Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008750.1 Hibiscus syriacus cultivar Beakdansim tig00111841_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: 3719443
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 18
Found at i:1236625 original size:17 final size:18
Alignment explanation
Indices: 1236563--1236681 Score: 85
Period size: 17 Copynumber: 6.8 Consensus size: 18
1236553 GTGTCTACAA
*
1236563 TAATATAAAATATATAAG
1 TAATATAAAGTATATAAG
1236581 T-AT-TAAA-TATA-AAG
1 TAATATAAAGTATATAAG
*
1236595 TATATATACA-TATATAA-
1 TA-ATATAAAGTATATAAG
1236612 TAATATAAAGTATATAAG
1 TAATATAAAGTATATAAG
*
1236630 AATTAAATATAAAGTATTTAAG
1 ---T-AATATAAAGTATATAAG
*
1236652 T-ATATAAAGTACAT-A-
1 TAATATAAAGTATATAAG
1236667 TACATATAAAGTATA
1 TA-ATATAAAGTATA
1236682 AGTGTGTATA
Statistics
Matches: 83, Mismatches: 6, Indels: 25
0.73 0.05 0.22
Matches are distributed among these distances:
14 4 0.05
15 5 0.06
16 13 0.16
17 40 0.48
18 3 0.04
19 1 0.01
21 1 0.01
22 16 0.19
ACGTcount: A:0.55, C:0.03, G:0.07, T:0.35
Consensus pattern (18 bp):
TAATATAAAGTATATAAG
Found at i:1236641 original size:22 final size:22
Alignment explanation
Indices: 1236564--1236651 Score: 95
Period size: 22 Copynumber: 3.8 Consensus size: 22
1236554 TGTCTACAAT
* *
1236564 AATATAAAATATATAAGTATTA
1 AATATAAAGTATATAAGAATTA
*
1236586 AATATAAAGTATATATACATATATAA
1 AATATAAAGTATATA-AGA-AT-T-A
1236612 TAATATAAAGTATATAAGAATTA
1 -AATATAAAGTATATAAGAATTA
*
1236635 AATATAAAGTATTTAAG
1 AATATAAAGTATATAAG
1236652 TATATAAAGT
Statistics
Matches: 56, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
22 30 0.54
23 2 0.04
24 3 0.05
25 3 0.05
26 3 0.05
27 15 0.27
ACGTcount: A:0.57, C:0.01, G:0.07, T:0.35
Consensus pattern (22 bp):
AATATAAAGTATATAAGAATTA
Found at i:1236693 original size:2 final size:2
Alignment explanation
Indices: 1236688--1236738 Score: 52
Period size: 2 Copynumber: 25.5 Consensus size: 2
1236678 TATAAGTGTG
* *
1236688 TA TA TA TA TA TA TA GA TA TGA TA TA -A TA TA -A TA TA AA CTA TA
1 TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA -TA TA
1236730 TA TA TA TA T
1 TA TA TA TA T
1236739 TATTTTATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
1 2 0.05
2 36 0.88
3 3 0.07
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (2 bp):
TA
Found at i:1237237 original size:2 final size:2
Alignment explanation
Indices: 1237217--1237268 Score: 67
Period size: 2 Copynumber: 28.0 Consensus size: 2
1237207 TAACATTCAT
*
1237217 TA TA CA TA T- TA TA TA -A 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 TA TA
1237257 TA TA -A TA T- TA TA
1 TA TA TA TA TA TA TA
1237269 ATTGTTTTAA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
1 4 0.09
2 40 0.91
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1237522 original size:532 final size:532
Alignment explanation
Indices: 1236691--1237692 Score: 1505
Period size: 532 Copynumber: 1.9 Consensus size: 532
1236681 AAGTGTGTAT
* *
1236691 ATATATATATAGATATGATATAATATAATATAAACTATATATATATATTATTTTATTTTTTCCCA
1 ATATATATATAGATATGATATAATATAATATAAACTATATATATATATTATTTTAATTTTCCCCA
1236756 ACTTTTGATATTAATGCAATTCAATCCATTTTACAATTTTTCTCACATTTTACAATTTTTTTGAT
66 ACTTTTGATATTAATGCAATTCAATCCATTTTACAATTTTTCTCACATTTTACAA-TTTTTTGAT
*
1236821 TTGATCCTTTTATGTTGTTTATTGTATTTTAATTTTAATTTCTAATTTCATATTTATTCAATTTA
130 TTGATCCTTTTATGTTGTTTATTGTATTTAAATTTTAATTTCTAATTTCATATTTATTCAATTTA
*
1236886 GTCATTCAAATTATATTAGAATATGAAATTGATCCATACTTATTTATATATTTTTGTAATTTACT
195 GTCATTCAAATTATATTAGAATATGAAATTAATCCATACTTATTTATATATTTTTGTAATTTACT
* *
1236951 TAAAACCCTATAAAATGTAAACATATAATAAATTTCTTTTCAAATTATGTTCATCAACTTTTT-A
260 TAAAACCCTATAAAATGTAAACACATAATAAATTTCTTTTCAAATTATGTTCACCAA-TTTTTAA
* * *
1237015 AATGTATGCAATTTAGTCCA-TTTTTATATTAATAT-TGACTTCACATTTTATAATTAATTCAAT
324 AATGTATGCAATTTAGTACATTTTTTATATTAATATCAG-CTTCACATTTTATAATTAATTAAAT
* *
1237078 TTCATCACTCATCAATGTGTGTTGCTTGATTTATTCAA-TTTTTATTTCCAATTTCATGTTTGTT
388 TTCATCACTCATCAATGTGTGTTGCTTAATTTATTCAATTTTTTATTTCCAATTTCATGTTTCTT
1237142 CAATTT-AGTACTTTATATATATATAAAGTATAATGTATATTATATATACATGCATCATATTATC
453 CAATTTGA-TACTTTATATATATATAAAGTATAATGTATATTATATATACATGCATCATATTATC
1237206 ATAACATTCATTATAC
517 ATAACATTCATTATAC
* *
1237222 ATAT-TATATA-ATAT-ATATATATATATATATATA-TATATAATATTATAATTGTTTTAATTTT
1 ATATATATATAGATATGATATA-ATATA-ATATAAACTATAT-ATA-TAT-ATTATTTTAATTTT
* *
1237283 CCCCAGCTTTTGA-ATTTAATGCAATTCAGTCCATTTTACAATTTTTCCTCACATTTTACAA-TT
61 CCCCAACTTTTGATA-TTAATGCAATTCAATCCATTTTACAATTTTT-CTCACATTTTACAATTT
* *
1237346 TTT-ATTTGATCCTTTTATTTTGTTTATTGTATTTAAATTTTAATTTGTAATTTCATATTT-TTC
124 TTTGATTTGATCCTTTTATGTTGTTTATTGTATTTAAATTTTAATTTCTAATTTCATATTTATTC
* *** *
1237409 AATTTAGTCCTTCAAATTATATTTTTATCTGAAATTAA-CTCATACTTA-TT-TATATTTTTGTA
189 AATTTAGTCATTCAAATTATATTAGAATATGAAATTAATC-CATACTTATTTATATATTTTTGTA
*
1237471 ATTTATTTAAAACAAACCCTATAAAATGTAAATCACATAATAAATTTCTTTTCAAATTATGTTCA
253 ATTTACTT---A-AAACCCTATAAAATGTAAA-CACATAATAAATTTCTTTTCAAATTATGTTCA
1237536 CCAATTTTTAAAATGTATGCAATTTAGTACATTTTTTATATTAATATCAGCTTCACATTTTATAA
313 CCAATTTTTAAAATGTATGCAATTTAGTACATTTTTTATATTAATATCAGCTTCACATTTTATAA
**
1237601 TTAATTAAATTTCATCTTTCATCAATGTGTGTTGCTTAATTTATTCAATTTTTTTATTTCCAATT
378 TTAATTAAATTTCATCACTCATCAATGTGTGTTGCTTAATTTATTCAA-TTTTTTATTTCCAATT
1237666 TCATGTTTCTTCAATTTGATACTTTAT
442 TCATGTTTCTTCAATTTGATACTTTAT
1237693 TTCCACCAGT
Statistics
Matches: 427, Mismatches: 25, Indels: 34
0.88 0.05 0.07
Matches are distributed among these distances:
527 19 0.04
528 8 0.02
529 57 0.13
530 70 0.16
531 37 0.09
532 107 0.25
533 88 0.21
534 1 0.00
535 39 0.09
536 1 0.00
ACGTcount: A:0.33, C:0.11, G:0.05, T:0.50
Consensus pattern (532 bp):
ATATATATATAGATATGATATAATATAATATAAACTATATATATATATTATTTTAATTTTCCCCA
ACTTTTGATATTAATGCAATTCAATCCATTTTACAATTTTTCTCACATTTTACAATTTTTTGATT
TGATCCTTTTATGTTGTTTATTGTATTTAAATTTTAATTTCTAATTTCATATTTATTCAATTTAG
TCATTCAAATTATATTAGAATATGAAATTAATCCATACTTATTTATATATTTTTGTAATTTACTT
AAAACCCTATAAAATGTAAACACATAATAAATTTCTTTTCAAATTATGTTCACCAATTTTTAAAA
TGTATGCAATTTAGTACATTTTTTATATTAATATCAGCTTCACATTTTATAATTAATTAAATTTC
ATCACTCATCAATGTGTGTTGCTTAATTTATTCAATTTTTTATTTCCAATTTCATGTTTCTTCAA
TTTGATACTTTATATATATATAAAGTATAATGTATATTATATATACATGCATCATATTATCATAA
CATTCATTATAC
Found at i:1238978 original size:21 final size:20
Alignment explanation
Indices: 1238932--1238971 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1238922 ATGCATGGAG
*
1238932 GAAAAGGATCGATTCCTTCAC
1 GAAAAGGATCGA-TCCCTCAC
*
1238953 CAAAAGGATCGATCCCTCA
1 GAAAAGGATCGATCCCTCA
1238972 ATGAAAATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.35, C:0.28, G:0.17, T:0.20
Consensus pattern (20 bp):
GAAAAGGATCGATCCCTCAC
Found at i:1239031 original size:20 final size:21
Alignment explanation
Indices: 1238984--1239033 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
1238974 GAAAATGATA
1238984 GATCCATTTCCCTAAAGGATC
1 GATCCATTTCCCTAAAGGATC
1239005 GAT-CATTTCCCTTAAA-GATC
1 GATCCATTTCCC-TAAAGGATC
1239025 G-TCCATTTC
1 GATCCATTTC
1239034 TTACATCAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
19 1 0.04
20 19 0.70
21 7 0.26
ACGTcount: A:0.26, C:0.28, G:0.12, T:0.34
Consensus pattern (21 bp):
GATCCATTTCCCTAAAGGATC
Found at i:1240395 original size:17 final size:16
Alignment explanation
Indices: 1240346--1240396 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 16
1240336 ATAAGACTCC
*
1240346 AAAAGAATAAGGAAGA
1 AAAAGAATGAGGAAGA
**
1240362 AAAAGAGATGAAAAAGA
1 AAAAGA-ATGAGGAAGA
1240379 AAAAGAATGAGGTAAGA
1 AAAAGAATGAGG-AAGA
1240396 A
1 A
1240397 TCGCCTTCAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
16 10 0.36
17 18 0.64
ACGTcount: A:0.67, C:0.00, G:0.25, T:0.08
Consensus pattern (16 bp):
AAAAGAATGAGGAAGA
Found at i:1241184 original size:30 final size:30
Alignment explanation
Indices: 1241148--1241222 Score: 141
Period size: 30 Copynumber: 2.5 Consensus size: 30
1241138 AGCCGTTTAA
1241148 ATTCAATTAGGTATCTCAGTTTTATTTTGT
1 ATTCAATTAGGTATCTCAGTTTTATTTTGT
1241178 ATTCAATTAGGTATCTCAGTTTTATTTTGT
1 ATTCAATTAGGTATCTCAGTTTTATTTTGT
*
1241208 ATTCAATCAGGTATC
1 ATTCAATTAGGTATC
1241223 AGTCAATTCC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.25, C:0.12, G:0.13, T:0.49
Consensus pattern (30 bp):
ATTCAATTAGGTATCTCAGTTTTATTTTGT
Found at i:1244569 original size:19 final size:19
Alignment explanation
Indices: 1244534--1244570 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1244524 ACCCCCTTTA
* *
1244534 TTATTAAAAGTTGCAAAAG
1 TTATTAAAAGCTACAAAAG
1244553 TTATTAAAAGCTACAAAA
1 TTATTAAAAGCTACAAAA
1244571 ATTCCTTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.08, G:0.11, T:0.30
Consensus pattern (19 bp):
TTATTAAAAGCTACAAAAG
Found at i:1249743 original size:120 final size:120
Alignment explanation
Indices: 1249530--1249768 Score: 478
Period size: 120 Copynumber: 2.0 Consensus size: 120
1249520 ATTTCATGGA
1249530 TCGTTCAGCTAGAGAGTTGAGAAAAAAGGCTTACCCTAAAGCACTTAAGAATCAGGAAGTAATAT
1 TCGTTCAGCTAGAGAGTTGAGAAAAAAGGCTTACCCTAAAGCACTTAAGAATCAGGAAGTAATAT
1249595 TTGTCAGAGATGAAGAAGAAAGATCATCAAAGCAAGCTAAACCCTGGGGGGGGGG
66 TTGTCAGAGATGAAGAAGAAAGATCATCAAAGCAAGCTAAACCCTGGGGGGGGGG
1249650 TCGTTCAGCTAGAGAGTTGAGAAAAAAGGCTTACCCTAAAGCACTTAAGAATCAGGAAGTAATAT
1 TCGTTCAGCTAGAGAGTTGAGAAAAAAGGCTTACCCTAAAGCACTTAAGAATCAGGAAGTAATAT
1249715 TTGTCAGAGATGAAGAAGAAAGATCATCAAAGCAAGCTAAACCCTGGGGGGGGG
66 TTGTCAGAGATGAAGAAGAAAGATCATCAAAGCAAGCTAAACCCTGGGGGGGGG
1249769 TGTTCCGACT
Statistics
Matches: 119, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
120 119 1.00
ACGTcount: A:0.38, C:0.15, G:0.27, T:0.19
Consensus pattern (120 bp):
