Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009611.1 Hibiscus syriacus cultivar Beakdansim tig00116997_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: 6671611
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 26 of 27
Found at i:6388436 original size:76 final size:76
Alignment explanation
Indices: 6387691--6388409 Score: 1316
Period size: 76 Copynumber: 9.5 Consensus size: 76
6387681 GATGAAAATG
* * *
6387691 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGTTTTGAAAACATTAAAAAGCT
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
6387756 CCCGAAGGCTT
66 CCCGAAGGCTT
* *
6387767 TTTGGAAACATCATGCACTGCAGGACTTATAGATGACCCTAAGGCTTTGAAAATATCAAAAAGCT
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
*
6387832 TCCGAAGGCTT
66 CCCGAAGGCTT
6387843 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
6387908 CCCGAAGGCTT
66 CCCGAAGGCTT
6387919 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
6387984 CCCGAAGGCTT
66 CCCGAAGGCTT
6387995 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
*
6388060 -CCTAAGGCTTT
66 CCCGAAGGC-TT
*
6388071 TTTTGAAACATCATGCACTGCA-GACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
*
6388135 CCCGAAGGATTT
66 CCCGAAGG-CTT
6388147 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
6388212 CCCGAAGGCTT
66 CCCGAAGGCTT
6388223 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
6388288 CCCGAAGGCTT
66 CCCGAAGGCTT
*
6388299 TTTGGAAACATCATGCACTGCAGGACTTACAGATAACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
6388364 CCCGAAGGCTT
66 CCCGAAGGCTT
6388375 TTTGGAAACATCATGCACTGCAGGACTTACAGATG
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATG
6388410 TGGGAAATAG
Statistics
Matches: 622, Mismatches: 17, Indels: 8
0.96 0.03 0.01
Matches are distributed among these distances:
75 49 0.08
76 523 0.84
77 50 0.08
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.24
Consensus pattern (76 bp):
TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTT
Found at i:6388845 original size:167 final size:168
Alignment explanation
Indices: 6388412--6388918 Score: 872
Period size: 167 Copynumber: 3.0 Consensus size: 168
6388402 TACAGATGTG
* *
6388412 GGAAATAGTTTATTAAGTAAAAAAACTAAGGAAATCATTTTCTTACTTTTCAACAATTTCATTTT
1 GGAAATAGTTTACTAAGTAAAAAAACTAAGAAAATCATTTTCTTACTTTTCAACAATTTCATTTT
** *
6388477 CAGAAAAGATTGAATGAGAAACTATGAAAATCGTTTTCTCATTATTTTTTTTCTTTTCAAAATAA
66 -AGAAAAGATAAAATGAGAAACTATGAAAATCGTTTTCTCATTA--TGTTTT-TTTT--AAATAA
*
6388542 CATGTTGATTGGGTAACATGCCCCAATCTCAAGATAAGGCTGTT
125 CATGTTGATTGGGTAACATGCCCCAATCTCAAGATAAGGCTATT
*
6388586 GGAAATAGTTTACTAAGTAAAAAAACTAAGAAAATCGTTTTCTTACTTTTCAACAATTTCATTTT
1 GGAAATAGTTTACTAAGTAAAAAAACTAAGAAAATCATTTTCTTACTTTTCAACAATTTCATTTT
6388651 AGAAAAGATAAAATGAGAAACTATGAAAATCGTTTTCTCATTATGTTTTTTTTAAATAACATGTT
66 AGAAAAGATAAAATGAGAAACTATGAAAATCGTTTTCTCATTATGTTTTTTTTAAATAACATGTT
6388716 GATTGGGTAACATGCCCCAATCTCAAGATAAGGCTATT
131 GATTGGGTAACATGCCCCAATCTCAAGATAAGGCTATT
6388754 GGAAATAGTTTACTAAGT-AAAAAACTAAGAAAATCATTTTCTTACTTTTCAACAATTTCATTTT
1 GGAAATAGTTTACTAAGTAAAAAAACTAAGAAAATCATTTTCTTACTTTTCAACAATTTCATTTT
*
6388818 AGAAAAGATAAAATGAGAAACTATGAAAATCGTTTTCTCATTCTGTTTTTTTTAAATAACATGTT
66 AGAAAAGATAAAATGAGAAACTATGAAAATCGTTTTCTCATTATGTTTTTTTTAAATAACATGTT
*
6388883 GATTGGGTAACATGCCCCAATCTCAAGATAATGCTA
131 GATTGGGTAACATGCCCCAATCTCAAGATAAGGCTA
6388919 ATTTTTGTGG
Statistics
Matches: 323, Mismatches: 10, Indels: 7
0.95 0.03 0.02
Matches are distributed among these distances:
167 144 0.45
168 67 0.21
170 4 0.01
171 5 0.02
173 41 0.13
174 62 0.19
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (168 bp):
GGAAATAGTTTACTAAGTAAAAAAACTAAGAAAATCATTTTCTTACTTTTCAACAATTTCATTTT
AGAAAAGATAAAATGAGAAACTATGAAAATCGTTTTCTCATTATGTTTTTTTTAAATAACATGTT
GATTGGGTAACATGCCCCAATCTCAAGATAAGGCTATT
Found at i:6389453 original size:22 final size:22
Alignment explanation
Indices: 6389428--6389482 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
6389418 AATAAAGCTT
6389428 TCATCTTTGAAAAGAGAA-TCTA
1 TCATCTTTGAAAAGAGAACT-TA
*
6389450 TCATCTTTAAAAAGAGAACTTA
1 TCATCTTTGAAAAGAGAACTTA
6389472 TCATCTTTGAA
1 TCATCTTTGAA
6389483 GAGTGTAGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 29 0.97
23 1 0.03
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAACTTA
Found at i:6392224 original size:114 final size:114
Alignment explanation
Indices: 6392024--6392475 Score: 744
Period size: 114 Copynumber: 4.0 Consensus size: 114
6392014 AATCATGCAG
* * * * *
6392024 TTCATCTTTCAATTACAATGATTGGTTCTGGGGTTCATACCAAACCAGATCATATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATATCAAACCAGATCAGATAACTCAAAGA
* * *
6392089 ACACTTCCAGAAGATGCTATTGAG-CCTCTTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTTC-TTATTTCTGCTATGAGCAAA
*
6392138 TTCATCTTTCAAATCTAATGATTGGTTTTGGGGTTCATATCAAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATATCAAACCAGATCAGATAACTCAAAGA
* *
6392203 ACACTTCCAGAAGATGCTATTGGGTCTTTTTATTTCTTCTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTGCTATGAGCAAA
*
6392252 TTCATCTTTCAAATCCAATGATTGGTTTTAGGGTTCATATCAAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATATCAAACCAGATCAGATAACTCAAAGA
*
6392317 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTGCTATAAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTGCTATGAGCAAA
* *
6392366 TTCATCTTTCAAATCCAATGATTGGTTTTTGGGTTCATATCAAACCGGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATATCAAACCAGATCAGATAACTCAAAGA
*
6392431 ACAATTCCAGAAGATGCTATTGGGTCTTCTTATTTCTGCTATGAG
66 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTGCTATGAG
6392476 AACGTGGCAT
Statistics
Matches: 318, Mismatches: 19, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
114 316 0.99
115 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.34
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATATCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTGCTATGAGCAAA
Found at i:6394649 original size:22 final size:24
Alignment explanation
Indices: 6394624--6394671 Score: 64
Period size: 22 Copynumber: 2.0 Consensus size: 24
6394614 TCATTTTTCA
6394624 TTTTTCATTTT-TT-TTCTTTCTT
1 TTTTTCATTTTCTTCTTCTTTCTT
*
6394646 TTTTTCTTTTTCCTTCTTCTTTCTT
1 TTTTTCATTTT-CTTCTTCTTTCTT
6394671 T
1 T
6394672 GCTGGATGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 10 0.45
24 2 0.09
25 10 0.45
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (24 bp):
TTTTTCATTTTCTTCTTCTTTCTT
Found at i:6394665 original size:21 final size:22
Alignment explanation
Indices: 6394624--6394667 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
6394614 TCATTTTTCA
*
6394624 TTTTTCATTTTTTTTCTTTCTT
1 TTTTTCATTTTTCTTCTTTCTT
6394646 TTTTTC-TTTTTCCTTC-TTCTT
1 TTTTTCATTTTT-CTTCTTTCTT
6394667 T
1 T
6394668 CTTTGCTGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (22 bp):
TTTTTCATTTTTCTTCTTTCTT
Found at i:6397532 original size:15 final size:14
Alignment explanation
Indices: 6397500--6397540 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
6397490 TAAAAGTATG
*
6397500 AATGCAAAATGAAA
1 AATGCAAAATGCAA
6397514 AATGCAAATATGCAA
1 AATGCAAA-ATGCAA
6397529 AATG-AAAATGCA
1 AATGCAAAATGCA
6397541 TATATGAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 5 0.20
14 11 0.44
15 9 0.36
ACGTcount: A:0.59, C:0.10, G:0.15, T:0.17
Consensus pattern (14 bp):
AATGCAAAATGCAA
Found at i:6397538 original size:21 final size:22
Alignment explanation
Indices: 6397501--6397550 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 22
6397491 AAAAGTATGA
6397501 ATGCAAAATGAAAAATGCAAAT
1 ATGCAAAATGAAAAATGCAAAT
*
6397523 ATGCAAAATG-AAAATGCATAT
1 ATGCAAAATGAAAAATGCAAAT
6397544 ATG-AAAA
1 ATGCAAAA
6397551 GGTGTTACTC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 4 0.15
21 13 0.48
22 10 0.37
ACGTcount: A:0.58, C:0.08, G:0.14, T:0.20
Consensus pattern (22 bp):
ATGCAAAATGAAAAATGCAAAT
Found at i:6401691 original size:3 final size:3
Alignment explanation
Indices: 6401664--6401716 Score: 70
Period size: 3 Copynumber: 17.0 Consensus size: 3
6401654 TTGGGTTTTG
* *
6401664 TAA TAT TAA TAAA TTA TATA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
6401711 TAA TAA
1 TAA TAA
6401717 ATTTAAATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
3 38 0.86
4 6 0.14
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:6404064 original size:34 final size:34
Alignment explanation
Indices: 6404026--6404094 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
6404016 GGTTCCTAAT
6404026 AAGATAAAACTACAATGTACTTAATAGTTAATAC
1 AAGATAAAACTACAATGTACTTAATAGTTAATAC
*
6404060 AAGATAAAACTACAATGTACTTGATAGTTAATAC
1 AAGATAAAACTACAATGTACTTAATAGTTAATAC
6404094 A
1 A
6404095 CTCCTCATTC
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:0.49, C:0.12, G:0.10, T:0.29
Consensus pattern (34 bp):
AAGATAAAACTACAATGTACTTAATAGTTAATAC
Found at i:6413679 original size:22 final size:23
Alignment explanation
Indices: 6413651--6413698 Score: 80
Period size: 22 Copynumber: 2.1 Consensus size: 23
6413641 TTTTGATAGG
6413651 ATAAAATTTCAAGGTGGACAC-C
1 ATAAAATTTCAAGGTGGACACAC
*
6413673 ATAAAATTTCAGGGTGGACACAC
1 ATAAAATTTCAAGGTGGACACAC
6413696 ATA
1 ATA
6413699 TATTAGTGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.42, C:0.17, G:0.19, T:0.23
Consensus pattern (23 bp):
ATAAAATTTCAAGGTGGACACAC
Found at i:6414598 original size:2 final size:2
Alignment explanation
Indices: 6414591--6414615 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6414581 TTAAGCTCCG
6414591 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
6414616 TAAAAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:6417992 original size:3 final size:3
Alignment explanation
Indices: 6417984--6418045 Score: 124
Period size: 3 Copynumber: 20.7 Consensus size: 3
6417974 ATACAATACG
6417984 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
6418032 ATT ATT ATT ATT AT
1 ATT ATT ATT ATT AT
6418046 GGTAAACTAC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:6418463 original size:27 final size:29
Alignment explanation
Indices: 6418425--6418482 Score: 93
Period size: 27 Copynumber: 2.1 Consensus size: 29
6418415 TATTGGCCAG
6418425 TGATTTACTTTGT-TCA-AGAAACTTGCA
1 TGATTTACTTTGTCTCACAGAAACTTGCA
*
6418452 TGATTTACTTTGTCTTACAGAAACTTGCA
1 TGATTTACTTTGTCTCACAGAAACTTGCA
6418481 TG
1 TG
6418483 GAAACATACT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
27 13 0.46
28 2 0.07
29 13 0.46
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.41
Consensus pattern (29 bp):
TGATTTACTTTGTCTCACAGAAACTTGCA
Found at i:6419094 original size:30 final size:30
Alignment explanation
Indices: 6419058--6419123 Score: 107
Period size: 30 Copynumber: 2.2 Consensus size: 30
6419048 AGAATATGTA
*
6419058 AATATTAAGGACCAAATGTATAATTATGCC
1 AATATTAAGGACCAAATATATAATTATGCC
*
6419088 AATATTAAGGACCAAATATATAATTATGTC
1 AATATTAAGGACCAAATATATAATTATGCC
6419118 AA-ATTA
1 AATATTA
6419124 TTAACGGACA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
29 4 0.12
30 30 0.88
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.32
Consensus pattern (30 bp):
AATATTAAGGACCAAATATATAATTATGCC
Found at i:6422078 original size:16 final size:15
Alignment explanation
