGATTCTTGATGATCAAATTGCTTTTAACATGTCTAGGAAATCATGGTTGTT
1637854 CTTGTGAGAACTATATTATCTGTCCAATTGCTTATCTTATAAGGACCG
66 CTTGTGAGAACTATATTATCTGTCCAATTGCTTATCTTATAAGGACCG
1637902 GCAAGGGTATTCTGGATTCTTGATGATCAAATTGCTTTTAACATGTCTAGGAAATCATGGTTGTT
1 GCAAGGGTATTCTGGATTCTTGATGATCAAATTGCTTTTAACATGTCTAGGAAATCATGGTTGTT
* *
1637967 CTCGTGAGAACTATATTATCTGTCCAACTGCTTATCTTATAAGGACCG
66 CTTGTGAGAACTATATTATCTGTCCAATTGCTTATCTTATAAGGACCG
1638015 AGTTAAACTA
Statistics
Matches: 896, Mismatches: 8, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
113 896 1.00
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.38
Consensus pattern (113 bp):
GCAAGGGTATTCTGGATTCTTGATGATCAAATTGCTTTTAACATGTCTAGGAAATCATGGTTGTT
CTTGTGAGAACTATATTATCTGTCCAATTGCTTATCTTATAAGGACCG
Found at i:1638373 original size:2 final size:2
Alignment explanation
Indices: 1638366--1638393 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1638356 TTGAACTTAG
1638366 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
1638394 TTAATATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1639139 original size:31 final size:31
Alignment explanation
Indices: 1639104--1639171 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
1639094 TTAAGGGAAA
*
1639104 TAGTCCCTAATATTATCAATCCATTCAATTT
1 TAGTCCCTAACATTATCAATCCATTCAATTT
* * * *
1639135 TAGTCCCTAACATTATCGATTCGTTCGATTT
1 TAGTCCCTAACATTATCAATCCATTCAATTT
1639166 TAGTCC
1 TAGTCC
1639172 TTTAGCCGTT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.26, C:0.24, G:0.09, T:0.41
Consensus pattern (31 bp):
TAGTCCCTAACATTATCAATCCATTCAATTT
Found at i:1643363 original size:49 final size:49
Alignment explanation
Indices: 1643269--1643363 Score: 136
Period size: 49 Copynumber: 1.9 Consensus size: 49
1643259 CTAACCGAAG
**
1643269 CAGGGGCGGACCTCCATGGAGCCCGGGATATCCCGGGCAACCCCTCATC
1 CAGGGGCGGACCTCCATGGAGCCCGGGATATCCCAAGCAACCCCTCATC
* * * *
1643318 CAGGGGTGGACCTCCATGGTGCCCGGGGTATCCCAAGCAATCCCTC
1 CAGGGGCGGACCTCCATGGAGCCCGGGATATCCCAAGCAACCCCTC
1643364 CACAAGTGCC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
49 40 1.00
ACGTcount: A:0.18, C:0.37, G:0.31, T:0.15
Consensus pattern (49 bp):
CAGGGGCGGACCTCCATGGAGCCCGGGATATCCCAAGCAACCCCTCATC
Found at i:1646064 original size:49 final size:49
Alignment explanation
Indices: 1645987--1646099 Score: 217
Period size: 49 Copynumber: 2.3 Consensus size: 49
1645977 ATCACTTTTT
*
1645987 TTTCTGGGATAAATTACTAATCATGTGTCTTTTTTATAAACCCAAAATA
1 TTTCAGGGATAAATTACTAATCATGTGTCTTTTTTATAAACCCAAAATA
1646036 TTTCAGGGATAAATTACTAATCATGTGTCTTTTTTATAAACCCAAAATA
1 TTTCAGGGATAAATTACTAATCATGTGTCTTTTTTATAAACCCAAAATA
1646085 TTTCAGGGATAAATT
1 TTTCAGGGATAAATT
1646100 TATAGTTTAA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 63 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (49 bp):
TTTCAGGGATAAATTACTAATCATGTGTCTTTTTTATAAACCCAAAATA
Found at i:1649899 original size:18 final size:19
Alignment explanation
Indices: 1649857--1649900 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
1649847 TTTGGTTCAC
1649857 GGAATATAAAATTACCAGT
1 GGAATATAAAATTACCAGT
1649876 GAGAATA-AAAGATTACCAG-
1 G-GAATATAAA-ATTACCAGT
1649895 GGAATA
1 GGAATA
1649901 GGATTATTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
18 5 0.22
19 5 0.22
20 13 0.57
ACGTcount: A:0.50, C:0.09, G:0.20, T:0.20
Consensus pattern (19 bp):
GGAATATAAAATTACCAGT
Found at i:1650644 original size:16 final size:15
Alignment explanation
Indices: 1650623--1650652 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1650613 TTTTTACCCC
1650623 TTCAATTTTCCTTTCT
1 TTCAATTTT-CTTTCT
1650639 TTCAATTTTCTTTC
1 TTCAATTTTCTTTC
1650653 CACCTTACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.13, C:0.23, G:0.00, T:0.63
Consensus pattern (15 bp):
TTCAATTTTCTTTCT
Found at i:1651328 original size:21 final size:21
Alignment explanation
Indices: 1651291--1651330 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1651281 GCTAATGTAT
*
1651291 AAAAATATATACCTAATTAAA
1 AAAAATATATACATAATTAAA
1651312 AAAAATATTATA-ATAATTA
1 AAAAATA-TATACATAATTA
1651331 TCTCTTAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (21 bp):
AAAAATATATACATAATTAAA
Found at i:1655692 original size:31 final size:31
Alignment explanation
Indices: 1655654--1655809 Score: 251
Period size: 31 Copynumber: 5.0 Consensus size: 31
1655644 AGGGTCGAGG
1655654 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
1655685 GTTTACCTATGTTCTTCAGGACAAATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1655716 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1655747 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
1655778 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
1655809 G
1 G
1655810 GTCCTTCGGG
Statistics
Matches: 117, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
31 116 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:1659778 original size:19 final size:19
Alignment explanation
Indices: 1659754--1659791 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1659744 TCGAATGCAT
1659754 TTCATGCACCGATGCACTC
1 TTCATGCACCGATGCACTC
*
1659773 TTCATGCATCGATGCACTC
1 TTCATGCACCGATGCACTC
1659792 GGAATATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.21, C:0.34, G:0.16, T:0.29
Consensus pattern (19 bp):
TTCATGCACCGATGCACTC
Found at i:1659786 original size:64 final size:61
Alignment explanation
Indices: 1659711--1659917 Score: 193
Period size: 64 Copynumber: 3.2 Consensus size: 61
1659701 TGCGTCAAAC
* *
1659711 CATGCATCGATGCACCTATGATTTAATTGAACATCGAATGCATTTCATGCACCGATGCACTCTT
1 CATGCATCGATGCACC-ATGATTT--TTAAACATCGAATGCATTTCATGCATCGATGCACTCTT
* * ****
1659775 CATGCATCGATGCACTCGGAAT-ATTTTCAAACATCGAATGCATTTGATGCATCGATGCACAAGC
1 CATGCATCGATGCAC-C---ATGATTTTTAAACATCGAATGCATTTCATGCATCGATGCACTCTT
* * *
1659839 CATGCATCGATGCACCAGGCTATTTTTCAAACATCGAATGCACTTCATGCATCGGTGCACTCTT
1 CATGCATCGATGCACCATG--ATTTTT-AAACATCGAATGCATTTCATGCATCGATGCACTCTT
*
1659903 -AGTGCACCGATGCAC
1 CA-TGCATCGATGCAC
1659918 TAGGAGTCCA
Statistics
Matches: 116, Mismatches: 19, Indels: 16
0.77 0.13 0.11
Matches are distributed among these distances:
60 1 0.01
63 7 0.06
64 101 0.87
65 1 0.01
66 4 0.03
67 2 0.02
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (61 bp):
CATGCATCGATGCACCATGATTTTTAAACATCGAATGCATTTCATGCATCGATGCACTCTT
Found at i:1663801 original size:32 final size:32
Alignment explanation
Indices: 1663720--1663801 Score: 94
Period size: 32 Copynumber: 2.6 Consensus size: 32
1663710 AAAGGTCGAT
* *
1663720 AAATTTAATGGCTATCTTACAACAGTTTGATA
1 AAATTTAATGACTATTTTACAACAGTTTGATA
* ** *
1663752 AAATTTAATGA-TCATTTTATAGTAGTTTTATA
1 AAATTTAATGACT-ATTTTACAACAGTTTGATA