TCGTTCAGCTAGAGAGTTGAGAAAAAAGGCTTACCCTAAAGCACTTAAGAATCAGGAAGTAATAT
TTGTCAGAGATGAAGAAGAAAGATCATCAAAGCAAGCTAAACCCTGGGGGGGGGG
Found at i:1249955 original size:2 final size:2
Alignment explanation
Indices: 1249924--1250039 Score: 168
Period size: 2 Copynumber: 60.0 Consensus size: 2
1249914 TTTCATTGGA
* * *
1249924 AT AT -T AT AT AC AT AC AT AC AT AT A- AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1249964 AT AT AT AT AG AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1250005 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1250040 GAAAGATACC
Statistics
Matches: 102, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
1 4 0.04
2 98 0.96
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1251743 original size:127 final size:127
Alignment explanation
Indices: 1251517--1251771 Score: 510
Period size: 127 Copynumber: 2.0 Consensus size: 127
1251507 CATATTTAAT
1251517 ACAGATCCAAAGACAAATTATGAATTTTTCGAGTTGATTACTGGCTCAAAGTTTGGACCAAAAGG
1 ACAGATCCAAAGACAAATTATGAATTTTTCGAGTTGATTACTGGCTCAAAGTTTGGACCAAAAGG
1251582 GGGAAAAAACAATAACGGTCCAACCTGAACATTATGGCATCTAAAGAAGAATTCATGAAGAA
66 GGGAAAAAACAATAACGGTCCAACCTGAACATTATGGCATCTAAAGAAGAATTCATGAAGAA
1251644 ACAGATCCAAAGACAAATTATGAATTTTTCGAGTTGATTACTGGCTCAAAGTTTGGACCAAAAGG
1 ACAGATCCAAAGACAAATTATGAATTTTTCGAGTTGATTACTGGCTCAAAGTTTGGACCAAAAGG
1251709 GGGAAAAAACAATAACGGTCCAACCTGAACATTATGGCATCTAAAGAAGAATTCATGAAGAA
66 GGGAAAAAACAATAACGGTCCAACCTGAACATTATGGCATCTAAAGAAGAATTCATGAAGAA
1251771 A
1 A
1251772 ATAGTCACAG
Statistics
Matches: 128, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
127 128 1.00
ACGTcount: A:0.42, C:0.16, G:0.20, T:0.23
Consensus pattern (127 bp):
ACAGATCCAAAGACAAATTATGAATTTTTCGAGTTGATTACTGGCTCAAAGTTTGGACCAAAAGG
GGGAAAAAACAATAACGGTCCAACCTGAACATTATGGCATCTAAAGAAGAATTCATGAAGAA
Found at i:1253264 original size:31 final size:31
Alignment explanation
Indices: 1253165--1253265 Score: 87
Period size: 32 Copynumber: 3.2 Consensus size: 31
1253155 TATTTAAAAG
* * *
1253165 TTACAAAGTGGTCATTTAAATTTATTGAA-TGA
1 TTACAAAATGATCA-TTAAATTTATAGAACT-A
** * * *
1253197 TTACAAAATGATCACCAGATTTTATGGAACTG
1 TTACAAAATGATCATTA-AATTTATAGAACTA
*
1253229 TTACAAAATGATCATTAAATTTACAGAACTA
1 TTACAAAATGATCATTAAATTTATAGAACTA
1253260 TTACAA
1 TTACAA
1253266 TTATTACCAA
Statistics
Matches: 54, Mismatches: 13, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
31 17 0.31
32 36 0.67
33 1 0.02
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.35
Consensus pattern (31 bp):
TTACAAAATGATCATTAAATTTATAGAACTA
Found at i:1254063 original size:20 final size:20
Alignment explanation
Indices: 1254038--1254075 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1254028 TTTGGTTCAC
*
1254038 GGAATATAAGATTACCAGTA
1 GGAATAAAAGATTACCAGTA
1254058 GGAATAAAAGATTACCAG
1 GGAATAAAAGATTACCAG
1254076 GAATAGAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.11, G:0.21, T:0.21
Consensus pattern (20 bp):
GGAATAAAAGATTACCAGTA
Found at i:1254079 original size:17 final size:18
Alignment explanation
Indices: 1254038--1254080 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
1254028 TTTGGTTCAC
*
1254038 GGAATATAAGATTACCAGTA
1 GGAATAAAAGATTACCA--A
1254058 GGAATAAAAGATTACC-A
1 GGAATAAAAGATTACCAA
1254075 GGAATA
1 GGAATA
1254081 GAATTACTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 7 0.32
20 15 0.68
ACGTcount: A:0.49, C:0.09, G:0.21, T:0.21
Consensus pattern (18 bp):
GGAATAAAAGATTACCAA
Found at i:1254545 original size:15 final size:15
Alignment explanation
Indices: 1254525--1254560 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
1254515 AGGAAATAGA
1254525 GGTAATGACATTCTC
1 GGTAATGACATTCTC
1254540 GGTAATGACATTCTC
1 GGTAATGACATTCTC
1254555 GGTAAT
1 GGTAAT
1254561 ATACTCCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (15 bp):
GGTAATGACATTCTC
Found at i:1255401 original size:40 final size:40
Alignment explanation
Indices: 1255357--1255447 Score: 182
Period size: 40 Copynumber: 2.3 Consensus size: 40
1255347 GTTGGCCATC
1255357 GTATTATATGTTCTCTAATTTATGTTCAACAATGAAATTT
1 GTATTATATGTTCTCTAATTTATGTTCAACAATGAAATTT
1255397 GTATTATATGTTCTCTAATTTATGTTCAACAATGAAATTT
1 GTATTATATGTTCTCTAATTTATGTTCAACAATGAAATTT
1255437 GTATTATATGT
1 GTATTATATGT
1255448 AAGTTTTAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.32, C:0.09, G:0.11, T:0.48
Consensus pattern (40 bp):
GTATTATATGTTCTCTAATTTATGTTCAACAATGAAATTT
Found at i:1255835 original size:23 final size:23
Alignment explanation
Indices: 1255809--1255852 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1255799 AAACAATTTT
1255809 AAAAAAAATCATTTTAAAGATAA
1 AAAAAAAATCATTTTAAAGATAA
* *
1255832 AAAAAAATTCATTTTTAAGAT
1 AAAAAAAATCATTTTAAAGAT
1255853 TCGAAAGTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.32
Consensus pattern (23 bp):
AAAAAAAATCATTTTAAAGATAA
Found at i:1263420 original size:19 final size:19
Alignment explanation
Indices: 1263396--1263445 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
1263386 GAACACTTAG
1263396 TGCATCGGTGCACTAAGGA
1 TGCATCGGTGCACTAAGGA
1263415 TGCATCGGTGCACTAAGGA
1 TGCATCGGTGCACTAAGGA
*
1263434 TGCATCGATGCA
1 TGCATCGGTGCA
1263446 TAAAATGCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.26, C:0.22, G:0.30, T:0.22
Consensus pattern (19 bp):
TGCATCGGTGCACTAAGGA
Found at i:1264603 original size:27 final size:27
Alignment explanation
Indices: 1264563--1264618 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
1264553 GTGCCGGAGG
* *
1264563 AGGTGGAGGTGGAGCACGAGAAGAACT
1 AGGTGCAGGAGGAGCACGAGAAGAACT
* **
1264590 AGGTGCAGGAGGAGCTCTTGAAGAACT
1 AGGTGCAGGAGGAGCACGAGAAGAACT
1264617 AG
1 AG
1264619 CTCTCGGAGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.32, C:0.12, G:0.41, T:0.14
Consensus pattern (27 bp):
AGGTGCAGGAGGAGCACGAGAAGAACT
Found at i:1269970 original size:22 final size:21
Alignment explanation
Indices: 1269928--1269967 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1269918 AAGACTATTT
1269928 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
**
1269949 TCATTTTTGTATTTTGAAA
1 TCATTTTTCAATTTTGAAA
1269968 ATAGAGTTTT
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:0.30, C:0.07, G:0.07, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATA
Found at i:1271926 original size:64 final size:64
Alignment explanation
Indices: 1271857--1272011 Score: 217
Period size: 64 Copynumber: 2.4 Consensus size: 64
1271847 TGCACTAAGG
* *
1271857 GTGCATCAATGCATAAAATGCATTCGATG-TTTCA-AACAAGCCTGGGTGCATCAATGCATGGTC
1 GTGCATCAATGCATAAAATGCATTCGATGTTTTCATAA-AAACCTGAGTGCATCAATGCATGG-C
1271920 TA
64 -A
* *
1271922 -TGCATCTATGCATAAAATGCATTCGATGTTTTCATAAAAACCTGAGTGCATCGATGCATGGCA
1 GTGCATCAATGCATAAAATGCATTCGATGTTTTCATAAAAACCTGAGTGCATCAATGCATGGCA
*
1271985 GTGCATCGATGCATAAAATGCATTCGA
1 GTGCATCAATGCATAAAATGCATTCGA
1272012 AATGATGTGT
Statistics
Matches: 82, Mismatches: 5, Indels: 7
0.87 0.05 0.07
Matches are distributed among these distances:
63 1 0.01
64 53 0.65
65 26 0.32
66 2 0.02
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (64 bp):
GTGCATCAATGCATAAAATGCATTCGATGTTTTCATAAAAACCTGAGTGCATCAATGCATGGCA
Found at i:1273032 original size:2 final size:2
Alignment explanation
Indices: 1273025--1273074 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1273015 TTTGATTGAA
1273025 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1273067 AT AT AT AT
1 AT AT AT AT
1273075 TCTTCATTTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1281143 original size:25 final size:28
Alignment explanation
Indices: 1281091--1281143 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
1281081 CTCTATTTTA
* *
1281091 TTTTATTATTAATTTTATGATATGAAAT
1 TTTTATTATTAATTTTATAATATAAAAT
1281119 TTTTATTATT-ATTTTA-AATA-AAAAT
1 TTTTATTATTAATTTTATAATATAAAAT
1281144 AAATTTGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 4 0.17
26 3 0.13
27 6 0.26
28 10 0.43
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.57
Consensus pattern (28 bp):
TTTTATTATTAATTTTATAATATAAAAT
Found at i:1286794 original size:20 final size:21
Alignment explanation
Indices: 1286754--1286800 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
1286744 CTAATAAGTG
1286754 AATTTTTAAATATTATTAAAT
1 AATTTTTAAATATTATTAAAT
1286775 AATTTTTAAA-ATT-TTCAAAT
1 AATTTTTAAATATTATT-AAAT
*
1286795 GATTTT
1 AATTTT
1286801 GCTATATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 2 0.08
20 12 0.50
21 10 0.42
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (21 bp):
AATTTTTAAATATTATTAAAT
Found at i:1287263 original size:27 final size:27
Alignment explanation
Indices: 1287209--1287273 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
1287199 TCTCAAAAAA
* * *
1287209 TCGGGTCGGGTGAAGGGTATATATTTT
1 TCGGGTCGGGTGAAGGATATAAAATTT
*
1287236 TCGGGTCGGGTGAAGGATGTAAAATTT
1 TCGGGTCGGGTGAAGGATATAAAATTT
*
1287263 TCGGGTTGGGT
1 TCGGGTCGGGT
1287274 CGGGTTGGCC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.18, C:0.08, G:0.40, T:0.34
Consensus pattern (27 bp):
TCGGGTCGGGTGAAGGATATAAAATTT
Found at i:1290610 original size:20 final size:20
Alignment explanation
Indices: 1290581--1290621 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1290571 TTAACTTTGT
*
1290581 AAAAATTATAAAAAAATATG
1 AAAAAGTATAAAAAAATATG
*
1290601 AAAAAGTATAAAAAAGTATG
1 AAAAAGTATAAAAAAATATG
1290621 A
1 A
1290622 TCTTTAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.10, T:0.22
Consensus pattern (20 bp):
AAAAAGTATAAAAAAATATG
Found at i:1292010 original size:49 final size:49
Alignment explanation
Indices: 1291620--1292010 Score: 293
Period size: 49 Copynumber: 8.0 Consensus size: 49
1291610 AGTGAGATCG
* * * *
