Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001999.1 Hibiscus syriacus cultivar Beakdansim tig00004090_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: 232417
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 2 of 2
Found at i:140984 original size:23 final size:23
Alignment explanation
Indices: 140924--140998 Score: 105
Period size: 24 Copynumber: 3.2 Consensus size: 23
140914 CATAATTCAA
*
140924 GTCAAGTATCATATCAGAATCCAG
1 GTCAA-TATCAGATCAGAATCCAG
* *
140948 GTCATGTATCAGATCAGAATCCAT
1 GTCA-ATATCAGATCAGAATCCAG
140972 GTCAATATCAGATCAGAATCCAG
1 GTCAATATCAGATCAGAATCCAG
140995 GTCA
1 GTCA
140999 GGATCATAAC
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
23 21 0.47
24 24 0.53
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.25
Consensus pattern (23 bp):
GTCAATATCAGATCAGAATCCAG
Found at i:141004 original size:23 final size:23
Alignment explanation
Indices: 140928--141013 Score: 109
Period size: 23 Copynumber: 3.7 Consensus size: 23
140918 ATTCAAGTCA
*
140928 AGTATCATATCAGAATCCAGGTC
1 AGTATCAGATCAGAATCCAGGTC
*
140951 ATGTATCAGATCAGAATCCATGTC
1 A-GTATCAGATCAGAATCCAGGTC
*
140975 AATATCAGATCAGAATCCAGGTC
1 AGTATCAGATCAGAATCCAGGTC
* * *
140998 AGGATCATAACAGAAT
1 AGTATCAGATCAGAAT
141014 TCAAAGTCGG
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
23 33 0.61
24 21 0.39
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.24
Consensus pattern (23 bp):
AGTATCAGATCAGAATCCAGGTC
Found at i:142178 original size:18 final size:18
Alignment explanation
Indices: 142157--142192 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
142147 CTTCCATCCG
*
142157 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
142175 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
142193 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:143558 original size:29 final size:29
Alignment explanation
Indices: 143501--143607 Score: 135
Period size: 29 Copynumber: 3.7 Consensus size: 29
143491 AGTCGACTAT
* *
143501 TTTACACA-AATAGCACCCAAACAGAAATTA
1 TTTAC-CAGAATAGCACCAAAACCG-AATTA
* *
143531 ATTCCCAGAATAGCACCAAAACCGAATTA
1 TTTACCAGAATAGCACCAAAACCGAATTA
143560 TTTACCAGAATAGCACCAAAACCGAATTA
1 TTTACCAGAATAGCACCAAAACCGAATTA
* *
143589 TTTATCAGAATAACACCAA
1 TTTACCAGAATAGCACCAA
143608 TTTCGAATTA
Statistics
Matches: 68, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
29 51 0.75
30 17 0.25
ACGTcount: A:0.47, C:0.24, G:0.08, T:0.21
Consensus pattern (29 bp):
TTTACCAGAATAGCACCAAAACCGAATTA
Found at i:143614 original size:29 final size:29
Alignment explanation
Indices: 143553--143649 Score: 113
Period size: 29 Copynumber: 3.3 Consensus size: 29
143543 GCACCAAAAC
* * ***
143553 CGAATTATTTACCAGAATAGCACCAAAAC
1 CGAATTATTTATCAGAATAACACCAATTT
143582 CGAATTATTTATCAGAATAACACCAATTT
1 CGAATTATTTATCAGAATAACACCAATTT
* * * *
143611 CGAATTATTTCTCAAAATATCACCACTTT
1 CGAATTATTTATCAGAATAACACCAATTT
143640 CGAATTATTT
1 CGAATTATTT
143650 CCATGCGACG
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 59 1.00
ACGTcount: A:0.39, C:0.21, G:0.07, T:0.33
Consensus pattern (29 bp):
CGAATTATTTATCAGAATAACACCAATTT
Found at i:145610 original size:35 final size:35
Alignment explanation
Indices: 145537--145611 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
145527 CGTCACTAAC
**
145537 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
*
145572 AGTAAGGCCCTGAGCACACAGCCGAGGAACCTCCA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
145607 AGTAA
1 AGTAA
145612 TCTTCCTCCA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.33, C:0.29, G:0.28, T:0.09
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
Found at i:145749 original size:23 final size:23
Alignment explanation
Indices: 145689--145763 Score: 105
Period size: 24 Copynumber: 3.2 Consensus size: 23
145679 CATAATTCAA
*
145689 GTCAAGTATCATATCAGAATCCAG
1 GTCAA-TATCAGATCAGAATCCAG
* *
145713 GTCATGTATCAGATCAGAATCCAT
1 GTCA-ATATCAGATCAGAATCCAG
145737 GTCAATATCAGATCAGAATCCAG
1 GTCAATATCAGATCAGAATCCAG
145760 GTCA
1 GTCA
145764 GGATCATAAC
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
23 21 0.47
24 24 0.53
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.25
Consensus pattern (23 bp):
GTCAATATCAGATCAGAATCCAG
Found at i:145769 original size:23 final size:23
Alignment explanation
Indices: 145693--145778 Score: 109
Period size: 23 Copynumber: 3.7 Consensus size: 23
145683 ATTCAAGTCA
*
145693 AGTATCATATCAGAATCCAGGTC
1 AGTATCAGATCAGAATCCAGGTC
*
145716 ATGTATCAGATCAGAATCCATGTC
1 A-GTATCAGATCAGAATCCAGGTC
*
145740 AATATCAGATCAGAATCCAGGTC
1 AGTATCAGATCAGAATCCAGGTC
* * *
145763 AGGATCATAACAGAAT
1 AGTATCAGATCAGAAT
145779 TCAAAGTCGG
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
23 33 0.61
24 21 0.39
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.24
Consensus pattern (23 bp):
AGTATCAGATCAGAATCCAGGTC
Found at i:146940 original size:18 final size:18
Alignment explanation
Indices: 146919--146959 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
146909 TTTTCCTTCC
* *
146919 ATTCGATCTTATTATTTA
1 ATTCAATCTTATCATTTA
146937 ATTCAATCTTATCATTTA
1 ATTCAATCTTATCATTTA
*
146955 CTTCA
1 ATTCA
146960 GTCCTTTCGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.29, C:0.17, G:0.02, T:0.51
Consensus pattern (18 bp):
ATTCAATCTTATCATTTA
Found at i:148324 original size:29 final size:29
Alignment explanation
Indices: 148267--148373 Score: 135
Period size: 29 Copynumber: 3.7 Consensus size: 29
148257 AGTCGACTAT
* *
148267 TTTACACA-AATAGCACCCAAACAGAAATTA
1 TTTAC-CAGAATAGCACCAAAACCG-AATTA
* *
148297 ATTCCCAGAATAGCACCAAAACCGAATTA
1 TTTACCAGAATAGCACCAAAACCGAATTA
148326 TTTACCAGAATAGCACCAAAACCGAATTA
1 TTTACCAGAATAGCACCAAAACCGAATTA
* *
148355 TTTATCAGAATAACACCAA
1 TTTACCAGAATAGCACCAA
148374 TTTCGAATTA
Statistics
Matches: 68, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
29 51 0.75
30 17 0.25
ACGTcount: A:0.47, C:0.24, G:0.08, T:0.21
Consensus pattern (29 bp):
TTTACCAGAATAGCACCAAAACCGAATTA
Found at i:148380 original size:29 final size:29
Alignment explanation
Indices: 148319--148415 Score: 113
Period size: 29 Copynumber: 3.3 Consensus size: 29
148309 GCACCAAAAC
* * ***
148319 CGAATTATTTACCAGAATAGCACCAAAAC
1 CGAATTATTTATCAGAATAACACCAATTT
148348 CGAATTATTTATCAGAATAACACCAATTT
1 CGAATTATTTATCAGAATAACACCAATTT
* * * *
148377 CGAATTATTTCTCAAAATATCACCACTTT
1 CGAATTATTTATCAGAATAACACCAATTT
148406 CGAATTATTT