1663784 AAATTTAATGACTATTTT
1 AAATTTAATGACTATTTT
1663802 GTTACTTTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
31 1 0.02
32 40 0.95
33 1 0.02
ACGTcount: A:0.38, C:0.07, G:0.10, T:0.45
Consensus pattern (32 bp):
AAATTTAATGACTATTTTACAACAGTTTGATA
Found at i:1664974 original size:20 final size:21
Alignment explanation
Indices: 1664949--1665000 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1664939 TTTTCCCAAT
*
1664949 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1664969 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1664990 TCGCAATGCGA
1 TCGCAATGCGA
1665001 TACTTACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1665013 original size:41 final size:41
Alignment explanation
Indices: 1664986--1665063 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
1664976 GCGAATTGGG
* * *
1664986 AAAATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTTACTATCGCAACGCGATAATAC
*
1665027 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATA
1 AAAATCGCAACGAGATACTTACTATCGCAACGCGATA
1665064 CTGACTTTCG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.23
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTTACTATCGCAACGCGATAATAC
Found at i:1665014 original size:20 final size:20
Alignment explanation
Indices: 1664989--1665082 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
1664979 AATTGGGAAA
*
1664989 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTTACT
* * *
1665009 ATCGCAATGCGATA-ATACAAA
1 ATCGCAACGCGATACTTAC--T
*
1665030 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTTACT
* *
1665050 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTTACT
*
1665070 TTCGCAACGCGAT
1 ATCGCAACGCGAT
1665083 TTACATAATC
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 3 0.05
20 44 0.71
21 12 0.19
22 3 0.05
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTTACT
Found at i:1665299 original size:22 final size:22
Alignment explanation
Indices: 1665271--1665314 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1665261 ACTCTCTCAC
1665271 CCATCTCCGACGAAATCCGTCT
1 CCATCTCCGACGAAATCCGTCT
*
1665293 CCATCTCCGGCGAAATCCGTCT
1 CCATCTCCGACGAAATCCGTCT
1665315 ATCTAAATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.41, G:0.16, T:0.23
Consensus pattern (22 bp):
CCATCTCCGACGAAATCCGTCT
Found at i:1666842 original size:21 final size:21
Alignment explanation
Indices: 1666816--1666860 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1666806 GATTTCTGGG
* *
1666816 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1666837 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1666858 CAA
1 CAA
1666861 ACGAACAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1667538 original size:23 final size:24
Alignment explanation
Indices: 1667495--1667541 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
1667485 ATATGGCATG
*
1667495 TGATATGAAAGTGTATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
1667519 TGATATGAAA-TATATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
1667542 ACAAGTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.34
Consensus pattern (24 bp):
TGATATGAAAGTATATATGTGAAA
Found at i:1667854 original size:31 final size:31
Alignment explanation
Indices: 1667816--1668033 Score: 366
Period size: 31 Copynumber: 7.0 Consensus size: 31
1667806 AGGGTCGAGG
1667816 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1667847 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1667878 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1667909 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1667940 GTTTACCTATGTTCTTCGGGACATACGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
1667971 GCTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
1668002 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
1668033 G
1 G
1668034 GTCCTTCGGG
Statistics
Matches: 178, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
31 177 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:1669517 original size:18 final size:18
Alignment explanation
Indices: 1669496--1669540 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
1669486 TCCACTTTGG
* *
1669496 GAGCCATCACCTCGCCCA
1 GAGCCATCACCCCACCCA
*
1669514 GAGCTATCACCCCACCCA
1 GAGCCATCACCCCACCCA
1669532 GAGCCATCA
1 GAGCCATCA
1669541 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.47, G:0.16, T:0.11
Consensus pattern (18 bp):
GAGCCATCACCCCACCCA
Found at i:1670037 original size:19 final size:18
Alignment explanation
Indices: 1670013--1670127 Score: 85
Period size: 19 Copynumber: 6.3 Consensus size: 18
1670003 TAGTTTACTT
*
1670013 TCGCAACACGAAATGACTA
1 TCGCAACACGAAATGA-AA
* **
1670032 TCGCAACGCGGAAATGGCTA
1 TCGCAACAC-GAAAT-GAAA
**
1670052 TCGCAATGCGAAATGAAAA
1 TCGCAACACGAAATG-AAA
*
1670071 TCGC-A-ACGACA--AAA
1 TCGCAACACGAAATGAAA
*
1670085 TCGCAACGCGAAATGAAA
1 TCGCAACACGAAATGAAA
1670103 TCGCAACACGAAATGAAAA
1 TCGCAACACGAAATG-AAA
1670122 TCGCAA
1 TCGCAA
1670128 TGCGATTTGT
Statistics
Matches: 78, Mismatches: 10, Indels: 16
0.75 0.10 0.15
Matches are distributed among these distances:
14 7 0.09
15 1 0.01
16 4 0.05
17 4 0.05
18 19 0.24
19 27 0.35
20 15 0.19
21 1 0.01
ACGTcount: A:0.43, C:0.23, G:0.20, T:0.13
Consensus pattern (18 bp):
TCGCAACACGAAATGAAA
Found at i:1670164 original size:14 final size:14
Alignment explanation
Indices: 1670145--1670201 Score: 60
Period size: 14 Copynumber: 3.8 Consensus size: 14
1670135 TGTGTTTCGT
1670145 GTTGCGATTTTGTC
1 GTTGCGATTTTGTC
* *
1670159 GTTGCGGTTTCATTTCGC
1 GTTGCGATTT--TGT--C
1670177 GTTGCGATTTTGTC
1 GTTGCGATTTTGTC
1670191 GTTGCGATTTT
1 GTTGCGATTTT
1670202 CATTTCGCAT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
14 21 0.60
16 4 0.11
18 10 0.29
ACGTcount: A:0.07, C:0.16, G:0.28, T:0.49
Consensus pattern (14 bp):
GTTGCGATTTTGTC
Found at i:1670181 original size:32 final size:33
Alignment explanation
Indices: 1670139--1670217 Score: 124
Period size: 32 Copynumber: 2.4 Consensus size: 33
1670129 GCGATTTGTG
*
1670139 TTTCGTGTTGCGATTTTGTCGTTGCG-GTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGAGTTTCA
*
1670171 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGAGTTTCA
*
1670204 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
1670218 AGCCATTTCC
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
32 25 0.58
33 18 0.42
ACGTcount: A:0.09, C:0.18, G:0.25, T:0.48
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGAGTTTCA
Found at i:1670216 original size:19 final size:19
Alignment explanation
Indices: 1670190--1670256 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
1670180 GCGATTTTGT
**
1670190 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