1291620 CCCTCAAACGAAAATCTCAAAAGGGTTTGAACATTCCCAAGCAAGCTCG
1 CCCTCAAACAAAAATCTCCAAAGGGTTTGAACACTCCCAAGCAAGCTCA
** * * * * *
1291669 CCCTCAAATGAAAATCACTAAAGGGTTTGAACAATCGCAAGCGAA-CTCG
1 CCCTCAAACAAAAATCTCCAAAGGGTTTGAACACTCCCAAGC-AAGCTCA
* * * * *
1291718 CCCTCAAACAAAAATCTCCTAAGGGTTTGAACATTCGCAACCAAGCTCG
1 CCCTCAAACAAAAATCTCCAAAGGGTTTGAACACTCCCAAGCAAGCTCA
* * * ** ** * *
1291767 CCTTTAAA-AGAAAATCTCCAAAGGATTCAAATGCTTCCAAGCGAGCTCA
1 CCCTCAAACA-AAAATCTCCAAAGGGTTTGAACACTCCCAAGCAAGCTCA
* * * * * **
1291816 CCCTTAAACAAAAATATCCAAAGGGTTCGAACACACTCAAGCAAAATCA
1 CCCTCAAACAAAAATCTCCAAAGGGTTTGAACACTCCCAAGCAAGCTCA
* * * * * * *
1291865 CCCTTAAACAATAATCTTCAAAGTGTTTGAACGCTCCCAAGCGAA-ATTA
1 CCCTCAAACAAAAATCTCCAAAGGGTTTGAACACTCCCAAGC-AAGCTCA
* * * * *
1291914 CCCTTAAATAAAAATCTCCAAAGAGTTTGAACGCTCCCAAGCGAGCTCA
1 CCCTCAAACAAAAATCTCCAAAGGGTTTGAACACTCCCAAGCAAGCTCA
* ** * *
1291963 CCCTCAAATAAAAATCTCCAAAGGGTTCAAACACTCACGAGCAAGCTC
1 CCCTCAAACAAAAATCTCCAAAGGGTTTGAACACTCCCAAGCAAGCTC
1292011 TTCCAAGCAA
Statistics
Matches: 274, Mismatches: 62, Indels: 12
0.79 0.18 0.03
Matches are distributed among these distances:
48 4 0.01
49 265 0.97
50 5 0.02
ACGTcount: A:0.39, C:0.27, G:0.14, T:0.20
Consensus pattern (49 bp):
CCCTCAAACAAAAATCTCCAAAGGGTTTGAACACTCCCAAGCAAGCTCA
Found at i:1292260 original size:34 final size:34
Alignment explanation
Indices: 1292112--1292262 Score: 169
Period size: 34 Copynumber: 4.4 Consensus size: 34
1292102 TGATGCTTAA
* **
1292112 AAACATTCGCCACTCCAAATAAAAGTGTGCTCAC
1 AAACATTCGTCACTTTAAATAAAAGTGTGCTCAC
*
1292146 AAACATTCGTCACTTTAAATAAAAGTGAGCTCAC
1 AAACATTCGTCACTTTAAATAAAAGTGTGCTCAC
** * * *
1292180 AAACATTCACCA-ATTATAATAAAAGTGTACTTAC
1 AAACATTCGTCACTTTA-AATAAAAGTGTGCTCAC
* * *
1292214 AAACATTCGTCACTTTAAACAAAAGTGTGTTCAT
1 AAACATTCGTCACTTTAAATAAAAGTGTGCTCAC
*
1292248 AAACATTTGTCACTT
1 AAACATTCGTCACTT
1292263 CCAAGTAAGT
Statistics
Matches: 96, Mismatches: 19, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
33 3 0.03
34 90 0.94
35 3 0.03
ACGTcount: A:0.40, C:0.21, G:0.10, T:0.28
Consensus pattern (34 bp):
AAACATTCGTCACTTTAAATAAAAGTGTGCTCAC
Found at i:1293482 original size:42 final size:41
Alignment explanation
Indices: 1293417--1293538 Score: 136
Period size: 42 Copynumber: 2.9 Consensus size: 41
1293407 TGAGAACAAA
* * *
1293417 AAATGCTGCAATAGGTCAAGATCTATAGCGGCGTTTTTGGGAC
1 AAATGCCGCAA-AGGTC-AGATCTATAGCGGCGTTTTTCGAAC
* *
1293460 AAATGCCGCAAAGGTCGAGATCTATAGTGGCATTTTTCGAAC
1 AAATGCCGCAAAGGTC-AGATCTATAGCGGCGTTTTTCGAAC
* * *
1293502 AAACGCCGCAAAAGGACAGATCTATAGCGTCGTTTTT
1 AAATGCCGC-AAAGGTCAGATCTATAGCGGCGTTTTT
1293539 TTGGATACAA
Statistics
Matches: 67, Mismatches: 11, Indels: 3
0.83 0.14 0.04
Matches are distributed among these distances:
42 51 0.76
43 16 0.24
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (41 bp):
AAATGCCGCAAAGGTCAGATCTATAGCGGCGTTTTTCGAAC
Found at i:1299922 original size:2 final size:2
Alignment explanation
Indices: 1299915--1299941 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1299905 GCAAGTAAAA
1299915 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1299942 CATACACATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1303203 original size:23 final size:23
Alignment explanation
Indices: 1303156--1303204 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1303146 CAGCTCGTAT
* * *
1303156 AAAATGCACCGAAGTACCGTGTA
1 AAAATGCACCAAAGTACCATATA
*
1303179 AAAATGCACCAAAGTGCCATATA
1 AAAATGCACCAAAGTACCATATA
1303202 AAA
1 AAA
1303205 TGTCCTAAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.47, C:0.20, G:0.16, T:0.16
Consensus pattern (23 bp):
AAAATGCACCAAAGTACCATATA
Found at i:1303230 original size:21 final size:21
Alignment explanation
Indices: 1303204--1303327 Score: 79
Period size: 21 Copynumber: 5.8 Consensus size: 21
1303194 GCCATATAAA
*
1303204 ATGTCCTAAAGGACCACATAT
1 ATGTCCCAAAGGACCACATAT
* *
1303225 ATGTCCCGTAA-GACCACATAGA
1 ATGTCCC-AAAGGACCACATA-T
** * * *
1303247 ATTGTCCCGTATGACCAAATAC
1 A-TGTCCCAAAGGACCACATAT
* * *
1303269 ATTTCCAAAAAGGACCGCATAT
1 ATGTCC-CAAAGGACCACATAT
* *
1303291 ATGTTCCAAAGGATCACATAT
1 ATGTCCCAAAGGACCACATAT
*
1303312 ATGTCCCGAAGGACCA
1 ATGTCCCAAAGGACCA
1303328 TGTAGAAACC
Statistics
Matches: 75, Mismatches: 23, Indels: 10
0.69 0.21 0.09
Matches are distributed among these distances:
21 44 0.59
22 17 0.23
23 14 0.19
ACGTcount: A:0.36, C:0.25, G:0.16, T:0.23
Consensus pattern (21 bp):
ATGTCCCAAAGGACCACATAT
Found at i:1305590 original size:31 final size:31
Alignment explanation
Indices: 1305550--1305645 Score: 122
Period size: 31 Copynumber: 3.1 Consensus size: 31
1305540 AAGAATCGAG
1305550 GGTTACCTATGTCCTTCGGGACATATGTG-CA
1 GGTTACCTATGTCCTTCGGGACATATG-GACA
* *
1305581 GTTTACCTATGTCCTTCAGGACATATGGACA
1 GGTTACCTATGTCCTTCGGGACATATGGACA
* * * *
1305612 GGTTACCTATGTTCTTCGGAACATAAGGATA
1 GGTTACCTATGTCCTTCGGGACATATGGACA
1305643 GGT
1 GGT
1305646 CATTTGGGAC
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
30 1 0.02
31 55 0.98
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (31 bp):
GGTTACCTATGTCCTTCGGGACATATGGACA
Found at i:1307116 original size:2 final size:2
Alignment explanation
Indices: 1307109--1307142 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1307099 AATGTATAAA
1307109 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1307143 ATCACATAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1308084 original size:106 final size:106
Alignment explanation
Indices: 1307895--1308563 Score: 881
Period size: 106 Copynumber: 6.3 Consensus size: 106
1307885 ATTATTCCAT
* * * *
1307895 GTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTAGAACTGGGAAATTATTTGTTGACAGC
1 GTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTAAAATTGGGAAATTATTTGTTGACAAC
* * * * *
1307959 CAGCCGCCCCTTCGCTGTGAAGTTGAGCTTATGCTGTATCGA
65 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCTCGA
* * * * * *
1308001 ATCTAATATCATTCGCTGTGAAGTTGAAATTGACTCTAAAATTGGGAATTTGTTTGTTGACAACC
1 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAATTATTTGTTGACAACC
* * *
1308066 AGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTATCTTGA
66 AGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCTCGA
* * *
1308107 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAGTTGTTTGTTGACAACC
1 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAATTATTTGTTGACAACC
* *
1308172 AGCCGTCCCTTCGTTGTGAAGTTGAAATTGTACTGTCTCGA
66 AGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCTCGA
** *
1308213 GTCCAATGCCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACAACC
1 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAATTATTTGTTGACAACC
* * *
1308278 AGTCGTCCCTTCTTTGTGAAGTTGAACTTGTGTTGTCTCGA
66 AGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCTCGA
** * * *
1308319 GTCCAATGCCCTTCGCTGTGAAGTTGAAACTGGCTCTGAAATTGGGAAATTATTTGTTGAAAACC
1 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAATTATTTGTTGACAACC
* *
1308384 AGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGA
66 AGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCTCGA
* * *
1308425 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACC
1 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAATTATTTGTTGACAACC
* * *
1308490 AGCCATCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAA
66 AGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCTCG-A
* * * *
1308532 TGGCACGATATCCTTCGTTGTGGAGTTGAAAT
1 -GTC-CAATATCCTTCGCTGTGAAGTTGAAAT
1308564 CGTGGATGTG
Statistics
Matches: 503, Mismatches: 56, Indels: 5
0.89 0.10 0.01
Matches are distributed among these distances:
106 475 0.94
107 2 0.00
108 2 0.00
109 24 0.05
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.35
Consensus pattern (106 bp):
GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAATTATTTGTTGACAACC
AGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCTCGA
Found at i:1310299 original size:22 final size:22
Alignment explanation
Indices: 1310273--1310323 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
1310263 TTGTGTTTGG
1310273 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
* *
1310295 TCAAAGGTTTGGTATTTGATTC
1 TCAAAGGTTTGGCATTTGATGC
1310317 TCAAAGG
1 TCAAAGG
1310324 ATTGATGGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.37
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:1310966 original size:37 final size:37
Alignment explanation
Indices: 1310925--1310995 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 37
1310915 GCTTTTTTCC
**
1310925 CTTGTCCTTTGGATTTTTGCTTCTTTTCTTTTTTGTT
1 CTTGTCCTTTCCATTTTTGCTTCTTTTCTTTTTTGTT
** *
1310962 CTTGTGTTTTCCTTTTTTGCTTCTTTTCTTTTTT
1 CTTGTCCTTTCCATTTTTGCTTCTTTTCTTTTTT
1310996 CTTTTTTCCC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 29 1.00
ACGTcount: A:0.01, C:0.17, G:0.11, T:0.70
Consensus pattern (37 bp):
CTTGTCCTTTCCATTTTTGCTTCTTTTCTTTTTTGTT
Found at i:1311008 original size:16 final size:17
Alignment explanation
Indices: 1310938--1311015 Score: 67
Period size: 16 Copynumber: 4.6 Consensus size: 17
1310928 GTCCTTTGGA
1310938 TTTTTGCTTCTTTT-CT
1 TTTTTGCTTCTTTTCCT
*
1310954 TTTTTGTTCTTGTGTTTTCCT
1 TTTTTG--C-T-TCTTTTCCT
1310975 TTTTTGCTTCTTTT-CT
1 TTTTTGCTTCTTTTCCT
*
1310991 TTTTT-CTT-TTTTCCC
1 TTTTTGCTTCTTTTCCT
1311006 TTTTTG-TTCT
1 TTTTTGCTTCT
1311016 GATTGAATCT
Statistics
Matches: 51, Mismatches: 3, Indels: 16
0.73 0.04 0.23
Matches are distributed among these distances:
14 4 0.08
15 11 0.22
16 14 0.27
17 5 0.10
18 2 0.04
19 2 0.04
20 5 0.10
21 8 0.16
ACGTcount: A:0.00, C:0.18, G:0.08, T:0.74
Consensus pattern (17 bp):
TTTTTGCTTCTTTTCCT
