Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009574.1 Hibiscus syriacus cultivar Beakdansim tig00116939_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: 2686660
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 14
Found at i:1345166 original size:23 final size:23
Alignment explanation
Indices: 1345139--1345183 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1345129 GATTTTGAAT
*
1345139 TTCCACCTTT-TCAAAATGTTTTG
1 TTCCAACTTTATCAAAA-GTTTTG
1345162 TTCCAACTTTATCAAAAGTTTT
1 TTCCAACTTTATCAAAAGTTTT
1345184 AAGATCATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.27, C:0.20, G:0.07, T:0.47
Consensus pattern (23 bp):
TTCCAACTTTATCAAAAGTTTTG
Found at i:1345374 original size:22 final size:21
Alignment explanation
Indices: 1345332--1345371 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1345322 GAGTTTGTTT
*
1345332 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1345353 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1345372 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1347761 original size:2 final size:2
Alignment explanation
Indices: 1347756--1347809 Score: 99
Period size: 2 Copynumber: 26.5 Consensus size: 2
1347746 TGTGTGTGTG
1347756 TA TA 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 TA TA
1347798 TA TA TA TCA TA T
1 TA TA TA T-A TA T
1347810 TATCATATTA
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 49 0.96
3 2 0.04
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1353252 original size:32 final size:32
Alignment explanation
Indices: 1353183--1353274 Score: 127
Period size: 32 Copynumber: 2.9 Consensus size: 32
1353173 AAGAGTCGAG
*
1353183 GGTTACCTATGTCTTTC-GAGACATATGGATA
1 GGTTACCTATGTCTTTCGGAGACATATGGACA
* *
1353214 GTTTACCTATGT-TCTTCGGAAACATATGGACA
1 GGTTACCTATGTCT-TTCGGAGACATATGGACA
1353246 GGTTACCTATGTCTTTCGG-GACATATGGA
1 GGTTACCTATGTCTTTCGGAGACATATGGA
1353275 AAGTGGTCCT
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
30 1 0.02
31 23 0.43
32 28 0.53
33 1 0.02
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (32 bp):
GGTTACCTATGTCTTTCGGAGACATATGGACA
Found at i:1357154 original size:18 final size:16
Alignment explanation
Indices: 1357126--1357169 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
1357116 TGTGTGTAAT
*
1357126 ATGAGTATATGTATTAC
1 ATGATTATATGTA-TAC
*
1357143 ATGATTTATATGTATGC
1 ATGA-TTATATGTATAC
1357160 ATGATTATAT
1 ATGATTATAT
1357170 AATGGTGATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 6 0.25
17 10 0.42
18 8 0.33
ACGTcount: A:0.34, C:0.05, G:0.16, T:0.45
Consensus pattern (16 bp):
ATGATTATATGTATAC
Found at i:1357170 original size:18 final size:18
Alignment explanation
Indices: 1357131--1357169 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
1357121 GTAATATGAG
1357131 TATATGTATTACATGATT
1 TATATGTATTACATGATT
*
1357149 TATATGTA-TGCATGA-T
1 TATATGTATTACATGATT
1357165 TATAT
1 TATAT
1357170 AATGGTGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 6 0.30
17 6 0.30
18 8 0.40
ACGTcount: A:0.33, C:0.05, G:0.13, T:0.49
Consensus pattern (18 bp):
TATATGTATTACATGATT
Found at i:1357482 original size:31 final size:31
Alignment explanation
Indices: 1357441--1357503 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
1357431 AAGAATCGAG
* * *
1357441 GGTTATCTATGTTCTTCGGAATATATGGATA
1 GGTTACCTATGTCCTTCGGAACATATGGATA
*
1357472 GGTTACCTATGTCCTTCGGGACATATGGATA
1 GGTTACCTATGTCCTTCGGAACATATGGATA
1357503 G
1 G
1357504 TGGTCCTTCG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.24, C:0.14, G:0.25, T:0.37
Consensus pattern (31 bp):
GGTTACCTATGTCCTTCGGAACATATGGATA
Found at i:1358356 original size:15 final size:15
Alignment explanation
Indices: 1358336--1358365 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1358326 AAATGTTTAG
*
1358336 CATTTTATAAGTTAA
1 CATTTTATAAATTAA
1358351 CATTTTATAAATTAA
1 CATTTTATAAATTAA
1358366 TTTAATGATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (15 bp):
CATTTTATAAATTAA
Found at i:1359066 original size:2 final size:2
Alignment explanation
Indices: 1359061--1359104 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1359051 AGAATATTAC
1359061 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
1359103 AT
1 AT
1359105 GAGTAAATTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1359329 original size:60 final size:60
Alignment explanation
Indices: 1359222--1359363 Score: 173
Period size: 60 Copynumber: 2.4 Consensus size: 60
1359212 CCTAATCAAT
* * * *
1359222 TTTTTAATATTCTAATTTCATCCTTAAACTATGACTCTCATTATAAATTAGTCCTT-AAAC
1 TTTTGAATATTTTAATTTCATCATTAAACTATGACCCTCATTATAAATTAGT-CTTCAAAC
* *
1359282 TTTTGAA-ATTTATAATTTCATCATTAAACTATGACCCT-ATTTCTAAATTGGTCTTCAAAC
1 TTTTGAATATTT-TAATTTCATCATTAAACTATGACCCTCA-TTATAAATTAGTCTTCAAAC
*
1359342 TTTTGAATATTTCAATTTCATC
1 TTTTGAATATTTTAATTTCATC
1359364 CCCAAAATAT
Statistics
Matches: 71, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
59 7 0.10
60 60 0.85
61 4 0.06
ACGTcount: A:0.32, C:0.17, G:0.05, T:0.46
Consensus pattern (60 bp):
TTTTGAATATTTTAATTTCATCATTAAACTATGACCCTCATTATAAATTAGTCTTCAAAC
Found at i:1359596 original size:60 final size:59
Alignment explanation
Indices: 1359489--1359657 Score: 153
Period size: 60 Copynumber: 2.8 Consensus size: 59
1359479 ATTTATGCGT
* * ** * *
1359489 ATAGTTTA-GGATGAAATTAGAATGTTAAAAAATTTTAGGGTTCAATTTAGAATGA-AGGTA
1 ATAGTTTAGGGATGAAATTAGAATATT-AAAAAGTTTAGGACT-AATTTAGAAAGATA-ATA
* * *
1359549 ATAGTTTAGGGATGAAATTAAAATATTCAAAAGTTTGAGGACTAATTTAGAAAGATAATC
1 ATAGTTTAGGGATGAAATTAGAATATTAAAAAGTTT-AGGACTAATTTAGAAAGATAATA
* * * * *
1359609 ATAGTTTAGGAATAAAATTGGAATATTTAAAAGTTTAGGGACCAATTTA
1 ATAGTTTAGGGATGAAATTAGAATATTAAAAAGTTTA-GGACTAATTTA
1359658 AAATAAAAAT
Statistics
Matches: 90, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
59 1 0.01
60 68 0.76
61 21 0.23
ACGTcount: A:0.43, C:0.04, G:0.20, T:0.34
Consensus pattern (59 bp):
ATAGTTTAGGGATGAAATTAGAATATTAAAAAGTTTAGGACTAATTTAGAAAGATAATA
Found at i:1359669 original size:60 final size:60
Alignment explanation
Indices: 1359549--1359671 Score: 142
Period size: 60 Copynumber: 2.0 Consensus size: 60
1359539 AATGAAGGTA
* * * * *
1359549 ATAGTTTAGGGATGAAATTAAAATATTCAAAAGTTTGAGGACTAATTTAGAAAGATAATC
1 ATAGTTTAGGAATAAAATTAAAATATTCAAAAGTTTGAGGACCAATTTAGAAAAAAAATC
** *
1359609 ATAGTTTAGGAATAAAATTGGAATATTTAAAAGTTT-AGGGACCAATTTA-AAATAAAAATC
1 ATAGTTTAGGAATAAAATTAAAATATTCAAAAGTTTGA-GGACCAATTTAGAAA-AAAAATC
1359669 ATA
1 ATA
1359672 CTTTGATGAC
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
59 4 0.08
60 49 0.92
ACGTcount: A:0.47, C:0.05, G:0.16, T:0.32