* *
1670209 CATTGCGATAGCCATTTCCG
1 CGTTGCGATAGTCATTT-CG
1670229 CGTTGCGATAGTCATTTCG
1 CGTTGCGATAGTCATTTCG
1670248 CGTTGCGAT
1 CGTTGCGAT
1670257 TTTAAGTTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.37
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:1670236 original size:20 final size:19
Alignment explanation
Indices: 1670202--1670256 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
1670192 TTGCGATTTT
*
1670202 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
1670221 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
1670241 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
1670257 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:1672271 original size:19 final size:19
Alignment explanation
Indices: 1672247--1672317 Score: 106
Period size: 19 Copynumber: 3.7 Consensus size: 19
1672237 AAAACAGACT
*
1672247 ATCGCAACGCGAAATGGAA
1 ATCGCAACGCGAAATGAAA
*
1672266 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
1672285 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
1672304 ATCGCAACGAGAAA
1 ATCGCAACGCGAAA
1672318 ATCGCAATGC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 48 1.00
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:1672318 original size:33 final size:36
Alignment explanation
Indices: 1672247--1672329 Score: 109
Period size: 38 Copynumber: 2.3 Consensus size: 36
1672237 AAAACAGACT
* *
1672247 ATCGCAACGCGAAATGGAAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAAA
1672285 ATCGCAATGCGAAATGAAAATCGCAA-CG-A-GAAA
1 ATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAA
1672318 ATCGCAATGCGA
1 ATCGCAATGCGA
1672330 TTTTCATTTC
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
33 16 0.37
34 1 0.02
36 2 0.05
38 24 0.56
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.13
Consensus pattern (36 bp):
ATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAA
Found at i:1672373 original size:20 final size:20
Alignment explanation
Indices: 1672348--1672425 Score: 138
Period size: 20 Copynumber: 3.9 Consensus size: 20
1672338 TCGCATTGCG
* *
1672348 ATTTTCTCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAGCC
1672368 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
1672388 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
1672408 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
1672426 TCAAATGAAT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 56 1.00
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.37
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:1673489 original size:24 final size:24
Alignment explanation
Indices: 1673462--1673515 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1673452 GTATTCGAAA
* *
1673462 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
1673486 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
1673510 TTTGAT
1 TTTGAT
1673516 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:1676045 original size:33 final size:33
Alignment explanation
Indices: 1676003--1676129 Score: 193
Period size: 33 Copynumber: 3.8 Consensus size: 33
1675993 GGAAATTACT
1676003 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
1676036 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
1676068 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
1676102 ATCGCAATGCGAAATGAAAATCGTAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
1676130 CGAATTTCAT
Statistics
Matches: 84, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
32 1 0.01
33 82 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1676110 original size:66 final size:66
Alignment explanation
Indices: 1676004--1676137 Score: 241
Period size: 66 Copynumber: 2.0 Consensus size: 66
1675994 GAAATTACTA
*
1676004 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1676069 T
66 T
* *
1676070 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGTAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1676135 T
66 T
1676136 TC
1 TC
1676138 ATTTCGCATT
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.41, C:0.19, G:0.22, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:1676279 original size:14 final size:14
Alignment explanation
Indices: 1676260--1676296 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1676250 CATCAATTAA
1676260 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1676274 ACAAATCACCTTTT
1 ACAAATCAACTTTT
1676288 ACAAATCAA
1 ACAAATCAA
1676297 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1677709 original size:21 final size:21
Alignment explanation
Indices: 1677643--1677709 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1677633 GTGAATCGGG
*
1677643 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
1677663 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
1677685 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
1677706 CTCT
1 CTCT
1677710 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:1677728 original size:42 final size:41
Alignment explanation
Indices: 1677643--1677765 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
1677633 GTGAATCGGG
* * * * *
1677643 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
1677685 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
1677727 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
1677766 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:1679812 original size:39 final size:37
Alignment explanation
Indices: 1679769--1679895 Score: 127
Period size: 39 Copynumber: 3.4 Consensus size: 37
1679759 TCTTTTGGTT
*
1679769 GAAATGAAAATCGCAACGAGATAATGAGAATCGCAACGC
1 GAAATGAAAATCGCAACG-GA-AATGAAAATCGCAACGC
** * * *
1679808 GAAATGACTATCGCGAC---CA-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGGAAATGAAAATCGCAACGC
*
1679841 GAAATGAAAATCGCAACCGCGAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAA-CG-GAAATGAAAATCGCAACGC
1679880 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1679896 TGCGATTTTG
Statistics
Matches: 71, Mismatches: 11, Indels: 12
0.76 0.12 0.13
Matches are distributed among these distances:
33 26 0.37
34 2 0.03
38 1 0.01
39 42 0.59
ACGTcount: A:0.46, C:0.22, G:0.20, T:0.12
Consensus pattern (37 bp):
GAAATGAAAATCGCAACGGAAATGAAAATCGCAACGC
Found at i:1679820 original size:19 final size:19
Alignment explanation
Indices: 1679769--1679900 Score: 139
Period size: 19 Copynumber: 7.1 Consensus size: 19
1679759 TCTTTTGGTT
*
1679769 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
1679788 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
** *
1679808 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
1679826 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