Found at i:1315060 original size:2 final size:2
Alignment explanation
Indices: 1315053--1315093 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1315043 TGTGTAAATA
1315053 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1315094 ATCACATAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1323544 original size:31 final size:31
Alignment explanation
Indices: 1323477--1323536 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
1323467 CAATTTAAGG
*
1323477 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
1323508 CAAAAT-GTATTTGGACTT-AATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
1323537 TTCAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.42
Consensus pattern (31 bp):
CAAAATGGTATTTGGACTTGAATTGAATTTA
Found at i:1323633 original size:19 final size:19
Alignment explanation
Indices: 1323611--1323665 Score: 74
Period size: 19 Copynumber: 2.9 Consensus size: 19
1323601 GAATAGTAAT
1323611 TTACTATTTGAACAATAAA
1 TTACTATTTGAACAATAAA
*
1323630 TTACTATTTGAACAGTAAA
1 TTACTATTTGAACAATAAA
* * *
1323649 TCACTGTTTGAATAATA
1 TTACTATTTGAACAATA
1323666 CCCCGAGGCT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.38
Consensus pattern (19 bp):
TTACTATTTGAACAATAAA
Found at i:1323810 original size:21 final size:21
Alignment explanation
Indices: 1323771--1323811 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1323761 ATTTGAATAT
* *
1323771 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCAATTCCC
1323792 TATGAAGGGGTACCAATTCC
1 TATGAAGGGGTACCAATTCC
1323812 TCCCATTCTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.27
Consensus pattern (21 bp):
TATGAAGGGGTACCAATTCCC
Found at i:1323874 original size:21 final size:21
Alignment explanation
Indices: 1323841--1323880 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
1323831 TTTTTGCAGA
*
1323841 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
1323863 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
1323881 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:1325957 original size:21 final size:23
Alignment explanation
Indices: 1325911--1325957 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1325901 AGCTCGTATA
* *
1325911 AAATGCACCGAAGTATCACGTAT
1 AAATGCACCGAAGTAGCACATAT
1325934 AAATGCACCGAAGT-GC-CATAT
1 AAATGCACCGAAGTAGCACATAT
1325955 AAA
1 AAA
1325958 ATATCCCGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.43, C:0.21, G:0.17, T:0.19
Consensus pattern (23 bp):
AAATGCACCGAAGTAGCACATAT
Found at i:1325993 original size:21 final size:21
Alignment explanation
Indices: 1325961--1326049 Score: 79
Period size: 21 Copynumber: 4.1 Consensus size: 21
1325951 ATATAAAATA
*
1325961 TCCCGAAGGACCACATATATG
1 TCCCGTAGGACCACATATATG
* *
1325982 TCTCGTAGGACCACATAGAATTG
1 TCCCGTAGGACCACATA-TA-TG
*
1326005 TCCCGTATGACCACATATATG
1 TCCCGTAGGACCACATATATG
* ** * *
1326026 TTCCAAATGACCAAATATATG
1 TCCCGTAGGACCACATATATG
1326047 TCC
1 TCC
1326050 AAAAAGGACC
Statistics
Matches: 55, Mismatches: 11, Indels: 4
0.79 0.16 0.06
Matches are distributed among these distances:
21 36 0.65
22 2 0.04
23 17 0.31
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.26
Consensus pattern (21 bp):
TCCCGTAGGACCACATATATG
Found at i:1326078 original size:21 final size:22
Alignment explanation
Indices: 1326013--1326098 Score: 79
Period size: 21 Copynumber: 4.0 Consensus size: 22
1326003 TGTCCCGTAT
* *
1326013 GACCACATATATGTTCC-AAAT
1 GACCAAATATATGTTCCAAAAG
1326034 GACCAAATATATG-TCCAAAAAG
1 GACCAAATATATGTTCC-AAAAG
**
1326056 GACCGTATATATGTTCC-AAAG
1 GACCAAATATATGTTCCAAAAG
* * *
1326077 GATCACATATATGTTCCGAAAG
1 GACCAAATATATGTTCCAAAAG
1326099 ACTACGCAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
20 3 0.06
21 30 0.56
22 18 0.33
23 3 0.06
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.26
Consensus pattern (22 bp):
GACCAAATATATGTTCCAAAAG
Found at i:1331008 original size:23 final size:23
Alignment explanation
Indices: 1330982--1331036 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
1330972 TGGAATCCCT
1330982 GATGGAATTCAATTCCCTTGTTG
1 GATGGAATTCAATTCCCTTGTTG
1331005 GATGGAATTCAATTCCCTTGTTG
1 GATGGAATTCAATTCCCTTGTTG
*
1331028 GAGGGAATT
1 GATGGAATT
1331037 GAAATTTGAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.24, C:0.15, G:0.25, T:0.36
Consensus pattern (23 bp):
GATGGAATTCAATTCCCTTGTTG
Found at i:1331150 original size:31 final size:31
Alignment explanation
Indices: 1331112--1331188 Score: 92
Period size: 26 Copynumber: 2.6 Consensus size: 31
1331102 TTTTTATTAT
*
1331112 TTCGGGTCGGGTCGGGTTTCTAATTCATATA
1 TTCGGGTCGGGTCAGGTTTCTAATTCATATA
*
1331143 -T----TCGGGTCAGGTTTCTAATTTATATA
1 TTCGGGTCGGGTCAGGTTTCTAATTCATATA
1331169 TTCGGGTCGGGTTCAGGTTT
1 TTCGGGTCGGG-TCAGGTTT
1331189 AGGGTAAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
26 23 0.61
27 1 0.03
30 1 0.03
31 5 0.13
32 8 0.21
ACGTcount: A:0.16, C:0.14, G:0.29, T:0.42
Consensus pattern (31 bp):
TTCGGGTCGGGTCAGGTTTCTAATTCATATA
Found at i:1331155 original size:26 final size:26
Alignment explanation
Indices: 1331118--1331181 Score: 110
Period size: 26 Copynumber: 2.5 Consensus size: 26
1331108 TTATTTCGGG
1331118 TCGGGTCGGGTTTCTAATTCATATAT
1 TCGGGTCGGGTTTCTAATTCATATAT
* *
1331144 TCGGGTCAGGTTTCTAATTTATATAT
1 TCGGGTCGGGTTTCTAATTCATATAT
1331170 TCGGGTCGGGTT
1 TCGGGTCGGGTT
1331182 CAGGTTTAGG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.17, C:0.14, G:0.27, T:0.42
Consensus pattern (26 bp):
TCGGGTCGGGTTTCTAATTCATATAT
Found at i:1331444 original size:37 final size:37
Alignment explanation
Indices: 1331353--1331445 Score: 116
Period size: 37 Copynumber: 2.5 Consensus size: 37
1331343 TTTATTTTGT
*
1331353 TCGGGTCGGG-TCAGGTTTTTTAAGTGTAATATTCGGG
1 TCGGGTCGGGTTC-GGGTTTTTAAGTGTAATATTCGGG
* * ** *
1331390 TCGAGTTGGGTGGGGGTTTTTAAGTGTGATATTCGGG
1 TCGGGTCGGGTTCGGGTTTTTAAGTGTAATATTCGGG
1331427 TCGGGTCGGGTTCGGGTTT
1 TCGGGTCGGGTTCGGGTTT
1331446 AGGGTGAAAA
Statistics
Matches: 45, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
37 45 1.00
ACGTcount: A:0.12, C:0.10, G:0.41, T:0.38
Consensus pattern (37 bp):
TCGGGTCGGGTTCGGGTTTTTAAGTGTAATATTCGGG
Found at i:1331648 original size:37 final size:37
Alignment explanation
Indices: 1331606--1331693 Score: 133
Period size: 38 Copynumber: 2.4 Consensus size: 37
1331596 TTTATTTTAT
1331606 TCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTC-GAG
1 TCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCAG-G
**
1331643 TCGGGTCGATTTTTTTTAAGTGTGATATTCGGGTCAGG
1 TCGGGTCG-GGTTTTTTAAGTGTGATATTCGGGTCAGG
1331681 TCGGGTCGGGTTT
1 TCGGGTCGGGTTT
1331694 GGGTTTAGGG
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
37 11 0.24
38 33 0.73
39 1 0.02
ACGTcount: A:0.12, C:0.11, G:0.36, T:0.40
Consensus pattern (37 bp):
TCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCAGG
Found at i:1331651 original size:258 final size:244
Alignment explanation
Indices: 1331170--1331741 Score: 697
Period size: 258 Copynumber: 2.2 Consensus size: 244
1331160 ATTTATATAT
* *
1331170 TCGGGTCGGGTTCAGGTTTAGGGT-AAAAAAATCGGACCGACCCGAAAATATATATAATTCAGGT
1 TCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAATATATATAATTCAGGT
* *
1331234 CGGGTCGGATTAAGTCATTGTTTTCATTAAATAAAAATATTTTTTTATTATTTCGGGTCGGGTCG
66 CGGGTCGGATTAAGTCACTGTTTTCATTAAATAAAAATAATTTTTTATTATTTCGGGTCGGGTC-
* *
1331299 GGTTGGATTTCTAATTCATATATTCAGGTCGTGTCGGATGAAACTTTATTTTGTTCGGGTCGGGT
130 -G--GGATTTCTAATTCATATATTCAGGTCGGGTCGGATGAAACTTTATTTTATTCGGGTC-GG-
*
1331364 CAGGTTTTTTAAGTGTAATATTCGGGTCGAGTTGGGTGGGGGTTTTTAAGTGTGATATTC-G-GG
190 -AGGTTTTTTAAGTGTAATAGTCGGGTCGA-TT---T-----TTTTTAAGTGTGATATTCGGAGG
* * *
1331427 TCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAACCGGACCGGCCTGAAAATATATATAATTCGGGT
1 TCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAATATATATAATTCAGGT
*
1331492 CGGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAATAATTTTTTATTATTTCGGGTCGGGTC-
66 CGGGTCGGATTAAGTCACTGTTTTCATTAAATAAAAATAATTTTTTATTATTTCGGGTCGGGTCG
*
1331556 GGATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAACTTTATTTTATTCGGGTC-G-GGTTT
131 GGATTTCTAATTCATATATTCAGGTCGGGTCGGATGAAACTTTATTTTATTCGGGTCGGAGGTTT
1331619 TTTAAGTGTGATATTCGGGTCGAGTCGGGTCGATTTTTTTTAAGTGTGATATTCGGGTCAGG
196 TTTAAGTGT-A-A------T--AGTCGGGTCGATTTTTTTTAAGTGTGATATTC-GG--AGG
* * *
1331681 TCGGGTCGGGTTTGGGTTTAGGGTGAAAAAAACCGGACCAACCCGAAAAAAATATATAATT
1 TCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCG-AAAATATATATAATT
1331742 TTACCTTATA
Statistics
Matches: 281, Mismatches: 17, Indels: 36
0.84 0.05 0.11
Matches are distributed among these distances:
248 14 0.05
249 19 0.07
250 1 0.00
251 2 0.01
253 54 0.19
254 44 0.16
255 14 0.05
256 1 0.00
257 25 0.09
258 107 0.38
ACGTcount: A:0.24, C:0.12, G:0.28, T:0.36
Consensus pattern (244 bp):
TCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAATATATATAATTCAGGT
CGGGTCGGATTAAGTCACTGTTTTCATTAAATAAAAATAATTTTTTATTATTTCGGGTCGGGTCG
GGATTTCTAATTCATATATTCAGGTCGGGTCGGATGAAACTTTATTTTATTCGGGTCGGAGGTTT
TTTAAGTGTAATAGTCGGGTCGATTTTTTTTAAGTGTGATATTCGGAGG
Found at i:1332294 original size:16 final size:18
Alignment explanation
Indices: 1332273--1332317 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
1332263 TATGGAATTG
1332273 GATTCCAATTCC-T-ACA
1 GATTCCAATTCCTTCACA
1332289 GATTCCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
1332307 GATTCCAATTC
1 GATTCCAATTC
1332318 TCTCATAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 12 0.44
17 1 0.04
18 14 0.52
ACGTcount: A:0.29, C:0.31, G:0.07, T:0.33
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:1333372 original size:25 final size:26
Alignment explanation