Consensus pattern (60 bp):
ATAGTTTAGGAATAAAATTAAAATATTCAAAAGTTTGAGGACCAATTTAGAAAAAAAATC
Found at i:1364543 original size:34 final size:33
Alignment explanation
Indices: 1364479--1364562 Score: 159
Period size: 34 Copynumber: 2.5 Consensus size: 33
1364469 CGATTATATA
1364479 TATATATATAATATTTTATATTTTTATATTAAT
1 TATATATATAATATTTTATATTTTTATATTAAT
1364512 TATATATATAATATTTTATATATTTTATATTAAT
1 TATATATATAATATTTTATAT-TTTTATATTAAT
1364546 TATATATATAATATTTT
1 TATATATATAATATTTT
1364563 TCGGGTTCGG
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
33 21 0.42
34 29 0.58
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (33 bp):
TATATATATAATATTTTATATTTTTATATTAAT
Found at i:1364559 original size:9 final size:9
Alignment explanation
Indices: 1364471--1364559 Score: 60
Period size: 9 Copynumber: 9.8 Consensus size: 9
1364461 CCCCGCCCCG
1364471 ATTATATAT
1 ATTATATAT
1364480 ATATATATAAT
1 AT-TATAT-AT
*
1364491 ATTTTATAT
1 ATTATATAT
*
1364500 -TTTTATATT
1 ATTATATA-T
1364509 AATTATATAT
1 -ATTATATAT
1364519 A-TA-ATAT
1 ATTATATAT
*
1364526 TTTATATAT
1 ATTATATAT
*
1364535 TTTATAT-T
1 ATTATATAT
1364543 AATTATATAT
1 -ATTATATAT
*
1364553 ATAATAT
1 ATTATAT
1364560 TTTTCGGGTT
Statistics
Matches: 66, Mismatches: 5, Indels: 18
0.74 0.06 0.20
Matches are distributed among these distances:
7 4 0.06
8 12 0.18
9 29 0.44
10 11 0.17
11 10 0.15
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (9 bp):
ATTATATAT
Found at i:1365184 original size:16 final size:17
Alignment explanation
Indices: 1365155--1365194 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
1365145 ACATGTCACC
*
1365155 ATTTAATTAGATAAAAA
1 ATTTAATTAAATAAAAA
1365172 ATTT-ATTAAATAAAAA
1 ATTTAATTAAATAAAAA
1365188 ATATTAA
1 AT-TTAA
1365195 AAAAATATCC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 13 0.65
17 6 0.30
18 1 0.05
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
ATTTAATTAAATAAAAA
Found at i:1367608 original size:21 final size:21
Alignment explanation
Indices: 1367582--1367635 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
1367572 GTTTCCAGAT
*
1367582 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
1367603 TCGCAATGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
1367624 TCGCAATGCGAA
1 TCGCAATGCGAA
1367636 TATGTAAATC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (21 bp):
TCGCAATGCGAACTTCGACTA
Found at i:1368197 original size:6 final size:6
Alignment explanation
Indices: 1368176--1368214 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
1368166 CCGTCGTCTG
1368176 GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCG
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCG
1368215 ATCGAAGTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 10 0.30
6 23 0.70
ACGTcount: A:0.00, C:0.18, G:0.54, T:0.28
Consensus pattern (6 bp):
GGTCGT
Found at i:1370923 original size:21 final size:21
Alignment explanation
Indices: 1370897--1370972 Score: 152
Period size: 21 Copynumber: 3.6 Consensus size: 21
1370887 GATTCTGACT
1370897 ATCGCAACGCGATAATACATA
1 ATCGCAACGCGATAATACATA
1370918 ATCGCAACGCGATAATACATA
1 ATCGCAACGCGATAATACATA
1370939 ATCGCAACGCGATAATACATA
1 ATCGCAACGCGATAATACATA
1370960 ATCGCAACGCGAT
1 ATCGCAACGCGAT
1370973 TCTGACTATC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 55 1.00
ACGTcount: A:0.41, C:0.25, G:0.16, T:0.18
Consensus pattern (21 bp):
ATCGCAACGCGATAATACATA
Found at i:1371184 original size:22 final size:22
Alignment explanation
Indices: 1371158--1371208 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
1371148 CTACGGCGAC
1371158 ATCCGTCCCCATCTCCGACAAA
1 ATCCGTCCCCATCTCCGACAAA
*
1371180 ATCCGTCCCCATCTCCGGCAAA
1 ATCCGTCCCCATCTCCGACAAA
1371202 ATCCGTC
1 ATCCGTC
1371209 TATCTCCATC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.24, C:0.45, G:0.12, T:0.20
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACAAA
Found at i:1371586 original size:19 final size:19
Alignment explanation
Indices: 1371564--1371629 Score: 116
Period size: 19 Copynumber: 3.5 Consensus size: 19
1371554 AGGATCGCAA
1371564 TGCGATTTT-AGTTTCGCGT
1 TGCGATTTTCA-TTTCGCGT
1371583 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
1371602 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
1371621 TGCGATTTT
1 TGCGATTTT
1371630 AAGTTTCAGA
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
19 45 0.98
20 1 0.02
ACGTcount: A:0.11, C:0.18, G:0.23, T:0.48
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:1372760 original size:21 final size:20
Alignment explanation
Indices: 1372725--1372838 Score: 95
Period size: 20 Copynumber: 5.6 Consensus size: 20
1372715 TTATGTATTT
* *
1372725 ATCGCGTTACGATAGTCAGA
1 ATCGCGTTGCGATAGTCAAA
1372745 ATCGCGTTTGCGATAGTCAAA
1 ATCGCG-TTGCGATAGTCAAA
* *
1372766 ATCGCGTTGCGAT-TTACATA
1 ATCGCGTTGCGATAGT-CAAA
* * **
1372786 TTCGCATTGCGATTTTCTAAA
1 ATCGCGTTGCGATAGTC-AAA
***
1372807 ATCGCAACGCGATAGTCAAA
1 ATCGCGTTGCGATAGTCAAA
1372827 ATCGCGTTGCGA
1 ATCGCGTTGCGA
1372839 ATCTGGAAAC
Statistics
Matches: 75, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
19 1 0.01
20 40 0.53
21 34 0.45
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAAA
Found at i:1373964 original size:20 final size:20
Alignment explanation
Indices: 1373818--1373964 Score: 130
Period size: 20 Copynumber: 7.7 Consensus size: 20
1373808 ATCGCAACAA
1373818 GATTTT-AGTTTCGCGTTGC
1 GATTTTCAGTTTCGCGTTGC
* * * *
1373837 AATTTTTATTTTCACGTTGC
1 GATTTTCAGTTTCGCGTTGC
1373857 GA---T-A-TTT-GCGTTGC
1 GATTTTCAGTTTCGCGTTGC
1373871 GATTTTCTAGTTTCGCGTTGC
1 GATTTTC-AGTTTCGCGTTGC
*
1373892 GATTTTCA-TGTTCACGTTGC
1 GATTTTCAGT-TTCGCGTTGC
* *
1373912 GATTTTCATTTTCGTGTTGC
1 GATTTTCAGTTTCGCGTTGC
*
1373932 GATTTTCATTTTCGCGTTGC
1 GATTTTCAGTTTCGCGTTGC
* *
1373952 GAATTTAAGTTTC
1 GATTTTCAGTTTC
1373965 AGAAACTACT
Statistics
Matches: 106, Mismatches: 12, Indels: 19
0.77 0.09 0.14
Matches are distributed among these distances:
14 8 0.08
15 3 0.03
16 1 0.01
17 2 0.02
19 7 0.07
20 70 0.66
21 15 0.14
ACGTcount: A:0.14, C:0.16, G:0.20, T:0.49
Consensus pattern (20 bp):
GATTTTCAGTTTCGCGTTGC
Found at i:1376140 original size:21 final size:21
Alignment explanation
Indices: 1376052--1376150 Score: 94
Period size: 21 Copynumber: 4.7 Consensus size: 21
1376042 TATGCACCTA
* **
1376052 TCATCGTTCAAGAGGTACCTC
1 TCATCATTCAAGAGGCCCCTC
*
1376073 -CTATCATTCAAGAAGCCCCTC
1 TC-ATCATTCAAGAGGCCCCTC
*
1376094 TCATCA-TCGAAGAGGCACCTC
1 TCATCATTC-AAGAGGCCCCTC
* *
1376115 CCATCATTCAAGAGGCCCCTG
1 TCATCATTCAAGAGGCCCCTC
*
1376136 TCATCGTTCAAGAGG
1 TCATCATTCAAGAGG
1376151 TCACGTCCGC
Statistics