1 CGAATTATTT
148416 CCATGCGACG
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 59 1.00
ACGTcount: A:0.39, C:0.21, G:0.07, T:0.33
Consensus pattern (29 bp):
CGAATTATTTATCAGAATAACACCAATTT
Found at i:151756 original size:21 final size:21
Alignment explanation
Indices: 151730--151774 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
151720 GATTTCTGGG
* *
151730 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
151751 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
151772 CAA
1 CAA
151775 ACGAACAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:152378 original size:18 final size:18
Alignment explanation
Indices: 152355--152389 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
152345 CTAGGAGATT
152355 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
152373 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
152390 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:152486 original size:22 final size:21
Alignment explanation
Indices: 152446--152489 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 21
152436 GTTGTATGAT
152446 AGAAATTTATGAAGTTATATG
1 AGAAATTTATGAAGTTATATG
152467 AGAAGATTATATG-AGTTATATG
1 AGAA-ATT-TATGAAGTTATATG
152489 A
1 A
152490 AATTGAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 4 0.19
22 13 0.62
23 4 0.19
ACGTcount: A:0.43, C:0.00, G:0.20, T:0.36
Consensus pattern (21 bp):
AGAAATTTATGAAGTTATATG
Found at i:153465 original size:149 final size:149
Alignment explanation
Indices: 153285--153599 Score: 614
Period size: 149 Copynumber: 2.1 Consensus size: 149
153275 GAGTCGAGGG
153285 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
153350 ATATGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ATATGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
153415 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
153434 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
153499 ATATGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ATATGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
153564 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
153583 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
153600 TGCAATTATA
Statistics
Matches: 165, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
148 1 0.01
149 164 0.99
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
ATATGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:153600 original size:23 final size:23
Alignment explanation
Indices: 153567--153611 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
153557 ATCATTATAT
*
153567 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
153590 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
153612 AGCTGTAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:156883 original size:21 final size:21
Alignment explanation
Indices: 156857--156901 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
156847 GATTTCTGGG
* *
156857 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
156878 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
156899 CAA
1 CAA
156902 ACGAACAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:157505 original size:18 final size:18
Alignment explanation
Indices: 157482--157516 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
157472 CTAGGAGATT
157482 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
157500 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
157517 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:158580 original size:149 final size:149
Alignment explanation
Indices: 158399--158713 Score: 605
Period size: 149 Copynumber: 2.1 Consensus size: 149
158389 GAGTCGAGGG
158399 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
158464 ATATGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ATATGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
158529 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
*
158548 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
158613 ATATGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ATATGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
158678 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
158697 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
158714 TGCAATTATA
Statistics
Matches: 163, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
149 163 1.00
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
ATATGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:158714 original size:23 final size:23
Alignment explanation
Indices: 158681--158725 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
158671 ATCATTATAT
*
158681 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
158704 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
158726 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:161348 original size:21 final size:21
Alignment explanation
Indices: 161318--161360 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
161308 AGCAAAATTA
*
161318 TGCATTGATGCACTACTACAG
1 TGCATCGATGCACTACTACAG
*
161339 TGCATCGATGCACTTCTACAG
1 TGCATCGATGCACTACTACAG
161360 T
1 T
161361 ACTTTCGTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.30
Consensus pattern (21 bp):
TGCATCGATGCACTACTACAG
Found at i:162092 original size:31 final size:30
Alignment explanation
Indices: 162035--162190 Score: 123
Period size: 32 Copynumber: 5.0 Consensus size: 30
162025 CCTTGGCAAC
* * *
162035 TGTCCATAGGTCCCATAGAACCTAGGTAAAT
1 TGTCCATATGT-CCTTAGAACATAGGTAAAT
* * *
162066 TGTACATATATTCCTTAGAACATAGGTATAT
1 TGTCCATAT-GTCCTTAGAACATAGGTAAAT
* * *
162097 TGTCCATATGTCCTGAAAGACATAGGTAATTT
1 TGTCCATATGTCCTTAGA-ACATAGGTAA-AT
** * *
162129 TGTCCATATGTCCCGAAAGACATAGGTAATT
1 TGTCCATATGTCCTTAGA-ACATAGGTAAAT
*
162160 CTGTCCATATGTTCCGTAGAACATAGGTAAA
1 -TGTCCATATG-TCCTTAGAACATAGGTAAA
162191 CCCTCGACTC
Statistics
Matches: 103, Mismatches: 17, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
30 6 0.06
31 42 0.41
32 50 0.49
33 5 0.05
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (30 bp):
TGTCCATATGTCCTTAGAACATAGGTAAAT
Found at i:162136 original size:32 final size:32
Alignment explanation
Indices: 162085--162189 Score: 142
Period size: 32 Copynumber: 3.3 Consensus size: 32
162075 ATTCCTTAGA
* *
162085 ACATAGGT-ATATTGTCCATATGTCCTGAAAG
1 ACATAGGTAATTTTGTCCATATGTCCCGAAAG
162116 ACATAGGTAATTTTGTCCATATGTCCCGAAAG
1 ACATAGGTAATTTTGTCCATATGTCCCGAAAG