1679841 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
1679861 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
1679880 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
1679899 GA
1 GA
1679901 TTTTGGTTTC
Statistics
Matches: 95, Mismatches: 11, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
14 10 0.11
15 2 0.02
18 2 0.02
19 46 0.48
20 35 0.37
ACGTcount: A:0.45, C:0.22, G:0.21, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:1679929 original size:19 final size:19
Alignment explanation
Indices: 1679896--1679976 Score: 73
Period size: 19 Copynumber: 4.5 Consensus size: 19
1679886 AAAATCGCAA
**
1679896 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
1679915 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
1679934 TGCGA---TTA--TCTCGT
1 TGCGATTTTTATTTCGCGT
**
1679948 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
1679968 TGCGATTTT
1 TGCGATTTT
1679977 CATTCTCGAA
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
14 10 0.20
16 3 0.06
17 3 0.06
19 23 0.46
20 11 0.22
ACGTcount: A:0.11, C:0.17, G:0.25, T:0.47
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:1680587 original size:20 final size:20
Alignment explanation
Indices: 1680494--1680587 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
1680484 CGCTATGTAA
* *
1680494 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTAAGT
*
1680514 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTAAGT
* * *
1680534 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCGTTGCGA--TAGTAAGT
*
1680555 ATCGCATTGCGATAGTAAGT
1 ATCGCGTTGCGATAGTAAGT
*
1680575 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
1680588 TTTCCCAATT
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 3 0.05
20 45 0.73
21 12 0.19
22 2 0.03
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTAAGT
Found at i:1680605 original size:21 final size:21
Alignment explanation
Indices: 1680576--1680668 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
1680566 ATAGTAAGTA
1680576 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
1680597 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
1680617 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
1680638 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
1680658 TCGCATTGCGA
1 TCGCATTGCGA
1680669 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:1680606 original size:41 final size:41
Alignment explanation
Indices: 1680515--1680649 Score: 148
Period size: 41 Copynumber: 3.3 Consensus size: 41
1680505 AAAGTCAGTA
* * * ** *
1680515 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-GTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
*
1680555 ATCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
1680597 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
1680638 TCGCGTTGCGAT
1 TCGCGTTGCGAT
1680650 TTACTTATTC
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
40 4 0.05
41 75 0.93
42 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:1680650 original size:41 final size:41
Alignment explanation
Indices: 1680576--1680668 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
1680566 ATAGTAAGTA
1680576 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1680617 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1680658 TCGCATTGCGA
1 TCGCATTGCGA
1680669 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:1681077 original size:18 final size:19
Alignment explanation
Indices: 1681054--1681100 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
1681044 CTGTTACTAG
1681054 TGAACCGGAAG-GAACCGT
1 TGAACCGGAAGTGAACCGT
**
1681072 TGAACCGGCTGTGAACCGT
1 TGAACCGGAAGTGAACCGT
1681091 TCGAACCGGA
1 T-GAACCGGA
1681101 TCGGACCTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 9 0.38
19 8 0.33
20 7 0.29
ACGTcount: A:0.28, C:0.26, G:0.32, T:0.15
Consensus pattern (19 bp):
TGAACCGGAAGTGAACCGT
Found at i:1682627 original size:60 final size:60
Alignment explanation
Indices: 1682551--1682733 Score: 230
Period size: 60 Copynumber: 3.0 Consensus size: 60
1682541 ATATATCCCT
*
1682551 AAACTAT-AACCATCATTTTAAATTAG-CCGCTAAACTTTTAAATATTCTAATTTTATCCAC
1 AAACTATGAACC-TCATTTTAAATTAGTCC-CTAAACTTTTAAATATTCTAATTTTATCCTC
* * *
1682611 AAACTATGAATCTCATTTTAAATTAGTCCTTAAACTTTTGAAA-ATTCTAATTTTATCCTT
1 AAACTATGAACCTCATTTTAAATTAGTCCCTAAACTTTT-AAATATTCTAATTTTATCCTC
* * * *
1682671 AAACTATGACCCTC-TTTCAGAATTAGTCCCCAAACTTTTAGATATTCTAATTTTATCCTC
1 AAACTATGAACCTCATTTTA-AATTAGTCCCTAAACTTTTAAATATTCTAATTTTATCCTC
1682731 AAA
1 AAA
1682734 TTCATTCTAA
Statistics
Matches: 107, Mismatches: 11, Indels: 10
0.84 0.09 0.08
Matches are distributed among these distances:
59 6 0.06
60 93 0.87
61 8 0.07
ACGTcount: A:0.36, C:0.20, G:0.05, T:0.40
Consensus pattern (60 bp):
AAACTATGAACCTCATTTTAAATTAGTCCCTAAACTTTTAAATATTCTAATTTTATCCTC
Found at i:1683040 original size:60 final size:60
Alignment explanation
Indices: 1682927--1683045 Score: 148
Period size: 60 Copynumber: 2.0 Consensus size: 60
1682917 CAGGGTTTGG
* * * * * * *
1682927 GGATGAAATTGAAATGTTCAAAAGTTTGAGGACCAATTTAGAATCATTATCATAGTTTAA
1 GGATGAAATTAAAATATTCAAAAGTTTAAGGACCAATTTAAAATAATGATCATACTTTAA
* * *
1682987 GGATGAAATTAAAATATTTAAAAGTTTAAGGACTAATTTAAAATAATGGTCATACTTTA
1 GGATGAAATTAAAATATTCAAAAGTTTAAGGACCAATTTAAAATAATGATCATACTTTA
1683046 TGGACATGTG
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 49 1.00
ACGTcount: A:0.43, C:0.07, G:0.16, T:0.34
Consensus pattern (60 bp):
GGATGAAATTAAAATATTCAAAAGTTTAAGGACCAATTTAAAATAATGATCATACTTTAA
Found at i:1683326 original size:10 final size:10
Alignment explanation
Indices: 1683313--1683430 Score: 56
Period size: 10 Copynumber: 10.5 Consensus size: 10
1683303 CGAACGGATG
1683313 TAAACGAACA
1 TAAACGAACA
*
1683323 TAAATGAACACAA
1 TAAACG-A-AC-A
1683336 TAAACGAACA
1 TAAACGAACA
*
1683346 CAAACGAACGAA
1 TAAACGAAC--A
*
1683358 CGTAAACGATCA
1 --TAAACGAACA
1683370 TAAACGAACACAA
1 TAAACG-A-AC-A
* *
1683383 AAAATGAACA
1 TAAACGAACA
1683393 TAAACGAACAAAA
1 TAAACGAAC---A
*
1683406 CAAACGAACA
1 TAAACGAACA
*
1683416 TAAATGAACA
1 TAAACGAACA
1683426 TAAAC
1 TAAAC
1683431 CACAACAACA
Statistics
Matches: 81, Mismatches: 14, Indels: 26
0.67 0.12 0.21
Matches are distributed among these distances:
10 41 0.51
11 6 0.07
12 7 0.09
13 20 0.25
14 7 0.09
ACGTcount: A:0.60, C:0.19, G:0.10, T:0.10
Consensus pattern (10 bp):
TAAACGAACA
Found at i:1683343 original size:23 final size:23
Alignment explanation
Indices: 1683277--1683425 Score: 129
Period size: 23 Copynumber: 6.3 Consensus size: 23
1683267 TTAAATGATG
* *
1683277 AACGAACACAAATGAACGAATATA
1 AACGAACAC-AATAAACGAACATA