Matches: 63, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
20 3 0.05
21 57 0.90
22 3 0.05
ACGTcount: A:0.26, C:0.32, G:0.18, T:0.23
Consensus pattern (21 bp):
TCATCATTCAAGAGGCCCCTC
Found at i:1376149 original size:42 final size:42
Alignment explanation
Indices: 1376052--1376150 Score: 137
Period size: 42 Copynumber: 2.4 Consensus size: 42
1376042 TATGCACCTA
* *
1376052 TCATCGTTCAAGAGGTACCTCCTATCATTCAAGAAGCCCCTC
1 TCATCGTTCAAGAGGCACCTCCCATCATTCAAGAAGCCCCTC
* * *
1376094 TCATC-ATCGAAGAGGCACCTCCCATCATTCAAGAGGCCCCTG
1 TCATCGTTC-AAGAGGCACCTCCCATCATTCAAGAAGCCCCTC
1376136 TCATCGTTCAAGAGG
1 TCATCGTTCAAGAGG
1376151 TCACGTCCGC
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
41 2 0.04
42 45 0.92
43 2 0.04
ACGTcount: A:0.26, C:0.32, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATCGTTCAAGAGGCACCTCCCATCATTCAAGAAGCCCCTC
Found at i:1377592 original size:50 final size:55
Alignment explanation
Indices: 1377538--1377671 Score: 152
Period size: 64 Copynumber: 2.4 Consensus size: 55
1377528 ATTTGTTCTC
1377538 TTTGTAAAAGTTGATTTGTTGA-G-G-AAATAAGAATTATTTTTT-CTTG-TTGA
1 TTTGTAAAAGTTGATTTGTTGATGTGTAAATAAGAATTATTTTTTACTTGTTTGA
1377588 TTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAAGAATTATTTTTTACTTGTTTCATTGA
1 TTTGTAAAAGTTGATTTG-----TTGATGTGTAAATAAGAATTATTTTTTACTTG--T--TTGA
1377652 TTTGTAAAAGTTGATTTGTT
1 TTTGTAAAAGTTGATTTGTT
1377672 TAAATTCAAT
Statistics
Matches: 70, Mismatches: 0, Indels: 19
0.79 0.00 0.21
Matches are distributed among these distances:
50 18 0.26
55 4 0.06
56 1 0.01
57 1 0.01
58 18 0.26
59 6 0.09
64 22 0.31
ACGTcount: A:0.29, C:0.02, G:0.18, T:0.51
Consensus pattern (55 bp):
TTTGTAAAAGTTGATTTGTTGATGTGTAAATAAGAATTATTTTTTACTTGTTTGA
Found at i:1377752 original size:20 final size:20
Alignment explanation
Indices: 1377727--1377805 Score: 95
Period size: 20 Copynumber: 4.0 Consensus size: 20
1377717 GTGCACTTTC
*
1377727 GCAACGTGAAAGTCAAATTT
1 GCAACGCGAAAGTCAAATTT
*
1377747 GCAACGCGAAAGTCAAATTC
1 GCAACGCGAAAGTCAAATTT
*** *
1377767 GCGTTGCGATAGTCAAATTT
1 GCAACGCGAAAGTCAAATTT
*
1377787 GCAACGTGAAAGTCAAATT
1 GCAACGCGAAAGTCAAATT
1377806 CGCGTTGCAA
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.24
Consensus pattern (20 bp):
GCAACGCGAAAGTCAAATTT
Found at i:1377781 original size:40 final size:40
Alignment explanation
Indices: 1377737--1377813 Score: 145
Period size: 40 Copynumber: 1.9 Consensus size: 40
1377727 GCAACGTGAA
1377737 AGTCAAATTTGCAACGCGAAAGTCAAATTCGCGTTGCGAT
1 AGTCAAATTTGCAACGCGAAAGTCAAATTCGCGTTGCGAT
*
1377777 AGTCAAATTTGCAACGTGAAAGTCAAATTCGCGTTGC
1 AGTCAAATTTGCAACGCGAAAGTCAAATTCGCGTTGC
1377814 AATTTTCGGT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.26
Consensus pattern (40 bp):
AGTCAAATTTGCAACGCGAAAGTCAAATTCGCGTTGCGAT
Found at i:1378130 original size:18 final size:18
Alignment explanation
Indices: 1378107--1378142 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1378097 AAGCTGGTTG
*
1378107 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
1378125 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
1378143 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:1380464 original size:24 final size:24
Alignment explanation
Indices: 1380413--1380464 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
1380403 ATCCGAGTAT
** *
1380413 TGACCAAGATCAAAGTACGGGTAT
1 TGACCAAGATCAAAGTACGAATAC
* *
1380437 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTACGAATAC
1380461 TGAC
1 TGAC
1380465 TAGTACTCAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (24 bp):
TGACCAAGATCAAAGTACGAATAC
Found at i:1381434 original size:20 final size:20
Alignment explanation
Indices: 1381386--1381518 Score: 112
Period size: 20 Copynumber: 6.7 Consensus size: 20
1381376 AACTAAAACC
*
1381386 TGTTGCGAAATT-AAATTCG
1 TGTTGCGAATTTGAAATTCG
* *
1381405 TGTTGTGAATTTGAAAATCG
1 TGTTGCGAATTTGAAATTCG
*
1381425 AGTTGCGAATTTGAAATTCAG
1 TGTTGCGAATTTGAAATTC-G
*
1381446 TGTTGCGAATTTG-ACTTCTG
1 TGTTGCGAATTTGAAATTC-G
* * *
1381466 TGTTACGAATTTG-ACTTATG
1 TGTTGCGAATTTGAAATT-CG
*
1381486 TGTTGCG-ATTTACAAATTCG
1 TGTTGCGAATTT-GAAATTCG
*
1381506 CGTTGCGAATTTG
1 TGTTGCGAATTTG
1381519 GAAACTGGGT
Statistics
Matches: 91, Mismatches: 17, Indels: 11
0.76 0.14 0.09
Matches are distributed among these distances:
19 14 0.15
20 57 0.63
21 20 0.22
ACGTcount: A:0.26, C:0.11, G:0.23, T:0.40
Consensus pattern (20 bp):
TGTTGCGAATTTGAAATTCG
Found at i:1386915 original size:25 final size:25
Alignment explanation
Indices: 1386887--1386935 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
1386877 TTTCAAAAAA
1386887 TTTT-ATTAAACATTTTTCAAAATTC
1 TTTTAATTAAAC-TTTTTCAAAATTC
* *
1386912 TTTTAATTGATCTTTTTCAAAATT
1 TTTTAATTAAACTTTTTCAAAATT
1386936 TGAAAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 16 0.76
26 5 0.24
ACGTcount: A:0.33, C:0.10, G:0.02, T:0.55
Consensus pattern (25 bp):
TTTTAATTAAACTTTTTCAAAATTC
Found at i:1389171 original size:36 final size:34
Alignment explanation
Indices: 1389057--1389163 Score: 88
Period size: 36 Copynumber: 3.0 Consensus size: 34
1389047 TGTTTATCTC
* *
1389057 GAAACAAAGTTTCGTCTCGTTTGAGACAGTGTTTCTT
1 GAAACAAA-TTTCATCTCGCTTGAGACA-T-TTTCTT
* * * * *
1389094 GAAACAAAATTGATCTCACTTGAGATTATTTTCCTA
1 GAAACAAATTTCATCTCGCTTGAGA-CATTTT-CTT
* *
1389130 AAAACAAATTTTATCTCGCTTGAGACATTTTCTT
1 GAAACAAATTTCATCTCGCTTGAGACATTTTCTT
1389164 TTGAAACATA
Statistics
Matches: 55, Mismatches: 13, Indels: 7
0.73 0.17 0.09
Matches are distributed among these distances:
34 2 0.04
35 8 0.15
36 36 0.65
37 9 0.16
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (34 bp):
GAAACAAATTTCATCTCGCTTGAGACATTTTCTT
Found at i:1389248 original size:66 final size:66
Alignment explanation
Indices: 1389130--1389255 Score: 148
Period size: 66 Copynumber: 1.9 Consensus size: 66
1389120 TATTTTCCTA
* * * * * *
1389130 AAAACAAATTTTATCTCGCTTGAGACATTTTCTTTTGAAACATAAGCCTTTGAGATTGTTCCTCT
1 AAAACAAATTTTATCTCGCTTGAAACAATTTCCTTCGAAACATAAGACTTTGAAATTGTTCCTCT
1389195 T
66 T
* *
1389196 AAAAC-AATTTTCGTCTCGCTTGAAACAGATTTCCTTCGAAACATAA-ATTTTGAAATTGTT
1 AAAACAAATTTT-ATCTCGCTTGAAACA-ATTTCCTTCGAAACATAAGACTTTGAAATTGTT
1389256 TCACTTGAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
65 6 0.12
66 29 0.58
67 15 0.30
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.39
Consensus pattern (66 bp):
AAAACAAATTTTATCTCGCTTGAAACAATTTCCTTCGAAACATAAGACTTTGAAATTGTTCCTCT
T
Found at i:1390405 original size:137 final size:137
Alignment explanation
Indices: 1389927--1390596 Score: 761
Period size: 137 Copynumber: 4.9 Consensus size: 137
1389917 TTTTACTTAC