Indices: 6422057--6422091 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
6422047 CCATCTAATT
6422057 TTTTTTAATTTATAGA
1 TTTTTTAATTTATA-A
*
6422073 TTTTTTATTTTATAA
1 TTTTTTAATTTATAA
6422088 TTTT
1 TTTT
6422092 AAAAAAGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (15 bp):
TTTTTTAATTTATAA
Found at i:6422227 original size:12 final size:12
Alignment explanation
Indices: 6422210--6422234 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6422200 AATGAATTTT
6422210 AAGATTTTACAA
1 AAGATTTTACAA
6422222 AAGATTTTACAA
1 AAGATTTTACAA
6422234 A
1 A
6422235 TTTATATTCG
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:0.52, C:0.08, G:0.08, T:0.32
Consensus pattern (12 bp):
AAGATTTTACAA
Found at i:6422493 original size:19 final size:19
Alignment explanation
Indices: 6422469--6422507 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
6422459 TCGAATGCAT
6422469 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
6422488 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
6422507 T
1 T
6422508 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:6422632 original size:64 final size:65
Alignment explanation
Indices: 6422455--6422617 Score: 204
Period size: 65 Copynumber: 2.5 Consensus size: 65
6422445 GAATTAATTG
* * * *
6422455 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAA
* * ** **
6422520 AACATCGAATGCATTTGATGCATCGATGCATAAGCCATGCATCGATGCAC-CAGGCTATTTTTC-
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATA-TTTTCA
6422583 A
65 A
*
6422584 AACATCGAATGCATTTCATGCATCGGTGCACACT
1 AACATCGAATGCATTTCATGCATCGATGCACACT
6422618 TGGTGCACCG
Statistics
Matches: 82, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
64 34 0.41
65 48 0.59
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:6424164 original size:117 final size:117
Alignment explanation
Indices: 6423962--6424174 Score: 263
Period size: 117 Copynumber: 1.8 Consensus size: 117
6423952 ATCTTATTTT
*
6423962 GAAAGCTAAAAAGGACTTGGAAAATAAAAATGAAATGTTGAAAAGGAGTTAGAGCTTTCAAAAAT
1 GAAAGCTAAAAAGGACTTGGAAAATAAAAATGAAATGTTGAAAAGAAGTTAGAGCTTTCAAAAAT
*
6424027 AAAATCGGAAAACTTTGAAAAAGAAATTTTCAAATTAAACAAACTTCTTCTA
66 AAAATCGGAAAACTTGGAAAAAGAAATTTTCAAATTAAACAAACTTCTTCTA
* * * *
6424079 GAAA-CTAAAATGGATTTTGAAAA-ACAAAATGAAAT-TTCGAAGAAGAATTTAGAGCTTTCAAA
1 GAAAGCTAAAAAGGACTTGGAAAATA-AAAATGAAATGTT-GAA-AAGAAGTTAGAGCTTTCAAA
* ** * *
6424141 GATAAAATTTG-AAAGTATGGAAAAGGAAATTTTC
63 AATAAAATCGGAAAACT-TGGAAAAAGAAATTTTC
6424175 TATTTAGAAG
Statistics
Matches: 81, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
115 3 0.04
116 33 0.41
117 45 0.56
ACGTcount: A:0.50, C:0.08, G:0.16, T:0.26
Consensus pattern (117 bp):
GAAAGCTAAAAAGGACTTGGAAAATAAAAATGAAATGTTGAAAAGAAGTTAGAGCTTTCAAAAAT
AAAATCGGAAAACTTGGAAAAAGAAATTTTCAAATTAAACAAACTTCTTCTA
Found at i:6424742 original size:20 final size:21
Alignment explanation
Indices: 6424709--6424748 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
6424699 TTTTAACGTA
6424709 ATTGATATTCATTTT-AAACC
1 ATTGATATTCATTTTCAAACC
6424729 ATTGATA-TCAATTTTCAAAC
1 ATTGATATTC-ATTTTCAAAC
6424749 AATTTGATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 2 0.11
20 12 0.67
21 4 0.22
ACGTcount: A:0.38, C:0.15, G:0.05, T:0.42
Consensus pattern (21 bp):
ATTGATATTCATTTTCAAACC
Found at i:6424756 original size:22 final size:20
Alignment explanation
Indices: 6424708--6424752 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
6424698 ATTTTAACGT
6424708 AATTGATATTCATTTTAAAC
1 AATTGATATTCATTTTAAAC
*
6424728 CATTGATA-TCAATTTTCAAAC
1 AATTGATATTC-ATTTT-AAAC
6424749 AATT
1 AATT
6424753 TGATTTTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
19 2 0.10
20 12 0.57
21 7 0.33
ACGTcount: A:0.40, C:0.13, G:0.04, T:0.42
Consensus pattern (20 bp):
AATTGATATTCATTTTAAAC
Found at i:6429750 original size:19 final size:19
Alignment explanation
Indices: 6429726--6429764 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
6429716 TCGAATGCAT
6429726 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
6429745 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
6429764 T
1 T
6429765 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:6429781 original size:65 final size:64
Alignment explanation
Indices: 6429712--6429855 Score: 173
Period size: 65 Copynumber: 2.2 Consensus size: 64
6429702 GAATTAATTG
*** * *
6429712 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATA-TTTTCA
1 AACATCGAATGCATTCCATGCACCGATGCACAAGCCATACATCGATGCAC-CAGAATATTTTTC-
6429776 A
64 A
** * **
6429777 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATACATCGATGCACCAGGCTATTTTTCA
1 AACATCGAATGCATTCCATGCACCGATGCACAAGCCATACATCGATGCACCAGAATATTTTTCA
6429841 AACATCGAATGCATT
1 AACATCGAATGCATT
6429856 TCAAGCCTAT
Statistics
Matches: 68, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
64 20 0.29
65 48 0.71
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.27
Consensus pattern (64 bp):
AACATCGAATGCATTCCATGCACCGATGCACAAGCCATACATCGATGCACCAGAATATTTTTCA
Found at i:6433703 original size:20 final size:19
Alignment explanation
Indices: 6433671--6433708 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
6433661 CCTGACATTA
6433671 CATTCCTCTTTAAATTTTCT
1 CATTCCTCTTT-AATTTTCT
6433691 CATTCCT-TCTTAATTTTC
1 CATTCCTCT-TTAATTTTC
6433709 AGTTCATCCC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.18, C:0.26, G:0.00, T:0.55
Consensus pattern (19 bp):
CATTCCTCTTTAATTTTCT
Found at i:6435980 original size:23 final size:26
Alignment explanation
Indices: 6435940--6436007 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 26
6435930 ATTTAATAAA
6435940 TATTATAATAATAATAAAT-ATTAAT
1 TATTATAATAATAATAAATAATTAAT
6435965 TATTA-AAT-ATAATAAATAATTAA-
1 TATTATAATAATAATAAATAATTAAT
*
6435988 -AATATAATAATATATAAATA
1 TATTATAATAATA-ATAAATA
6436008 TAGTAATCAA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
22 3 0.08
23 12 0.32
24 11 0.29
25 12 0.32
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (26 bp):
TATTATAATAATAATAAATAATTAAT
Found at i:6435990 original size:18 final size:18
Alignment explanation
Indices: 6435928--6435997 Score: 61
Period size: 18 Copynumber: 3.6 Consensus size: 18
6435918 GAAATTTAAT
*
6435928 AAATTTAATAAAT-ATTA
1 AAATATAATAAATAATTA
*
6435945 TAATAATAATAAATATTAATTA
1 AAAT-ATAAT-AA-A-TAATTA
6435967 TTAAATATAATAAATAATTA
1 --AAATATAATAAATAATTA
6435987 AAATATAATAA
1 AAATATAATAA
6435998 TATATAAATA
Statistics
Matches: 43, Mismatches: 3, Indels: 13
0.73 0.05 0.22
Matches are distributed among these distances:
17 3 0.07
18 15 0.35
19 2 0.05
20 7 0.16
21 2 0.05
22 6 0.14
23 5 0.12
24 3 0.07
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
AAATATAATAAATAATTA
Found at i:6436007 original size:34 final size:31
Alignment explanation
Indices: 6435935--6436014 Score: 81
Period size: 34 Copynumber: 2.5 Consensus size: 31
6435925 AATAAATTTA
* *
6435935 ATAAATATTATAATAATAATAAATATTAATT
1 ATAAATATAATAATAATAATAAATAATAATT
6435966 ATTAAATATAATAAATAATTAA-AATATAATAATAT
1 A-TAAATATAAT-AATAA-TAATAA-ATAATAAT-T
*
6436001 ATAAATATAGTAAT
1 ATAAATATAATAAT
6436015 CAAAATAGAT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
31 1 0.02
32 9 0.22
33 10 0.24
34 19 0.46
35 2 0.05
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (31 bp):
ATAAATATAATAATAATAATAAATAATAATT
Found at i:6436008 original size:16 final size:17
Alignment explanation
Indices: 6435936--6436014 Score: 69
Period size: 16 Copynumber: 4.8 Consensus size: 17
6435926 ATAAATTTAA
* *
6435936 TAAATATTATAATAATAA
1 TAAATATAATAAT-ATAT
6435954 TAAATAT--TAAT-TAT
1 TAAATATAATAATATAT
6435968 TAAATATAATAA-ATAAT
1 TAAATATAATAATAT-AT
6435985 TAAAATATAATAATATA-
1 T-AAATATAATAATATAT
*
6436002 TAAATATAGTAAT
1 TAAATATAATAAT
6436015 CAAAATAGAT
Statistics
Matches: 53, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
14 9 0.17
16 19 0.36
17 4 0.08
18 19 0.36
19 2 0.04
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (17 bp):
TAAATATAATAATATAT
Found at i:6450383 original size:25 final size:25
Alignment explanation
Indices: 6450355--6450405 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
6450345 TTAATCCAAA
*
6450355 TAATGTACCCATAACAATGTTCAAT
1 TAATGTACCCACAACAATGTTCAAT
*
6450380 TAATGTACCCACAACAATGTTTAAT
1 TAATGTACCCACAACAATGTTCAAT
6450405 T
1 T
6450406 GATTTGTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.33
Consensus pattern (25 bp):
TAATGTACCCACAACAATGTTCAAT
Found at i:6450732 original size:22 final size:23
Alignment explanation
Indices: 6450663--6450714 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
6450653 ACACTTTACA
* *
6450663 ATATAACCACTACCTATTACATT
1 ATATAAACAATACCTATTACATT
6450686 ATATAAACAATACCTATTACATT
1 ATATAAACAATACCTATTACATT
6450709 ATATAA
1 ATATAA
6450715 GGGCTACTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.46, C:0.19, G:0.00, T:0.35
Consensus pattern (23 bp):
ATATAAACAATACCTATTACATT
Found at i:6451137 original size:23 final size:22
Alignment explanation
Indices: 6451082--6451150 Score: 88
Period size: 21 Copynumber: 3.2 Consensus size: 22
6451072 ACACTTTACA
6451082 ATATAAC-ATACCTATTACATT
1 ATATAACGATACCTATTACATT
6451103 ATA-AACGATACCTATTACATT
1 ATATAACGATACCTATTACATT
* * *
6451124 ATATAAGGGCTACCTATTACATC
1 ATATAA-CGATACCTATTACATT
6451147 ATAT
1 ATAT
6451151 GTTTACCTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
20 3 0.07
21 20 0.48
22 2 0.05
23 17 0.40
ACGTcount: A:0.41, C:0.19, G:0.06, T:0.35
Consensus pattern (22 bp):
ATATAACGATACCTATTACATT
Found at i:6451229 original size:419 final size:417
Alignment explanation
Indices: 6450431--6451248 Score: 1422
Period size: 419 Copynumber: 2.0 Consensus size: 417
6450421 TTTCAATTTG
6450431 AATATTGATTTTAATTTCATTTGCACAAAAAATTTGATTGTTTTGATATTTTAAAAATAATATTT
1 AATATTGATTTTAATTTCATTTGCACAAAAAATTTGATTGTTTTGATATTTTAAAAATAATATTT
* *
6450496 AGAATTTTTAATTAATAATAATATATATGTAACGTAAAAATAAATCATTATACGCCTATAATTAC
66 AGAATTTTTAATTAATAATAATATATACGTAACGTAAAAATAAATCATTAGACGCCTATAATTAC
6450561 TAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAA
131 TAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAA
6450626 GTATGGACACTTTTATAAAAAAGATAGACACTTTACAATATAACCACTACCTATTACATTATATA
196 GTATGGACACTTTTATAAAAAAGATAGACACTTTACAATATAACCACTACCTATTACATTATATA
6450691 AACAATACCTATTACATTATATAAGGGCTACTATTACATTATGTTTACCTATTATATGAAAGTGT
261 AACAATACCTATTACATTATATAAGGGCTACTATTACATTATGTTTACCTATTATATGAAAGTGT
6450756 CCATACTTTTTATAAAAAGGATCGATACTTTTTTAAAACTTATGTAATTTATGTTTCAATTTTTT
326 CCATACTTTTTATAAAAAGGATCGATACTTTTTTAAAACTTATGTAATTTATGTTTCAATTTTTT
6450821 TAACAGTGTTTCATGTTTTCCACCTAC
391 TAACAGTGTTTCATGTTTTCCACCTAC
6450848 AATATTGATTTAATAATTTCATTTGCACAAAAATTATTTGATTGTTTT-ATATTTTAAAAAT-AT
1 AATATTGATTT--TAATTTCATTTGCACAAAAA--ATTTGATTGTTTTGATATTTTAAAAATAAT
6450911 A-TTAGAATTTTTAATTTAATAAT-ATATATACCGTAACGTAAAAAATAAA-CATTAGACGCCTA
62 ATTTAGAATTTTTAA-TTAATAATAATATATA-CGTAACGT-AAAAATAAATCATTAGACGCCTA
6450973 TAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGT
124 TAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGT
*
6451038 GAAAAAAGTATGGACACTTTTATAAAAAGGATAGACACTTTACAATATAA-CA-TACCTATTACA
189 GAAAAAAGTATGGACACTTTTATAAAAAAGATAGACACTTTACAATATAACCACTACCTATTACA