** *
1683301 AACGAACGGATGTAAACGAACATA
1 AACGAACACA-ATAAACGAACATA
* *
1683325 AATGAACACAATAAACGAACACA
1 AACGAACACAATAAACGAACATA
* *
1683348 AACGAACGA-ACGTAAACGATCATA
1 AACGAAC-ACA-ATAAACGAACATA
* *
1683372 AACGAACACAAAAAATGAACATA
1 AACGAACACAATAAACGAACATA
* *
1683395 AACGAACAAAACAAACGAACATA
1 AACGAACACAATAAACGAACATA
*
1683418 AATGAACA
1 AACGAACA
1683426 TAAACCACAA
Statistics
Matches: 99, Mismatches: 22, Indels: 9
0.76 0.17 0.07
Matches are distributed among these distances:
23 56 0.57
24 43 0.43
ACGTcount: A:0.58, C:0.19, G:0.13, T:0.10
Consensus pattern (23 bp):
AACGAACACAATAAACGAACATA
Found at i:1683351 original size:47 final size:47
Alignment explanation
Indices: 1683280--1683425 Score: 168
Period size: 47 Copynumber: 3.1 Consensus size: 47
1683270 AATGATGAAC
* * * *
1683280 GAACACAAATGAACGAATATAAACGAACGGATGTAAACGAACATAAAT
1 GAACAC-AATAAACGAACATAAACGAACGAAAGTAAACGAACATAAAT
* * * *
1683328 GAACACAATAAACGAACACAAACGAACGAACGTAAACGATCATAAAC
1 GAACACAATAAACGAACATAAACGAACGAAAGTAAACGAACATAAAT
* * **
1683375 GAACACAAAAAATGAACATAAACGAAC-AAAACAAACGAACATAAAT
1 GAACACAATAAACGAACATAAACGAACGAAAGTAAACGAACATAAAT
1683421 GAACA
1 GAACA
1683426 TAAACCACAA
Statistics
Matches: 83, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
46 19 0.23
47 58 0.70
48 6 0.07
ACGTcount: A:0.58, C:0.18, G:0.13, T:0.10
Consensus pattern (47 bp):
GAACACAATAAACGAACATAAACGAACGAAAGTAAACGAACATAAAT
Found at i:1683586 original size:14 final size:14
Alignment explanation
Indices: 1683567--1683609 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
1683557 AGATTGGGCT
*
1683567 AAACATAAATGAAC
1 AAACATAAACGAAC
1683581 AAACATAAACGAAC
1 AAACATAAACGAAC
*
1683595 GAAA-GTAAACGAAC
1 -AAACATAAACGAAC
1683609 A
1 A
1683610 TAAACAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
13 1 0.04
14 22 0.85
15 3 0.12
ACGTcount: A:0.63, C:0.16, G:0.12, T:0.09
Consensus pattern (14 bp):
AAACATAAACGAAC
Found at i:1688930 original size:22 final size:22
Alignment explanation
Indices: 1688905--1688947 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1688895 GATTTTTTTG
1688905 GAAAATA-AAAACAAAAATAAAT
1 GAAAATATAAAA-AAAAATAAAT
*
1688927 GAAAATATAAAAAAACATAAA
1 GAAAATATAAAAAAAAATAAA
1688948 AAATATGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.77, C:0.05, G:0.05, T:0.14
Consensus pattern (22 bp):
GAAAATATAAAAAAAAATAAAT
Found at i:1705072 original size:30 final size:30
Alignment explanation
Indices: 1705009--1705080 Score: 74
Period size: 30 Copynumber: 2.4 Consensus size: 30
1704999 GATATGATAT
* * *
1705009 ATATTATATAATCATTTTGAATGATGTGAC
1 ATATCATATAATCACTTTGAATGATGAGAC
* * *
1705039 ATATCATATCATCACTTTGAGTGATGAGGC
1 ATATCATATAATCACTTTGAATGATGAGAC
1705069 ATAT-ATTATAAT
1 ATATCA-TATAAT
1705081 GTTATTTCAG
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
29 1 0.03
30 33 0.97
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.40
Consensus pattern (30 bp):
ATATCATATAATCACTTTGAATGATGAGAC
Found at i:1705556 original size:2 final size:2
Alignment explanation
Indices: 1705549--1705581 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1705539 TATCATATTA
1705549 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 A
1705582 ATAGCATAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1705656 original size:24 final size:25
Alignment explanation
Indices: 1705602--1705656 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
1705592 ACATGACACG
* *
1705602 ATATCATTTTAGACACATACATCTT
1 ATATTATTTTAGACACACACATCTT
*
1705627 ATTATTATTTTAGACACACATATC-T
1 A-TATTATTTTAGACACACACATCTT
1705652 ATATT
1 ATATT
1705657 TCCAAACAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
24 4 0.15
25 3 0.12
26 19 0.73
ACGTcount: A:0.36, C:0.16, G:0.04, T:0.44
Consensus pattern (25 bp):
ATATTATTTTAGACACACACATCTT
Found at i:1706373 original size:2 final size:2
Alignment explanation
Indices: 1706356--1706442 Score: 142
Period size: 2 Copynumber: 44.5 Consensus size: 2
1706346 TAAATAGCCA
* *
1706356 AT AT AA AT AA AT AT AT AT AT AT AT AT AT AT AT -T 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
1706397 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- 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
1706438 AT AT A
1 AT AT A
1706443 ACTCTTTTAG
Statistics
Matches: 79, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
1 2 0.03
2 77 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1708886 original size:4 final size:4
Alignment explanation
Indices: 1708877--1708909 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
1708867 TATGTTTATG
1708877 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
1708910 ATACTATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TGTA
Found at i:1710098 original size:17 final size:17
Alignment explanation
Indices: 1710072--1710106 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1710062 TTTAAAATCG
1710072 TTTACCTAATGCTTCGT
1 TTTACCTAATGCTTCGT
* *
1710089 TTTACGTAATTCTTCGT
1 TTTACCTAATGCTTCGT
1710106 T
1 T
1710107 GGGATTTGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.17, C:0.20, G:0.11, T:0.51
Consensus pattern (17 bp):
TTTACCTAATGCTTCGT
Found at i:1716088 original size:55 final size:56
Alignment explanation
Indices: 1715891--1716077 Score: 243
Period size: 56 Copynumber: 3.4 Consensus size: 56
1715881 CCTTATTTTT
* * *
1715891 TAGATATATTCGATTTCGAGACTCCTATTTTTATGTTTCTTAATGGCAACAAGTGA
1 TAGATATACTCGATTTCGGGACTCCTATTTTTATGTTTCTTAATGGCAACAACTGA
* * * * *
1715947 TACATATATTTGATTTCGGGAC-CTCTATTTTTATATTTCTTAATGACAACAACTGA
1 TAGATATACTCGATTTCGGGACTC-CTATTTTTATGTTTCTTAATGGCAACAACTGA
* * * *
1716003 TAGATATACTCAATTTCGGGACTCCTA-TTTTATGTTTATTAATGGCAATAACTTA
1 TAGATATACTCGATTTCGGGACTCCTATTTTTATGTTTCTTAATGGCAACAACTGA
1716058 TAGATATACTCGATTTCGGG
1 TAGATATACTCGATTTCGGG
1716078 GTTCTTATTT
Statistics
Matches: 113, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
55 43 0.38
56 69 0.61
57 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.14, T:0.41
Consensus pattern (56 bp):
TAGATATACTCGATTTCGGGACTCCTATTTTTATGTTTCTTAATGGCAACAACTGA
Found at i:1725034 original size:2 final size:2
Alignment explanation
Indices: 1725029--1725055 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1725019 TATTTTAAAT
1725029 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1725056 TTATTTATTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1727508 original size:16 final size:17
Alignment explanation
Indices: 1727468--1727513 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
1727458 TATTATTACT
* *
1727468 ATATAATATTAATCAAA
1 ATATTATATTAAACAAA
*
1727485 ATATTATATTAAACCAA
1 ATATTATATTAAACAAA