* * * * * * *
1389927 CAAGAAGGAATAATGTCGTCCATCGACCAGATCTCCTCAATGCGAAGGAGTAATCTCATCCTCGG
1 CAAGAAGGAACAATGTCGTCCACCGACCAGATCTCCTCAACGCGAAGGAGCAGTGTCATCCTCAG
* * *
1389992 ACAATCAGACTTCCTCAACGCGAAGGAACCATGTTGTCTCCAAATTATCTC-CATATACGGCTAG
66 ACAATCAGACTTCCTCAACGCGAAGGAACCGTGTTGTCTCCAAATTATC-CAAAAATA--GCTAG
*
1390056 ACATCCTC-A
128 ACGTCCTCAA
* * *
1390065 CTAAGAAGGAACAATGTCGTCCACCAACCAGATCTCCTCAACTCGAAGGAGCAGTGTCATCCTAA
1 C-AAGAAGGAACAATGTCGTCCACCGACCAGATCTCCTCAACGCGAAGGAGCAGTGTCATCCTCA
* * *
1390130 GACAATCAGACTTCCTCAATGTGAAGGAACCGTGTTGTCTCCAAATTATCTTCAAATATAGCTAG
65 GACAATCAGACTTCCTCAACGCGAAGGAACCGTGTTGTCTCCAAATTATC--CAAAAATAGCTAG
* * *
1390195 ACTTCCCCAC
128 ACGTCCTCAA
* * * * * * * *
1390205 CAAAAAGGAACAATATCGTCCACTGACTATATCTCCTCAACGCGAAAGAGTAGTGTCATCCTTAG
1 CAAGAAGGAACAATGTCGTCCACCGACCAGATCTCCTCAACGCGAAGGAGCAGTGTCATCCTCAG
* * * * * *
1390270 AAAATCAGACTTCCTCAACGCAAAGGAACCGTGTTATCTCCAAACTATCCAAAAATGGCTAGATG
66 ACAATCAGACTTCCTCAACGCGAAGGAACCGTGTTGTCTCCAAATTATCCAAAAATAGCTAGACG
1390335 TCCTCAA
131 TCCTCAA
* * * * * * * *
1390342 CACGAAGGAAAAATATCGTCCATCGACCAGATCTCCTTAACGCAAAGTAGCAGTGTCATCCTTAG
1 CAAGAAGGAACAATGTCGTCCACCGACCAGATCTCCTCAACGCGAAGGAGCAGTGTCATCCTCAG
* * *
1390407 ATAATCAGACTTCCTCAACGAGAAGGAACCATGTTGTCTCCAAATTATCCAAAAATAGCTAGACG
66 ACAATCAGACTTCCTCAACGCGAAGGAACCGTGTTGTCTCCAAATTATCCAAAAATAGCTAGACG
1390472 TCCTCAA
131 TCCTCAA
* * * *
1390479 CACA-AAAGAACAATGTCGTCCACCGACCAGATCTCTTCAATGCGAAGAAGCAGTGTCATCCTCA
1 CA-AGAAGGAACAATGTCGTCCACCGACCAGATCTCCTCAACGCGAAGGAGCAGTGTCATCCTCA
* * * * * *
1390543 GATAACCAGACTTCCTCAACACGGAGGAACTGTGTTGTCTCCAAATTACCCAAA
65 GACAATCAGACTTCCTCAACGCGAAGGAACCGTGTTGTCTCCAAATTATCCAAA
1390597 TACTTCTAGA
Statistics
Matches: 450, Mismatches: 77, Indels: 11
0.84 0.14 0.02
Matches are distributed among these distances:
137 233 0.52
138 1 0.00
139 208 0.46
140 3 0.01
141 5 0.01
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.23
Consensus pattern (137 bp):
CAAGAAGGAACAATGTCGTCCACCGACCAGATCTCCTCAACGCGAAGGAGCAGTGTCATCCTCAG
ACAATCAGACTTCCTCAACGCGAAGGAACCGTGTTGTCTCCAAATTATCCAAAAATAGCTAGACG
TCCTCAA
Found at i:1390444 original size:276 final size:274
Alignment explanation
Indices: 1389925--1390596 Score: 812
Period size: 276 Copynumber: 2.4 Consensus size: 274
1389915 AGTTTTACTT
* * * * *
1389925 ACCAAGAAGGAATAATGTCGTCCA-TCGACCAGATCTCCTCAATGCGAAGGAGTAATCTCATCCT
1 ACCAAAAAGGAACAATGTCGTCCACT-GACCAGATCTCCTCAATGCGAAAGAGTAGTGTCATCCT
* * * * *
1389989 CGGACAATCAGACTTCCTCAACGCGAAGGAACCATGTTGTCTCCAAATTATCTCCATATACGGCT
65 CAGAAAATCAGACTTCCTCAACGCGAAGGAACCGTGTTGTCTCCAAATTA--TCCAAAAACGGCT
* * * *
1390054 AGACATCCTCACTAAGAAGGAACAATGTCGTCCACCAACCAGATCTCCTCAACTCGAAGGAGCAG
128 AGACATCCTCACTAAGAAGGAAAAATATCGTCCACCAACCAGATCTCCTCAACGCAAAGGAGCAG
* * *
1390119 TGTCATCCTAAGACAATCAGACTTCCTCAATGTGAAGGAACCGTGTTGTCTCCAAATTATCTTCA
193 TGTCATCCTAAGACAATCAGACTTCCTCAACGAGAAGGAACCATGTTGTCTCCAAATTATC--CA
* *
1390184 AATATAGCTAGACTTCCCC
256 AAAATAGCTAGACGTCCCC
* * * * *
1390203 ACCAAAAAGGAACAATATCGTCCACTGACTATATCTCCTCAACGCGAAAGAGTAGTGTCATCCTT
1 ACCAAAAAGGAACAATGTCGTCCACTGACCAGATCTCCTCAATGCGAAAGAGTAGTGTCATCCTC
* * * *
1390268 AGAAAATCAGACTTCCTCAACGCAAAGGAACCGTGTTATCTCCAAACTATCCAAAAATGGCTAGA
66 AGAAAATCAGACTTCCTCAACGCGAAGGAACCGTGTTGTCTCCAAATTATCCAAAAACGGCTAGA
** * * * * *
1390333 TGTCCTCAAC-ACGAAGGAAAAATATCGTCCATCGACCAGATCTCCTTAACGCAAAGTAGCAGTG
131 CATCCTC-ACTAAGAAGGAAAAATATCGTCCACCAACCAGATCTCCTCAACGCAAAGGAGCAGTG
* *
1390397 TCATCCTTAGATAATCAGACTTCCTCAACGAGAAGGAACCATGTTGTCTCCAAATTATCCAAAAA
195 TCATCCTAAGACAATCAGACTTCCTCAACGAGAAGGAACCATGTTGTCTCCAAATTATCCAAAAA
*
1390462 TAGCTAGACGTCCTC
260 TAGCTAGACGTCCCC
* * * *
1390477 AACACAAAA-GAACAATGTCGTCCACCGACCAGATCTCTTCAATGCG-AAGAAGCAGTGTCATCC
1 ACCA-AAAAGGAACAATGTCGTCCACTGACCAGATCTCCTCAATGCGAAAG-AGTAGTGTCATCC
* * * * * *
1390540 TCAGATAACCAGACTTCCTCAACACGGAGGAACTGTGTTGTCTCCAAATTACCCAAA
64 TCAGAAAATCAGACTTCCTCAACGCGAAGGAACCGTGTTGTCTCCAAATTATCCAAA
1390597 TACTTCTAGA
Statistics
Matches: 334, Mismatches: 56, Indels: 12
0.83 0.14 0.03
Matches are distributed among these distances:
273 3 0.01
274 111 0.33
275 4 0.01
276 117 0.35
277 2 0.01
278 96 0.29
279 1 0.00
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.22
Consensus pattern (274 bp):
ACCAAAAAGGAACAATGTCGTCCACTGACCAGATCTCCTCAATGCGAAAGAGTAGTGTCATCCTC
AGAAAATCAGACTTCCTCAACGCGAAGGAACCGTGTTGTCTCCAAATTATCCAAAAACGGCTAGA
CATCCTCACTAAGAAGGAAAAATATCGTCCACCAACCAGATCTCCTCAACGCAAAGGAGCAGTGT
CATCCTAAGACAATCAGACTTCCTCAACGAGAAGGAACCATGTTGTCTCCAAATTATCCAAAAAT
AGCTAGACGTCCCC
Found at i:1390948 original size:122 final size:121
Alignment explanation
Indices: 1390686--1390950 Score: 386
Period size: 122 Copynumber: 2.2 Consensus size: 121
1390676 AAGCGGCCAT
* *
1390686 AACTCTTCAACGTGGATGAGTAGTGTTGTCTTCAACACCAAATTATATCAGATTGACCTGATTTC
1 AACTCTTCAACGTGGATGAGCAGAGTTGTCTTCAACACCAAATTATATCAGATTGACCTGATTTC
* * * *
1390751 CTCAACGAGAAGGAACATCGTCATCTTCAGCAAACAATTTACCTGAAAACAATCGG
66 CTCAACAAGAAGGAACAACGTCATCTTCAACAAACAATTTACCTGAAAACAATCAG
* * * * *
1390807 AACTCTTCAACATGGATGAGCAGAGTTGTGTTCAACACCATATTATCTCCAGATTGACTTGATTT
1 AACTCTTCAACGTGGATGAGCAGAGTTGTCTTCAACACCAAATTATAT-CAGATTGACCTGATTT
*
1390872 CCTCAACAAGAAGGAACAACGTCATCTTCAACAAACAATTTACCTGAAAGCAATCAG
65 CCTCAACAAGAAGGAACAACGTCATCTTCAACAAACAATTTACCTGAAAACAATCAG
* * *
1390929 ATCTCTTCAATGTGAATGAGCA
1 AACTCTTCAACGTGGATGAGCA
1390951 ATGTCATTTT
Statistics
Matches: 127, Mismatches: 16, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
121 42 0.33
122 85 0.67
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (121 bp):
AACTCTTCAACGTGGATGAGCAGAGTTGTCTTCAACACCAAATTATATCAGATTGACCTGATTTC
CTCAACAAGAAGGAACAACGTCATCTTCAACAAACAATTTACCTGAAAACAATCAG
Found at i:1393059 original size:21 final size:20
Alignment explanation
Indices: 1393030--1393070 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1393020 ACACTAACAT
* *
1393030 TTTATTTTTATTACATTTTTA
1 TTTAATTTTA-TACACTTTTA
1393051 TTTAATTTTATACACTTTTA
1 TTTAATTTTATACACTTTTA
1393071 AATTTATGCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTAATTTTATACACTTTTA
Found at i:1395665 original size:17 final size:17
Alignment explanation
Indices: 1395643--1395676 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1395633 TAATGGCAGA
1395643 GTCAACTGAACTTACTG
1 GTCAACTGAACTTACTG
1395660 GTCAACTGAACTTACTG
1 GTCAACTGAACTTACTG
1395677 CCATTCAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (17 bp):
GTCAACTGAACTTACTG
Found at i:1407966 original size:3 final size:3
Alignment explanation
Indices: 1407958--1407999 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