* * *
162148 ACATAGGTAATTCTGTCCATATGTTCCG-TAG
1 ACATAGGTAATTTTGTCCATATGTCCCGAAAG
162179 AACATAGGTAA
1 -ACATAGGTAA
162190 ACCCTCGACT
Statistics
Matches: 67, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
31 10 0.15
32 57 0.85
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.31
Consensus pattern (32 bp):
ACATAGGTAATTTTGTCCATATGTCCCGAAAG
Found at i:167476 original size:2 final size:2
Alignment explanation
Indices: 167471--167495 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
167461 AAATAAATAA
167471 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
167496 ACAATGTAAA
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:167932 original size:33 final size:33
Alignment explanation
Indices: 167867--167932 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
167857 AAAATGTTTC
167867 GTTTTAGTGTTTCAATAAGACTCAAATACGTTG
1 GTTTTAGTGTTTCAATAAGACTCAAATACGTTG
*
167900 GTTTTAGTGTTTCAATAGGACTCAAATACGTTG
1 GTTTTAGTGTTTCAATAAGACTCAAATACGTTG
167933 ATTTATTTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (33 bp):
GTTTTAGTGTTTCAATAAGACTCAAATACGTTG
Found at i:168006 original size:3 final size:3
Alignment explanation
Indices: 167995--168056 Score: 92
Period size: 3 Copynumber: 20.7 Consensus size: 3
167985 AAATAAAAAA
167995 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT ATAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
168043 ATAT AAT -AT AAT AA
1 A-AT AAT AAT AAT AA
168057 AATGTTTTTG
Statistics
Matches: 56, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
2 4 0.07
3 45 0.80
4 7 0.12
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:169437 original size:21 final size:21
Alignment explanation
Indices: 169411--169732 Score: 154
Period size: 21 Copynumber: 15.6 Consensus size: 21
169401 GTTTCCAGAT
* *
169411 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTGGACTA
*
169432 TCGCAATACGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
169453 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
* * *
169474 TCGCTATGCGAA-TATGTA-AA
1 TCGCAATGCGAACT-TGGACTA
** * *
169494 TCGCAAACCGATA-GTCGACTA
1 TCGCAATGCGA-ACTTGGACTA
* *
169515 TCGCAATGCGAA-TATGTA-AA
1 TCGCAATGCGAACT-TGGACTA
* * *
169535 TCGTAATGCGATA-GTCGACTA
1 TCGCAATGCGA-ACTTGGACTA
* *
169556 TCGCAATGCGAA-TATGTA-AA
1 TCGCAATGCGAACT-TGGACTA
* *
169576 TCGCAATGCGATA-GTCGACTA
1 TCGCAATGCGA-ACTTGGACTA
* *
169597 TCGCAATGCGAA-TATGTA-AA
1 TCGCAATGCGAACT-TGGACTA
* *
169617 TCGCAATGCGATA-GTCGACTA
1 TCGCAATGCGA-ACTTGGACTA
* *
169638 TCGCAATGCGAA-TATGTA-AA
1 TCGCAATGCGAACT-TGGACTA
* *
169658 TCGCAATGCGATA-GTCGACTA
1 TCGCAATGCGA-ACTTGGACTA
* *
169679 TCGCAATGCGATA-ATCGACTA
1 TCGCAATGCGA-ACTTGGACTA
*
169700 TCGCAATGCGAACTTTGACTA
1 TCGCAATGCGAACTTGGACTA
*
169721 TTGCAATGCGAA
1 TCGCAATGCGAA
169733 TATGTAAATC
Statistics
Matches: 231, Mismatches: 54, Indels: 32
0.73 0.17 0.10
Matches are distributed among these distances:
20 72 0.31
21 159 0.69
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (21 bp):
TCGCAATGCGAACTTGGACTA
Found at i:169514 original size:41 final size:41
Alignment explanation
Indices: 169425--169813 Score: 545
Period size: 41 Copynumber: 9.4 Consensus size: 41
169415 AACGCGAACT
* * * *
169425 TCGACTATCGCAATACGAACT-TGGACTATCGCAATGCGA-ACT
1 TCGACTATCGCAATGCGAA-TATGTA-AATCGCAATGCGATA-G
* * **
169467 TGGACTATCGCTATGCGAATATGTAAATCGCAAACCGATAG
1 TCGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAG
*
169508 TCGACTATCGCAATGCGAATATGTAAATCGTAATGCGATAG
1 TCGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAG
169549 TCGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAG
1 TCGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAG
169590 TCGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAG
1 TCGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAG
169631 TCGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAG
1 TCGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAG
* *
169672 TCGACTATCGCAATGCG-ATAATCG-ACTATCGCAATGCGA-ACT
1 TCGACTATCGCAATGCGAAT-AT-GTA-AATCGCAATGCGATA-G
* *
169714 TTGACTATTGCAATGCGAATATGTAAATCGCAATGCGATAG
1 TCGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAG
*
169755 TCGACTATCGTAATGCGAATATGTAAATCGCAATGCGATAG
1 TCGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAG
*
169796 TCGACTATCGCATTGCGA
1 TCGACTATCGCAATGCGA
169814 TACTCCAAAA
Statistics
Matches: 313, Mismatches: 25, Indels: 19
0.88 0.07 0.05
Matches are distributed among these distances:
40 2 0.01
41 257 0.82
42 52 0.17
43 2 0.01
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.25
Consensus pattern (41 bp):
TCGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAG
Found at i:169826 original size:21 final size:21
Alignment explanation
Indices: 169779--169829 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
169769 GCGAATATGT
* *
169779 AAATCGCAATGCGATAGTCGA
1 AAATCGCAATGCGATACTCCA
** *
169800 CTATCGCATTGCGATACTCCA
1 AAATCGCAATGCGATACTCCA
169821 AAATCGCAA
1 AAATCGCAA
169830 CGACTGGTGG
Statistics
Matches: 22, Mismatches: 8, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (21 bp):
AAATCGCAATGCGATACTCCA
Found at i:169827 original size:124 final size:123
Alignment explanation
Indices: 169452--169829 Score: 580
Period size: 124 Copynumber: 3.1 Consensus size: 123
169442 AACTTGGACT
* * **
169452 ATCGCAATGCGAACTTGGACTATCGCTATGCGAATATGTAAATCGCAAACCGATAGTCGACTATC
1 ATCGCAATGCGAACTTCGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGACTATC
* *
169517 GCAATGCGAATATGTAAATCGTAATGCGATAGTCGACTATCGCAATGCGAATAT-GTAA
66 GCAATGCGAATATGTAAATCGCAATGCGATAGTCGACTATCGCAATGCG-ATATCGAAA
*
169575 ATCGCAATGCGATA-GTCGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGACTAT
1 ATCGCAATGCGA-ACTTCGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGACTAT
**
169639 CGCAATGCGAATATGTAAATCGCAATGCGATAGTCGACTATCGCAATGCGATAATCGACT
65 CGCAATGCGAATATGTAAATCGCAATGCGATAGTCGACTATCGCAATGCGAT-ATCGAAA
* *
169699 ATCGCAATGCGAACTTTGACTATTGCAATGCGAATATGTAAATCGCAATGCGATAGTCGACTATC
1 ATCGCAATGCGAACTTCGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGACTATC
* * *
169764 GTAATGCGAATATGTAAATCGCAATGCGATAGTCGACTATCGCATTGCGATACTCCAAA
66 GCAATGCGAATATGTAAATCGCAATGCGATAGTCGACTATCGCAATGCGATA-TCGAAA
169823 ATCGCAA
1 ATCGCAA
169830 CGACTGGTGG
Statistics
Matches: 233, Mismatches: 17, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
122 2 0.01
123 110 0.47
124 121 0.52