1727502 A-ATTATATTAAA
1 ATATTATATTAAA
1727514 TATACATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
16 11 0.42
17 15 0.58
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.37
Consensus pattern (17 bp):
ATATTATATTAAACAAA
Found at i:1729574 original size:18 final size:18
Alignment explanation
Indices: 1729551--1729586 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1729541 TGGAAAGACG
* *
1729551 GCGGCATCTTATATGGCT
1 GCGGCATCATAAATGGCT
1729569 GCGGCATCATAAATGGCT
1 GCGGCATCATAAATGGCT
1729587 ACGGTGGCTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (18 bp):
GCGGCATCATAAATGGCT
Found at i:1732580 original size:20 final size:19
Alignment explanation
Indices: 1732557--1732605 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 19
1732547 CGATATACCA
1732557 GGTAAAATTATGATAAAACC
1 GGTAAAATTATGAT-AAACC
*
1732577 GGTAACAA-AATGATAAACC
1 GGTAA-AATTATGATAAACC
1732596 GGTAAAATTA
1 GGTAAAATTA
1732606 AAAGTGTCGA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
18 2 0.08
19 11 0.44
20 10 0.40
21 2 0.08
ACGTcount: A:0.51, C:0.10, G:0.16, T:0.22
Consensus pattern (19 bp):
GGTAAAATTATGATAAACC
Found at i:1735102 original size:33 final size:33
Alignment explanation
Indices: 1735060--1735125 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1735050 AAATAGATGG
*
1735060 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
***
1735093 AGTGGTGAAAGAAGTTTCGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
1735126 TATTAAGATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.29, C:0.02, G:0.45, T:0.24
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:1736971 original size:19 final size:19
Alignment explanation
Indices: 1736908--1736970 Score: 110
Period size: 19 Copynumber: 3.4 Consensus size: 19
1736898 AATGTCGAGT
*
1736908 TAATTTTGTATAAGATTTA
1 TAATTTTGTATACGATTTA
1736927 TAATTTTGTATACGATTTA
1 TAATTTTGTATACGATTTA
1736946 TAATTTTGTATACGATTTA
1 TAATTTTGTATACGATTTA
1736965 T-ATTTT
1 TAATTTT
1736971 TTTATGTGAA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
18 5 0.12
19 38 0.88
ACGTcount: A:0.32, C:0.03, G:0.10, T:0.56
Consensus pattern (19 bp):
TAATTTTGTATACGATTTA
Found at i:1737832 original size:395 final size:397
Alignment explanation
Indices: 1737053--1738206 Score: 2142
Period size: 395 Copynumber: 2.9 Consensus size: 397
1737043 TTAAGGGTCA
* *
1737053 TGTCGATACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGAATCA
1737117 ATAAAGTGTCGATCCATATA-AAAAAAGTGTCGATCCC-AAATCATCGAACCCAAAAGTATAATG
66 ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
1737180 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
* ***
1737245 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTG
196 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATT-TTTACAAGGTG
* * *
1737310 CACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTA
260 AATCAATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTA
1737375 TAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTC
324 TAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTC
1737440 TAAATAATG
389 TAAATAATG
1737449 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGAATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGAATCA
1737514 ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
1737579 TAATATGTAATTTTTTAATCTAACCGGTACAATTATA-CGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
1737643 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGA
196 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGA
1737708 ATCAATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATA
261 ATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATA
*
1737772 ATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTA
326 ATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTA
1737837 AATAATG
391 AATAATG
1737844 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGAATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGAATCA
1737909 ATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
1737973 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
1738038 AATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAATTTTTACAAGGTGA
196 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGA
1738102 ATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATA
261 ATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATA
1738167 ATGTAATATGTAATTTTTCAATCTAACCGGTACAAATTAT
326 ATGTAATATGTAATTTTTCAATCTAACCGGTAC-AATTAT
1738207 CTTTGTACGT
Statistics
Matches: 741, Mismatches: 11, Indels: 12
0.97 0.01 0.02
Matches are distributed among these distances:
394 136 0.18
395 327 0.44
396 34 0.05
397 85 0.11
398 96 0.13
399 63 0.09
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (397 bp):
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGAATCA
ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGA
ATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATA
ATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTA
AATAATG
Found at i:1737861 original size:197 final size:198
Alignment explanation
Indices: 1737053--1738206 Score: 2129
Period size: 198 Copynumber: 5.8 Consensus size: 198
1737043 TTAAGGGTCA
* *
1737053 TGTCGATACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGAATCA
*
1737117 ATAAAGTGTCGATCCATATAAAAAAAGTGTCGATCCC-AAATCATCGAACCCAAAAGTATAATGT
66 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
1737181 AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
131 AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
1737246 ATG
196 ATG
* *** * *
1737249 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATT-TTTACAAGGTGAATC
*
1737314 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
65 AATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
*
1737379 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
129 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
1737444 TAATG
194 TAATG
1737449 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGAATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGAATCA
1737514 ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 ATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
1737579 TAATATGTAATTTTTTAATCTAACCGGTACAATTATA-CGGTTTTATGAGAGAATAAGTCTAAAT
130 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
1737643 AATG
195 AATG
1737647 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGAATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGAATCA
1737712 ATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
66 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
1737776 AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