1407948 CCTGTAAATA
* *
1407958 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GAT AAT ATT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1408000 GTCGGGACGA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:1408057 original size:17 final size:17
Alignment explanation
Indices: 1408035--1408068 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1408025 AGATGAAAAA
* *
1408035 TAATTCTAAGTTGAATT
1 TAATTCAAAGTTAAATT
1408052 TAATTCAAAGTTAAATT
1 TAATTCAAAGTTAAATT
1408069 GTTTATTTGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (17 bp):
TAATTCAAAGTTAAATT
Found at i:1408516 original size:6 final size:6
Alignment explanation
Indices: 1408507--1408569 Score: 51
Period size: 6 Copynumber: 10.5 Consensus size: 6
1408497 AATAATATAT
* * *
1408507 TTAATA TTAATA TCAATA TTAAATA TATAAAA TTAA-A TTTAA-A ATAAT-
1 TTAATA TTAATA TTAATA TT-AATA T-TAATA TTAATA -TTAATA TTAATA
1408555 TTAATA TTAATA TTA
1 TTAATA TTAATA TTA
1408570 TTTAGTATAG
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
5 8 0.17
6 29 0.62
7 9 0.19
8 1 0.02
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (6 bp):
TTAATA
Found at i:1414884 original size:25 final size:24
Alignment explanation
Indices: 1414827--1414892 Score: 66
Period size: 25 Copynumber: 2.8 Consensus size: 24
1414817 GGTTTTGAAA
* *
1414827 ATATA-ATATATATTATATAATAT
1 ATATATATATATATTTTTTAATAT
*
1414850 -T-TATAAATATATTGTTTTAATAT
1 ATATATATATATATT-TTTTAATAT
1414873 ATATATATATATATTATTTT
1 ATATATATATATATT-TTTT
1414893 CTTCTTTTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
21 2 0.06
22 9 0.26
23 7 0.21
24 1 0.03
25 15 0.44
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (24 bp):
ATATATATATATATTTTTTAATAT
Found at i:1417163 original size:12 final size:13
Alignment explanation
Indices: 1417136--1417170 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1417126 TTTCACTAAC
1417136 TTTTTTCTTTTCA
1 TTTTTTCTTTTCA
1417149 TTTTTTCTTTT-A
1 TTTTTTCTTTTCA
1417161 -TTTTTCTTTT
1 TTTTTTCTTTT
1417171 TATTATTTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 10 0.45
12 1 0.05
13 11 0.50
ACGTcount: A:0.06, C:0.11, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTTTCTTTTCA
Found at i:1417171 original size:12 final size:12
Alignment explanation
Indices: 1417137--1417174 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1417127 TTCACTAACT
*
1417137 TTTTTCTTTTCA
1 TTTTTCTTTTTA
1417149 TTTTT-TCTTTTA
1 TTTTTCT-TTTTA
1417161 TTTTTCTTTTTA
1 TTTTTCTTTTTA
1417173 TT
1 TT
1417175 ATTTGCATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
11 1 0.04
12 21 0.91
13 1 0.04
ACGTcount: A:0.08, C:0.11, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTTCTTTTTA
Found at i:1421300 original size:21 final size:20
Alignment explanation
Indices: 1421276--1421315 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1421266 TTAACCTTTA
* *
1421276 AATTTTATTTCTTTTCTTTTC
1 AATTTAATTT-TTTTATTTTC
1421297 AATTTAATTTTTTTATTTT
1 AATTTAATTTTTTTATTTT
1421316 GTTTTTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.72
Consensus pattern (20 bp):
AATTTAATTTTTTTATTTTC
Found at i:1423575 original size:25 final size:23
Alignment explanation
Indices: 1423521--1423577 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 23
1423511 AAATTATATT
*
1423521 AAATTTGTGTAATTTAAATTATG
1 AAATTTGTGTAATTAAAATTATG
*
1423544 AATATTTGTTTAATTAATAATTATTG
1 AA-ATTTGTGTAATTAA-AATTA-TG
*
1423570 TAATTTGT
1 AAATTTGT
1423578 AAATTTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
23 2 0.07
24 12 0.43
25 11 0.39
26 3 0.11
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.53
Consensus pattern (23 bp):
AAATTTGTGTAATTAAAATTATG
Found at i:1431459 original size:20 final size:20
Alignment explanation
Indices: 1431426--1431465 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1431416 CCCATCAGAT
1431426 TGTACATACATACATACATA
1 TGTACATACATACATACATA
* *
1431446 TGTACGTACGTACATACATA
1 TGTACATACATACATACATA
1431466 CATAGGGACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.30
Consensus pattern (20 bp):
TGTACATACATACATACATA
Found at i:1434005 original size:59 final size:57
Alignment explanation
Indices: 1433942--1434072 Score: 142
Period size: 59 Copynumber: 2.2 Consensus size: 57
1433932 ATTTTGATTG
*
1433942 CATCCTAAACTATGGCTACCAGTCTAAATTAGT-TCTCAAA-CTTTTGAATATTCCAATTT
1 CATCCTAAACTAT-G--ACCAGTCTAAATTAGTCTC-CAAATCTTTTGAACATTCCAATTT
* * *
1434001 CATCCCCCAAACTATGACCATTCTAAATTAGTCTCCAAATTTTTTGAACATTCCAATTT
1 CAT--CCTAAACTATGACCAGTCTAAATTAGTCTCCAAATCTTTTGAACATTCCAATTT
1434060 CAT-CTCAAACTAT
1 CATCCT-AAACTAT
1434073 ACGTATATAC
Statistics
Matches: 62, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
56 1 0.02
57 7 0.11
58 19 0.31
59 25 0.40
60 1 0.02
61 9 0.15
ACGTcount: A:0.33, C:0.25, G:0.06, T:0.36
Consensus pattern (57 bp):
CATCCTAAACTATGACCAGTCTAAATTAGTCTCCAAATCTTTTGAACATTCCAATTT
Found at i:1434321 original size:60 final size:60
Alignment explanation
Indices: 1434195--1434323 Score: 152
Period size: 60 Copynumber: 2.1 Consensus size: 60
1434185 TATTTGAATG
* ** * * * *
1434195 AATTTGGATATGAAATTAGAATGTTCAAAAGTTTAAGGACTGATTTAGAATAAGAGTCAT
1 AATTTGGAGATGAAATTAGAATACTCAAAAGTTTAAGGACTAAATTAAAATAAGACTCAT
* * *
1434255 AGTTTGGGGATGAAATTAGAATACTCAAAAGTTTAAGGACTAAATTAAAATGAGAACT-AT
1 AATTTGGAGATGAAATTAGAATACTCAAAAGTTTAAGGACTAAATTAAAATAAG-ACTCAT
1434315 AATTTGGAG
1 AATTTGGAG
1434324 GCATATGATG
Statistics
Matches: 56, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
60 54 0.96
61 2 0.04
ACGTcount: A:0.43, C:0.05, G:0.21, T:0.31
Consensus pattern (60 bp):
AATTTGGAGATGAAATTAGAATACTCAAAAGTTTAAGGACTAAATTAAAATAAGACTCAT
Found at i:1435850 original size:25 final size:26
Alignment explanation
Indices: 1435803--1435852 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
1435793 GAAGATGAAA
*
1435803 TTATAAAATTTTAAGAAGTGACAAAT
1 TTATAAAATTTTAAGAAGAGACAAAT
1435829 TTATAAAATTTTAAG-AGAGACAAA
1 TTATAAAATTTTAAGAAGAGACAAA
1435853 AATAAATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 8 0.35
26 15 0.65
ACGTcount: A:0.52, C:0.04, G:0.12, T:0.32
Consensus pattern (26 bp):
TTATAAAATTTTAAGAAGAGACAAAT
Found at i:1448187 original size:117 final size:117
Alignment explanation
Indices: 1447965--1448187 Score: 254
Period size: 117 Copynumber: 1.9 Consensus size: 117
1447955 ATCTTTCAAA
* * * *
1447965 TTGAAATTTTCTTTTTCAATACTTTCAAATTTCATTTTTGAGAGTTATAAATCCTTCTTCAAGAT
1 TTGAAAATTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTATAAATCCTTCTTCAACAT
* * *
1448030 TTCATTTTGATTTTCAAAATCCATTTTCATTTTTAGAAGAAGTTTGTTTAAT