Indices: 1333334--1333404 Score: 90
Period size: 25 Copynumber: 2.7 Consensus size: 26
1333324 AAATTAAATT
*
1333334 TATAATTTATTATATTTTTTA-TACA
1 TATAATTTAATATATTTTTTATTACA
**
1333359 TATAATTTAATATATTTTTTATTATT
1 TATAATTTAATATATTTTTTATTACA
*
1333385 TCTAATTTATATATATTTTT
1 TATAATTTA-ATATATTTTT
1333405 AATAAAACTT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
25 20 0.50
26 10 0.25
27 10 0.25
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (26 bp):
TATAATTTAATATATTTTTTATTACA
Found at i:1336709 original size:13 final size:14
Alignment explanation
Indices: 1336685--1336713 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1336675 TACTTACCCC
1336685 ATATTAATTAAAAA
1 ATATTAATTAAAAA
1336699 ATATT-ATTAAAAA
1 ATATTAATTAAAAA
1336712 AT
1 AT
1336714 TAGAATTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
ATATTAATTAAAAA
Found at i:1340837 original size:3 final size:3
Alignment explanation
Indices: 1340831--1340898 Score: 136
Period size: 3 Copynumber: 22.7 Consensus size: 3
1340821 GATGATGATG
1340831 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1340879 ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA AT
1340899 GATATCATGG
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1349318 original size:12 final size:12
Alignment explanation
Indices: 1349301--1349325 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1349291 TTACTTTTTG
1349301 TTGTTGTTGATA
1 TTGTTGTTGATA
1349313 TTGTTGTTGATA
1 TTGTTGTTGATA
1349325 T
1 T
1349326 ATAAGTTAGT
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:0.00, G:0.24, T:0.60
Consensus pattern (12 bp):
TTGTTGTTGATA
Found at i:1352625 original size:21 final size:21
Alignment explanation
Indices: 1352601--1352642 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1352591 CTATGAACAG
*
1352601 TGCTACAGTGTATCGATGTAT
1 TGCTACAGTGCATCGATGTAT
1352622 TGCTACAGTGCATCGATGTAT
1 TGCTACAGTGCATCGATGTAT
1352643 CAAAAATTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.36
Consensus pattern (21 bp):
TGCTACAGTGCATCGATGTAT
Found at i:1352687 original size:21 final size:21
Alignment explanation
Indices: 1352663--1352706 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
1352653 AAGCAAAATT
1352663 GTGCATCGATGCACTGCTACA
1 GTGCATCGATGCACTGCTACA
1352684 GTGCATCGATGCACTGCTACA
1 GTGCATCGATGCACTGCTACA
1352705 GT
1 GT
1352707 ACTGCTACAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.27, G:0.25, T:0.25
Consensus pattern (21 bp):
GTGCATCGATGCACTGCTACA
Found at i:1353210 original size:31 final size:31
Alignment explanation
Indices: 1353165--1353287 Score: 104
Period size: 31 Copynumber: 4.0 Consensus size: 31
1353155 CTCGAAGGAC
* *
1353165 CAGTCCATAGGTTTCTAAGAACCTAGGTAAT
1 CAGTCCATAGGTTTCGAAGAACATAGGTAAT
* *
1353196 CAGTCTATATGTTTCGAAGAACATAGGTAAAT
1 CAGTCCATAGGTTTCGAAGAACATAGGT-AAT
* * ** * *
1353228 -AATCCATATGTCCCAAAGAACATAGGTAAA
1 CAGTCCATAGGTTTCGAAGAACATAGGTAAT
** **
1353258 CAGTCCATATATCCCGAAGAACATAGGTAA
1 CAGTCCATAGGTTTCGAAGAACATAGGTAA
1353288 ACCCTCGACC
Statistics
Matches: 77, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
30 2 0.03
31 72 0.94
32 3 0.04
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.25
Consensus pattern (31 bp):
CAGTCCATAGGTTTCGAAGAACATAGGTAAT
Found at i:1353288 original size:31 final size:31
Alignment explanation
Indices: 1353181--1353289 Score: 137
Period size: 31 Copynumber: 3.5 Consensus size: 31
1353171 ATAGGTTTCT
* * * **
1353181 AAGAACCTAGGTAATCAGTCTATATGTTTCG
1 AAGAACATAGGTAAACAGTCCATATGTCCCG
* * *
1353212 AAGAACATAGGTAAATAATCCATATGTCCCA
1 AAGAACATAGGTAAACAGTCCATATGTCCCG
*
1353243 AAGAACATAGGTAAACAGTCCATATATCCCG
1 AAGAACATAGGTAAACAGTCCATATGTCCCG
1353274 AAGAACATAGGTAAAC
1 AAGAACATAGGTAAAC
1353290 CCTCGACCCT
Statistics
Matches: 66, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 66 1.00
ACGTcount: A:0.42, C:0.18, G:0.17, T:0.23
Consensus pattern (31 bp):
AAGAACATAGGTAAACAGTCCATATGTCCCG
Found at i:1384611 original size:18 final size:18
Alignment explanation
Indices: 1384588--1384630 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1384578 AATAAATATT
1384588 ATTATTGAACTACAATG-A
1 ATTATT-AACTACAATGAA
* *
1384606 ATTATTTATTACAATGAA
1 ATTATTAACTACAATGAA
1384624 ATTATTA
1 ATTATTA
1384631 CCTTAATGCA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (18 bp):
ATTATTAACTACAATGAA
Found at i:1386649 original size:23 final size:24
Alignment explanation
Indices: 1386590--1386662 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 24
1386580 CTGCTCATAT
1386590 AATTTG-CACCGAAGGACTGCGTAG
1 AATTTGTC-CCGAAGGACTGCGTAG
* *
1386614 AATTTGTCTCGAAGGACTACGTAG
1 AATTTGTCCCGAAGGACTGCGTAG
*
1386638 AA-TTGTCCCGAAGGACCGCGTAG
1 AATTTGTCCCGAAGGACTGCGTAG
1386661 AA
1 AA
1386663 CCCTCAACTC
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
23 20 0.47
24 22 0.51
25 1 0.02
ACGTcount: A:0.30, C:0.21, G:0.27, T:0.22
Consensus pattern (24 bp):
AATTTGTCCCGAAGGACTGCGTAG
Found at i:1386806 original size:15 final size:15
Alignment explanation
Indices: 1386788--1386840 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
1386778 CACATAAGGT
*
1386788 ATTTTCACGTAGAAC
1 ATTTTCACATAGAAC
* *
1386803 ATTTTTCGCATAGCAC
1 A-TTTTCACATAGAAC
1386819 ATTTTCACATA-ACAC
1 ATTTTCACATAGA-AC
1386834 ATTTTCA
1 ATTTTCA
1386841 TATACCCATA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
15 19 0.61
16 12 0.39
ACGTcount: A:0.32, C:0.23, G:0.08, T:0.38
Consensus pattern (15 bp):
ATTTTCACATAGAAC
Found at i:1389100 original size:40 final size:40
Alignment explanation
Indices: 1389055--1389186 Score: 126
Period size: 41 Copynumber: 3.2 Consensus size: 40
1389045 TTATTGAAAT
*
1389055 AATGCCACTATAGGTGACCCTATTGCGGTGTTTATATAAA
1 AATGCCACTATAGGTAACCCTATTGCGGTGTTTATATAAA
* * * ** *
1389095 AATGCCGCTAAAGATCTAA-TATGTTGCGGTGTTTAT-TGAAAA
1 AATGCCACTATAG--GTAACCCTATTGCGGTGTTTATAT--AAA
*
1389137 AAT-CCAGTATAGGTTAACCCTATTGCGGTGTTTATATAAA
1 AATGCCACTATAGG-TAACCCTATTGCGGTGTTTATATAAA
1389177 AATGCCACTA
1 AATGCCACTA
1389187 AATTACTACT
Statistics
Matches: 69, Mismatches: 15, Indels: 15
0.70 0.15 0.15
Matches are distributed among these distances:
40 21 0.30
41 39 0.57
42 9 0.13
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.33
Consensus pattern (40 bp):
AATGCCACTATAGGTAACCCTATTGCGGTGTTTATATAAA
Found at i:1389202 original size:82 final size:82
Alignment explanation
Indices: 1389030--1389243 Score: 243
Period size: 82 Copynumber: 2.6 Consensus size: 82
1389020 GTATAAGACC
** * * *
1389030 AATATGTTATGGCATTTATTGAAATAATGCCACTATAGG-TGACCCTATTGCGGTGTTTATATAA
1 AATATGTTGCGGCGTTTATTGAAAAAAT-CCACTATAGGTTAACCCTATTGCGGTGTTTATATAA
*
1389094 AAATGCCGCTAAAGATCT
65 AAATGCCACTAAAGATCT
* *
1389112 AATATGTTGCGGTGTTTATTGAAAAAATCCAGTATAGGTTAACCCTATTGCGGTGTTTATATAAA
1 AATATGTTGCGGCGTTTATTGAAAAAATCCACTATAGGTTAACCCTATTGCGGTGTTTATATAAA
*
1389177 AATGCCACTAAA-TTACT
66 AATGCCACTAAAGAT-CT
* * * * * * *
1389194 ACTCTGTTGTGGCGTTTGTTGAAAAAACGCCACTATAGATTAACACTATT
1 AATATGTTGCGGCGTTTATTGAAAAAA-TCCACTATAGGTTAACCCTATT
1389244 ATAGCATTTG
Statistics
Matches: 111, Mismatches: 18, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
81 10 0.09
82 83 0.75
83 18 0.16
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.35
Consensus pattern (82 bp):
AATATGTTGCGGCGTTTATTGAAAAAATCCACTATAGGTTAACCCTATTGCGGTGTTTATATAAA
AATGCCACTAAAGATCT
Found at i:1391589 original size:31 final size:31
Alignment explanation
Indices: 1391554--1391612 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
1391544 TATAGTCCCC
1391554 CAACATTTAGTCCGTTTACAATATGGTCTCT
1 CAACATTTAGTCCGTTTACAATATGGTCTCT
**
1391585 CAACATTTAGTCCGTTTGTAATATGGTC
1 CAACATTTAGTCCGTTTACAATATGGTC
1391613 CCCGACGTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.39
Consensus pattern (31 bp):
CAACATTTAGTCCGTTTACAATATGGTCTCT
Found at i:1392004 original size:3 final size:3
Alignment explanation
Indices: 1391996--1392090 Score: 73
Period size: 3 Copynumber: 31.7 Consensus size: 3
1391986 TATTAGTAGA
* * * * * * *
1391996 AGG AGG AGG AGG GGG AGG AGA AGA AGA AGA AGG AGA AGG AGG AGG GGG
1 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG
* * * * * *
1392044 AGG AGA AGA AGA AGA AGG AGA AGG AGG AGG AGG AGG AGG AGG GGG AG
1 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AG
1392091 AAGAAGAGTA
Statistics
Matches: 78, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 78 1.00
ACGTcount: A:0.41, C:0.00, G:0.59, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:1392093 original size:33 final size:33
Alignment explanation
Indices: 1391999--1392081 Score: 157
Period size: 33 Copynumber: 2.5 Consensus size: 33
1391989 TAGTAGAAGG
1391999 AGGAGGAGGGGGAGGAGAAGAAGAAGAAGGAGA
1 AGGAGGAGGGGGAGGAGAAGAAGAAGAAGGAGA
1392032 AGGAGGAGGGGGAGGAGAAGAAGAAGAAGGAGA
1 AGGAGGAGGGGGAGGAGAAGAAGAAGAAGGAGA
*
1392065 AGGAGGAGGAGGAGGAG
1 AGGAGGAGGGGGAGGAG
1392082 GAGGGGGAGA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.43, C:0.00, G:0.57, T:0.00
Consensus pattern (33 bp):
AGGAGGAGGGGGAGGAGAAGAAGAAGAAGGAGA
Found at i:1393198 original size:29 final size:29
Alignment explanation
Indices: 1393126--1393189 Score: 119
Period size: 29 Copynumber: 2.2 Consensus size: 29
1393116 TTTCATTTAG
*
1393126 GTCCCCAAATTTTTAAAACTTGCAATACA
1 GTCCCCAAAATTTTAAAACTTGCAATACA
1393155 GTCCCCAAAATTTTAAAACTTGCAATACA
1 GTCCCCAAAATTTTAAAACTTGCAATACA
1393184 GTCCCC
1 GTCCCC
1393190 CAACATTTAG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.36, C:0.28, G:0.08, T:0.28
Consensus pattern (29 bp):
GTCCCCAAAATTTTAAAACTTGCAATACA
Found at i:1393275 original size:31 final size:31