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (123 bp):
ATCGCAATGCGAACTTCGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGACTATC
GCAATGCGAATATGTAAATCGCAATGCGATAGTCGACTATCGCAATGCGATATCGAAA
Found at i:177115 original size:21 final size:21
Alignment explanation
Indices: 177081--177124 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
177071 GTAAAAAAAA
* *
177081 TTCTTAAAATATTATTATTTT
1 TTCTTAAAACATTAATATTTT
* *
177102 TTCTTAAAGCATTAATGTTTT
1 TTCTTAAAACATTAATATTTT
177123 TT
1 TT
177125 TAATATTTTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.07, G:0.05, T:0.59
Consensus pattern (21 bp):
TTCTTAAAACATTAATATTTT
Found at i:180280 original size:22 final size:19
Alignment explanation
Indices: 180254--180293 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 19
180244 TAACTAAAAT
180254 ATAAATTATCATATAGAATATG
1 ATAAATT-T-ATATA-AATATG
180276 ATAAATTTATATAAATAT
1 ATAAATTTATATAAATAT
180294 ATTAAATACT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.28
20 5 0.28
21 1 0.06
22 7 0.39
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.40
Consensus pattern (19 bp):
ATAAATTTATATAAATATG
Found at i:186725 original size:33 final size:33
Alignment explanation
Indices: 186680--186756 Score: 136
Period size: 33 Copynumber: 2.3 Consensus size: 33
186670 GAATAGAGAA
*
186680 AGGAGCATGGGTGATTTAGCGCATTGCAAGGCG
1 AGGAGCACGGGTGATTTAGCGCATTGCAAGGCG
*
186713 AGGAGCACGGGTGATTTAGTGCATTGCAAGGCG
1 AGGAGCACGGGTGATTTAGCGCATTGCAAGGCG
186746 AGGAGCACGGG
1 AGGAGCACGGG
186757 GACGAACAGG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.25, C:0.16, G:0.42, T:0.18
Consensus pattern (33 bp):
AGGAGCACGGGTGATTTAGCGCATTGCAAGGCG
Found at i:188523 original size:13 final size:13
Alignment explanation
Indices: 188505--188549 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
188495 GAAACAAAAA
188505 CAAAATGCCACTG
1 CAAAATGCCACTG
** *
188518 CAAAATGAAAC-A
1 CAAAATGCCACTG
188530 CAAAATGCCACTG
1 CAAAATGCCACTG
188543 CAAAATG
1 CAAAATG
188550 AAACTAACAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
12 9 0.36
13 16 0.64
ACGTcount: A:0.49, C:0.24, G:0.13, T:0.13
Consensus pattern (13 bp):
CAAAATGCCACTG
Found at i:188533 original size:25 final size:25
Alignment explanation
Indices: 188504--188553 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
188494 TGAAACAAAA
188504 ACAAAATGCCACTGCAAAATGAAAC
1 ACAAAATGCCACTGCAAAATGAAAC
188529 ACAAAATGCCACTGCAAAATGAAAC
1 ACAAAATGCCACTGCAAAATGAAAC
188554 TAACATACCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.52, C:0.24, G:0.12, T:0.12
Consensus pattern (25 bp):
ACAAAATGCCACTGCAAAATGAAAC
Found at i:190203 original size:2 final size:2
Alignment explanation
Indices: 190196--190233 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
190186 TTGTTAAGTG
190196 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
190234 AAGTTGAGTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:191729 original size:42 final size:42
Alignment explanation
Indices: 191681--191843 Score: 263
Period size: 42 Copynumber: 3.9 Consensus size: 42
191671 GAGCCTAGGA
* * * *
191681 AAACTGTAAGGCTCACCCTCGCATACAGCAAAGGGACCTGGG
1 AAACTGTAAGGCTTACCTTTGCACACAGCAAAGGGACCTGGG
191723 AAACTGTAAGGCTTACCTTTGCACACAGCAAAGGGACCTGGG
1 AAACTGTAAGGCTTACCTTTGCACACAGCAAAGGGACCTGGG
* *
191765 AAACTGTAAGTCTTACCTTTGCACACAACAAAGGGACCTGGG
1 AAACTGTAAGGCTTACCTTTGCACACAGCAAAGGGACCTGGG
*
191807 AAACTGTAAGGCTTACCTTTGCACACATCAAAGGGAC
1 AAACTGTAAGGCTTACCTTTGCACACAGCAAAGGGAC
191844 TTGATAATAC
Statistics
Matches: 113, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 113 1.00
ACGTcount: A:0.33, C:0.25, G:0.23, T:0.19
Consensus pattern (42 bp):
AAACTGTAAGGCTTACCTTTGCACACAGCAAAGGGACCTGGG
Found at i:192736 original size:29 final size:29
Alignment explanation
Indices: 192687--192825 Score: 163
Period size: 29 Copynumber: 4.8 Consensus size: 29
192677 AAATAGCATA
192687 ATTTTC-AAATAATTACCAAAATATCACC
1 ATTTTCAAAATAATTACCAAAATATCACC
* **
192715 ATTTTCAAAATAATTACTAAAATATCAAT
1 ATTTTCAAAATAATTACCAAAATATCACC
* * * ** *
192744 TTTTTTAAAAAAATTATGAAAATAACACC
1 ATTTTCAAAATAATTACCAAAATATCACC
* *
192773 ATTTTCAAAATAATTACCAGAATACCACC
1 ATTTTCAAAATAATTACCAAAATATCACC
*
192802 ATTTTCCAAATAATTACCAAAATA
1 ATTTTCAAAATAATTACCAAAATA
192826 CCGTCCGGTC
Statistics
Matches: 90, Mismatches: 20, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
28 6 0.07
29 84 0.93
ACGTcount: A:0.49, C:0.17, G:0.01, T:0.33
Consensus pattern (29 bp):
ATTTTCAAAATAATTACCAAAATATCACC
Found at i:195418 original size:235 final size:235
Alignment explanation
Indices: 195006--195476 Score: 906
Period size: 235 Copynumber: 2.0 Consensus size: 235
194996 AGTGGGTTTA
195006 ACCTGCAACTCTGCTAACAGACTGTTATCATCAAATAAACTCCAGTTGGCGAATAAGGCTCTGAG
1 ACCTGCAACTCTGCTAACAGACTGTTATCATCAAATAAACTCCAGTTGGCGAATAAGGCTCTGAG
*
195071 ATCTTATATCGCCTTACGGCTCAAGGCGTCTGCCACTACATTAGCCTTCCCTAGATGATATTCTA
66 ATCTGATATCGCCTTACGGCTCAAGGCGTCTGCCACTACATTAGCCTTCCCTAGATGATATTCTA
* * *
195136 TCTCTAAATCATAGTCCTTTAAAAGCTCCAACCAGTGACGTTGTCTTAAATTCAATTCTTTCTTA
131 TCTCTAAATCATAGTCATTTAAAAGCTCCAACCAGTGACGCTGTCTTAAATTCAATTATTTCTTA
195201 GTAAGCATATACTTCAGACTCTTATGATCAGTATAAATAT
196 GTAAGCATATACTTCAGACTCTTATGATCAGTATAAATAT
195241 ACCTGCAACTCTGCTAACAGACTGTTATCATCAAATAAACTCCAGTTGGCGAATAAGGCTCTGAG
1 ACCTGCAACTCTGCTAACAGACTGTTATCATCAAATAAACTCCAGTTGGCGAATAAGGCTCTGAG
195306 ATCTGATATCGCCTTACGGCTCAAGGCGTCTGCCACTACATTAGCCTTCCCTAGATGATATTCTA
66 ATCTGATATCGCCTTACGGCTCAAGGCGTCTGCCACTACATTAGCCTTCCCTAGATGATATTCTA
195371 TCTCTAAATCATAGTCATTTAAAAGCTCCAACCAGTGACGCTGTCTTAAATTCAATTATTTCTTA
131 TCTCTAAATCATAGTCATTTAAAAGCTCCAACCAGTGACGCTGTCTTAAATTCAATTATTTCTTA
195436 GTAAGCATATACTTCAGACTCTTATGATCAGTATAAATAT
196 GTAAGCATATACTTCAGACTCTTATGATCAGTATAAATAT
195476 A
1 A
195477 ACACTTTTCT
Statistics
Matches: 232, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
235 232 1.00
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (235 bp):
ACCTGCAACTCTGCTAACAGACTGTTATCATCAAATAAACTCCAGTTGGCGAATAAGGCTCTGAG
ATCTGATATCGCCTTACGGCTCAAGGCGTCTGCCACTACATTAGCCTTCCCTAGATGATATTCTA
TCTCTAAATCATAGTCATTTAAAAGCTCCAACCAGTGACGCTGTCTTAAATTCAATTATTTCTTA
GTAAGCATATACTTCAGACTCTTATGATCAGTATAAATAT
Found at i:199161 original size:42 final size:42
Alignment explanation
Indices: 199110--199275 Score: 262
Period size: 42 Copynumber: 4.0 Consensus size: 42
199100 GAGCTTAGGA
* **