*
6451101 -T-TATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTAT
254 TTATATAAACAATACCTATTACATTATATAAGGGCTA-CTATTACAT--TATGTTTACCTATTAT
6451164 ATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAA-TTATG
316 A-TGAAAGTGTCCATACTTTTTATAAAAAGGATCGATAC-TTTTTTAAAACTTATGTAATTTATG
6451228 TTTCAATTTTTTTAACAGTGT
379 TTTCAATTTTTTTAACAGTGT
6451249 ACTGCGAATT
Statistics
Matches: 385, Mismatches: 4, Indels: 22
0.94 0.01 0.05
Matches are distributed among these distances:
415 33 0.09
416 10 0.03
417 22 0.06
418 39 0.10
419 227 0.59
420 41 0.11
421 13 0.03
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.39
Consensus pattern (417 bp):
AATATTGATTTTAATTTCATTTGCACAAAAAATTTGATTGTTTTGATATTTTAAAAATAATATTT
AGAATTTTTAATTAATAATAATATATACGTAACGTAAAAATAAATCATTAGACGCCTATAATTAC
TAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAA
GTATGGACACTTTTATAAAAAAGATAGACACTTTACAATATAACCACTACCTATTACATTATATA
AACAATACCTATTACATTATATAAGGGCTACTATTACATTATGTTTACCTATTATATGAAAGTGT
CCATACTTTTTATAAAAAGGATCGATACTTTTTTAAAACTTATGTAATTTATGTTTCAATTTTTT
TAACAGTGTTTCATGTTTTCCACCTAC
Found at i:6451841 original size:3 final size:3
Alignment explanation
Indices: 6451833--6451904 Score: 72
Period size: 3 Copynumber: 24.0 Consensus size: 3
6451823 ACTTGTTTGG
* * * ** *
6451833 ATC ATC ATC TTC ATC ATC ATC ATC ATC GTC ATC ATC TTC ATC GCC AGC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* *
6451881 TTC ATC GTC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC
6451905 GTCAGCTTCA
Statistics
Matches: 54, Mismatches: 15, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.25, C:0.35, G:0.06, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:6451850 original size:12 final size:12
Alignment explanation
Indices: 6451833--6451919 Score: 66
Period size: 12 Copynumber: 7.0 Consensus size: 12
6451823 ACTTGTTTGG
6451833 ATCATCATCTTC
1 ATCATCATCTTC
6451845 ATCATCATCATCATC
1 ATCATCATC-T--TC
*
6451860 GTCATCATCTTC
1 ATCATCATCTTC
** *
6451872 ATCGCCAGCTTC
1 ATCATCATCTTC
* *
6451884 ATCGTCATCATC
1 ATCATCATCTTC
*
6451896 ATCATCATCGTC
1 ATCATCATCTTC
* *
6451908 AGCTTCATCTTC
1 ATCATCATCTTC
6451920 TGCGACCGCT
Statistics
Matches: 59, Mismatches: 13, Indels: 6
0.76 0.17 0.08
Matches are distributed among these distances:
12 47 0.80
13 1 0.02
14 1 0.02
15 10 0.17
ACGTcount: A:0.23, C:0.34, G:0.07, T:0.36
Consensus pattern (12 bp):
ATCATCATCTTC
Found at i:6451886 original size:30 final size:30
Alignment explanation
Indices: 6451852--6451916 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
6451842 TTCATCATCA
* *
6451852 TCATCATCGTCATCATCTTCATCGCCAGCT
1 TCATCATCATCATCATCATCATCGCCAGCT
* *
6451882 TCATCGTCATCATCATCATCATCGTCAGCT
1 TCATCATCATCATCATCATCATCGCCAGCT
6451912 TCATC
1 TCATC
6451917 TTCTGCGACC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.22, C:0.35, G:0.09, T:0.34
Consensus pattern (30 bp):
TCATCATCATCATCATCATCATCGCCAGCT
Found at i:6454524 original size:193 final size:196
Alignment explanation
Indices: 6453471--6454604 Score: 1902
Period size: 191 Copynumber: 5.9 Consensus size: 196
6453461 TATTTAAATT
6453471 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTTCTCATAAAACCGGTAT
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATA-TTCTCATAAAACCGGTAT
6453536 AATTGTA-CGGTTAGATTGAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
65 AATTGTACCGGTTAGATTGAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
6453600 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGAAA
130 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGAAA
6453665 AA
195 AA
6453667 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTC-TCAAAACCGGTAT
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCAT-AAAACCGGTAT
6453731 AATTGTACCGGTTAGATTGAAAATTA-ATATTACATT-TACTTTTGGGTTCGATGATTTTGGGAT
65 AATTGTACCGGTTAGATTGAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
6453794 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTG-TTTCCATTCATTATGGGAAA
130 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGAAA
6453858 AA
195 AA
6453860 AGTATCGACACAAACTATATTAGTGTCG--ACATTATTTAGACATATTCTCTCATAAAACCGGTT
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATA-T-TCTCATAAAACCGG-T
6453923 ATAATTGTACCGGTTAGATTGAAAA-T---TATTACATTATACTTTT-GGTTCGATGATTTTGGG
63 ATAATTGTACCGGTTAGATTGAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
*
6453983 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTATGGG-
128 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGA
6454047 AAAA
193 AAAA
6454051 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTC-TCAAAACCGGTAT
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCAT-AAAACCGGTAT
6454115 AA--GTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTC---GATTTTGGGA
65 AATTGTACCGGTTAGATTG-AAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGA
6454175 -CGA-ACTTTTT-TATATGGATCGACACTTTATGGGTGCACC-TGTTTTCCATTCATTCTGGG-A
129 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGAA
6454235 AAA
194 AAA
6454238 AGTATCG--ACAAACTATATTAGTGTCGACACA-TATTTAGACATATTCTCATATAAAACCGGTA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTC--ATAAAACCGGTA
6454300 TAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
64 TAATTGTACCGGTTAGATTG-AAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
6454365 ATCGACAC-TTTT-TATATGGATCGACACTTTA-GGGTGCACCTTG-TTTCCATTCATTCTGGGA
128 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGA
6454426 AAAA
193 AAAA
6454430 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCATAAAACCGGTATA
1 AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCATAAAACCGGTATA
6454495 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTG-AAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
6454560 -GACACTTTTTTATATATGGATCGACACTTTA-GGGTGCACCCTGTT
130 CGACAC-TTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTT
6454605 GGTCATATTG
Statistics
Matches: 899, Mismatches: 3, Indels: 72
0.92 0.00 0.07
Matches are distributed among these distances:
184 17 0.02
185 24 0.03
186 13 0.01
187 31 0.03
188 92 0.10
189 11 0.01
190 10 0.01
191 178 0.20
192 70 0.08
193 176 0.20
194 132 0.15
195 80 0.09
196 65 0.07
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.37
Consensus pattern (196 bp):
AGTATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATC
GACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTCCATTCATTCTGGGAAAA
A
Found at i:6454756 original size:19 final size:19
Alignment explanation
Indices: 6454723--6454770 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
6454713 TTATATTCAC
*
6454723 ATACAAAA-AATAAATCGT
1 ATACAAAATTATAAATCGT
*
6454741 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
6454760 ATACAAAATTA
1 ATACAAAATTA
6454771 ACTCGACACA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 8 0.30
19 19 0.70
ACGTcount: A:0.58, C:0.10, G:0.02, T:0.29
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:6456529 original size:21 final size:22
Alignment explanation
Indices: 6456516--6456556 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
6456506 GACTCTCTCG
6456516 AGTTTCTCTACGACT-TGATCA
1 AGTTTCTCTACGACTCTGATCA
*
6456537 AGTTTCTCTTCGACTCTGAT
1 AGTTTCTCTACGACTCTGAT
6456557 TGTCTTTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.20, C:0.24, G:0.15, T:0.41
Consensus pattern (22 bp):
AGTTTCTCTACGACTCTGATCA
Found at i:6458770 original size:17 final size:18
Alignment explanation
Indices: 6458748--6458790 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
6458738 ATATATCCGG
6458748 TATCATT-TTACCGGTTT
1 TATCATTGTTACCGGTTT
6458765 TATCATTTTGTTACCGGTTT
1 TATCA--TTGTTACCGGTTT
6458785 TATCAT
1 TATCAT
6458791 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 5 0.22
18 1 0.04
19 2 0.09
20 15 0.65
ACGTcount: A:0.19, C:0.16, G:0.12, T:0.53
Consensus pattern (18 bp):
TATCATTGTTACCGGTTT
Found at i:6458780 original size:20 final size:20
Alignment explanation
Indices: 6458753--6458799 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
6458743 TCCGGTATCA
6458753 TTTTACCGGTTTTATCAT-T
1 TTTTACCGGTTTTATCATAT
6458772 TTGTTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCATAT
6458793 TTTTACC
1 TTTTACC
6458800 TGTTATATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.55
Consensus pattern (20 bp):
TTTTACCGGTTTTATCATAT
Found at i:6458947 original size:20 final size:20
Alignment explanation
Indices: 6458921--6458966 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
6458911 CACTTTTAAA
6458921 TTTACCGGTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
6458940 TGTTACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCATATT
6458961 TTTACC
1 TTTACC
6458967 TGGTATATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (20 bp):
TTTACCGGTTTTATCATATT
Found at i:6459429 original size:224 final size:225
Alignment explanation
Indices: 6459032--6459473 Score: 725
Period size: 224 Copynumber: 2.0 Consensus size: 225
6459022 TTAAAACTGC
6459032 TTTTAAAGTTATGTAATTTATTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATAT
1 TTTTAAAGTTATGTAATTTATTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATAT
*
6459097 TAATTTAATAATTTAATTTACACAAAATTATATTTGATTGTTTTGATATTTTATAAAATATTATT
66 TAATTTAATAATTTAATTTACACAAAAATATATTTGATTGTTTTGATATTTTATAAAATATTATT
* *
6459162 AGAATTTAAATTTAACAATATTAACCAAATATAATAATAAATATGTTTTCAACAATGAAATAAGT
131 AGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTC-ACAATGAAATAAGT
*
6459227 ATGGACACTTTTATAAAAATGATATATACTT
195 ATGGACACTTTTATAAAAAGGATATATACTT
*
6459258 TTTTGAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTT-CACCTAC-AT
1 TTTT-AAAGTTATGTAATTTAT-TTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAAT
*
6459321 ATTAA-TTAATAATTTCATTTACACAAAAA-ATTATTTGATTGTTTTGATA-TTTATAAAATATT
64 ATTAATTTAATAATTTAATTTACACAAAAATA-TATTTGATTGTTTTGATATTTTATAAAATATT
* *
6459383 ATTTAG-ATTTAAATTTAACAATATTAACTAAAGATAATAATAAATATATTTTCACAGTGAAATA
128 A-TTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTCACAATGAAATA
6459447 AGTATGGACACTTTTATAAAAAGGATA
192 AGTATGGACACTTTTATAAAAAGGATA
6459474 GATAATTTAC
Statistics
Matches: 204, Mismatches: 8, Indels: 11
0.91 0.04 0.05
Matches are distributed among these distances:
223 36 0.18
224 59 0.29
225 44 0.22
226 11 0.05
227 24 0.12
228 30 0.15
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.45
Consensus pattern (225 bp):
TTTTAAAGTTATGTAATTTATTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATAT
TAATTTAATAATTTAATTTACACAAAAATATATTTGATTGTTTTGATATTTTATAAAATATTATT
AGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTCACAATGAAATAAGTA
TGGACACTTTTATAAAAAGGATATATACTT
Found at i:6461721 original size:3 final size:3
Alignment explanation
Indices: 6461713--6461742 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
6461703 AAAGACTCGA
6461713 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
6461743 TTGACCCAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:6463088 original size:83 final size:83
Alignment explanation
Indices: 6462949--6463114 Score: 305
Period size: 83 Copynumber: 2.0 Consensus size: 83
6462939 AAAACATTAA
* *
6462949 AATGCTTGAAAAGAGGACAAGCTTATTCTACCCTGCCACTAGGCCCTATACATGGTTGGCCTTGG