Alignment explanation
Indices: 1393174--1393281 Score: 153
Period size: 31 Copynumber: 3.5 Consensus size: 31
1393164 ATTTTAAAAC
** *
1393174 TTGCAATACAGTCCCCCAACATTTAGTCCAT
1 TTGCAATATGGTCCCTCAACATTTAGTCCAT
* *
1393205 TTGCAATATGATCCCTCAATATTTAGTCCAT
1 TTGCAATATGGTCCCTCAACATTTAGTCCAT
* *
1393236 TTACAATATGGTCCCTCAACATTTAGTCCGT
1 TTGCAATATGGTCCCTCAACATTTAGTCCAT
1393267 TTGCAATATGGTCCC
1 TTGCAATATGGTCCC
1393282 CGACGTAACT
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 67 1.00
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.34
Consensus pattern (31 bp):
TTGCAATATGGTCCCTCAACATTTAGTCCAT
Found at i:1406847 original size:20 final size:20
Alignment explanation
Indices: 1406822--1406859 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1406812 TTCCCCTTTA
1406822 AGTGCATCGATGCATTCTAC
1 AGTGCATCGATGCATTCTAC
1406842 AGTGCATCGATGCATTCT
1 AGTGCATCGATGCATTCT
1406860 TTAACATGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.32
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:1409265 original size:21 final size:22
Alignment explanation
Indices: 1409231--1409277 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
1409221 ATTTTAAATT
1409231 TAAACTATAAAAATA-TAGAAAA
1 TAAACTATAAAAATATTA-AAAA
*
1409253 TAAA-TATATAAATATTAAAAA
1 TAAACTATAAAAATATTAAAAA
1409274 TAAA
1 TAAA
1409278 AATGAATTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (22 bp):
TAAACTATAAAAATATTAAAAA
Found at i:1409627 original size:6 final size:6
Alignment explanation
Indices: 1409616--1409665 Score: 73
Period size: 6 Copynumber: 8.0 Consensus size: 6
1409606 TTTTTACATA
*
1409616 AATTTT AATTTT AATTTT AATTTT AATTCT AATTTTT AAATTTT AATTTT
1 AATTTT AATTTT AATTTT AATTTT AATTTT AA-TTTT -AATTTT AATTTT
1409666 TATAAGACTT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
6 31 0.77
7 7 0.17
8 2 0.05
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (6 bp):
AATTTT
Found at i:1409927 original size:24 final size:23
Alignment explanation
Indices: 1409875--1409928 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
1409865 AATTTAATAT
* **
1409875 ATATTTTTATATTTAATTTTTAA
1 ATATTTTTATATTTAAATTAGAA
*
1409898 ACATTTTTATATTTTAAATTAGAA
1 ATATTTTTATA-TTTAAATTAGAA
1409922 ATATTTT
1 ATATTTT
1409929 AATTTTTCTA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 10 0.40
24 15 0.60
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (23 bp):
ATATTTTTATATTTAAATTAGAA
Found at i:1410974 original size:20 final size:21
Alignment explanation
Indices: 1410937--1410976 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1410927 AAATTAAGTT
1410937 AAATGAATTTTAAGATTTTAC
1 AAATGAATTTTAAGATTTTAC
1410958 AAATG-ATTTTACA-ATTTTA
1 AAATGAATTTTA-AGATTTTA
1410977 TATTCGATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (21 bp):
AAATGAATTTTAAGATTTTAC
Found at i:1411262 original size:65 final size:63
Alignment explanation
Indices: 1411144--1411352 Score: 233
Period size: 65 Copynumber: 3.2 Consensus size: 63
1411134 TTATTTGAGG
* * * *
1411144 TGATGCACCGATGCATCAACCATGCATCGATGCATTAGTGAAT-TAATTGAAACATCGAATGCAT
1 TGATGCACCGATGCATC-ACCATGCATCGATGCACT-CTGAATAT-TTTCAAACATCGAATGCAT
1411208 T
63 T
** *
1411209 CCATGCACCGATGCATTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATT
1 TGATGCACCGATGCA-TCACCATGCATCGATGCACTCTGAATATTTTC-AAACATCGAATGCATT
* * **
1411274 TGATGCATCGATGCA-CAAGCCATGCATCGATGCACTCAGGCTATTTTCAAACATCGAATGCATT
1 TGATGCACCGATGCATC-A-CCATGCATCGATGCACTCTGAATATTTTCAAACATCGAATGCATT
*
1411338 TGATGCATCGATGCA
1 TGATGCACCGATGCA
1411353 CACTTGGTGC
Statistics
Matches: 125, Mismatches: 14, Indels: 11
0.83 0.09 0.07
Matches are distributed among these distances:
63 1 0.01
64 38 0.30
65 84 0.67
66 2 0.02
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.28
Consensus pattern (63 bp):
TGATGCACCGATGCATCACCATGCATCGATGCACTCTGAATATTTTCAAACATCGAATGCATT
Found at i:1413451 original size:20 final size:21
Alignment explanation
Indices: 1413418--1413457 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1413408 TTTTAACGTA
1413418 ATTGATATTCATTTT-AAACC
1 ATTGATATTCATTTTCAAACC
1413438 ATTGATA-TCAATTTTCAAAC
1 ATTGATATTC-ATTTTCAAAC
1413458 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:1413465 original size:22 final size:20
Alignment explanation
Indices: 1413417--1413461 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
1413407 ATTTTAACGT
1413417 AATTGATATTCATTTTAAAC
1 AATTGATATTCATTTTAAAC
*
1413437 CATTGATA-TCAATTTTCAAAC
1 AATTGATATTC-ATTTT-AAAC
1413458 AATT
1 AATT
1413462 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:1418392 original size:21 final size:21
Alignment explanation
Indices: 1418350--1418393 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1418340 ACCCCGGGAG
*
1418350 CTAGTTCTTCACGAGCTGCTC
1 CTAGTTCTTCACGAGCTCCTC
* *
1418371 CTAGTTCTTCTCGTGCTCCTC
1 CTAGTTCTTCACGAGCTCCTC
1418392 CT
1 CT
1418394 CCTCCTCCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.36, G:0.16, T:0.39
Consensus pattern (21 bp):
CTAGTTCTTCACGAGCTCCTC
Found at i:1419488 original size:65 final size:64
Alignment explanation
Indices: 1419372--1419580 Score: 219
Period size: 65 Copynumber: 3.2 Consensus size: 64
1419362 ATTTGAGGTG
* * * *
1419372 ATGCACCGATGCATCAA-CCATGCATCGATGCA-TTAGTGAAT-TAATTGAAACATCGAATGCAT
1 ATGCATCGATGCA-CAAGCCATGCATCGATGCACTCA--GAATAT-TTTCAAACATCGAATGCAT
*
1419434 TCC
62 TTC
* ****
1419437 ATGCACCGATGCATTCTCCATGCATCGATGCACTCTA-AATATTTTCAAAACATCGAATGCATTT
1 ATGCATCGATGCACAAGCCATGCATCGATGCACTC-AGAATATTTTC-AAACATCGAATGCATTT
*
1419501 G
64 C
**
1419502 ATGCATCGATGCACAAGCCATGCATCGATGCACTCAGGCTATTTTCAAACATCGAATGCATTTC
1 ATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAAACATCGAATGCATTTC
1419566 ATGCATCGATGCACA
1 ATGCATCGATGCACA
1419581 CTTGGTGCAC
Statistics
Matches: 122, Mismatches: 16, Indels: 13
0.81 0.11 0.09
Matches are distributed among these distances:
64 38 0.31
65 82 0.67
66 1 0.01
67 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (64 bp):
ATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAAACATCGAATGCATTTC
Found at i:1419597 original size:64 final size:65
Alignment explanation
Indices: 1419419--1419582 Score: 224
Period size: 65 Copynumber: 2.5 Consensus size: 65
1419409 GAATTAATTG
* * **
1419419 AAACATCGAATGCATTCCATGCACCGATGCATTCTCCATGCATCGATGCACTCTAAATATTTTCA
1 AAACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCTAAATATTTTCA
* ** **
1419484 AAACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCACTC-AGGCTATTTTC
1 AAACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCTA-AATATTTTC
1419548 -
65 A
1419548 AAACATCGAATGCATTTCATGCATCGATGCACACT
1 AAACATCGAATGCATTTCATGCATCGATGCACACT
1419583 TGGTGCACCG
Statistics
Matches: 86, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
64 33 0.38
65 53 0.62
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.27
Consensus pattern (65 bp):
AAACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCTAAATATTTTCA
Found at i:1427093 original size:9 final size:9
Alignment explanation
Indices: 1427079--1427105 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
1427069 TTAAGAATTT
1427079 ATTTAAAAA
1 ATTTAAAAA
1427088 ATTTAAAAA
1 ATTTAAAAA
1427097 ATTTAAAAA
1 ATTTAAAAA
1427106 TATTATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
ATTTAAAAA
Found at i:1428801 original size:2 final size:2
Alignment explanation
Indices: 1428794--1428845 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
1428784 GTTAATACTA
1428794 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1428836 AT AT AT AT AT
1 AT AT AT AT AT
1428846 CAAGAATATG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1431515 original size:24 final size:24
Alignment explanation
Indices: 1431486--1431535 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1431476 TGGTGGTTGA
*
1431486 TTTAATGGT-TGTTTAAACTTTATT
1 TTTAATGGTATATTT-AACTTTATT
*
1431510 TTTAATGGTATATTTAAGTTTATT
1 TTTAATGGTATATTTAACTTTATT
1431534 TT
1 TT
1431536 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.26, C:0.02, G:0.12, T:0.60
Consensus pattern (24 bp):
TTTAATGGTATATTTAACTTTATT
Found at i:1432037 original size:17 final size:16
Alignment explanation
Indices: 1432006--1432039 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1431996 CACGTGGGAA
1432006 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
1432022 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
1432039 T
1 T
1432040 ACTATTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:1441469 original size:24 final size:24
Alignment explanation
Indices: 1441442--1441491 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1441432 TGGTGGTTGA
*
1441442 TTTAATGGT-TGTTTAAACTTTATT
1 TTTAATGGTATATTT-AACTTTATT
*
1441466 TTTAATGGTATATTTAAGTTTATT
1 TTTAATGGTATATTTAACTTTATT
1441490 TT
1 TT
1441492 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.26, C:0.02, G:0.12, T:0.60
Consensus pattern (24 bp):
TTTAATGGTATATTTAACTTTATT
Found at i:1441997 original size:17 final size:16
Alignment explanation
Indices: 1441966--1441999 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1441956 CACGTGAGGA
1441966 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
1441982 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
1441999 T
1 T
1442000 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:1444083 original size:42 final size:41
Alignment explanation
Indices: 1444031--1444132 Score: 132
Period size: 42 Copynumber: 2.5 Consensus size: 41
1444021 TCCAAAATTT
* *
1444031 ATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATG
1 ATAAATCCTTCGGGCCATCAGTAAGTCTTTCGAGCAAGATG