199110 AAACTGTAAGGCTTACCCTCGCACACAACAAAGGGAATTGGG
1 AAACTGTAAGGCTTACCTTCGCACACAACAAAGGGACCTGGG
*
199152 AAACTGTAAGGCTTACCTTTGCACACAACAAAGGGACCTGGG
1 AAACTGTAAGGCTTACCTTCGCACACAACAAAGGGACCTGGG
* *
199194 AAACTGTAAGGCTTACCTTAGCACACAACAAAGGGACCTGAG
1 AAACTGTAAGGCTTACCTTCGCACACAACAAAGGGACCTGGG
199236 AAACTGTAAGGCTTACCTTTC-CACACAACAAAGGGACCTG
1 AAACTGTAAGGCTTACC-TTCGCACACAACAAAGGGACCTG
199276 ATAATACTTC
Statistics
Matches: 116, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
42 114 0.98
43 2 0.02
ACGTcount: A:0.36, C:0.25, G:0.22, T:0.18
Consensus pattern (42 bp):
AAACTGTAAGGCTTACCTTCGCACACAACAAAGGGACCTGGG
Found at i:200135 original size:29 final size:29
Alignment explanation
Indices: 200102--200254 Score: 134
Period size: 29 Copynumber: 5.4 Consensus size: 29
200092 CTATTGTACG
*
200102 AAAATAGCATCATTTTCAAAATAATTACC
1 AAAATAGCACCATTTTCAAAATAATTACC
* * * *
200131 AAAATATCACCATTTTTAAAATAGTTACT
1 AAAATAGCACCATTTTCAAAATAATTACC
* * ** *
200160 AAAATATCA-C-TTTT-AAAAAAAAAACG
1 AAAATAGCACCATTTTCAAAATAATTACC
*
200186 AAAATAGCA-TATTTTCAAAAATAATTACC
1 AAAATAGCACCATTTTC-AAAATAATTACC
* * *
200215 AGAATACCACCATTTTCGAAATAATTACC
1 AAAATAGCACCATTTTCAAAATAATTACC
*
200244 AAAATACCACC
1 AAAATAGCACC
200255 CGGTCAACGG
Statistics
Matches: 99, Mismatches: 21, Indels: 8
0.77 0.16 0.06
Matches are distributed among these distances:
26 15 0.15
27 8 0.08
28 1 0.01
29 69 0.70
30 6 0.06
ACGTcount: A:0.50, C:0.18, G:0.04, T:0.29
Consensus pattern (29 bp):
AAAATAGCACCATTTTCAAAATAATTACC
Found at i:202112 original size:38 final size:37
Alignment explanation
Indices: 202032--202121 Score: 94
Period size: 38 Copynumber: 2.4 Consensus size: 37
202022 CAAATGGGTG
*
202032 TCCCACGTGTCTTTTTCTTTTTATTTTTTTATTCATA
1 TCCCACGTGTCTTTTTCTTTTTATTTTATTATTCATA
* * *
202069 GCCCACGTGTCATTTTAT-TTTTTAATTTTATTGTT-GTA
1 TCCCACGTGTC-TTTT-TCTTTTT-ATTTTATTATTCATA
202107 TCCCACGTGTACTTT
1 TCCCACGTGT-CTTT
202122 CGGTTTGGGT
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
37 10 0.23
38 23 0.52
39 11 0.25
ACGTcount: A:0.16, C:0.19, G:0.10, T:0.56
Consensus pattern (37 bp):
TCCCACGTGTCTTTTTCTTTTTATTTTATTATTCATA
Found at i:202317 original size:42 final size:42
Alignment explanation
Indices: 202270--202385 Score: 214
Period size: 42 Copynumber: 2.8 Consensus size: 42
202260 CCCGAATTCT
* *
202270 CGTGTTTGTTTTACGTAATTCGTTTTCCGGAAAATGTTTTCC
1 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTTTTCC
202312 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTTTTCC
1 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTTTTCC
202354 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
202386 TGTAATTCAT
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 72 1.00
ACGTcount: A:0.16, C:0.19, G:0.20, T:0.45
Consensus pattern (42 bp):
CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTTTTCC
Found at i:202615 original size:21 final size:21
Alignment explanation
Indices: 202574--202632 Score: 52
Period size: 21 Copynumber: 2.9 Consensus size: 21
202564 TAATTATTAA
*
202574 AATATTTAAAATATATTTATT
1 AATATTTAAAATATATATATT
*
202595 AATATTTATAATA-ATAATATT
1 AATATTTAAAATATAT-ATATT
* *
202616 -ATTTTTAATAT-TATATA
1 AATATTTAAAATATATATA
202633 AATAATCAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
19 3 0.10
20 12 0.39
21 16 0.52
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
AATATTTAAAATATATATATT
Found at i:202679 original size:29 final size:29
Alignment explanation
Indices: 202667--202742 Score: 95
Period size: 28 Copynumber: 2.7 Consensus size: 29
202657 AGATATTATA
202667 TTTTTAT-TTTAATAATATATAATAATTT
1 TTTTTATATTTAATAATATATAATAATTT
*
202695 TTTTTATATTTAATAATGA-ATAAT-ATTA
1 TTTTTATATTTAATAAT-ATATAATAATTT
*
202723 TTTATATATTTCAATAATAT
1 TTTTTATATTT-AATAATAT
202743 TTTAGTAAAG
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
28 21 0.50
29 20 0.48
30 1 0.02
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (29 bp):
TTTTTATATTTAATAATATATAATAATTT
Found at i:202686 original size:24 final size:23
Alignment explanation
Indices: 202654--202700 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
202644 ATATAATAAT
* *
202654 ATAAGATATTATATTTTTATTTTA
1 ATAAGATATAATAATTTT-TTTTA
*
202678 ATAATATATAATAATTTTTTTTA
1 ATAAGATATAATAATTTTTTTTA
202701 TATTTAATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
ATAAGATATAATAATTTTTTTTA
Found at i:202696 original size:26 final size:27
Alignment explanation
Indices: 202667--202742 Score: 84
Period size: 29 Copynumber: 2.7 Consensus size: 27
202657 AGATATTATA
202667 TTTTTAT-TTTAATAATATATAATAATTT
1 TTTTTATATTTAATAATATATAAT-A-TT
202695 TTTTTATATTTAATAATGA-ATAATATT
1 TTTTTATATTTAATAAT-ATATAATATT
*
202722 ATTTATATATTTCAATAATAT
1 -TTTTTATATTT-AATAATAT
202743 TTTAGTAAAG
Statistics
Matches: 42, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
27 2 0.05
28 19 0.45
29 20 0.48
30 1 0.02
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (27 bp):
TTTTTATATTTAATAATATATAATATT
Found at i:202985 original size:20 final size:20
Alignment explanation
Indices: 202908--202977 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
202898 TTTCCAGATG
202908 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
202928 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
202948 TTTTACAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
202968 TTTTCCAGAA
1 TTTTCCAGAA
202978 TTCAAATTTT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:202996 original size:15 final size:15
Alignment explanation
Indices: 202976--203026 Score: 84
Period size: 15 Copynumber: 3.4 Consensus size: 15
202966 CATTTTCCAG
*
202976 AATTCAAATTTTAGT
1 AATTCAAATTTCAGT
*
202991 AATTCAAATTCCAGT
1 AATTCAAATTTCAGT
203006 AATTCAAATTTCAGT
1 AATTCAAATTTCAGT
203021 AATTCA
1 AATTCA
203027 TTTTCTGGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.41, C:0.14, G:0.06, T:0.39
Consensus pattern (15 bp):
AATTCAAATTTCAGT
Found at i:203002 original size:29 final size:30
Alignment explanation
Indices: 202960--203026 Score: 100
Period size: 30 Copynumber: 2.3 Consensus size: 30
202950 TTACAGAAAT
** *
202960 GTAATTCATTTTCCAG-AATTCAAATTTTA
1 GTAATTCAAATTCCAGTAATTCAAATTTCA
202989 GTAATTCAAATTCCAGTAATTCAAATTTCA
1 GTAATTCAAATTCCAGTAATTCAAATTTCA
203019 GTAATTCA
1 GTAATTCA
203027 TTTTCTGGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 14 0.41
30 20 0.59
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.40