1 AATGCTTGAAAAGAGGACAAGCTTAGTCTACCCTACCACTAGGCCCTATACATGGTTGGCCTTGG
6463014 CGTACCTACCCGGTTGTG
66 CGTACCTACCCGGTTGTG
*
6463032 AATGCTTGAAAAGAGGACAAGCTTAGTCTACCCTACCACTAGGCCTTATACATGGTTGGCCTTGG
1 AATGCTTGAAAAGAGGACAAGCTTAGTCTACCCTACCACTAGGCCCTATACATGGTTGGCCTTGG
6463097 CGTACCTACCCGGTTGTG
66 CGTACCTACCCGGTTGTG
6463115 GCCCCATAAA
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
83 80 1.00
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.27
Consensus pattern (83 bp):
AATGCTTGAAAAGAGGACAAGCTTAGTCTACCCTACCACTAGGCCCTATACATGGTTGGCCTTGG
CGTACCTACCCGGTTGTG
Found at i:6467709 original size:15 final size:15
Alignment explanation
Indices: 6467689--6467722 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
6467679 TGCACAACTG
6467689 GCTCGGTAGCTTCCT
1 GCTCGGTAGCTTCCT
6467704 GCTCGGTAGCTTCCT
1 GCTCGGTAGCTTCCT
6467719 GCTC
1 GCTC
6467723 TACACCTCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.06, C:0.35, G:0.26, T:0.32
Consensus pattern (15 bp):
GCTCGGTAGCTTCCT
Found at i:6468011 original size:55 final size:56
Alignment explanation
Indices: 6467950--6468216 Score: 286
Period size: 55 Copynumber: 4.8 Consensus size: 56
6467940 GAATCCATAG
* *
6467950 CACCTCTGTGCTAG-AATTAACGATTGAGCACCTCTGTGCTTCAATCGAGAGCTGA
1 CACCTCTGTGCTAGCAATAAATGATTGAGCACCTCTGTGCTTCAATCGAGAGCTGA
* *
6468005 CACCTCTGTG-TAGCCAA-AAGTGATTGAGCACCTCTGTGCTTCAATCGAGAACTGA
1 CACCTCTGTGCTAG-CAATAAATGATTGAGCACCTCTGTGCTTCAATCGAGAGCTGA
* * * ** *
6468060 CACCTCTGTGC-AGTTAAAAAAATGACTGAGCACCTCTGTGCTTCAGCCGGGAGCTGA
1 CACCTCTGTGCTAG--CAATAAATGATTGAGCACCTCTGTGCTTCAATCGAGAGCTGA
*
6468117 CACCTCTGTG-TAGC--TAAGATGATTGAGCACCTCTGTCCTTCAATCGAG-GACTGA
1 CACCTCTGTGCTAGCAATAA-ATGATTGAGCACCTCTGTGCTTCAATCGAGAG-CTGA
*
6468171 CACCTCTGTGC-AGCCAACT--ATGACTGAGCACCTCTGTGCTTCAATC
1 CACCTCTGTGCTAG-CAA-TAAATGATTGAGCACCTCTGTGCTTCAATC
6468217 TAAATTCTGG
Statistics
Matches: 178, Mismatches: 21, Indels: 26
0.79 0.09 0.12
Matches are distributed among these distances:
53 3 0.02
54 44 0.25
55 82 0.46
56 4 0.02
57 44 0.25
58 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (56 bp):
CACCTCTGTGCTAGCAATAAATGATTGAGCACCTCTGTGCTTCAATCGAGAGCTGA
Found at i:6468069 original size:27 final size:27
Alignment explanation
Indices: 6467974--6468216 Score: 135
Period size: 27 Copynumber: 8.8 Consensus size: 27
6467964 AATTAACGAT
6467974 TGAGCACCTCTGTGCTTCAATCGAGAGC
1 TGAGCACCTCTGTGCTTCAATCGAGA-C
* ** * *
6468002 TGA-CACCTCTGTG-TAGCCAAAAGTGAT
1 TGAGCACCTCTGTGCT--TCAATCGAGAC
6468029 TGAGCACCTCTGTGCTTCAATCGAGAAC
1 TGAGCACCTCTGTGCTTCAATCGAG-AC
* ***
6468057 TGA-CACCTCTGTGCAGTTAAAAAAATGAC
1 TGAGCACCTCTGTGC--TTCAATCGA-GAC
** *
6468086 TGAGCACCTCTGTGCTTCAGCCGGGAGC
1 TGAGCACCTCTGTGCTTCAATCGAGA-C
* *
6468114 TGA-CACCTCTGTG-TAGCTAA--GATGAT
1 TGAGCACCTCTGTGCT-TC-AATCGA-GAC
*
6468140 TGAGCACCTCTGTCCTTCAATCGAGGAC
1 TGAGCACCTCTGTGCTTCAATCGA-GAC
** *
6468168 TGA-CACCTCTGTGCAGCCAA-CTATGAC
1 TGAGCACCTCTGTGC-TTCAATCGA-GAC
6468195 TGAGCACCTCTGTGCTTCAATC
1 TGAGCACCTCTGTGCTTCAATC
6468217 TAAATTCTGG
Statistics
Matches: 160, Mismatches: 35, Indels: 40
0.68 0.15 0.17
Matches are distributed among these distances:
26 8 0.05
27 75 0.47
28 54 0.34
29 11 0.07
30 12 0.08
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (27 bp):
TGAGCACCTCTGTGCTTCAATCGAGAC
Found at i:6468270 original size:109 final size:110
Alignment explanation
Indices: 6467974--6468270 Score: 330
Period size: 109 Copynumber: 2.7 Consensus size: 110
6467964 AATTAACGAT
* * * * *
6467974 TGAGCACCTCTGTGCTTCAATCGAGAGCTGACACCTCTGTGTAGCCAAAAGTGATTGAGCACCTC
1 TGAGCACCTCTGTGCTTCAACCGAAAGCTGACACCTCTGTGCAGCTAAGA-TGATTGAGCACCTC
6468039 TGTGCTTCAATCGAGAACTGACACCTCTGTGCAGTTAAAAAAATGAC
65 TGTGCTTCAATCGAGAACTGACACCTCTGTGCAG-TAAAAAAATGAC
* ** *
6468086 TGAGCACCTCTGTGCTTCAGCCGGGAGCTGACACCTCTGTGTAGCTAAGATGATTGAGCACCTCT
1 TGAGCACCTCTGTGCTTCAACCGAAAGCTGACACCTCTGTGCAGCTAAGATGATTGAGCACCTCT
* * ** **
6468151 GTCCTTCAATCGAGGACTGACACCTCTGTGCAG-CCAACTATGAC
66 GTGCTTCAATCGAGAACTGACACCTCTGTGCAGTAAAAAAATGAC
* * * * * **
6468195 TGAGCACCTCTGTGCTTCAATCTAAATTCTGGCTCCTCTGTGCA--TTGGAATGATTGAGCACCT
1 TGAGCACCTCTGTGCTTCAACCGAAA-GCTGACACCTCTGTGCAGCTAAG-ATGATTGAGCACCT
*
6468258 CTGTGCTACAATC
64 CTGTGCTTCAATC
6468271 TAAAATCAAG
Statistics
Matches: 159, Mismatches: 24, Indels: 7
0.84 0.13 0.04
Matches are distributed among these distances:
108 2 0.01
109 53 0.33
110 13 0.08
111 46 0.29
112 45 0.28
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.27
Consensus pattern (110 bp):
TGAGCACCTCTGTGCTTCAACCGAAAGCTGACACCTCTGTGCAGCTAAGATGATTGAGCACCTCT
GTGCTTCAATCGAGAACTGACACCTCTGTGCAGTAAAAAAATGAC
Found at i:6469077 original size:83 final size:83
Alignment explanation
Indices: 6468936--6469100 Score: 276
Period size: 83 Copynumber: 2.0 Consensus size: 83
6468926 AAAACATTAA
* * * *
6468936 AATGCTTGAAAAGATGACAAGCTTATTCTACCCTGCCACTAGGCCCTATACATGGTTGGCCTTGG
1 AATGCTTGAAAAGAGGACAAGCTTATTCTACCCTACCACTAGACCCTATACATAGTTGGCCTTGG
* *
6469001 TGTACCTACCCGGTTGTG
66 CGTACCTACCCAGTTGTG
6469019 AATGCTTGAAAAGAGGACAAGCTTATTCTACCCTACCACTAGACCCTATACATAGTTGGCCTTGG
1 AATGCTTGAAAAGAGGACAAGCTTATTCTACCCTACCACTAGACCCTATACATAGTTGGCCTTGG
6469084 CGTACCTACCCAGTTGT
66 CGTACCTACCCAGTTGT
6469101 TGCCCCATAA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
83 76 1.00
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28
Consensus pattern (83 bp):
AATGCTTGAAAAGAGGACAAGCTTATTCTACCCTACCACTAGACCCTATACATAGTTGGCCTTGG
CGTACCTACCCAGTTGTG
Found at i:6473433 original size:12 final size:12
Alignment explanation
Indices: 6473407--6473440 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
6473397 GAGTCGATTG
6473407 AAGCTCGAGACTC
1 AAGCTCGA-ACTC
6473420 AAGCTCGAACTC
1 AAGCTCGAACTC
*
6473432 AAACTCGAA
1 AAGCTCGAA
6473441 TTTGAACCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.38, C:0.29, G:0.18, T:0.15
Consensus pattern (12 bp):
AAGCTCGAACTC
Found at i:6478568 original size:26 final size:28
Alignment explanation
Indices: 6478531--6478594 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 28
6478521 TATGTATTTG
6478531 TTTCTA-ATATTT-CAATGTAAT-TGCAT
1 TTTCTACATATTTCCAATGT-ATGTGCAT
*
6478557 TTTCTACA-ATTTCCCAATGTATGTGTAT
1 TTTCTACATATTT-CCAATGTATGTGCAT
6478585 TTTCTACATA
1 TTTCTACATA
6478595 AATTTCTCAC
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
26 10 0.31
27 3 0.09
28 18 0.56
29 1 0.03
ACGTcount: A:0.28, C:0.16, G:0.08, T:0.48
Consensus pattern (28 bp):
TTTCTACATATTTCCAATGTATGTGCAT
Found at i:6478718 original size:51 final size:51
Alignment explanation
Indices: 6478652--6478774 Score: 176
Period size: 51 Copynumber: 2.4 Consensus size: 51
6478642 ATCGAACCTT
* *
6478652 ACCCTAAACCACTTTAACCTACACAACCCTTGACCA-TTCTCACCTTAAAAA
1 ACCCTAAACCACTTTAACCTACAAAACCCTTCACCACTT-TCACCTTAAAAA
**
6478703 ACCCTAAACCACTTTAACCTACAAAACCCTTCACCACTTTCACCTTAACGA
1 ACCCTAAACCACTTTAACCTACAAAACCCTTCACCACTTTCACCTTAAAAA
* *
6478754 ACCTTATACCACTTTAACCTA
1 ACCCTAAACCACTTTAACCTA
6478775 AAATCACTCA
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
51 63 0.97
52 2 0.03
ACGTcount: A:0.36, C:0.37, G:0.02, T:0.25
Consensus pattern (51 bp):
ACCCTAAACCACTTTAACCTACAAAACCCTTCACCACTTTCACCTTAAAAA
Found at i:6478722 original size:26 final size:25
Alignment explanation
Indices: 6478652--6478777 Score: 101
Period size: 25 Copynumber: 5.0 Consensus size: 25
6478642 ATCGAACCTT
* *
6478652 ACCCTAAACCACTTTAACCTACACA
1 ACCCTAAACCACTTTAACCTAAAAA
** *
6478677 ACCCTTGACCA-TTCTCACCTTAAAAA
1 ACCCTAAACCACTT-TAACC-TAAAAA
*
6478703 ACCCTAAACCACTTTAACCTACAAA
1 ACCCTAAACCACTTTAACCTAAAAA
** * **
6478728 ACCCTTCACCACTTTCACCTTAACGA
1 ACCCTAAACCACTTTAACC-TAAAAA
* *
6478754 ACCTTATACCACTTTAACCTAAAA
1 ACCCTAAACCACTTTAACCTAAAA
6478778 TCACTCAAAC
Statistics
Matches: 76, Mismatches: 21, Indels: 8
0.72 0.20 0.08
Matches are distributed among these distances:
24 2 0.03
25 37 0.49
26 35 0.46
27 2 0.03
ACGTcount: A:0.37, C:0.37, G:0.02, T:0.25
Consensus pattern (25 bp):
ACCCTAAACCACTTTAACCTAAAAA
Found at i:6479773 original size:12 final size:11
Alignment explanation
Indices: 6479755--6479797 Score: 50
Period size: 12 Copynumber: 3.7 Consensus size: 11
6479745 AGTTTTAAAT
6479755 TTAATTTTATA
1 TTAATTTTATA
* *
6479766 TTATATTTGATT
1 TTA-ATTTTATA
6479778 TTAATTTTAATA
1 TTAATTTT-ATA
6479790 TTAATTTT
1 TTAATTTT
6479798 TTAAATAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
11 7 0.27
12 19 0.73
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (11 bp):
TTAATTTTATA
Found at i:6479873 original size:64 final size:62
Alignment explanation
Indices: 6479749--6479915 Score: 243
Period size: 64 Copynumber: 2.7 Consensus size: 62
6479739 CAAAGAAGTT
* *
6479749 TTAAAT-TTAA-TTTT-ATATTATAT-TTGATTTTAATTTTAATATTAATTTTTTAAATAAA
1 TTAAATATTAATTTTTAATATTATATATAGATATTAATTTTAATATTAATTTTTTAAATAAA
6479807 TTAAATATTAATTTTTAATATTATACTATAGATATTAATTTTAATATTAATTTTTTTAAATAAA
1 TTAAATATTAATTTTTAATATTATA-TATAGATATTAATTTTAATATTAA-TTTTTTAAATAAA
6479871 TTAAATATTAATTTTTTAATATTATATTATAGATATTTAATTTTA
1 TTAAATATTAA-TTTTTAATATTATA-TATAGATA-TTAATTTTA
6479916 TATCATATAA
Statistics
Matches: 98, Mismatches: 3, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
58 6 0.06
59 4 0.04
60 4 0.04
61 8 0.08
62 1 0.01
63 20 0.20
64 24 0.24
65 22 0.22
66 9 0.09
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (62 bp):
TTAAATATTAATTTTTAATATTATATATAGATATTAATTTTAATATTAATTTTTTAAATAAA
Found at i:6479949 original size:65 final size:63
Alignment explanation
Indices: 6479778--6479950 Score: 185
Period size: 65 Copynumber: 2.7 Consensus size: 63
6479768 ATATTTGATT
*
6479778 TTAATTTTAATATTAATT-TTTTAAATAAATTAAATATTAA-TTTTTAATATTATACTATAGATA
1 TTAATTTTAATATTAATTATTTT-AATAAATT-AATATAAATTTTTTAATATTATACTATAGATA
* * *
6479841 TTAATTTTAATATTAATTTTTTTAAATAAATTAAATATTAATTTTTTAATATTATATTATAGATA
1 TTAATTTTAATATTAATTATTTT-AATAAATT-AATATAAATTTTTTAATATTATACTATAGATA
*
6479906 TTTAATTTTATATCATATAAATTATTTT-ATATATT-AT-TAAATTTT
1 -TTAATTTTA-AT-AT-T-AATTATTTTAATAAATTAATATAAATTTT
6479951 ATATTTATTT
Statistics
Matches: 99, Mismatches: 4, Indels: 12
0.86 0.03 0.10
Matches are distributed among these distances:
63 18 0.18
64 22 0.22
65 29 0.29
66 11 0.11
67 2 0.02
68 8 0.08
69 1 0.01
70 8 0.08
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (63 bp):
TTAATTTTAATATTAATTATTTTAATAAATTAATATAAATTTTTTAATATTATACTATAGATA
Found at i:6480464 original size:31 final size:31
Alignment explanation
Indices: 6480429--6480488 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
6480419 TAGTTGTATG
* * *
6480429 AATTATTTAAATTTTAGTATTGTAAAACTAA
1 AATTATTTAAATCTTAATATTGCAAAACTAA
6480460 AATTATTTAAATCTTAATATTGCAAAACT
1 AATTATTTAAATCTTAATATTGCAAAACT
6480489 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (31 bp):
AATTATTTAAATCTTAATATTGCAAAACTAA
Found at i:6487083 original size:33 final size:33
Alignment explanation
Indices: 6487040--6487111 Score: 128
Period size: 33 Copynumber: 2.2 Consensus size: 33
6487030 TTTAACACTA
6487040 GATGATCATAATGAAACCAAAATGTAACATTAGT
1 GATGATCATAATGAAACCAAAATGTAACATT-GT
6487074 GATGA-CATAATGAAACCAAAATGTAACATTGT
1 GATGATCATAATGAAACCAAAATGTAACATTGT
6487106 GATGAT