66 TTCATTTTGATTTTCAAAATCCATTTTCACTTTCAAAAGAAGTTTGTTTAAT
* * * * *
1448082 TTGAAAATTTCTTTTTCAA-AGTTTTCAGATTTTATTTTTGAAAGCTCTAACTCCTT-TCTCAAC
1 TTGAAAATTTCTTTTTCAATA-CTTTCAAATTTCATTTTTGAAAGCTATAAATCCTTCT-TCAAC
* * **
1448145 ATTTCATTTTGATTTTCCAATTCTGTTTT-AGCTTTCAAAAGAA
64 ATTTCATTTTGATTTTCAAAATCCATTTTCA-CTTTCAAAAGAA
1448188 TATCATTTTT
Statistics
Matches: 87, Mismatches: 16, Indels: 6
0.80 0.15 0.06
Matches are distributed among these distances:
116 3 0.03
117 84 0.97
ACGTcount: A:0.28, C:0.14, G:0.09, T:0.49
Consensus pattern (117 bp):
TTGAAAATTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTATAAATCCTTCTTCAACAT
TTCATTTTGATTTTCAAAATCCATTTTCACTTTCAAAAGAAGTTTGTTTAAT
Found at i:1450969 original size:2 final size:2
Alignment explanation
Indices: 1450962--1450989 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1450952 CAATTTTGTA
1450962 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
1450990 TTATGAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1451197 original size:18 final size:19
Alignment explanation
Indices: 1451174--1451216 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
1451164 CAGTAATCCT
1451174 ATTCCCA-GGTAATCTTAC
1 ATTCCCATGGTAATCTTAC
*
1451192 ATTCCCATTGGTAATCTTAT
1 ATTCCCA-TGGTAATCTTAC
1451212 ATTCC
1 ATTCC
1451217 GTGAACCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.32
20 15 0.68
ACGTcount: A:0.26, C:0.26, G:0.09, T:0.40
Consensus pattern (19 bp):
ATTCCCATGGTAATCTTAC
Found at i:1452603 original size:60 final size:60
Alignment explanation
Indices: 1452478--1452662 Score: 210
Period size: 60 Copynumber: 3.1 Consensus size: 60
1452468 TGGATGAATA
* * * * * *
1452478 TGGGGATGAAATTGGAATATTCAAAAG-TTCAGTACTAATTTAGAAAGAGGGTCATGGTT
1 TGGGGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAGAATGAGAGTCATAGTT
* * * *
1452537 TAGGGATGAAATTAGAATGTTCAAAAGTTTTAGGGCTAATTTAGAATGAGAGTCATAGTT
1 TGGGGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAGAATGAGAGTCATAGTT
* * * * * * *
1452597 TGGGGATGAAATTTGAATATTCAAAAGTGTAAAGACTAATCTAAAATGAAAGTTATAGTT
1 TGGGGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAGAATGAGAGTCATAGTT
1452657 TGGGGA
1 TGGGGA
1452663 CATATGATGC
Statistics
Matches: 105, Mismatches: 20, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
59 24 0.23
60 81 0.77
ACGTcount: A:0.38, C:0.05, G:0.25, T:0.31
Consensus pattern (60 bp):
TGGGGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAGAATGAGAGTCATAGTT
Found at i:1453716 original size:64 final size:64
Alignment explanation
Indices: 1453602--1453725 Score: 151
Period size: 64 Copynumber: 1.9 Consensus size: 64
1453592 AGAAAGTTTA
* * * *
1453602 TTCATTTCAATAAAAAAATATCAATTTAATTTATGACGGAACAATGATTCCGTCGAAAATTTTG
1 TTCATTTCAATAAAAAAATACCAATTTAAATTATGACGGAACAATCATTCCATCGAAAATTTTG
* * * * *
1453666 TTCACTTT-AATAAAAATATACCAATTTAAATTGTGATGGAATAATCATTCCATCGGAAAT
1 TTCA-TTTCAATAAAAAAATACCAATTTAAATTATGACGGAACAATCATTCCATCGAAAAT
1453726 AACAAAATAA
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
64 47 0.94
65 3 0.06
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.35
Consensus pattern (64 bp):
TTCATTTCAATAAAAAAATACCAATTTAAATTATGACGGAACAATCATTCCATCGAAAATTTTG
Found at i:1453833 original size:27 final size:27
Alignment explanation
Indices: 1453762--1453825 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
1453752 CGGTAAACAA
1453762 TTATATTTATATGTATTTATCCTTTGCTT
1 TTAT-TTTATATGTATTTATCCTTT-CTT
*
1453791 TT-TTTTATATGCATTTAT-CTTT-TT
1 TTATTTTATATGTATTTATCCTTTCTT
1453815 TTATTTTATAT
1 TTATTTTATAT
1453826 TGTAATTTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
24 4 0.12
25 8 0.24
26 4 0.12
27 14 0.42
28 1 0.03
29 2 0.06
ACGTcount: A:0.20, C:0.08, G:0.05, T:0.67
Consensus pattern (27 bp):
TTATTTTATATGTATTTATCCTTTCTT
Found at i:1454557 original size:88 final size:89
Alignment explanation
Indices: 1454397--1454573 Score: 293
Period size: 88 Copynumber: 2.0 Consensus size: 89
1454387 AAATATTATT
* *
1454397 TTTAGAAAAATGTATTTTAAATTTGTGACGGAATTTATGGTCCCGTCACAAATTTATGACAGATC
1 TTTAGAAAAATGTATTTTAAATTTGTGACGGAATTTATGGACCCGTCACAAATTTATGACAAATC
* *
1454462 CACCTATTTCGTCACAAATTTGTG
66 CACCTATTCCGTCAAAAATTTGTG
* *
1454486 TTTAGAAAAA-GTATTTTAAATTTGTGACGGAATTTGTGGACCCGTCACAAATTTCTGACAAATC
1 TTTAGAAAAATGTATTTTAAATTTGTGACGGAATTTATGGACCCGTCACAAATTTATGACAAATC
1454550 CACCTATTCCGTCAAAAATTTGTG
66 CACCTATTCCGTCAAAAATTTGTG
1454574 ATGGGTCCAC
Statistics
Matches: 82, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
88 72 0.88
89 10 0.12
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (89 bp):
TTTAGAAAAATGTATTTTAAATTTGTGACGGAATTTATGGACCCGTCACAAATTTATGACAAATC
CACCTATTCCGTCAAAAATTTGTG
Found at i:1455368 original size:15 final size:16
Alignment explanation
Indices: 1455335--1455370 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
1455325 ATTTTTTTAA
1455335 ATTAA-TGTAATTATT
1 ATTAATTGTAATTATT
1455350 -TTAATTGT-ATTATT
1 ATTAATTGTAATTATT
1455364 ATTAATT
1 ATTAATT
1455371 TTTGGCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 10 0.53
15 9 0.47
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (16 bp):
ATTAATTGTAATTATT
Found at i:1461216 original size:60 final size:59
Alignment explanation
Indices: 1461142--1461257 Score: 153
Period size: 60 Copynumber: 1.9 Consensus size: 59
1461132 TATTTGGATG
* * * *
1461142 ACCATTTTGTAACTTGTAAT-AGTCGAGGGACTCAATAAAGCAACATCCTAGAGTCGGAGA
1 ACCATTTTGTAACTTGTAATAACT-AAGAGACTCAATAAAGAAACA-CCTAGAGTCGGAGA
* *
1461202 ACCATTTTGTAACTTTTAATAACTAAGAGACTCAATAAAGAAACACCTATAGTCGG
1 ACCATTTTGTAACTTGTAATAACTAAGAGACTCAATAAAGAAACACCTAGAGTCGG
1461258 GGGATCATTT
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
59 10 0.20
60 37 0.76
61 2 0.04
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (59 bp):
ACCATTTTGTAACTTGTAATAACTAAGAGACTCAATAAAGAAACACCTAGAGTCGGAGA
Found at i:1465032 original size:21 final size:21
Alignment explanation
Indices: 1465004--1465059 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
1464994 TGTGCAGGGT
1465004 GTACCGGTACACTATGAATGG
1 GTACCGGTACACTATGAATGG
*
1465025 GTATCGGTACACTATGAATGG
1 GTACCGGTACACTATGAATGG
*
1465046 GTACCGATACACTA
1 GTACCGGTACACTA
1465060 AGACCAATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (21 bp):
GTACCGGTACACTATGAATGG
Found at i:1465174 original size:19 final size:19
Alignment explanation
Indices: 1465150--1465200 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
1465140 AATGTAATTT
*
1465150 GTGTACTGATACATAGGCA
1 GTGTACCGATACATAGGCA
1465169 GTGTACCGATACATAGGCA
1 GTGTACCGATACATAGGCA
1465188 GTGTACCGATACA
1 GTGTACCGATACA