* * * *
1444072 CTTAAATCCTTCGGGTCATCTGTAAGTCTTTTGAGCAAGATG
1 -ATAAATCCTTCGGGCCATCAGTAAGTCTTTCGAGCAAGATG
*
1444114 ATAAGTCCTTCGGGCCATC
1 ATAAATCCTTCGGGCCATC
1444133 CATAAGACAT
Statistics
Matches: 51, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
41 16 0.31
42 35 0.69
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.31
Consensus pattern (41 bp):
ATAAATCCTTCGGGCCATCAGTAAGTCTTTCGAGCAAGATG
Found at i:1444402 original size:233 final size:233
Alignment explanation
Indices: 1443942--1444628 Score: 984
Period size: 233 Copynumber: 2.9 Consensus size: 233
1443932 TAAAAATGAA
* * * * * *
1443942 ATGAGAAATATTTCTCATTTAAATTTGAAAATTCAATTTTTTTGAAAAGTAAGAAAGCTTTCTTA
1 ATGAGAAAGATTTCTCATTTAAATCTGAAATTTGAA-ATTTTTGAAAAGTAAGAAAGGTTTCTTA
*
1444007 CCTAGTAAACTATTTCCAAAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATG
65 CCTAGTAAACTATTTCCAAAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATC
* *
1444072 CTTAAATCCTTCGGGTCATCTGTAAGTCTTTTGAGCAAGATGATAAGTCCTTCGGGCCATCCATA
130 CTTAAATCCTTCGGGTCATCTGTAAGTCTTTAGAGCAAGATGATAAGTCCTTCGAGCCATCCATA
* * * **
1444137 AGACATTTGGGCATGATGTTTTCACGTGTCTATTGAAAT
195 AGACATTTGGACAGGATGTTTTCACATGTCTATCAAAAT
*
1444176 ATGAGAAAGATTTCTCATTTAAATCTGAAATTTGAAATTTTTGGAAAGTAAGAAAGGTTTCTTAC
1 ATGAGAAAGATTTCTCATTTAAATCTGAAATTTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTAC
* *
1444241 CTAGTAAACTATTTCTAAAATTTATAAGTCCTTCGGGTCATCAGTAAGTCTTTCGAGCATGATCC
66 CTAGTAAACTATTTCCAAAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATCC
* * * * * * *
1444306 TTAAATCATTCTGGTCATCTGTAAGCCTTTAGAGCAAGA-AATTAAGTCCTTCTAGCTATCTATA
131 TTAAATCCTTCGGGTCATCTGTAAGTCTTTAGAGCAAGATGA-TAAGTCCTTCGAGCCATCCATA
* *
1444370 AGACATTTGTACAGGATGTTTTTACATGTCTATCAAAAT
195 AGACATTTGGACAGGATGTTTTCACATGTCTATCAAAAT
* * *
1444409 ATGAGAAAGGTTTCTCATTTAAATCTAAAAATTTGAAATTTTTGAAAAGTAAGAAAGGTTTATTA
1 ATGAGAAAGATTTCTCATTTAAATCT-GAAATTTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTA
*
1444474 CCTACGTAAACTATTTCCAAAATTTATAAGTCTTTCGGGCCATCAGTAAGTCTTTCGAGCATGAT
65 CCTA-GTAAACTATTTCCAAAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGAT
* *
1444539 GCC-TATATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTC-AGGCCATCC
129 -CCTTAAATCCTTCGGGTCATCTGTAAGTCTTTAGAGCAAGATGATAAGTCCTTCGA-GCCATCC
* * *
1444602 ATAAGACCTTTGGGCAAGATGTTTTCA
192 ATAAGACATTTGGACAGGATGTTTTCA
1444629 AAGGTCCATC
Statistics
Matches: 401, Mismatches: 46, Indels: 11
0.88 0.10 0.02
Matches are distributed among these distances:
232 1 0.00
233 198 0.49
234 72 0.18
235 127 0.32
236 3 0.01
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (233 bp):
ATGAGAAAGATTTCTCATTTAAATCTGAAATTTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTAC
CTAGTAAACTATTTCCAAAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATCC
TTAAATCCTTCGGGTCATCTGTAAGTCTTTAGAGCAAGATGATAAGTCCTTCGAGCCATCCATAA
GACATTTGGACAGGATGTTTTCACATGTCTATCAAAAT
Found at i:1444924 original size:22 final size:22
Alignment explanation
Indices: 1444871--1444925 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
1444861 TTTTCGTCCC
* *
1444871 ATTTTTATGTTATTACTATTATT
1 ATTTTT-TATTATTAATATTATT
** *
1444894 ATTAATTATTATTAATATTTTT
1 ATTTTTTATTATTAATATTATT
1444916 ATTTTTTATT
1 ATTTTTTATT
1444926 TATCTTGCAG
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
22 21 0.84
23 4 0.16
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (22 bp):
ATTTTTTATTATTAATATTATT
Found at i:1449709 original size:23 final size:23
Alignment explanation
Indices: 1449678--1449730 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
1449668 ATGTTGCTTG
*
1449678 ATTGTTAGCTTGAGAATTATATT
1 ATTGATAGCTTGAGAATTATATT
1449701 ATTGATAGCTTGAGAATTATATT
1 ATTGATAGCTTGAGAATTATATT
1449724 ATTGATA
1 ATTGATA
1449731 TTTATTCAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.34, C:0.04, G:0.17, T:0.45
Consensus pattern (23 bp):
ATTGATAGCTTGAGAATTATATT
Found at i:1451629 original size:20 final size:21
Alignment explanation
Indices: 1451604--1451655 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1451594 TTTTCCCAAT
*
1451604 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1451624 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1451645 TCGCAATGCGA
1 TCGCAATGCGA
1451656 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1451669 original size:20 final size:20
Alignment explanation
Indices: 1451644--1451798 Score: 152
Period size: 20 Copynumber: 7.7 Consensus size: 20
1451634 AATTGGGAAA
1451644 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
1451664 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
1451684 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
1451704 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
1451725 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * * *
1451745 TTTGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* * *
1451765 TTCGCAACGCGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
1451785 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
1451799 TTTCAAAGCG
Statistics
Matches: 114, Mismatches: 16, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
19 4 0.04
20 84 0.74
21 24 0.21
22 2 0.02
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:1451729 original size:61 final size:61
Alignment explanation
Indices: 1451664--1451798 Score: 180
Period size: 61 Copynumber: 2.2 Consensus size: 61
1451654 GATACTGACT
* * *
1451664 ATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATACAAA
1 ATCGCAATGCGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATACAAA
* * * * * * *
1451725 ATCGCAACGAGATACTGACTTTTGCAACGCGATTCTGACTTTCGCAACGCGATAATACATA
1 ATCGCAATGCGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATACAAA
1451786 ATCGCAATGCGAT
1 ATCGCAATGCGAT
1451799 TTTCAAAGCG
Statistics
Matches: 62, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (61 bp):
ATCGCAATGCGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATACAAA
Found at i:1452521 original size:25 final size:24
Alignment explanation
Indices: 1452467--1452521 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
1452457 TGTTTATTAT
* *
1452467 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
1452491 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
1452517 TGTTT
1 TGTTT
1452522 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:1454202 original size:20 final size:20
Alignment explanation
Indices: 1454177--1454222 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
1454167 TAGTTTACTT
1454177 TCGCAACACAAAAATGACTA
1 TCGCAACACAAAAATGACTA
* ** *
1454197 TCGCAACGCGGAAATGGCTA
1 TCGCAACACAAAAATGACTA
1454217 TCGCAA
1 TCGCAA
1454223 TGCGAAATGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.39, C:0.26, G:0.20, T:0.15
Consensus pattern (20 bp):
TCGCAACACAAAAATGACTA
Found at i:1454231 original size:19 final size:20
Alignment explanation
Indices: 1454188--1454243 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
1454178 CGCAACACAA
1454188 AAATGACTATCGCAACGCGG
1 AAATGACTATCGCAACGCGG
* *
1454208 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAACGCGG
**
1454227 AAATGAAAATCGCAACG
1 AAATGACTATCGCAACG
1454244 ACAAAATCGC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.39, C:0.21, G:0.23, T:0.16
Consensus pattern (20 bp):
AAATGACTATCGCAACGCGG
Found at i:1454251 original size:14 final size:14
Alignment explanation
Indices: 1454232--1454289 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1454222 ATGCGAAATG
1454232 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1454246 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
1454262 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
1454278 AAAATCGCAACG
1 AAAATCGCAACG
1454290 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1454274 original size:32 final size:33
Alignment explanation
Indices: 1454216--1454294 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
1454206 GGAAATGGCT
1454216 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1454249 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
1454281 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
1454295 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 29 0.64
33 16 0.36
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:1454344 original size:20 final size:20
Alignment explanation
Indices: 1454310--1454365 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
1454300 ATCGCATTTT
*
1454310 CATTTC-GCATTGCGATAGC
1 CATTTCTGCGTTGCGATAGC
*
1454329 CATTTCTGCGTTGCGATAGT
1 CATTTCTGCGTTGCGATAGC
1454349 CATTT-TCGCGTTGCGAT
1 CATTTCT-GCGTTGCGAT
1454366 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 7 0.21
20 26 0.79
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.38
Consensus pattern (20 bp):
CATTTCTGCGTTGCGATAGC
Found at i:1456254 original size:14 final size:14
Alignment explanation
Indices: 1456235--1456270 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1456225 ATTGTTTAAT
1456235 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1456249 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1456263 TGATTTGT
1 TGATTTGT
1456271 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1456519 original size:20 final size:20
Alignment explanation
Indices: 1456496--1456583 Score: 97
Period size: 20 Copynumber: 4.4 Consensus size: 20
1456486 AGATTTTCTA
*
1456496 GTTGCGATAGCCATTTCCGC
1 GTTGCGATAGCCATTTTCGC
* *** *
1456516 GTTGCAATTTTTCA-TTTCGA
1 GTTGCGA-TAGCCATTTTCGC
*
1456536 ATTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
1456556 GTTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
1456576 GTTGCGAT
1 GTTGCGAT