Consensus pattern (30 bp):
GTAATTCAAATTCCAGTAATTCAAATTTCA
Found at i:203647 original size:2 final size:2
Alignment explanation
Indices: 203594--203628 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
203584 CATTACTTTC
203594 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
203629 AATTAATTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:208210 original size:23 final size:23
Alignment explanation
Indices: 208184--208245 Score: 97
Period size: 23 Copynumber: 2.7 Consensus size: 23
208174 AATAACATAT
*
208184 TAGGTAGAGCTTATATAATGTAA
1 TAGGTAGCGCTTATATAATGTAA
*
208207 TAGGTAGCGCTTGTATAATGTAA
1 TAGGTAGCGCTTATATAATGTAA
*
208230 TAAGTAGCGCTTATAT
1 TAGGTAGCGCTTATAT
208246 TGACCTATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.34, C:0.08, G:0.23, T:0.35
Consensus pattern (23 bp):
TAGGTAGCGCTTATATAATGTAA
Found at i:208597 original size:198 final size:198
Alignment explanation
Indices: 208273--208762 Score: 569
Period size: 198 Copynumber: 2.5 Consensus size: 198
208263 AAATCGGTAA
* * * * * *
208273 ATTTAAACCGGTTACATTATAAATTGACCTATTACATTATAAATATTGGTTTCGATGTTTTCGGG
1 ATTTTAACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGATTTCGGG
* * *** *
208338 ATCGATA-TAATTTT-AAATGTATCGACACTTTATGTGTGCAACTCGTTTGTGTTTTATTTTGGA
66 ATCGATACT--TTTTAAAATGTATCGACACTTTATGCGTACAACTCGTTTGCCATTCATTTTGGA
* * * *
208401 AAAAAGTATCGACACATATTTAAAGAGTGTCGATACATAATGTAGACCTATT-TGCTAATTAACC
129 AAAAAGTATCGACACAAATTAAAAAAGTGTCGATACATAATGTAGACCTATTCT-CTAATGAACC
*
208465 GA-TAT
193 CAGTAT
* * * *
208470 ATTTTAACCGGTTACATTGTAAATTTACATGTTACATAATAATTATCGATTTCGATG-TTTCGAG
1 ATTTTAACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGATTTCG-G
*
208534 GATCGATACTTTTTACAAATGTATCGACACTTTATGCGTACACCTCGTTTGCCATTCATTTTGGA
65 GATCGATACTTTTTA-AAATGTATCGACACTTTATGCGTACAACTCGTTTGCCATTCATTTTGGA
* * * * *
208599 AAAATGTATCGACACAAATTAAAAAAGTGTCGATACTTTATGTTGACCTATTCTCTCATGAACCC
129 AAAAAGTATCGACACAAATTAAAAAAGTGTCGATACATAATGTAGACCTATTCTCTAATGAACCC
208664 AGTAT
194 AGTAT
* * ** *
208669 ATTTCT-ACCGGTTACATTGGAAATTTACCTATTACATTATAATTATCGGTCTCTTTGATTTTGG
1 ATTT-TAACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGATTTCGG
* *
208733 GATTGATACTTGTTATAAATGTATCGACAC
65 GATCGATACTTTTTA-AAATGTATCGACAC
208763 AAAATCTAAC
Statistics
Matches: 247, Mismatches: 38, Indels: 14
0.83 0.13 0.05
Matches are distributed among these distances:
196 9 0.04
197 57 0.23
198 97 0.39
199 79 0.32
200 5 0.02
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (198 bp):
ATTTTAACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGATTTCGGG
ATCGATACTTTTTAAAATGTATCGACACTTTATGCGTACAACTCGTTTGCCATTCATTTTGGAAA
AAAGTATCGACACAAATTAAAAAAGTGTCGATACATAATGTAGACCTATTCTCTAATGAACCCAG
TAT
Found at i:212385 original size:21 final size:21
Alignment explanation
Indices: 212361--212412 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
212351 TGTTTTTGGG
212361 ATCGACACTTGTTATAAATGT
1 ATCGACACTTGTTATAAATGT
212382 ATCGACACTTGTTATAAATGT
1 ATCGACACTTGTTATAAATGT
212403 ATCGACACTT
1 ATCGACACTT
212413 TTTTCATGCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (21 bp):
ATCGACACTTGTTATAAATGT
Found at i:212389 original size:200 final size:199
Alignment explanation
Indices: 211984--212879 Score: 846
Period size: 200 Copynumber: 4.4 Consensus size: 199
211974 TGTTTTTAGG
*
211984 ATCGACACTTTTTCGTGAACTTGTTTGGAAAATTTATTATGGACATAAAGTGTCGACACAAATGT
1 ATCGACACTTTTTCGTGAACTTGTTTGGAAAATTTATTATGGACATAAAGTATCGACACAAATGT
* *
212049 ATAAAGTATTGATACATTATGTATACCTTTTTTTTAATAACCGGTATATTTAGACC-GCTTACAT
66 ATAAAGTATCGATACATTATGTATACCTTTTTTTTAATAACCGGTATATTTAGACCTGGTTACAT
* * *
212113 TGTTATGTTACCTATTACATTATAATTATGGGTTTCGATATTTTTGGGATCGACACTTGTTATAA
131 TGTTATATTACCCATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTGTTATAA
212178 ATGT
196 ATGT
* *
212182 GTCGACACTTTTTCGTGAACTTGTTTGGAAAATTTATTATGGACATAAAGTGTCGACACAAATGT
1 ATCGACACTTTTTCGTGAACTTGTTTGGAAAATTTATTATGGACATAAAGTATCGACACAAATGT
212247 ATAAAGTATCGATACATTATGTATACCTTTCTTTTTTAATAACCGGTATATTTAGA-CTGGTTAC
66 ATAAAGTATCGATACATTATGTATACC-TT-TTTTTTAATAACCGGTATATTTAGACCTGGTTAC
* *
212311 ATTGTTATATTACCCATTATATTATAATTATGTGTTTCGATGTTTTTGGGATCGACACTTGTTAT
129 ATTGTTATATTACCCATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTGTTAT
212376 AAATGT
194 AAATGT
* ** * * **
212382 ATCGACACTTGTTATAAATGTATCGACACTT-TTTTCATGCACTTGGTT-TGGAAATACATTCTG
1 ATCGACACTT-TT-T---CG--T-GA-ACTTGTTTGGA--AAATTTATTATGG----ACA---T-
* * * *
212445 GACAACATGTATCGACACAAATGAATAAAGTGTCGATACA-TATTGTAGACCTATTTTCTCATAA
47 ---AA-A-GTATCGACACAAATGTATAAAGTATCGATACATTA-TGTATACCT-TTTT-T-TTAA
* * * * * * * *
212509 -AACCAGTAAATTTA-ATCTGGTTACATTG-TAAAGTGACCTATTACATTATAGTTACGGGTTTC
103 TAACCGGTATATTTAGACCTGGTTACATTGTTATA-TTACCCATTACATTATAATTATGGGTTTC
* *
212571 GATGTTTTTGGGATTGACACTTGATATAAATGT
167 GATGTTTTTGGGATCGACACTTGTTATAAATGT
* ** * *
212604 ATCGACACTTATTT-ATGAACTTGTTTTGGTTGGAAAATACATTATGGACACAAAGTATCAACAC
1 ATCGACACTT-TTTCGTGAACTTG---T--TTGGAAAATTTATTATGGACATAAAGTATCGACAC
* * * * * *
212668 AAATGTATAAAGTGTCGATACTTTATGTATACATCTTTTCTCATAAACCGGTATATTTAGACCT-
60 AAATGTATAAAGTATCGATACATTATGTATACCTTTTTTTTAAT-AACCGGTATATTTAGACCTG
* * *
212732 GTTACATTGTTAT-TTTCCCTATTACATTATAATTATGGGTCTCGATGTTTTTGGGATCGATACT
124 GTTACATTGTTATATTACCC-ATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACT
*
212796 TTTTATAAATGT
188 TGTTATAAATGT
* ** * * *
212808 ATCGACACTTTGTTCGTGCACTTGGTTTGG-AAATACATTCTGGACA-ACATGTATCGACACGAA
1 ATCGACACTTT-TTCGTGAACTT-GTTTGGAAAATTTATTATGGACATA-AAGTATCGACACAAA
*
212871 TGAATAAAG
63 TGTATAAAG
212880 CAAATTCATT
Statistics
Matches: 577, Mismatches: 71, Indels: 98
0.77 0.10 0.13
Matches are distributed among these distances:
198 90 0.16
199 4 0.01
200 140 0.24
201 6 0.01
202 3 0.01
203 6 0.01
204 85 0.15
205 48 0.08
206 4 0.01
207 3 0.01
208 6 0.01
209 7 0.01
210 5 0.01
213 7 0.01
214 5 0.01
215 1 0.00
216 1 0.00
217 5 0.01
218 3 0.01
219 3 0.01
220 2 0.00
221 12 0.02
222 128 0.22
223 3 0.01
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.39
Consensus pattern (199 bp):
ATCGACACTTTTTCGTGAACTTGTTTGGAAAATTTATTATGGACATAAAGTATCGACACAAATGT
ATAAAGTATCGATACATTATGTATACCTTTTTTTTAATAACCGGTATATTTAGACCTGGTTACAT
TGTTATATTACCCATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTGTTATAA
ATGT
Found at i:212572 original size:222 final size:218
Alignment explanation
Indices: 212161--212817 Score: 705