1465201 CTAGTGAAGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.24
Consensus pattern (19 bp):
GTGTACCGATACATAGGCA
Found at i:1470754 original size:16 final size:17
Alignment explanation
Indices: 1470728--1470760 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1470718 TTGCACATGC
*
1470728 ATCACAATTTTATCTTT
1 ATCACAATTTTAGCTTT
1470745 ATCA-AATTTTAGCTTT
1 ATCACAATTTTAGCTTT
1470761 GACAACCTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.30, C:0.15, G:0.03, T:0.52
Consensus pattern (17 bp):
ATCACAATTTTAGCTTT
Found at i:1471734 original size:21 final size:21
Alignment explanation
Indices: 1471697--1471736 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1471687 TCGGTTTTCA
*
1471697 ATTTTGAAATATCTTTCTTGT
1 ATTTTGAAATATATTTCTTGT
1471718 ATTTTGAAA-ATAATTTCTT
1 ATTTTGAAATAT-ATTTCTT
1471737 ATAATCCGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.55
Consensus pattern (21 bp):
ATTTTGAAATATATTTCTTGT
Found at i:1478657 original size:16 final size:15
Alignment explanation
Indices: 1478624--1478662 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1478614 ACTAAATTTT
*
1478624 TATGATTTTTTTAAA
1 TATGATTTGTTTAAA
*
1478639 TATGATATTGTTTATA
1 TATGAT-TTGTTTAAA
1478655 TATGATTT
1 TATGATTT
1478663 TTAAATGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.31, C:0.00, G:0.10, T:0.59
Consensus pattern (15 bp):
TATGATTTGTTTAAA
Found at i:1479393 original size:23 final size:23
Alignment explanation
Indices: 1479366--1479432 Score: 80
Period size: 23 Copynumber: 2.8 Consensus size: 23
1479356 TATTTTTACC
**
1479366 CTCTAAAATTTTATAAATTCGTT
1 CTCTAAAATTTTATAAATTCACT
*
1479389 CTCTAAAATTTTATAAGTTCACT
1 CTCTAAAATTTTATAAATTCACT
*
1479412 CATCCTGAAATTTTATAAATT
1 C-T-CTAAAATTTTATAAATT
1479433 TATCTCTTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 21 0.57
24 1 0.03
25 15 0.41
ACGTcount: A:0.36, C:0.15, G:0.04, T:0.45
Consensus pattern (23 bp):
CTCTAAAATTTTATAAATTCACT
Found at i:1480954 original size:2 final size:2
Alignment explanation
Indices: 1480949--1480974 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1480939 GTGGAGGTTA
1480949 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
1480975 TAAATAACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1485550 original size:15 final size:16
Alignment explanation
Indices: 1485530--1485560 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1485520 ATTTAATATA
1485530 AAACCTAAA-TAACCT
1 AAACCTAAACTAACCT
1485545 AAACCTAAACTAACCT
1 AAACCTAAACTAACCT
1485561 CACGTAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.52, C:0.29, G:0.00, T:0.19
Consensus pattern (16 bp):
AAACCTAAACTAACCT
Found at i:1487124 original size:55 final size:54
Alignment explanation
Indices: 1487064--1487359 Score: 254
Period size: 55 Copynumber: 5.5 Consensus size: 54
1487054 GATGAGCCCA
* *
1487064 CTCCCTATTCCTTCAGGAAGTATAAGACTCAAACAATCTTCAGCAAATGTGTCTG
1 CTCCCTATTCCTTCAGGAAGTATAAGACTC-AACAATCTTCAACAAACGTGTCTG
* ** * *
1487119 GTCCCTATTTGTTCAGGGAGTATAAGACTCGAACAATCTTCATACAACAAGT-TC-G
1 CTCCCTATTCCTTCAGGAAGTATAAGACTC-AACAATCTTCA-ACAA-ACGTGTCTG
* * ** *
1487174 CTCCCTATTCGTTCAGGGAGTAT-AGAACTCGAACAATCTTCAGTAAATGTGTCTG
1 CTCCCTATTCCTTCAGGAAGTATAAG-ACTC-AACAATCTTCAACAAACGTGTCTG
* * * * * * *
1487229 CTCCCTAATCGTTTAGGGAGCATAAGACTC--GAA-CTTCAACAAACGTGTCCG
1 CTCCCTATTCCTTCAGGAAGTATAAGACTCAACAATCTTCAACAAACGTGTCTG
*
1487280 CTCCCTATTCCTTCA-GAGAGTATAGGACT---CAATCTTCAACAAACGTGTCTG
1 CTCCCTATTCCTTCAGGA-AGTATAAGACTCAACAATCTTCAACAAACGTGTCTG
*
1487331 CTCCCTATTTCTTCA-GAGAGTATAAGACT
1 CTCCCTATTCCTTCAGGA-AGTATAAGACT
1487360 TTATCTTCAT
Statistics
Matches: 203, Mismatches: 30, Indels: 20
0.80 0.12 0.08
Matches are distributed among these distances:
50 3 0.01
51 79 0.39
52 2 0.01
53 3 0.01
54 6 0.03
55 100 0.49
56 7 0.03
57 3 0.01
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (54 bp):
CTCCCTATTCCTTCAGGAAGTATAAGACTCAACAATCTTCAACAAACGTGTCTG
Found at i:1487209 original size:110 final size:105
Alignment explanation
Indices: 1487064--1487359 Score: 334
Period size: 110 Copynumber: 2.8 Consensus size: 105
1487054 GATGAGCCCA
* *
1487064 CTCCCTATTCCTTCAGGAAGTATA-AGACTCAAACAATCTTCAGCAAATGTGTCTGGTCCCTATT
1 CTCCCTATTCCTTCAGGGAGTATAGA-ACTC-AACAATCTTCAGCAAATGTGTCTGCTCCCTATT
1487128 TGTTCAGGGAGTATAAGACTCGAACAATCTTCATACAACAAGT-T-CG
64 TGTTCAGGGAGTATAAGACTCG---AA-CTTCA-ACAA-AAGTGTCCG
* * * *
1487174 CTCCCTATTCGTTCAGGGAGTATAGAACTCGAACAATCTTCAGTAAATGTGTCTGCTCCCTAATC
1 CTCCCTATTCCTTCAGGGAGTATAGAACTC-AACAATCTTCAGCAAATGTGTCTGCTCCCTATTT
* * *
1487239 GTTTAGGGAGCATAAGACTCGAACTTCAACAAACGTGTCCG
65 GTTCAGGGAGTATAAGACTCGAACTTCAACAAAAGTGTCCG
* * * * *
1487280 CTCCCTATTCCTTCAGAGAGTATAGGACT---CAATCTTCAACAAACGTGTCTGCTCCCTATTTC
1 CTCCCTATTCCTTCAGGGAGTATAGAACTCAACAATCTTCAGCAAATGTGTCTGCTCCCTATTTG
*
1487342 TTCAGAGAGTATAAGACT
66 TTCAGGGAGTATAAGACT
1487360 TTATCTTCAT
Statistics
Matches: 161, Mismatches: 22, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
102 42 0.26
104 3 0.02
105 5 0.03
106 33 0.20
107 2 0.01
110 75 0.47
111 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (105 bp):
CTCCCTATTCCTTCAGGGAGTATAGAACTCAACAATCTTCAGCAAATGTGTCTGCTCCCTATTTG
TTCAGGGAGTATAAGACTCGAACTTCAACAAAAGTGTCCG
Found at i:1487461 original size:37 final size:37
Alignment explanation
Indices: 1487383--1487488 Score: 133
Period size: 37 Copynumber: 2.9 Consensus size: 37
1487373 ATGAGTTTGC
* * *
1487383 TTCACTACTCTTCCATGAAGGCTTATAGATT-ATTTGC
1 TTCACTACTCTTCCGTGAAGGCTTA-AGATTGAATTGA
*
1487420 TTCACTACTCTTCCGTGAAGGCTTAACATTGAATTGA
1 TTCACTACTCTTCCGTGAAGGCTTAAGATTGAATTGA
* * *
1487457 TTCACTGCTCTTTCGTGAATGCTTAAGATTGA
1 TTCACTACTCTTCCGTGAAGGCTTAAGATTGA
1487489 CTCGTTTCGA
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
36 4 0.07
37 56 0.93
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.39
Consensus pattern (37 bp):
TTCACTACTCTTCCGTGAAGGCTTAAGATTGAATTGA
Found at i:1488766 original size:40 final size:40
Alignment explanation
Indices: 1488722--1488805 Score: 100
Period size: 40 Copynumber: 2.1 Consensus size: 40
1488712 ATTTTTCTTC
*
1488722 CATTTTCC--CATATTCCCATTTTTCTCTCTTTTTTCCTTTT
1 CATTTTCCATCAT-TTCCCATTTTTCTC-ATTTTTTCCTTTT
* **
1488762 CATTTTTCATCATTTTTCATTTTTCTCATTTTTTCCTTTT
1 CATTTTCCATCATTTCCCATTTTTCTCATTTTTTCCTTTT
1488802 CATT
1 CATT
1488806 CCTTTTTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
40 23 0.61
41 12 0.32
42 3 0.08
ACGTcount: A:0.12, C:0.25, G:0.00, T:0.63
Consensus pattern (40 bp):
CATTTTCCATCATTTCCCATTTTTCTCATTTTTTCCTTTT
Found at i:1488769 original size:41 final size:40
Alignment explanation