1456584 TTCCCCGTTG
Statistics
Matches: 53, Mismatches: 13, Indels: 4
0.76 0.19 0.06
Matches are distributed among these distances:
19 3 0.06
20 47 0.89
21 3 0.06
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.38
Consensus pattern (20 bp):
GTTGCGATAGCCATTTTCGC
Found at i:1456822 original size:20 final size:20
Alignment explanation
Indices: 1456797--1456846 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
1456787 TTGAAGATGA
1456797 TTGCGATTTTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
***
1456817 TTGCGAAAGTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
1456837 TTGCGATTTT
1 TTGCGATTTT
1456847 GTATTATCTC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (20 bp):
TTGCGATTTTCAGAATCTCG
Found at i:1456876 original size:20 final size:20
Alignment explanation
Indices: 1456811--1456876 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
1456801 GATTTTCAGA
* * *
1456811 ATCTCGTTGCGAAAGTCAGA
1 ATCTCGTTGCGATAGTTAGT
** *
1456831 ATCTCGTTGCGATTTTGTATT
1 ATCTCGTTGCGATAGT-TAGT
1456852 ATCTCGTTGCGATAGTTAGT
1 ATCTCGTTGCGATAGTTAGT
1456872 ATCTC
1 ATCTC
1456877 ATTATGATTT
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
20 21 0.58
21 15 0.42
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.39
Consensus pattern (20 bp):
ATCTCGTTGCGATAGTTAGT
Found at i:1457724 original size:24 final size:24
Alignment explanation
Indices: 1457697--1457750 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1457687 GTATTCGAAA
*
1457697 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
1457721 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
1457745 TTTGAT
1 TTTGAT
1457751 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:1457941 original size:12 final size:12
Alignment explanation
Indices: 1457924--1457948 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1457914 ATATAATCTT
1457924 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1457936 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1457948 G
1 G
1457949 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1460261 original size:19 final size:19
Alignment explanation
Indices: 1460219--1460369 Score: 98
Period size: 19 Copynumber: 8.7 Consensus size: 19
1460209 CTTAATGTCT
* **
1460219 ATCGCAATGCGGAAATTACT
1 ATCGCAATGC-GAAATGAAA
1460239 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1460258 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1460272 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
1460291 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
1460305 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
1460324 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
1460338 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1460357 ATCGCAACGCGAA
1 ATCGCAATGCGAA
1460370 TTTAATTTCG
Statistics
Matches: 100, Mismatches: 16, Indels: 31
0.68 0.11 0.21
Matches are distributed among these distances:
14 27 0.27
15 3 0.03
16 6 0.06
17 6 0.06
18 3 0.03
19 45 0.45
20 10 0.10
ACGTcount: A:0.42, C:0.20, G:0.23, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1460281 original size:33 final size:33
Alignment explanation
Indices: 1460239--1460365 Score: 202
Period size: 33 Copynumber: 3.8 Consensus size: 33
1460229 GGAAATTACT
1460239 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
1460272 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
1460304 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1460338 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
1460366 CGAATTTAAT
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
32 1 0.01
33 83 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1460346 original size:66 final size:66
Alignment explanation
Indices: 1460240--1460372 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
1460230 GAAATTACTA
*
1460240 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1460305 T
66 T
*
1460306 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1460371 T
66 T
1460372 T
1 T
1460373 AATTTCGCGT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:1460387 original size:19 final size:19
Alignment explanation
Indices: 1460365--1460439 Score: 70
Period size: 19 Copynumber: 4.2 Consensus size: 19
1460355 AAATCGCAAC
*
1460365 GCGAATTTAATTTCGCGTT
1 GCGAATTTCATTTCGCGTT
*
1460384 GCG-A-TTC---TCTCGTT
1 GCGAATTTCATTTCGCGTT
*
1460398 GCGATTTTCATTTCGCGTT
1 GCGAATTTCATTTCGCGTT
* *
1460417 GCGATTTTCATTTCGCATT
1 GCGAATTTCATTTCGCGTT
1460436 GCGA
1 GCGA
1460440 TAGTACTTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
14 9 0.20
16 3 0.07
17 2 0.04
18 1 0.02
19 31 0.67
ACGTcount: A:0.15, C:0.21, G:0.21, T:0.43
Consensus pattern (19 bp):
GCGAATTTCATTTCGCGTT
Found at i:1460440 original size:19 final size:19
Alignment explanation
Indices: 1460396--1460440 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
1460386 GATTCTCTCG
*
1460396 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
1460415 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1460434 TTGCGAT
1 TTGCGAT
1460441 AGTACTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.13, C:0.20, G:0.20, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1460566 original size:14 final size:14
Alignment explanation
Indices: 1460547--1460583 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1460537 CATCAATTAA
1460547 ACAAATCAACTTTT
1 ACAAATCAACTTTT
* *
1460561 ACAAATTACCTTTT
1 ACAAATCAACTTTT
1460575 ACAAATCAA
1 ACAAATCAA
1460584 TTAAACAATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1462025 original size:42 final size:41
Alignment explanation
Indices: 1461979--1462142 Score: 168
Period size: 42 Copynumber: 3.9 Consensus size: 41
1461969 CGATGACAGT
*
1461979 GGCCTCTTGAACGGTGGAAGGGGACTCTCGAGGAATGATAAG
1 GGCCTCTTCAACGGTGG-AGGGGACTCTCGAGGAATGATAAG
* * * * *
1462021 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA-CAG
1 GGCCTCTTCAACGGT-GGAGGGGACTCTCGAGGAATGATAAG
* *
1462062 TGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 -GGCCTCTTCAACGGT-GGAGGGGACTCTCGAGGAATGATAAG
* * * *
1462105 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 GGCCTCTTCAACGGT-GGAGGGGACTCTCGAGGAATGA
1462143 CAGGCGAGTC
Statistics
Matches: 99, Mismatches: 20, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
41 2 0.02
42 94 0.95
43 3 0.03
ACGTcount: A:0.24, C:0.18, G:0.37, T:0.21
Consensus pattern (41 bp):
GGCCTCTTCAACGGTGGAGGGGACTCTCGAGGAATGATAAG
Found at i:1462085 original size:84 final size:84
Alignment explanation
Indices: 1461970--1462145 Score: 334
Period size: 84 Copynumber: 2.1 Consensus size: 84
1461960 CCTCTTCAAC
1461970 GATGACAGTGGCCTCTTGAACGGTGGAAGGGGACTCTCGAGGAATGATAAGGGCCTCTTCAACGA
1 GATGACAGTGGCCTCTTGAACGGTGGAAGGGGACTCTCGAGGAATGATAAGGGCCTCTTCAACGA
1462035 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
* *
1462054 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
1 GATGACAGTGGCCTCTTGAACGGTGGAAGGGGACTCTCGAGGAATGATAAGGGCCTCTTCAACGA
1462119 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
1462138 GATGACAG
1 GATGACAG
1462146 GCGAGTCGGG
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 90 1.00
ACGTcount: A:0.24, C:0.18, G:0.37, T:0.21
Consensus pattern (84 bp):
GATGACAGTGGCCTCTTGAACGGTGGAAGGGGACTCTCGAGGAATGATAAGGGCCTCTTCAACGA
TAGGAGTGGACTCTTGAGG
Found at i:1462541 original size:91 final size:90
Alignment explanation
Indices: 1462366--1462550 Score: 291
Period size: 91 Copynumber: 2.0 Consensus size: 90
1462356 ATTTCAAACT
* *
1462366 TTCAACCAAAAGATAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
1462431 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
1462459 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
*
1462523 GTATTGGCAGCAACCGAATAAATTTAC
64 GAATTGGCAGCAACCGAATAAATTTAC
1462550 T
1 T
1462551 AAGCAATCTA
Statistics
Matches: 87, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
91 42 0.48
93 18 0.21
95 27 0.31
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:1464313 original size:33 final size:33
Alignment explanation
Indices: 1464253--1464349 Score: 158
Period size: 33 Copynumber: 2.9 Consensus size: 33
1464243 ACGAGATAAT
*
1464253 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGAATATCGCAACGA
*
1464287 GAGAATCGCAACGCGAAATGAATATCGCGACGA
1 GAGAATCGCAACGCGAAATGAATATCGCAACGA
*
1464320 GAGAATCGCAACGCGAAATGAAAATCGCAA
1 GAGAATCGCAACGCGAAATGAATATCGCAA
1464350 GGCGAAATGA
Statistics
Matches: 59, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 45 0.76
34 14 0.24
ACGTcount: A:0.41, C:0.22, G:0.26, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGAATATCGCAACGA
Found at i:1464345 original size:19 final size:19
Alignment explanation
Indices: 1464228--1464373 Score: 114
Period size: 19 Copynumber: 8.1 Consensus size: 19
1464218 TCTTTTGGTT
*
1464228 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
1464247 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
1464267 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
1464285 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
* *
1464301 GAAATGAATATCGCGA--C
1 GAAATGAAAATCGCAACGC
*
1464318 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
1464334 GAAATGAAAATCGCAAGGC
1 GAAATGAAAATCGCAACGC
*
1464353 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
1464372 GA
1 GA
1464374 TTTTGGTTTC
Statistics
Matches: 100, Mismatches: 15, Indels: 24
0.72 0.11 0.17
Matches are distributed among these distances:
14 17 0.17
15 2 0.02
16 4 0.04
17 3 0.03
18 3 0.03
19 42 0.42
20 27 0.27
21 2 0.02
ACGTcount: A:0.43, C:0.19, G:0.25, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Done.