131 AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
1737841 ATG
196 ATG
1737844 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGAATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGAATCA
1737909 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
66 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
1737974 AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
131 AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
1738039 ATG
196 ATG
1738042 TGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAATTTTTACAAGGTGAATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGAATCA
1738106 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
66 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
*
1738171 AATATGTAATTTTTCAATCTAACCGGTACAAATTAT
131 AATATGTAATTTTTTAATCTAACCGGTAC-AATTAT
1738207 CTTTGTACGT
Statistics
Matches: 933, Mismatches: 18, Indels: 12
0.97 0.02 0.01
Matches are distributed among these distances:
196 107 0.11
197 263 0.28
198 294 0.32
199 127 0.14
200 142 0.15
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (198 bp):
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGAATCA
ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
ATG
Found at i:1739285 original size:23 final size:23
Alignment explanation
Indices: 1739254--1739316 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
1739244 ATAGGTAAAC
*
1739254 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
1739277 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
1739300 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
1739317 ATGGTTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:1739324 original size:23 final size:23
Alignment explanation
Indices: 1739254--1739326 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
1739244 ATAGGTAAAC
* * **
1739254 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCGGTT
*
1739277 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
1739300 ATATAATGTAATAGGTAAT-GGTT
1 ATATAATGTAATAGGT-ATCGGTT
1739323 ATAT
1 ATAT
1739327 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 42 0.95
24 2 0.05
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGGTT
Found at i:1739712 original size:23 final size:23
Alignment explanation
Indices: 1739681--1739743 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
1739671 ATAGGTAAAC
*
1739681 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
1739704 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
1739727 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
1739744 ATGGTTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:1739751 original size:23 final size:23
Alignment explanation
Indices: 1739681--1739753 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
1739671 ATAGGTAAAC
* * **
1739681 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCGGTT
*
1739704 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
1739727 ATATAATGTAATAGGTAAT-GGTT
1 ATATAATGTAATAGGT-ATCGGTT
1739750 ATAT
1 ATAT
1739754 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 42 0.95
24 2 0.05
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGGTT
Found at i:1739950 original size:427 final size:427
Alignment explanation
Indices: 1739155--1740019 Score: 1698
Period size: 427 Copynumber: 2.0 Consensus size: 427
1739145 AATTCGCAGT
1739155 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
1739220 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
66 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
1739285 TAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTAT
131 TAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTAT
1739350 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
196 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
1739415 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTACGTTACGGTATATATTATTA
261 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTACGTTACGGTATATATTATTA
1739480 AATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATG
326 AATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATG
1739545 AAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
391 AAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
1739582 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
1739647 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
66 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
1739712 TAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTAT
131 TAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTAT
1739777 AAAAGTGTCCATAC-TTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
196 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
1739841 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTACGTTACGGTATATTTATTAT
261 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTACGTTACGGTATA--TATTAT
1739906 TAAATTAAAAATTCTAAATAATA-TTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAA
324 TAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAA
1739970 TGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
389 TGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
1740009 ACACTGTTAAA
1 ACACTGTTAAA
1740020 GTATCGATCC
Statistics
Matches: 436, Mismatches: 0, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
426 107 0.25
427 300 0.69
428 29 0.07
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (427 bp):
ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
TAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTAT
AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTACGTTACGGTATATATTATTA
AATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATG
AAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
Found at i:1746508 original size:12 final size:12
Alignment explanation
Indices: 1746491--1746515 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1746481 ATTACATCAG
1746491 ATACAACCAACA
1 ATACAACCAACA
1746503 ATACAACCAACA
1 ATACAACCAACA
1746515 A
1 A
1746516 AACACCCCAA
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:0.60, C:0.32, G:0.00, T:0.08
Consensus pattern (12 bp):
ATACAACCAACA
Found at i:1762272 original size:115 final size:115
Alignment explanation
Indices: 1762070--1762299 Score: 460
Period size: 115 Copynumber: 2.0 Consensus size: 115
1762060 TGAACTGTCG
1762070 TTATTGTAGAATTCAGAGTAATTCTCTGTAATTTCTTATTCTTTTCAATATGACAGATTACATAT
1 TTATTGTAGAATTCAGAGTAATTCTCTGTAATTTCTTATTCTTTTCAATATGACAGATTACATAT
1762135 TTATATACAAAATATCTCTCTAAAGTAGAAAACTCTAAGAAAGGAAAAAT
66 TTATATACAAAATATCTCTCTAAAGTAGAAAACTCTAAGAAAGGAAAAAT
1762185 TTATTGTAGAATTCAGAGTAATTCTCTGTAATTTCTTATTCTTTTCAATATGACAGATTACATAT