1 GATGAT
6487112 TATGGGAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
32 7 0.19
33 25 0.68
34 5 0.14
ACGTcount: A:0.46, C:0.11, G:0.17, T:0.26
Consensus pattern (33 bp):
GATGATCATAATGAAACCAAAATGTAACATTGT
Found at i:6487292 original size:3 final size:3
Alignment explanation
Indices: 6487284--6487309 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
6487274 TTTATTTGTT
6487284 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
6487310 CAAATATTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:6493638 original size:20 final size:22
Alignment explanation
Indices: 6493613--6493663 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 22
6493603 ATTATAAACT
*
6493613 TTTTTTAATTT-GATCATTA-A
1 TTTTTTAATTTGGATAATTAGA
6493633 TTTTTT-ATTTGGATAATTAGA
1 TTTTTTAATTTGGATAATTAGA
*
6493654 TTATTTAATT
1 TTTTTTAATT
6493664 ATTTAAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 4 0.15
20 13 0.50
21 6 0.23
22 3 0.12
ACGTcount: A:0.29, C:0.02, G:0.08, T:0.61
Consensus pattern (22 bp):
TTTTTTAATTTGGATAATTAGA
Found at i:6494187 original size:27 final size:27
Alignment explanation
Indices: 6494123--6494187 Score: 64
Period size: 27 Copynumber: 2.4 Consensus size: 27
6494113 TTAAAATAAA
6494123 AAAT-TAATAATTTTATATTTTTAACTT
1 AAATATAAT-ATTTTATATTTTTAACTT
*
6494150 AAATTTAATATTTT-TATTTTATAA-TT
1 AAATATAATATTTTATATTTT-TAACTT
*
6494176 CAATATATATAT
1 AAATATA-ATAT
6494188 ATATATATGA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
26 13 0.39
27 16 0.48
28 4 0.12
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (27 bp):
AAATATAATATTTTATATTTTTAACTT
Found at i:6494850 original size:16 final size:16
Alignment explanation
Indices: 6494829--6494867 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
6494819 AGAAATTTAG
6494829 CTTGTTCGTGTTCATT
1 CTTGTTCGTGTTCATT
6494845 CTTGTTCGTGTTCATT
1 CTTGTTCGTGTTCATT
*
6494861 ATTGTTC
1 CTTGTTC
6494868 ATTCGTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.08, C:0.18, G:0.18, T:0.56
Consensus pattern (16 bp):
CTTGTTCGTGTTCATT
Found at i:6494910 original size:24 final size:24
Alignment explanation
Indices: 6494882--6494944 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
6494872 GTTAAAATGA
* * *
6494882 TAAACTAACACAAACGAATGAACT
1 TAAACGAACACAAACGAATAAACG
*
6494906 TAAACGAACACAAGCGAATAAACG
1 TAAACGAACACAAACGAATAAACG
* *
6494930 TAAATGAGCACAAAC
1 TAAACGAACACAAAC
6494945 AAACGAATAT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.54, C:0.21, G:0.13, T:0.13
Consensus pattern (24 bp):
TAAACGAACACAAACGAATAAACG
Found at i:6495476 original size:2 final size:2
Alignment explanation
Indices: 6495469--6495493 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6495459 AAATCGGTGA
6495469 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
6495494 CCATGTAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6497111 original size:12 final size:12
Alignment explanation
Indices: 6497094--6497118 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6497084 CCACCGTCAC
6497094 CCTCATTATCTT
1 CCTCATTATCTT
6497106 CCTCATTATCTT
1 CCTCATTATCTT
6497118 C
1 C
6497119 TCTTAATAAC
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:0.16, C:0.36, G:0.00, T:0.48
Consensus pattern (12 bp):
CCTCATTATCTT
Found at i:6499622 original size:2 final size:2
Alignment explanation
Indices: 6499615--6499647 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
6499605 TTATCCTTAT
6499615 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6499648 GATCTTTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6499895 original size:21 final size:21
Alignment explanation
Indices: 6499871--6499919 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
6499861 GAAAACTCAA
*
6499871 ATTTCAGTAAATAAAATTCGG
1 ATTTCAGTAAAGAAAATTCGG
* * *
6499892 ATTTCAGTGAAGAAATTTTGG
1 ATTTCAGTAAAGAAAATTCGG
6499913 ATTTCAG
1 ATTTCAG
6499920 AATAAGCACG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.37, C:0.08, G:0.18, T:0.37
Consensus pattern (21 bp):
ATTTCAGTAAAGAAAATTCGG
Found at i:6502162 original size:20 final size:20
Alignment explanation
Indices: 6502139--6502190 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
6502129 AACGCGATCC
6502139 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
6502159 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
6502179 CCAAAATCGCAA
1 CCAGAATCGCAA
6502191 CGCGATTCTT
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:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:6502207 original size:21 final size:20
Alignment explanation
Indices: 6502180--6502278 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
6502170 AATCAGTTTC
6502180 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
6502201 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
6502222 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
6502242 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
6502263 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
6502279 ACACATAAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
20 16 0.27
21 43 0.73
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:6502307 original size:20 final size:20
Alignment explanation
Indices: 6502245--6502438 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
6502235 CGATTTTCCA
* ** *
6502245 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
6502265 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
6502285 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
6502305 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
6502325 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
6502345 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
6502365 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
6502385 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
6502405 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
6502426 AAATCGCAACGCG
1 AAATCGCAACGCG
6502439 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:6502329 original size:60 final size:60
Alignment explanation
Indices: 6502245--6502438 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
6502235 CGATTTTCCA
* ** * *
6502245 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
6502305 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
6502365 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
6502426 AAATCGCAACGCG
1 AAATCGCAACGCG
6502439 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:6502859 original size:33 final size:33
Alignment explanation
Indices: 6502820--6502890 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
6502810 TTCACTTAGA
*
6502820 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
6502853 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
6502886 TTTCA
1 TTTCA
6502891 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:6503028 original size:14 final size:14
Alignment explanation
Indices: 6503009--6503063 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
6502999 AGAATGACTG
6503009 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
6503023 TCGCAACGCGAAATGGAAA
1 TCGCAA--CGAGA--G-AA
6503042 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
6503056 TCGCAACG
1 TCGCAACG
6503064 CGAAACAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 16 0.47
15 1 0.03
16 4 0.12
17 4 0.12
18 1 0.03
19 8 0.24
ACGTcount: A:0.40, C:0.24, G:0.27, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:6503076 original size:33 final size:33
Alignment explanation
Indices: 6503009--6503079 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
6502999 AGAATGACTG
***
6503009 TCGCAACGAGAGAATCGCAACGCGAAATGGAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACAAAAA
6503042 TCGCAACGAGAGAATCGCAACGCGAAACAAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACAAAAA
6503075 TCGCA
1 TCGCA
6503080 TTGCGATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.44, C:0.24, G:0.24, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACAAAAA
Found at i:6503116 original size:14 final size:14
Alignment explanation
Indices: 6503097--6503186 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
6503087 TTTCATTTCG
6503097 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
6503111 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
6503130 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
6503144 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
*
6503161 CGCGTTACGATTCTCT
1 --CGTTGCGATTCTCT
6503177 CGTTGCGATT
1 CGTTGCGATT
6503187 TTCATTTCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 27 0.44
15 1 0.02
16 8 0.13
17 8 0.13
18 1 0.02
19 17 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:6503122 original size:33 final size:33
Alignment explanation
Indices: 6503080--6503194 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
6503070 AAAAATCGCA
6503080 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
6503113 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* * *
6503146 TTGCGATTGTCATCTCGCGTTACGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
6503179 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
6503195 AACCAAAAGA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 77 1.00
ACGTcount: A:0.10, C:0.24, G:0.20, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:6503166 original size:19 final size:18
Alignment explanation
Indices: 6503075--6503187 Score: 79
Period size: 19 Copynumber: 6.8 Consensus size: 18
6503065 GAAACAAAAA
* *
6503075 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGA-TTTCATC
6503094 TCGCGTTGCGA-TTC-TC
1 TCGCGTTGCGATTTCATC
*
6503110 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGA-TTTCATC
6503127 TCGCGTTGCGA-TTC-TC
1 TCGCGTTGCGATTTCATC
6503143 T--CGTTGCGATTGTCATC
1 TCGCGTTGCGATT-TCATC
*
6503160 TCGCGTTACGA-TTC-TC
1 TCGCGTTGCGATTTCATC
6503176 T--CGTTGCGATTT
1 TCGCGTTGCGATTT
6503188 TCATTTCAAC
Statistics
Matches: 77, Mismatches: 6, Indels: 26
0.71 0.06 0.24
Matches are distributed among these distances:
14 23 0.30
15 3 0.04
16 12 0.16
17 13 0.17
18 1 0.01
19 25 0.32
ACGTcount: A:0.11, C:0.25, G:0.21, T:0.43
Consensus pattern (18 bp):
TCGCGTTGCGATTTCATC
Found at i:6505107 original size:92 final size:93
Alignment explanation
Indices: 6504887--6505262 Score: 708
Period size: 92 Copynumber: 4.1 Consensus size: 93
6504877 TAGATTGCTT
*
6504887 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
6504952 -TTGTC-TTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
6504978 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
6505042 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
6505070 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTA-TCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
6505134 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
6505162 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
6505227 TTTGTCTTTG-TTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
6505254 AGTAAATTT
1 AGTAAATTT
6505263 ATCCATTCAA
Statistics
Matches: 280, Mismatches: 1, Indels: 7
0.97 0.00 0.02
Matches are distributed among these distances:
90 2 0.01
91 85 0.30
92 161 0.57
93 32 0.11