Period size: 222 Copynumber: 3.0 Consensus size: 218
212151 TATTTTTGGG
* **
212161 ATCGACACTTGTTATAAATGTGTCGACACTTTTTCGTGAACTT-GTTTGGAAAATTTATTATGGA
1 ATCGACACTTGTTATAAATGTATCGACACTTTTTC-TG-ACTTGGTTTGGAAAATACATTATGGA
* * **
212225 CATA-AAGTGTCGACACAAATGTATAAAGTATCGATACATTATGTATACCTTTCTT-TTTTAATA
64 CA-ACAAGTATCGACACAAATGTATAAAGTGTCGATACATTATGTATACCTTT-TTCTCATAA-A
* * * *
212288 ACCGGTATATTTAGACTGGTTACATTGTTATATTACCCATTATATTATAATTATGTGTTTCGATG
126 ACCGGTATATTTAGACTGGTTACATTG-TAAATTACCTATTACATTATAATTATGGGTTTCGATG
212353 TTTTTGGGATCGACACTTGTTATAAATGT
190 TTTTTGGGATCGACACTTGTTATAAATGT
*
212382 ATCGACACTTGTTATAAATGTATCGACACTTTTTTCATGCACTTGGTTTGG-AAATACATTCTGG
1 ATCGACACTTGTTATAAATGTATCGACAC-TTTTTC-TG-ACTTGGTTTGGAAAATACATTATGG
* * *
212446 ACAACATGTATCGACACAAATGAATAAAGTGTCGATACA-TATTGTAGACCTATTTTCTCATAAA
63 ACAACAAGTATCGACACAAATGTATAAAGTGTCGATACATTA-TGTATACCT-TTTTCTCATAAA
* * * * *
212510 ACCAGTAAATTTA-ATCTGGTTACATTGTAAAGTGACCTATTACATTATAGTTACGGGTTTCGAT
126 ACCGGTATATTTAGA-CTGGTTACATTGTAAA-TTACCTATTACATTATAATTATGGGTTTCGAT
* *
212574 GTTTTTGGGATTGACACTTGATATAAATGT
189 GTTTTTGGGATCGACACTTGTTATAAATGT
*
212604 ATCGACAC---TTAT---T-TAT-GA-AC-TTGT-T---TTGG-TTGGAAAATACATTATGGAC-
1 ATCGACACTTGTTATAAATGTATCGACACTTTTTCTGACTTGGTTTGGAAAATACATTATGGACA
* * *
212653 ACAAAGTATCAACACAAATGTATAAAGTGTCGATACTTTATGTATACATCTTTTCTCAT-AAACC
66 AC-AAGTATCGACACAAATGTATAAAGTGTCGATACATTATGTATACCT-TTTTCTCATAAAACC
** * *
212717 GGTATATTTAGACCT-GTTACATTGTTATTTTCCCTATTACATTATAATTATGGGTCTCGATGTT
129 GGTATATTTAGA-CTGGTTACATTG-TAAATTACCTATTACATTATAATTATGGGTTTCGATGTT
* *
212781 TTTGGGATCGATACTTTTTATAAATGT
192 TTTGGGATCGACACTTGTTATAAATGT
212808 ATCGACACTT
1 ATCGACACTT
212818 TGTTCGTGCA
Statistics
Matches: 374, Mismatches: 47, Indels: 45
0.80 0.10 0.10
Matches are distributed among these distances:
204 89 0.24
205 69 0.18
206 2 0.01
209 1 0.00
211 3 0.01
213 2 0.01
214 2 0.01
215 3 0.01
216 1 0.00
219 4 0.01
221 35 0.09
222 151 0.40
223 12 0.03
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.39
Consensus pattern (218 bp):
ATCGACACTTGTTATAAATGTATCGACACTTTTTCTGACTTGGTTTGGAAAATACATTATGGACA
ACAAGTATCGACACAAATGTATAAAGTGTCGATACATTATGTATACCTTTTTCTCATAAAACCGG
TATATTTAGACTGGTTACATTGTAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTG
GGATCGACACTTGTTATAAATGT
Found at i:212786 original size:204 final size:201
Alignment explanation
Indices: 212382--212879 Score: 576
Period size: 204 Copynumber: 2.5 Consensus size: 201
212372 TTATAAATGT
* * * *
212382 ATCGACACTTGTTATAAATGTATCGACACTTTTTTCATGCACTTGGTTTGGAAATACATTCTGGA
1 ATCGACACTTGTTATAAATGTATCGACACTTATTTCATGAACTTGGGTTGGAAATACATTATGGA
* * *
212447 CAACATGTATCGACACAAATGAATAAAGTGTCGATACATATTGTAGACCTATTTTCTCATAAAAC
66 CAACAAGTATCAACACAAATGAATAAAGTGTCGATACATATTGTAGACATATTTTCTCATAAAAC
* * *
212512 CAGTAAATTTAATCTGGTTACATTGTAAAGTGACCTATTACATTATAGTTACGGGTTTCGATGTT
131 CAGTAAATTTAACCTGGTTACATTGTAAAGTGACCTATTACATTATAATTACGGGTCTCGATGTT
212577 TTTGGG
196 TTTGGG
* *
212583 ATTGACACTTGATATAAATGTATCGACACTTATTT-ATGAACTTGTTTTGGTTGGAAAATACATT
1 ATCGACACTTGTTATAAATGTATCGACACTTATTTCATGAACTTG----GGTTGG-AAATACATT
* * * *
212647 ATGGAC-ACAAAGTATCAACACAAATGTATAAAGTGTCGATAC-TTTATGTATACATCTTTTCTC
61 ATGGACAAC-AAGTATCAACACAAATGAATAAAGTGTCGATACATAT-TGTAGACATATTTTCTC
* * * ** ** *
212710 AT-AAACCGGTATATTTAGACCT-GTTACATTGTTATTTTCCCTATTACATTATAATTATGGGTC
124 ATAAAACCAGTAAATTTA-ACCTGGTTACATTGTAAAGTGACCTATTACATTATAATTACGGGTC
212773 TCGATGTTTTTGGG
188 TCGATGTTTTTGGG
* * * * * *
212787 ATCGATACTTTTTATAAATGTATCGACACTT-TGTTCGTGCACTTGGTTTGGAAATACATTCTGG
1 ATCGACACTTGTTATAAATGTATCGACACTTAT-TTCATGAACTTGGGTTGGAAATACATTATGG
* * *
212851 ACAACATGTATCGACACGAATGAATAAAG
65 ACAACAAGTATCAACACAAATGAATAAAG
212880 CAAATTCATT
Statistics
Matches: 250, Mismatches: 36, Indels: 23
0.81 0.12 0.07
Matches are distributed among these distances:
200 42 0.17
201 39 0.16
203 1 0.00
204 98 0.39
205 70 0.28
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.37
Consensus pattern (201 bp):
ATCGACACTTGTTATAAATGTATCGACACTTATTTCATGAACTTGGGTTGGAAATACATTATGGA
CAACAAGTATCAACACAAATGAATAAAGTGTCGATACATATTGTAGACATATTTTCTCATAAAAC
CAGTAAATTTAACCTGGTTACATTGTAAAGTGACCTATTACATTATAATTACGGGTCTCGATGTT
TTTGGG
Found at i:215757 original size:15 final size:15
Alignment explanation
Indices: 215737--215772 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
215727 TGATTTCCTC
*
215737 AGAAGAGCTAGGTTG
1 AGAAGAGATAGGTTG
*
215752 AGAAGAGATGGGTTG
1 AGAAGAGATAGGTTG
215767 AGAAGA
1 AGAAGA
215773 TCCCCGATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.39, C:0.03, G:0.42, T:0.17
Consensus pattern (15 bp):
AGAAGAGATAGGTTG
Found at i:216467 original size:198 final size:198
Alignment explanation
Indices: 216255--216888 Score: 1042
Period size: 198 Copynumber: 3.2 Consensus size: 198
216245 TTACATTATA
216255 GACA-AAATGTATCGACACAAATTCAA-AGAGTGTCGATACTTTATGTACACCTATTTTCTCATA
1 GACACAAA-GTATCGACACAAATTCAACA-AGTGTCGATACTTTATGTACACCTATTTTCTCATA
* *
216318 AACCGGTGTATTTAGACCGATCATATTCATAATTTACCTATTACATTATAATTATGGGTCTCGAT
64 AACCGGTGTATTTAGACCGATTAGATTCATAATTTACCTATTACATTATAATTATGGGTCTCGAT
*
216383 GTTTTTGGAATCGATACTTTTTATAAATGTATCGACACATTATGGTGACCTTGGTAAGGAAATCA
129 GTTTTTGGGATCGATACTTTTTATAAATGTATCGACACATTATGGTGACCTTGGTAAGGAAATCA
216448 TTCTG
194 TTCTG
*
216453 GACACAAAGTATCGACACAAATTAAACAAGTGTCGATACTTTATGTACACCTATTTTCTCATAAA
1 GACACAAAGTATCGACACAAATTCAACAAGTGTCGATACTTTATGTACACCTATTTTCTCATAAA
* * * *
216518 CCGGTATATTTAGACCAATTAGATTGATAATTTACCTATTACTTTATAATTATGGGTCTCGATGT
66 CCGGTGTATTTAGACCGATTAGATTCATAATTTACCTATTACATTATAATTATGGGTCTCGATGT
*
216583 TTTTGGGATCGATATTTTTTATAAATGTATCGACACATTATGGTGACCTTGGTAAGGAAATCATT
131 TTTTGGGATCGATACTTTTTATAAATGTATCGACACATTATGGTGACCTTGGTAAGGAAATCATT
216648 CTG
196 CTG
* *
216651 GACACAAAGTATCGACACAAATTCAACAAGTGTTGATACTTTATGTACACCTGTTTTCTCATAAA
1 GACACAAAGTATCGACACAAATTCAACAAGTGTCGATACTTTATGTACACCTATTTTCTCATAAA
* *
216716 CCGGTGTATTTAGACCGGTTAGATTCATAATTTACCTATTACATTATAATTATGAGTCTCGATGT
66 CCGGTGTATTTAGACCGATTAGATTCATAATTTACCTATTACATTATAATTATGGGTCTCGATGT
* ** *
216781 TTTTGGGATCGATACTTGTTATAAATGTATCGACACATT-TCCATG-CACTTGGTAAAGAAATCA
131 TTTTGGGATCGATACTTTTTATAAATGTATCGACACATTAT-GGTGAC-CTTGGTAAGGAAATCA
216844 TTCTG
194 TTCTG
*
216849 GACACAAAGTATAGACACAAATTCAACAAGTGTCGATACT
1 GACACAAAGTATCGACACAAATTCAACAAGTGTCGATACT
216889 GTAACATCCC
Statistics