1 TTATTGTAGAATTCAGAGTAATTCTCTGTAATTTCTTATTCTTTTCAATATGACAGATTACATAT
1762250 TTATATACAAAATATCTCTCTAAAGTAGAAAACTCTAAGAAAGGAAAAAT
66 TTATATACAAAATATCTCTCTAAAGTAGAAAACTCTAAGAAAGGAAAAAT
1762300 AATAATCCTA
Statistics
Matches: 115, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
115 115 1.00
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.37
Consensus pattern (115 bp):
TTATTGTAGAATTCAGAGTAATTCTCTGTAATTTCTTATTCTTTTCAATATGACAGATTACATAT
TTATATACAAAATATCTCTCTAAAGTAGAAAACTCTAAGAAAGGAAAAAT
Found at i:1762385 original size:27 final size:27
Alignment explanation
Indices: 1762354--1762421 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
1762344 TCTATTTACA
1762354 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
1762381 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
1762408 AAATC--ATCTCTATA
1 AAATCATATCTCTATA
1762422 ATTCCTACAC
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 9 0.22
27 32 0.78
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (27 bp):
AAATCATATCTCTATAGGAATGGTAAC
Found at i:1766145 original size:27 final size:27
Alignment explanation
Indices: 1766114--1766181 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
1766104 TCTATTTGCA
1766114 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
1766141 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
1766168 AAATC--ATCTCTATA
1 AAATCATATCTCTATA
1766182 ATTCCTACAG
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 9 0.22
27 32 0.78
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (27 bp):
AAATCATATCTCTATAGGAATGGTAAC
Found at i:1777653 original size:27 final size:27
Alignment explanation
Indices: 1777622--1777685 Score: 71
Period size: 26 Copynumber: 2.4 Consensus size: 27
1777612 AAAATTTTAT
1777622 TTAAAATTAAACAGACT-CAATA-AAAAA
1 TTAAAATTAAA-AGA-TACAATATAAAAA
*
1777649 TTAAAA-TAAAAGATATAATATAAAAA
1 TTAAAATTAAAAGATACAATATAAAAA
1777675 TTAACAATTAA
1 TTAA-AATTAA
1777686 TATTAAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
24 1 0.03
25 7 0.22
26 13 0.41
27 8 0.25
28 3 0.09
ACGTcount: A:0.64, C:0.06, G:0.03, T:0.27
Consensus pattern (27 bp):
TTAAAATTAAAAGATACAATATAAAAA
Found at i:1780845 original size:15 final size:15
Alignment explanation
Indices: 1780822--1780852 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1780812 AATTGAACAT
1780822 TACGGTGAACATTTA
1 TACGGTGAACATTTA
*
1780837 TACGTTGAACATTTA
1 TACGGTGAACATTTA
1780852 T
1 T
1780853 CATCCTATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.39
Consensus pattern (15 bp):
TACGGTGAACATTTA
Found at i:1784508 original size:21 final size:23
Alignment explanation
Indices: 1784482--1784523 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
1784472 AGGGTTTTTT
*
1784482 TATTTTT-TAATTAA-AAAATAA
1 TATTTTTATAATCAAGAAAATAA
1784503 TATTTTTATAATCAAGAAAAT
1 TATTTTTATAATCAAGAAAAT
1784524 TAAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 6 0.33
23 5 0.28
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
TATTTTTATAATCAAGAAAATAA
Found at i:1784953 original size:2 final size:2
Alignment explanation
Indices: 1784946--1784972 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1784936 TTGAGTATGA
1784946 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
1784973 ATTAGATTAA
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:1787806 original size:67 final size:67
Alignment explanation
Indices: 1787698--1787833 Score: 272
Period size: 67 Copynumber: 2.0 Consensus size: 67
1787688 TGAGCTCTTG
1787698 GATCTCCTTGTTTTCCAAACCTTTGTTGAAGTCCTTCAAAAGCTTCCCGTACTGCTTTTGGATGT
1 GATCTCCTTGTTTTCCAAACCTTTGTTGAAGTCCTTCAAAAGCTTCCCGTACTGCTTTTGGATGT
1787763 CC
66 CC
1787765 GATCTCCTTGTTTTCCAAACCTTTGTTGAAGTCCTTCAAAAGCTTCCCGTACTGCTTTTGGATGT
1 GATCTCCTTGTTTTCCAAACCTTTGTTGAAGTCCTTCAAAAGCTTCCCGTACTGCTTTTGGATGT
1787830 CC
66 CC
1787832 GA
1 GA
1787834 GCTGATGGTA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 69 1.00
ACGTcount: A:0.18, C:0.26, G:0.17, T:0.38
Consensus pattern (67 bp):
GATCTCCTTGTTTTCCAAACCTTTGTTGAAGTCCTTCAAAAGCTTCCCGTACTGCTTTTGGATGT
CC
Found at i:1789773 original size:44 final size:44
Alignment explanation
Indices: 1789705--1789795 Score: 157
Period size: 44 Copynumber: 2.1 Consensus size: 44
1789695 CTAAAAGAAA
*
1789705 TGTTGTTCTTCTTGATGAACGAGTTCGAGTAACTTGTCTATTAG
1 TGTTGTTCTCCTTGATGAACGAGTTCGAGTAACTTGTCTATTAG
1789749 TGTTGTTCTCCTTTGATGAA-GAGTTCGAGTAACTTGTCTATTAG
1 TGTTGTTCTCC-TTGATGAACGAGTTCGAGTAACTTGTCTATTAG
1789793 TGT
1 TGT
1789796 GTAAGAATTT
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
44 37 0.82
45 8 0.18
ACGTcount: A:0.20, C:0.13, G:0.23, T:0.44
Consensus pattern (44 bp):
TGTTGTTCTCCTTGATGAACGAGTTCGAGTAACTTGTCTATTAG
Found at i:1790700 original size:23 final size:24
Alignment explanation
Indices: 1790659--1790720 Score: 72
Period size: 23 Copynumber: 2.6 Consensus size: 24
1790649 TTAGTATTTT
* *
1790659 ATATTACATCTTAACTTAAATTCAC
1 ATATTA-ATATTAAATTAAATTCAC
*
1790684 ATATT-ATATTAAATTAAATTGAC
1 ATATTAATATTAAATTAAATTCAC
*
1790707 ATCTTAATATTAAA
1 ATATTAATATTAAA
1790721 AATATATATT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
23 19 0.59
24 8 0.25
25 5 0.16
ACGTcount: A:0.45, C:0.11, G:0.02, T:0.42
Consensus pattern (24 bp):
ATATTAATATTAAATTAAATTCAC
Found at i:1790778 original size:45 final size:45
Alignment explanation
Indices: 1790724--1790862 Score: 208
Period size: 45 Copynumber: 3.1 Consensus size: 45
1790714 TATTAAAAAT
1790724 ATATATTTTATTTTTATCTTAATTTTAAAATATTATAATAATAAA
1 ATATATTTTATTTTTATCTTAATTTTAAAATATTATAATAATAAA
* **
1790769 ATATATTTTATTTTTATCTTAAATTTTAAAATAGTT-CAATTTTAAA
1 ATATATTTTATTTTTATCTT-AATTTTAAAATA-TTATAATAATAAA
* *
1790815 ATATATTTTATTTTTATCTTAATTTTAAAATATTATAAGAACAAA
1 ATATATTTTATTTTTATCTTAATTTTAAAATATTATAATAATAAA
1790860 ATA
1 ATA
1790863 ATTACAATTA
Statistics
Matches: 83, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
44 2 0.02
45 40 0.48
46 39 0.47
47 2 0.02
ACGTcount: A:0.43, C:0.04, G:0.01, T:0.52
Consensus pattern (45 bp):
ATATATTTTATTTTTATCTTAATTTTAAAATATTATAATAATAAA
Found at i:1790791 original size:23 final size:23
Alignment explanation
Indices: 1790765--1790836 Score: 63
Period size: 23 Copynumber: 3.1 Consensus size: 23
1790755 ATTATAATAA
1790765 TAAAATATATTTTATTTTTATCT
1 TAAAATATATTTTATTTTTATCT
* * *** * ** *
1790788 TAAATTTTAAAATAGTTCAATTT
1 TAAAATATATTTTATTTTTATCT
1790811 TAAAATATATTTTATTTTTATCT
1 TAAAATATATTTTATTTTTATCT
1790834 TAA
1 TAA
1790837 TTTTAAAATA
Statistics
Matches: 31, Mismatches: 18, Indels: 0
0.63 0.37 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.56
Consensus pattern (23 bp):
TAAAATATATTTTATTTTTATCT
Done.