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:6505346 original size:19 final size:19
Alignment explanation
Indices: 6505306--6505434 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
6505296 TAGTTTACTT
* *
6505306 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
6505326 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
6505345 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
6505364 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
6505378 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
* *
6505397 CCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
6505411 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
6505430 TCGCA
1 TCGCA
6505435 TTGCGATTTT
Statistics
Matches: 88, Mismatches: 11, Indels: 21
0.73 0.09 0.17
Matches are distributed among these distances:
14 18 0.20
15 2 0.02
16 4 0.05
17 4 0.05
18 2 0.02
19 45 0.51
20 13 0.15
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.08
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:6505385 original size:33 final size:32
Alignment explanation
Indices: 6505342--6505434 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 32
6505332 CGCGAAACCA
**
6505342 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
*
6505374 AGAATCGCAACGCGAAACCAAAACCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
6505407 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
6505435 TTGCGATTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
32 2 0.04
33 53 0.96
ACGTcount: A:0.46, C:0.29, G:0.18, T:0.06
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:6505432 original size:52 final size:52
Alignment explanation
Indices: 6505306--6505434 Score: 131
Period size: 52 Copynumber: 2.5 Consensus size: 52
6505296 TAGTTTACTT
** *
6505306 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAACCGCAACGCGAAA
* * *
6505358 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAACCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAACCGCAACG-CGAA-A
*
6505411 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
6505435 TTGCGATTTT
Statistics
Matches: 61, Mismatches: 10, Indels: 12
0.73 0.12 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 41 0.67
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.08
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAACCGCAACGCGAAA
Found at i:6505452 original size:19 final size:19
Alignment explanation
Indices: 6505430--6505564 Score: 137
Period size: 19 Copynumber: 7.6 Consensus size: 19
6505420 GAAACCAAAA
*
6505430 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
6505449 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
6505465 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
6505482 TCGCGTTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
6505498 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
6505515 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
6505534 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
6505554 TCGTGTTGCGA
1 TCGCGTTGCGA
6505565 AAGTAAACTA
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:6505471 original size:14 final size:14
Alignment explanation
Indices: 6505452--6505508 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
6505442 TTTCATTTCG
6505452 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
6505466 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
6505483 CGCGTTGCGATTCTGT
1 --CGTTGCGATTCTTT
6505499 CGTTGCGATT
1 CGTTGCGATT
6505509 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.09, C:0.21, G:0.25, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:6505477 original size:33 final size:33
Alignment explanation
Indices: 6505435--6505527 Score: 177
Period size: 33 Copynumber: 2.8 Consensus size: 33
6505425 CAAAATCGCA
*
6505435 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
6505468 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
6505501 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
6505528 TTGGTTTCGC
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:6507402 original size:36 final size:37
Alignment explanation
Indices: 6507371--6507440 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
6507361 ATTGATTGTT
6507371 TTTTGATTGTTTAA-TGATTTGTAAAAGTTGATTCAA
1 TTTTGATTGTTTAATTGATTTGTAAAAGTTGATTCAA
*
6507407 TTTTGATTGTTTAATTGATTTGTAAAAGATGATT
1 TTTTGATTGTTTAATTGATTTGTAAAAGTTGATT
6507441 TGTAAAAGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
36 14 0.44
37 18 0.56
ACGTcount: A:0.30, C:0.01, G:0.17, T:0.51
Consensus pattern (37 bp):
TTTTGATTGTTTAATTGATTTGTAAAAGTTGATTCAA
Found at i:6507439 original size:14 final size:14
Alignment explanation
Indices: 6507422--6507457 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
6507412 ATTGTTTAAT
6507422 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
6507436 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
6507450 TGATTTGT
1 TGATTTGT
6507458 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:6507578 original size:19 final size:19
Alignment explanation
Indices: 6507562--6507663 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
6507552 AAAAATGACT
6507562 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
6507581 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
6507600 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
6507614 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
6507633 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
6507653 ATCGCAATGCG
1 ATCGCAATGCG
6507664 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:6507716 original size:19 final size:19
Alignment explanation
Indices: 6507692--6508000 Score: 312
Period size: 19 Copynumber: 17.4 Consensus size: 19
6507682 GATTATCTCG
6507692 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
6507711 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
6507730 TTGTGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
6507744 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
6507763 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
6507782 TTGCGA-TTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
*
6507800 TTGCGATTTT-AATTCGCA
1 TTGCGATTTTCATTTCGCA
6507818 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
6507836 TTGCGATTCTCTCGTTT-TCA
1 TTGCGATT-T-TCATTTCGCA
6507856 TTTCGCGATTTTCA--T----
1 -TT-GCGATTTTCATTTCGCA
6507871 TT-CGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
6507889 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
6507908 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
6507926 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
6507940 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
6507960 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
6507974 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
6507993 TTGCGATT
1 TTGCGATT
6508001 GTATTTTCCG
Statistics
Matches: 247, Mismatches: 13, Indels: 60
0.77 0.04 0.19
Matches are distributed among these distances:
12 9 0.04
14 25 0.10
16 17 0.07
17 17 0.07
18 66 0.27
19 82 0.33
20 17 0.07
21 8 0.03
22 6 0.02
ACGTcount: A:0.15, C:0.20, G:0.17, T:0.48
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:6507732 original size:52 final size:53
Alignment explanation
Indices: 6507670--6507933 Score: 299
Period size: 52 Copynumber: 4.9 Consensus size: 53
6507660 TGCGTTTATA
*
6507670 ATTTCGCATTGCGATTATCTCG-TTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTATTTCGATTGCGATTTTCATTTCGCATTGCGATTTTC
* *
6507722 ATTTCGCATTGTGATTCTTTCG-TTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTATTTCGATTGCGATTTTCATTTCGCATTGCGATTTTC
*
6507774 ATTTCGCATTGCGATTTCATTTCGTATTGCGATTTT-AATTCGCATTGCGA-TTTC
1 ATTTCGCATTGCGA-TT-ATTTCG-ATTGCGATTTTCATTTCGCATTGCGATTTTC
* * * * * * *
6507828 ATTTCGCATTGCGATTCTCTCGTTTTC-ATTTCGCGATTT-TCATTTCGATTTTC
1 ATTTCGCATTGCGATTATTTCGATTGCGATTT-TC-ATTTCGCATTGCGATTTTC
6507881 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA-TTTCATTTCGCATTGCGATT
1 ATTTCGCATTGCGA--TT-ATTTCG-ATTGCGATTTTCATTTCGCATTGCGATT
6507934 CTCTCGTTGC
Statistics
Matches: 177, Mismatches: 21, Indels: 24
0.80 0.09 0.11
Matches are distributed among these distances:
50 4 0.02
51 3 0.02
52 73 0.41
53 25 0.14
54 23 0.13
55 19 0.11
56 24 0.14
57 5 0.03
58 1 0.01
ACGTcount: A:0.16, C:0.20, G:0.16, T:0.48
Consensus pattern (53 bp):
ATTTCGCATTGCGATTATTTCGATTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:6507869 original size:14 final size:14
Alignment explanation
Indices: 6507850--6507887 Score: 62
Period size: 12 Copynumber: 2.9 Consensus size: 14
6507840 GATTCTCTCG
6507850 TTTTCATTTCGCGA
1 TTTTCATTTCGCGA
6507864 TTTTCATTT--CGA
1 TTTTCATTTCGCGA
6507876 TTTTCATTTCGC
1 TTTTCATTTCGC
6507888 ATTGCGATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 12 0.55
14 10 0.45
ACGTcount: A:0.13, C:0.21, G:0.11, T:0.55
Consensus pattern (14 bp):
TTTTCATTTCGCGA
Found at i:6507891 original size:126 final size:122
Alignment explanation
Indices: 6507670--6507972 Score: 416
Period size: 126 Copynumber: 2.4 Consensus size: 122
6507660 TGCGTTTATA
* *
6507670 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGTG
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
*
6507735 ATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTC
66 ATTCTTTCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTC
* * * * *
6507792 ATTTCGTATTGCGATTTTAATTCGCATTGCGA-TTTCATTTCGCATTGCGATTCTCTCGTTT-TC
1 ATTTCGCATTGCGATTCT--CTCG--TTGCGATTTTCATTTCGCATTGCGATT-T-TCATTTCGC
*
6507855 ATTTCGCGA-T-TTTCATTTCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTC
60 A-TT-GCGATTCTTTCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTC
6507918 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCAT
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCAT
6507973 GTTGGGATTT
Statistics
Matches: 159, Mismatches: 12, Indels: 20
0.83 0.06 0.10
Matches are distributed among these distances:
122 25 0.16
123 9 0.06
124 18 0.11
125 20 0.13
126 76 0.48
127 8 0.05
128 3 0.02
ACGTcount: A:0.15, C:0.21, G:0.16, T:0.48
Consensus pattern (122 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
ATTCTTTCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTC
Found at i:6507967 original size:90 final size:90
Alignment explanation
Indices: 6507692--6508000 Score: 358
Period size: 90 Copynumber: 3.5 Consensus size: 90
6507682 GATTATCTCG
*
6507692 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGTGA-TTC-TTTCG--TTGCGATTT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTCATTTCGCATTGCGA--T
*
6507753 TCATTTCGCATTGCGATTTTCATTTCGCA
64 TC-TCTCG-ATTGCGATTTTCATTTCGCA
* *
6507782 TTGCGA-TTTCATTTCGTATTGCGATTTT-AATTCGCATTGCGATTTCATTTCGCATTGCGATTC
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTCATTTCGCATTGCGATTC
* * * *
6507845 TCTCGTTTTC-ATTTCGCGATTT-TCA
66 TCTCGATTGCGATTT-TC-ATTTCGCA
*
6507870 TTTCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTCATTTCGCATTGCGATTC
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTCATTTCGCATTGCGATTC
6507935 TCTCG-TTGCGATTTTCATTTCCGCA
66 TCTCGATTGCGATTTTCATTT-CGCA
* *
6507960 TTGCGATTTTCA--T-G--TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATT
6508001 GTATTTTCCG
Statistics
Matches: 191, Mismatches: 17, Indels: 27
0.81 0.07 0.11
Matches are distributed among these distances:
85 25 0.13
87 5 0.03
88 28 0.15
89 57 0.30
90 70 0.37
92 6 0.03
ACGTcount: A:0.15, C:0.20, G:0.17, T:0.48
Consensus pattern (90 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTCATTTCGCATTGCGATTC
TCTCGATTGCGATTTTCATTTCGCA
Found at i:6510382 original size:20 final size:20
Alignment explanation
Indices: 6510354--6510760 Score: 468
Period size: 20 Copynumber: 20.4 Consensus size: 20
6510344 AAATTTCAGT
* * * *
6510354 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
6510374 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
6510394 GTTGCGA-TTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
6510413 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
6510433 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
6510453 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
6510473 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
6510493 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
6510513 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
6510533 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
6510553 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
6510573 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
6510593 GTTGCG-GTTACGGATACGC
1 GTTGCGATTTACGGATACGC
6510612 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
6510632 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
6510652 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
6510672 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
6510692 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
6510712 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
6510732 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
6510752 GTTGCGATT
1 GTTGCGATT
6510761 ATGGAAAATC
Statistics
Matches: 339, Mismatches: 36, Indels: 24
0.85 0.09 0.06
Matches are distributed among these distances:
18 1 0.00
19 37 0.11
20 295 0.87
21 6 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:6512904 original size:17 final size:18
Alignment explanation
Indices: 6512871--6512908 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
6512861 CCCAAGGAAC
6512871 AAAAGAAATCATATAATA
1 AAAAGAAATCATATAATA
6512889 AAAAGAAA-CA-AGTAATA
1 AAAAGAAATCATA-TAATA
6512906 AAA
1 AAA
6512909 CCTAGGGGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 1 0.05
17 10 0.53
18 8 0.42
ACGTcount: A:0.71, C:0.05, G:0.08, T:0.16
Consensus pattern (18 bp):
AAAAGAAATCATATAATA
Found at i:6514417 original size:19 final size:18
Alignment explanation
Indices: 6514390--6514427 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
6514380 CATGACGACA
6514390 TTCATTTCTC-AAAATCTT
1 TTCATTTCTCTAAAA-CTT
6514408 TTCATATTCTCTAAAACTT
1 TTCAT-TTCTCTAAAACTT
6514427 T
1 T
6514428 GGATTCTCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.28
19 9 0.50
20 4 0.22
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (18 bp):
TTCATTTCTCTAAAACTT
Found at i:6519257 original size:189 final size:189
Alignment explanation
Indices: 6518937--6519283 Score: 515
Period size: 189 Copynumber: 1.8 Consensus size: 189
6518927 AACGATATTT
* * *
6518937 TTTAATTTGAATATTAGTAAGATAATTATTTTTTTAATAAGTCAATTTAAAAATGTATTTGATTT
1 TTTAATTTGAATATTAGTAAGATAATTACTCTTTGAATAAGTCAATTTAAAAATGTATTTGATTT
* * *
6519002 TTTTAATTTTGATTATTAAAAAGATAATTATATACTTTTGTATATTTCAAATTAAAATAATATCT
66 TTTTAACTTTGAATATTAAAAAGATAATTATATACTTTTGTATATTTCAAACTAAAATAATATCT
6519067 ATTTAAGTTTGAATAATAAAAGGAGTTTACCTTTTGAACATTGCAAATTAAATATACTA
131 ATTTAAGTTTGAATAATAAAAGGAGTTTACCTTTTGAACATTGCAAATTAAATATACTA
*
6519126 TTTAATTTGAATATTAGTAAGA-ATATTACTCTTTGAATATGTCAATTTAAAAA-GATATTTG-T
1 TTTAATTTGAATATTAGTAAGATA-ATTACTCTTTGAATAAGTCAATTTAAAAATG-TATTTGAT
*
6519188 TACGTTTTTTACTTTGAATATT-AAAA-ATAATTATATACTTTTGTATATTTCAAACTAAAATAA
64 T---TTTTTAACTTTGAATATTAAAAAGATAATTATATACTTTTGTATATTTCAAACTAAAATAA
** *
6519251 TATCTATTTAAGTTTGAATGGTAAAAGGTGTTT
126 TATCTATTTAAGTTTGAATAATAAAAGGAGTTT
6519284 TATATTTGAA
Statistics
Matches: 142, Mismatches: 11, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
188 4 0.03
189 119 0.84
190 4 0.03
191 15 0.11
ACGTcount: A:0.39, C:0.05, G:0.10, T:0.46
Consensus pattern (189 bp):
TTTAATTTGAATATTAGTAAGATAATTACTCTTTGAATAAGTCAATTTAAAAATGTATTTGATTT
TTTTAACTTTGAATATTAAAAAGATAATTATATACTTTTGTATATTTCAAACTAAAATAATATCT
ATTTAAGTTTGAATAATAAAAGGAGTTTACCTTTTGAACATTGCAAATTAAATATACTA
Found at i:6523459 original size:14 final size:14
Alignment explanation
Indices: 6523437--6523475 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
6523427 ACAGGTAAAA
*
6523437 TCTTTATTTCCCGT
1 TCTTGATTTCCCGT
6523451 TCTTGATTTTCCCGT
1 TCTTGA-TTTCCCGT
*
6523466 TCTGGATTTC
1 TCTTGATTTC
6523476 GATCTGCCAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.08, C:0.26, G:0.13, T:0.54
Consensus pattern (14 bp):
TCTTGATTTCCCGT
Found at i:6523463 original size:15 final size:15
Alignment explanation
Indices: 6523443--6523474 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
6523433 AAAATCTTTA
*
6523443 TTTCCCGTTCTTGAT
1 TTTCCCGTTCTGGAT
6523458 TTTCCCGTTCTGGAT
1 TTTCCCGTTCTGGAT
6523473 TT
1 TT
6523475 CGATCTGCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.25, G:0.16, T:0.53
Consensus pattern (15 bp):
TTTCCCGTTCTGGAT
Found at i:6528921 original size:25 final size:24
Alignment explanation
Indices: 6528888--6528944 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 24
6528878 ATATATTAAC
6528888 TTAAAATATTTTTA-TATTAACTTT
1 TTAAAATA-TTTTACTATTAACTTT
6528912 TTAAATATATTTTACTATTAACTTAAT
1 TTAAA-ATATTTTACTATTAACTT--T
6528939 TTAAAA
1 TTAAAA
6528945 ATAATTTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
24 10 0.34
25 12 0.41
26 1 0.03
27 6 0.21
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (24 bp):
TTAAAATATTTTACTATTAACTTT
Found at i:6528952 original size:27 final size:24
Alignment explanation
Indices: 6528898--6528953 Score: 67
Period size: 27 Copynumber: 2.2 Consensus size: 24
6528888 TTAAAATATT
* *
6528898 TTTATATTAACTTTTTAAATATAT
1 TTTATATTAACTTTTTAAAAATAA
6528922 TTTACTATTAACTTAATTTAAAAATAA
1 TTTA-TATTAACTT--TTTAAAAATAA
6528949 TTTAT
1 TTTAT
6528954 TTTCATTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 4 0.15
25 9 0.33
26 1 0.04
27 13 0.48
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (24 bp):
TTTATATTAACTTTTTAAAAATAA
Found at i:6530462 original size:31 final size:29
Alignment explanation
Indices: 6530427--6530508 Score: 78
Period size: 29 Copynumber: 2.7 Consensus size: 29
6530417 TATTTTTTTG
*
6530427 TTTCAATTCGATACTTGAATTTGATTTTAA
1 TTTCAATT-GATACTTGAATTTCATTTTAA
*
6530457 TTTTCAATATGATACTT--TTTTCATTTTAA
1 -TTTCAAT-TGATACTTGAATTTCATTTTAA
*
6530486 TCTCAAATTAGATACTTGAATTT
1 TTTC-AATT-GATACTTGAATTT
6530509 AACTTTTTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
28 4 0.10
29 20 0.48
31 17 0.40
32 1 0.02
ACGTcount: A:0.30, C:0.11, G:0.07, T:0.51
Consensus pattern (29 bp):
TTTCAATTGATACTTGAATTTCATTTTAA
Found at i:6530844 original size:21 final size:22
Alignment explanation
Indices: 6530820--6530868 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
6530810 GATCACTATT
6530820 ATAATTTACCCTTT-A-TTTTAA
1 ATAATTTA-CCTTTAATTTTTAA
*
6530841 ATAAGTTACCTTTAATTTTTAA
1 ATAATTTACCTTTAATTTTTAA
*
6530863 CTAATT
1 ATAATT
6530869 CATAATTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 5 0.22
21 8 0.35
22 10 0.43
ACGTcount: A:0.35, C:0.12, G:0.02, T:0.51
Consensus pattern (22 bp):
ATAATTTACCTTTAATTTTTAA
Found at i:6532714 original size:20 final size:20
Alignment explanation
Indices: 6532685--6532957 Score: 124
Period size: 20 Copynumber: 13.5 Consensus size: 20
6532675 GATTTTCCAG
* *
6532685 AATCGTAACGCGAATATGAA
1 AATCGCAACGCGAATACGAA
* *
6532705 AATCGCAACGCGAACA-TATA
1 AATCGCAACGCGAATACGA-A
* *
6532725 AATCGCAACGCG-ATTCTGAC
1 AATCGCAACGCGAATAC-GAA
* * * * *
6532745 TATCGCAATGAGTATCCGTAA
1 AATCGCAACGCGAATACG-AA
* * * *
6532766 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
*
6532786 AATCGCAATGAC-AATACGTAA
1 AATCGCAACG-CGAATACG-AA
* * *
6532807 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
* * *
6532827 AATCGCAACGAGAATAAGTA
1 AATCGCAACGCGAATACGAA
* * *
6532847 AATCGCAATGCGTAT-CTGTA
1 AATCGCAACGCGAATAC-GAA
* *
6532867 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGAA
* * * *
6532887 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
*
6532907 AATCGCAATGAC-AATACGTAA
1 AATCGCAACG-CGAATACG-AA
* * *
6532928 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
6532948 AATCGCAACG
1 AATCGCAACG
6532958 TTATCGATAA
Statistics
Matches: 196, Mismatches: 44, Indels: 26
0.74 0.17 0.10
Matches are distributed among these distances:
19 2 0.01
20 142 0.72
21 52 0.27
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
AATCGCAACGCGAATACGAA
Found at i:6532791 original size:41 final size:41
Alignment explanation
Indices: 6532746--6532955 Score: 316
Period size: 41 Copynumber: 5.2 Consensus size: 41
6532736 GATTCTGACT
* *
6532746 ATCGCAATGAGTATCCGTAAAATCGCAATGCGTATCCGTAA
1 ATCGCAATGAGAATACGTAAAATCGCAATGCGTATCCGTAA
* *
6532787 ATCGCAATGACAATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAATGAGAATACGTAAAATCGCAATGCGTATCCGTAA
* * *
6532828 ATCGCAACGAGAATAAGT-AAATCGCAATGCGTATCTGTAA
1 ATCGCAATGAGAATACGTAAAATCGCAATGCGTATCCGTAA
*
6532868 ATCGCAACGAGAATACGT-AAATCGCAATGCGTATCCGTAA
1 ATCGCAATGAGAATACGTAAAATCGCAATGCGTATCCGTAA
* *
6532908 ATCGCAATGACAATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAATGAGAATACGTAAAATCGCAATGCGTATCCGTAA
6532949 ATCGCAA
1 ATCGCAA
6532956 CGTTATCGAT
Statistics
Matches: 154, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
40 74 0.48
41 80 0.52
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (41 bp):
ATCGCAATGAGAATACGTAAAATCGCAATGCGTATCCGTAA
Found at i:6532861 original size:40 final size:41
Alignment explanation
Indices: 6532761--6532957 Score: 308
Period size: 40 Copynumber: 4.9 Consensus size: 41
6532751 AATGAGTATC
*
6532761 CGTAAAATCGCAATGCGTATCCGTAAATCGCAATGACAATA
1 CGTAAAATCGCAATGCGTATCCGTAAATCGCAACGACAATA
* *
6532802 CGTAAAATCGCAACGCGTATCCGTAAATCGCAACGAGAATA
1 CGTAAAATCGCAATGCGTATCCGTAAATCGCAACGACAATA
* * *
6532843 AGT-AAATCGCAATGCGTATCTGTAAATCGCAACGAGAATA
1 CGTAAAATCGCAATGCGTATCCGTAAATCGCAACGACAATA
*
6532883 CGT-AAATCGCAATGCGTATCCGTAAATCGCAATGACAATA
1 CGTAAAATCGCAATGCGTATCCGTAAATCGCAACGACAATA
*
6532923 CGTAAAATCGCAACGCGTATCCGTAAATCGCAACG
1 CGTAAAATCGCAATGCGTATCCGTAAATCGCAACG
6532958 TTATCGATAA
Statistics
Matches: 143, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
40 74 0.52
41 69 0.48
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (41 bp):
CGTAAAATCGCAATGCGTATCCGTAAATCGCAACGACAATA
Found at i:6533060 original size:21 final size:21
Alignment explanation
Indices: 6533034--6533073 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
6533024 GACTATCGCA
6533034 TTGCGATTTCCCAAATTCGAG
1 TTGCGATTTCCCAAATTCGAG
* *
6533055 TTGCGATTTTCCTAATTCG
1 TTGCGATTTCCCAAATTCG
6533074 TAATGCGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.23, G:0.17, T:0.40