Matches: 407, Mismatches: 25, Indels: 8
0.93 0.06 0.02
Matches are distributed among these distances:
197 2 0.00
198 401 0.99
199 4 0.01
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (198 bp):
GACACAAAGTATCGACACAAATTCAACAAGTGTCGATACTTTATGTACACCTATTTTCTCATAAA
CCGGTGTATTTAGACCGATTAGATTCATAATTTACCTATTACATTATAATTATGGGTCTCGATGT
TTTTGGGATCGATACTTTTTATAAATGTATCGACACATTATGGTGACCTTGGTAAGGAAATCATT
CTG
Found at i:218442 original size:23 final size:23
Alignment explanation
Indices: 218409--218476 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
218399 ATTTTTATAT
218409 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* * *
218432 GGCACTCCGGTGTAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
** *
218455 GGCACTTTGGTGCAATTATACG
1 GGCACTACGGTGCAATTCTACG
218477 AGCTGTGGTG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.21, C:0.25, G:0.26, T:0.28
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:220924 original size:23 final size:23
Alignment explanation
Indices: 220894--220954 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
220884 GCTATTACTA
220894 CGGTGCAATTCTACGCGGCACTC
1 CGGTGCAATTCTACGCGGCACTC
* *
220917 CGGTGCAATTCTACGTGGCACTT
1 CGGTGCAATTCTACGCGGCACTC
* *
220940 CGATGCAATTATACG
1 CGGTGCAATTCTACG
220955 AGCTGTGGTG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.21, C:0.28, G:0.25, T:0.26
Consensus pattern (23 bp):
CGGTGCAATTCTACGCGGCACTC
Found at i:222219 original size:19 final size:19
Alignment explanation
Indices: 222195--222240 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
222185 ATTCACATAC
*
222195 AAAATTATAAATCGTATAA
1 AAAATTAAAAATCGTATAA
* *
222214 AAAATTAAAAATCTTATAC
1 AAAATTAAAAATCGTATAA
222233 AAAATTAA
1 AAAATTAA
222241 CCCTACATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.30
Consensus pattern (19 bp):
AAAATTAAAAATCGTATAA
Found at i:223685 original size:18 final size:18
Alignment explanation
Indices: 223662--223700 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
223652 TTCTCTTCAT
*
223662 TTCCTCCATCTTTTCTTC
1 TTCCTCAATCTTTTCTTC
223680 TTCCTCAATCTTTTCTTC
1 TTCCTCAATCTTTTCTTC
223698 TTC
1 TTC
223701 AAATTTTCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.08, C:0.36, G:0.00, T:0.56
Consensus pattern (18 bp):
TTCCTCAATCTTTTCTTC
Found at i:224366 original size:22 final size:24
Alignment explanation
Indices: 224338--224393 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
224328 AACCTGAATT
224338 TATAATAAAAT-TA-ATCATTTTA
1 TATAATAAAATATACATCATTTTA
*
224360 TATAAT-AACTATACCATCATTTTA
1 TATAATAAAATATA-CATCATTTTA
*
224384 TATAAAAAAA
1 TATAATAAAA
224394 CAAAAACATT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
21 3 0.11
22 8 0.30
24 14 0.52
25 2 0.07
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (24 bp):
TATAATAAAATATACATCATTTTA
Found at i:226308 original size:20 final size:20
Alignment explanation
Indices: 226262--226308 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
226252 ACTGGTAGCG
226262 CTTTACCGGTTTTGTCATTT
1 CTTTACCGGTTTTGTCATTT
**
226282 CGATACCGGTTTTGTCATATT
1 CTTTACCGGTTTTGTCAT-TT
226303 -TTTACC
1 CTTTACC
226309 TATTATATTG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.15, C:0.21, G:0.15, T:0.49
Consensus pattern (20 bp):
CTTTACCGGTTTTGTCATTT
Found at i:226769 original size:183 final size:183
Alignment explanation
Indices: 226370--226787 Score: 589
Period size: 182 Copynumber: 2.3 Consensus size: 183
226360 GGCGCTTTTT
* **
226370 AGGCGCTATAACTTCTTCTCTTTTAAATT-AAGAAAGTGTCGATACTTATATTAATTTATCGACA
1 AGGCGCTATAACTTCTTTTCTTTTAAATTCAA-AAAGTGTCGATACTTATATTAACGTATCGACA
* *
226434 CTTTCAATATATCTAATAGCTTTTTACCGGTTTTATCATTTCGAGACCTGTTTTTGTCATATTCT
65 CTTTCAATATATCTAATAGCTTTTTACCGGTTTTATCATTTCGAGACCTGGTTTTGTCATATTCA
* * *
226499 TACATGTTATATTGCTATGGATCGATACATTTTTATAAAGTATCGACATTTTAT
130 TACATGTTATATTACTATGGATCGATACATTTTTATAAAGTATCGACACTTTAC
226553 AGGCGCTATAACTT-TTTCTCTTTTAAATTCAAAAAGTGTCGATACTTATATTAACGTATCGACA
1 AGGCGCTATAACTTCTTT-TCTTTTAAATTCAAAAAGTGTCGATACTTATATTAACGTATCGACA
* ** * *
226617 CTTTTAATATATCTGGTAG-TTCTTTATCGGTTTTATCATTTCGTGACC-GGTTTTGTCATACTT
65 CTTTCAATATATCTAATAGCTT-TTTACCGGTTTTATCATTTCGAGACCTGGTTTTGTCATA-TT
* * *
226680 -ATACCTGTTATATTATTATGGATCGATACGTTTTTATAAAGTATCGACACTTTAC
128 CATACATGTTATATTACTATGGATCGATACATTTTTATAAAGTATCGACACTTTAC
*
226735 AGGCGCTATTACTTCTTTTCTTTTAAATTTC-AAAAGTGTCGATACTTAT-TTAA
1 AGGCGCTATAACTTCTTTTCTTTTAAA-TTCAAAAAGTGTCGATACTTATATTAA
226788 ATATAATCGA
Statistics
Matches: 212, Mismatches: 17, Indels: 14
0.87 0.07 0.06
Matches are distributed among these distances:
181 4 0.02
182 103 0.49
183 103 0.49
184 2 0.01
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.44
Consensus pattern (183 bp):
AGGCGCTATAACTTCTTTTCTTTTAAATTCAAAAAGTGTCGATACTTATATTAACGTATCGACAC
TTTCAATATATCTAATAGCTTTTTACCGGTTTTATCATTTCGAGACCTGGTTTTGTCATATTCAT
ACATGTTATATTACTATGGATCGATACATTTTTATAAAGTATCGACACTTTAC
Found at i:227681 original size:23 final size:22
Alignment explanation
Indices: 227651--227695 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
227641 AAAAAATTAT
*
227651 TTTTTATTAAATATTTTTTAATA
1 TTTTTATTAAAT-TTTTTAAATA
*
227674 TTTTTATTTAATTTTTTAAATA
1 TTTTTATTAAATTTTTTAAATA
227696 ATTATGACGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTTTATTAAATTTTTTAAATA
Found at i:229671 original size:31 final size:31
Alignment explanation
Indices: 229627--229699 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 31
229617 AAAAATATGT
*
229627 TTTGATAAATTT-AATGAGTATTTTATAATAG
1 TTTGATAAATTTAAAT-AGTATTTTATAATAA
* * * *
229658 TTTGATCAGTTTAAATATTATTTTGTAATAA
1 TTTGATAAATTTAAATAGTATTTTATAATAA
229689 TTTGA-AAATTT
1 TTTGATAAATTT
229700 TTAATGACAA
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
30 4 0.12
31 27 0.79
32 3 0.09
ACGTcount: A:0.37, C:0.01, G:0.11, T:0.51
Consensus pattern (31 bp):
TTTGATAAATTTAAATAGTATTTTATAATAA
Found at i:231747 original size:17 final size:17
Alignment explanation
Indices: 231693--231747 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
231683 TTGTTAAGAG
*
231693 TTAAAGATTAAAATTAAT
1 TTAAAGATT-TAATTAAT
**
231711 TTAAAGATTTAATTGGT
1 TTAAAGATTTAATTAAT
**
231728 TTAATTATTTAATTAAT
1 TTAAAGATTTAATTAAT
231745 TTA
1 TTA
231748 TTTTTCAATT
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
17 21 0.70
18 9 0.30
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (17 bp):
TTAAAGATTTAATTAAT
Done.