Consensus pattern (21 bp):
TTGCGATTTCCCAAATTCGAG
Found at i:6533457 original size:20 final size:20
Alignment explanation
Indices: 6533420--6533508 Score: 117
Period size: 20 Copynumber: 4.5 Consensus size: 20
6533410 CAACGCAGAA
6533420 ATCGCAACGC-GAATATGACT
1 ATCGCAACGCGGAA-ATGACT
* *
6533440 ATCACAACACGGAAATGACT
1 ATCGCAACGCGGAAATGACT
* *
6533460 ATCGCAATGCGGAATTGACT
1 ATCGCAACGCGGAAATGACT
*
6533480 ATCGCAGCGCGGAAATGACT
1 ATCGCAACGCGGAAATGACT
6533500 ATCGCAACG
1 ATCGCAACG
6533509 AGAGAATCGC
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
20 55 0.95
21 3 0.05
ACGTcount: A:0.35, C:0.25, G:0.22, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:6533537 original size:19 final size:19
Alignment explanation
Indices: 6533513--6533613 Score: 140
Period size: 19 Copynumber: 5.5 Consensus size: 19
6533503 GCAACGAGAG
6533513 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
6533532 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
6533551 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
6533570 AATCGCAA--CG-AGTG--
1 AATCGCAATGCGAAATGAA
*
6533584 AATCGCAATACGAAAATGAA
1 AATCGCAATGCG-AAATGAA
6533604 AATCGCAATG
1 AATCGCAATG
6533614 TAAAATTAGT
Statistics
Matches: 73, Mismatches: 3, Indels: 11
0.84 0.03 0.13
Matches are distributed among these distances:
14 8 0.11
16 5 0.07
17 2 0.03
18 3 0.04
19 46 0.63
20 9 0.12
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.16
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:6533653 original size:20 final size:19
Alignment explanation
Indices: 6533623--6533690 Score: 74
Period size: 19 Copynumber: 3.8 Consensus size: 19
6533613 GTAAAATTAG
*
6533623 TTTCGCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
6533642 TTGTCGCATTGCGA--TTCA
1 TT-TCGCATTGCGATTTTCA
*
6533660 -CTCG--TTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
6533676 TTTCGCATTGCGATT
1 TTTCGCATTGCGATT
6533691 CTCTCGTTGC
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
14 6 0.15
16 7 0.17
17 3 0.08
18 4 0.10
19 10 0.25
20 10 0.25
ACGTcount: A:0.13, C:0.22, G:0.21, T:0.44
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTCA
Found at i:6533687 original size:33 final size:33
Alignment explanation
Indices: 6533628--6533712 Score: 134
Period size: 33 Copynumber: 2.5 Consensus size: 33
6533618 ATTAGTTTCG
6533628 CGTTGCGATTTTCATTGTCGCATTGCGATTCACT
1 CGTTGCGATTTTCATT-TCGCATTGCGATTCACT
*
6533662 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
**
6533695 CGTTGCGATAGTCATTTC
1 CGTTGCGATTTTCATTTC
6533713 CACGTTGCGA
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 32 0.67
34 16 0.33
ACGTcount: A:0.14, C:0.24, G:0.20, T:0.42
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCACT
Found at i:6533940 original size:20 final size:20
Alignment explanation
Indices: 6533915--6534003 Score: 126
Period size: 20 Copynumber: 4.5 Consensus size: 20
6533905 CAACGCGGAA
6533915 ATCGCAACGC-GAATATGACT
1 ATCGCAACGCGGAA-ATGACT
*
6533935 ATCGCAACACGGAAATGACT
1 ATCGCAACGCGGAAATGACT
* *
6533955 ATCGCAATGCGGAATTGACT
1 ATCGCAACGCGGAAATGACT
*
6533975 ATCGCAACGCGGAAATAACT
1 ATCGCAACGCGGAAATGACT
6533995 ATCGCAACG
1 ATCGCAACG
6534004 AGAGAATCGC
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
20 58 0.95
21 3 0.05
ACGTcount: A:0.36, C:0.25, G:0.21, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:6534019 original size:495 final size:495
Alignment explanation
Indices: 6533283--6534271 Score: 1852
Period size: 495 Copynumber: 2.0 Consensus size: 495
6533273 ATGCAAACGT
*
6533283 TGTATTATGTGTATATTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGA
1 TGTATTATGTGTATATTATGTATAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGA
*
6533348 GTTTGAACATTGCTATGATAAGTTCAGTTGTTATCACTTATTAGACATTCATTTGACTATCGCAA
66 GTTTGAACATTGCTATGATAAGTTCAATTGTTATCACTTATTAGACATTCATTTGACTATCGCAA
6533413 CGCAGAAATCGCAACGCGAATATGACTATCACAACACGGAAATGACTATCGCAATGCGGAATTGA
131 CGCAGAAATCGCAACGCGAATATGACTATCACAACACGGAAATGACTATCGCAATGCGGAATTGA
* *
6533478 CTATCGCAGCGCGGAAATGACTATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGC
196 CTATCGCAACGCGGAAATAACTATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGC
*
6533543 GAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGTGAATCGCAATACGAAAATGAAAATC
261 GAAATGAAAATCGCAATGCGAAATGAAAATCACAACGAGTGAATCGCAATACGAAAATGAAAATC
* *
6533608 GCAATGTAAAATTAGTTTCGCGTTGCGATTTTCATTGTCGCATTGCGATTCACTCGTTGCGATTT
326 GCAACGTAAAATTAGTTTCGCATTGCGATTTTCATTGTCGCATTGCGATTCACTCGTTGCGATTT
6533673 TCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCATTTCCACGTTGCGATAGTCTGTTTTGCAT
391 TCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCATTTCCACGTTGCGATAGTCTGTTTTGCAT
6533738 TCAACATAATGCAGATTGAAATCAACAAATCAACTATTAG
456 TCAACATAATGCAGATTGAAATCAACAAATCAACTATTAG
*
6533778 TGTATTATGTGTATATTATGTATGAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGA
1 TGTATTATGTGTATATTATGTATAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGA
6533843 GTTTGAACATTGCTATGATAAGTTCAATTGTTATCACTTATTAGACATTCATTTGACTATCGCAA
66 GTTTGAACATTGCTATGATAAGTTCAATTGTTATCACTTATTAGACATTCATTTGACTATCGCAA
* *
6533908 CGCGGAAATCGCAACGCGAATATGACTATCGCAACACGGAAATGACTATCGCAATGCGGAATTGA
131 CGCAGAAATCGCAACGCGAATATGACTATCACAACACGGAAATGACTATCGCAATGCGGAATTGA
6533973 CTATCGCAACGCGGAAATAACTATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGC
196 CTATCGCAACGCGGAAATAACTATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGC
*
6534038 GAAATGAAAATCGCAATGCGAAATGAAAATCACAACGAGTGAATCGCAATGCGAAAATGAAAATC
261 GAAATGAAAATCGCAATGCGAAATGAAAATCACAACGAGTGAATCGCAATACGAAAATGAAAATC
* *
6534103 GCAACGTGAAATTAGTTTCGCATTGCGATTTTCATTTTCGCATTGCGATTCACTCGTTGCGATTT
326 GCAACGTAAAATTAGTTTCGCATTGCGATTTTCATTGTCGCATTGCGATTCACTCGTTGCGATTT
*
6534168 TCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCATTTCCGCGTTGCGATAGTCTGTTTTGCAT
391 TCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCATTTCCACGTTGCGATAGTCTGTTTTGCAT
6534233 TCAACATAATGCAGATTGAAATCAACAAATCAACTATTA
456 TCAACATAATGCAGATTGAAATCAACAAATCAACTATTA
6534272 TATTTTAATC
Statistics
Matches: 480, Mismatches: 14, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
495 480 1.00
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (495 bp):
TGTATTATGTGTATATTATGTATAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGA
GTTTGAACATTGCTATGATAAGTTCAATTGTTATCACTTATTAGACATTCATTTGACTATCGCAA
CGCAGAAATCGCAACGCGAATATGACTATCACAACACGGAAATGACTATCGCAATGCGGAATTGA
CTATCGCAACGCGGAAATAACTATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGC
GAAATGAAAATCGCAATGCGAAATGAAAATCACAACGAGTGAATCGCAATACGAAAATGAAAATC
GCAACGTAAAATTAGTTTCGCATTGCGATTTTCATTGTCGCATTGCGATTCACTCGTTGCGATTT
TCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCATTTCCACGTTGCGATAGTCTGTTTTGCAT
TCAACATAATGCAGATTGAAATCAACAAATCAACTATTAG
Found at i:6534032 original size:19 final size:19
Alignment explanation
Indices: 6534008--6534106 Score: 136
Period size: 19 Copynumber: 5.4 Consensus size: 19
6533998 GCAACGAGAG
6534008 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
6534027 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
6534046 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* *
6534065 AATCACAA--CG-AGTG--
1 AATCGCAATGCGAAATGAA
6534079 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
6534099 AATCGCAA
1 AATCGCAA
6534107 CGTGAAATTA
Statistics
Matches: 70, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
14 7 0.10
16 5 0.07
17 2 0.03
18 3 0.04
19 45 0.64
20 8 0.11
ACGTcount: A:0.47, C:0.17, G:0.20, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:6534059 original size:38 final size:33
Alignment explanation
Indices: 6533995--6534108 Score: 140
Period size: 38 Copynumber: 3.3 Consensus size: 33
6533985 GGAAATAACT
6533995 ATCGCAACGAGA-GAATCGCAATGCGAAATGAAA
1 ATCGCAACGA-ATGAATCGCAATGCGAAATGAAA
6534028 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
1 ATCGCAA--CG-AATG--AATCGCAATGCGAAATGAAA
* *
6534066 ATCACAACGAGTGAATCGCAATGCGAAAATGAAA
1 ATCGCAACGAATGAATCGCAATGCG-AAATGAAA
6534100 ATCGCAACG
1 ATCGCAACG
6534109 TGAAATTAGT
Statistics
Matches: 71, Mismatches: 3, Indels: 13
0.82 0.03 0.15
Matches are distributed among these distances:
33 19 0.27
34 16 0.23
35 6 0.08
36 4 0.06
38 26 0.37
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (33 bp):
ATCGCAACGAATGAATCGCAATGCGAAATGAAA
Found at i:6534143 original size:20 final size:19
Alignment explanation
Indices: 6534118--6534185 Score: 83
Period size: 20 Copynumber: 3.8 Consensus size: 19
6534108 GTGAAATTAG
6534118 TTTCGCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
6534137 TTTTCGCATTGCGA--TTCA
1 -TTTCGCATTGCGATTTTCA
*
6534155 -CTCG--TTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
6534171 TTTCGCATTGCGATT
1 TTTCGCATTGCGATT
6534186 CTCTCGTTGC
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
14 6 0.15
16 7 0.17
17 3 0.07
18 4 0.10
19 8 0.20
20 13 0.32
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTCA
Found at i:6534168 original size:34 final size:34
Alignment explanation
Indices: 6534125--6534218 Score: 136
Period size: 33 Copynumber: 2.8 Consensus size: 34
6534115 TAGTTTCGCA
6534125 TTGCGATTTTCATTTTCGCATTGCGATTCACTCG
1 TTGCGATTTTCATTTTCGCATTGCGATTCACTCG
*
6534159 TTGCGATTTTCA-TTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTTCGCATTGCGATTCACTCG
** * *
6534192 TTGCGATAGTCATTTCCGCGTTGCGAT
1 TTGCGATTTTCATTTTCGCATTGCGAT
6534219 AGTCTGTTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 30 0.56
34 24 0.44
ACGTcount: A:0.14, C:0.23, G:0.20, T:0.43
Consensus pattern (34 bp):
TTGCGATTTTCATTTTCGCATTGCGATTCACTCG
Found at i:6534339 original size:14 final size:14
Alignment explanation
Indices: 6534320--6534356 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
6534310 CATCAATTAA
6534320 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
6534334 ACAAATCATCTTTT
1 ACAAATCAACATTT
6534348 ACAAATCAA
1 ACAAATCAA
6534357 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:6535818 original size:42 final size:42
Alignment explanation
Indices: 6535720--6535821 Score: 116
Period size: 42 Copynumber: 2.4 Consensus size: 42
6535710 TTGAGAGGGA
* * *
6535720 CCTCTTCAACGATGACAGTGGCCTCTTGAACGGTGGGAGGGG
1 CCTCTTAAACGATGACAGTGGCCTCTTGAACGATGGGAGAGG
* * ** *
6535762 ACTCTTGAGGGATGATAGTGGCCTCTTGAACGATAGGG-GAGG
1 CCTCTTAAACGATGACAGTGGCCTCTTGAACGAT-GGGAGAGG
6535804 CCTCTTAAACGATGACAG
1 CCTCTTAAACGATGACAG
6535822 GTGAGTCGGG
Statistics
Matches: 47, Mismatches: 12, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
42 44 0.94
43 3 0.06
ACGTcount: A:0.24, C:0.21, G:0.33, T:0.23
Consensus pattern (42 bp):
CCTCTTAAACGATGACAGTGGCCTCTTGAACGATGGGAGAGG
Found at i:6536325 original size:20 final size:20
Alignment explanation
Indices: 6536302--6536370 Score: 93
Period size: 20 Copynumber: 3.5 Consensus size: 20
6536292 GAAACTTAAA
6536302 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
6536322 ATCGCAATGTGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
6536342 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
6536362 ATCGCAACG
1 ATCGCAACG
6536371 AGAGAATCGC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Done.