Indices: 1488724--1488805 Score: 103
Period size: 41 Copynumber: 2.0 Consensus size: 40
1488714 TTTTCTTCCA
*
1488724 TTTTC-CCATATTCCCATTTTTCTCTCTTTTTTCCTTTTCAT
1 TTTTCACCAT-TTCCCATTTTTCTC-ATTTTTTCCTTTTCAT
* **
1488765 TTTTCATCATTTTTCATTTTTCTCATTTTTTCCTTTTCAT
1 TTTTCACCATTTCCCATTTTTCTCATTTTTTCCTTTTCAT
1488805 T
1 T
1488806 CCTTTTTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
40 16 0.44
41 17 0.47
42 3 0.08
ACGTcount: A:0.11, C:0.24, G:0.00, T:0.65
Consensus pattern (40 bp):
TTTTCACCATTTCCCATTTTTCTCATTTTTTCCTTTTCAT
Found at i:1488784 original size:16 final size:18
Alignment explanation
Indices: 1488758--1488801 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
1488748 TCTTTTTTCC
1488758 TTTTCATTTTTCATCA-T
1 TTTTCATTTTTCATCATT
1488775 TTTTCATTTTTC-TCATT
1 TTTTCATTTTTCATCATT
*
1488792 TTTTCCTTTT
1 TTTTCATTTT
1488802 CATTCCTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 3 0.12
17 22 0.88
ACGTcount: A:0.11, C:0.18, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTTCATTTTTCATCATT
Found at i:1488792 original size:50 final size:50
Alignment explanation
Indices: 1488673--1488811 Score: 151
Period size: 50 Copynumber: 2.7 Consensus size: 50
1488663 CTTTTTACTT
* *
1488673 ATTTTTCTTTTTTCATCATTTTTTCCTTTTTT-CTTTTACATTTTTCTTCC
1 ATTTTTCATTTTTC-TCATTTTTTCCTTTTTTCCTTTTACATTTTTCATCC
* * *
1488723 ATTTTCCCA-TATTCCCATTTTTCTCTCTTTTTTCCTTTT-CATTTTTCAT-C
1 ATTTT-TCATTTTTCTCATTTTT-TC-CTTTTTTCCTTTTACATTTTTCATCC
1488773 ATTTTTCATTTTTCTCATTTTTTCCTTTTCATTCCTTTT
1 ATTTTTCATTTTTCTCATTTTTTCCTTTT--TTCCTTTT
1488812 TTTTATTTCA
Statistics
Matches: 74, Mismatches: 8, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
48 5 0.07
49 11 0.15
50 36 0.49
51 17 0.23
52 5 0.07
ACGTcount: A:0.11, C:0.23, G:0.00, T:0.66
Consensus pattern (50 bp):
ATTTTTCATTTTTCTCATTTTTTCCTTTTTTCCTTTTACATTTTTCATCC
Found at i:1488796 original size:17 final size:17
Alignment explanation
Indices: 1488758--1488794 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
1488748 TCTTTTTTCC
1488758 TTTTCATTTTTCATCAT
1 TTTTCATTTTTCATCAT
1488775 TTTTCATTTTTC-TCAT
1 TTTTCATTTTTCATCAT
1488791 TTTT
1 TTTT
1488795 TCCTTTTCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTTCATTTTTCATCAT
Found at i:1494044 original size:38 final size:38
Alignment explanation
Indices: 1493993--1494069 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
1493983 GGAGGTGTAA
* *
1493993 TAACCACTTTCGGAGCTACCTTTTCAGCCAATTGATTC
1 TAACCACTTTCGGAGCTACCTTTTCAACCAATCGATTC
1494031 TAACCACTTTCGGAGCTACCTTTTCAACCAATCGATTC
1 TAACCACTTTCGGAGCTACCTTTTCAACCAATCGATTC
1494069 T
1 T
1494070 TGGGAGTAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.25, C:0.30, G:0.12, T:0.34
Consensus pattern (38 bp):
TAACCACTTTCGGAGCTACCTTTTCAACCAATCGATTC
Found at i:1500418 original size:15 final size:16
Alignment explanation
Indices: 1500398--1500428 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1500388 ATTTAATATA
1500398 AAACCTAAA-TAACCT
1 AAACCTAAACTAACCT
1500413 AAACCTAAACTAACCT
1 AAACCTAAACTAACCT
1500429 CACGCAGGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.52, C:0.29, G:0.00, T:0.19
Consensus pattern (16 bp):
AAACCTAAACTAACCT
Found at i:1505081 original size:177 final size:177
Alignment explanation
Indices: 1504773--1505096 Score: 477
Period size: 177 Copynumber: 1.8 Consensus size: 177
1504763 AAAGTAGACA
* * *
1504773 TGTATCAATACCTTTATAAGTATATGTATAAAAGTATCGAAACTTTAGTAATTTAAAAGAATTGA
1 TGTATCAATACATTTATAAGTATATGTACAAAAGTATCGAAACTTTAGAAATTTAAAAGAATTGA
* * * *
1504838 AACAAAAGCGCCTATAAAGTATCGATATCTTACACATATGTATCGATACATGACAATATAACATG
66 AACAAAAGCGCCTAAAAAGTATCGATACCTTACACACATATATCGATACATGACAATATAACATG
** *
1504903 TTGCAATTTGACAAAACCGGTAAAGAGCAACTGGAATTGTTGAAATT
131 TTAAAAATTGACAAAACCGGTAAAGAGCAACTGGAATTGTTGAAATT
* * * * *
1504950 TGTATCGATACATTTATAAGTATATGTACCAAAGTATTGATACTTTAGAAATTTAAAAGAATTGC
1 TGTATCAATACATTTATAAGTATATGTACAAAAGTATCGAAACTTTAGAAATTTAAAAGAATTGA
* * * *
1505015 AATAATAGCGTCTAAAAAGTATCGATACCTTAGACACATATATCGATACATGACAATATAACATG
66 AACAAAAGCGCCTAAAAAGTATCGATACCTTACACACATATATCGATACATGACAATATAACATG
1505080 TTAAAAATTGACAAAAC
131 TTAAAAATTGACAAAAC
1505097 TGGTTTCAAT
Statistics
Matches: 128, Mismatches: 19, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
177 128 1.00
ACGTcount: A:0.43, C:0.13, G:0.14, T:0.31
Consensus pattern (177 bp):
TGTATCAATACATTTATAAGTATATGTACAAAAGTATCGAAACTTTAGAAATTTAAAAGAATTGA
AACAAAAGCGCCTAAAAAGTATCGATACCTTACACACATATATCGATACATGACAATATAACATG
TTAAAAATTGACAAAACCGGTAAAGAGCAACTGGAATTGTTGAAATT
Found at i:1505249 original size:197 final size:197
Alignment explanation
Indices: 1504906--1505297 Score: 579
Period size: 197 Copynumber: 2.0 Consensus size: 197
1504896 TAACATGTTG
** *
1504906 CAATTTGACAAAACCGGTAAAGAGCAACTGGAATTGTTGAAATTTGTATCGATACATTTATAAGT
1 CAATTTGACAAAACCGGTAAAGAGCAACTAAAATGGTTGAAATTTGTATCGATACATTTATAAGT
* * *
1504971 ATATGTACCAAAGTATTGATACTTTAGAAATTTAAAAGAATTGCAATAATAGCGTCTAAAAAGTA
66 ATATGTACCAAAGTATCGATACTTTAGAAATTTAAAAGAATTACAATAATAGCGCCTAAAAAGTA
* *
1505036 TCGATACCTTAGACACATATATCGATACATGACAATATAACATGTTAAAAATTGACAAAACTGGT
131 TCAATACCTCAGACACATATATCGATACATGACAATATAACATGTTAAAAATTGACAAAACTGGT
1505101 TT
196 TT
* **
1505103 CAATTTGACAAAACCGGTAAAGAGCTA-TCAAAATGGTTGAAATTTGTATCGATATTTTTATAAG
1 CAATTTGACAAAACCGGTAAAGAGCAACT-AAAATGGTTGAAATTTGTATCGATACATTTATAAG
* * * * *
1505167 TATATGTACCAAAGTGTCGGTACTTTAGGAATTTAAAAGATTTACAATAATAGCGCCTATAAAGT
65 TATATGTACCAAAGTATCGATACTTTAGAAATTTAAAAGAATTACAATAATAGCGCCTAAAAAGT
* * * * *
1505232 ATCAATACCTCAGACACATGTATCGATATATGACAATATAGCATGTTGAAATTTGACAAAACTGG
130 ATCAATACCTCAGACACATATATCGATACATGACAATATAACATGTTAAAAATTGACAAAACTGG
1505297 T
195 T
1505298 AAAGCGTTAC
Statistics
Matches: 173, Mismatches: 21, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
196 1 0.01
197 172 0.99
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.31
Consensus pattern (197 bp):
CAATTTGACAAAACCGGTAAAGAGCAACTAAAATGGTTGAAATTTGTATCGATACATTTATAAGT
ATATGTACCAAAGTATCGATACTTTAGAAATTTAAAAGAATTACAATAATAGCGCCTAAAAAGTA
TCAATACCTCAGACACATATATCGATACATGACAATATAACATGTTAAAAATTGACAAAACTGGT
TT
Found at i:1506645 original size:117 final size:114
Alignment explanation
Indices: 1506482--1506712 Score: 410
Period size: 117 Copynumber: 2.0 Consensus size: 114
1506472 TGTAAATAAG
*
1506482 TGATAAACGATATATCAAACACTAACATTAATTTTTAAAAATGTAGGAAATGTCGAAAATGTGTA
1 TGATAAACGATATATAAAACACTAACATTAATTTTTAAAAATGTAGGAAATGTCGAAAATGTGTA
1506547 GCATCAAAAG-GTGAACTACATAATTGAACACTTGAAAGAGAAGAACAA
66 GCATCAAAAGAGTGAACTACATAATTGAACACTTGAAAGAGAAGAACAA
1506595 TGATAAACGATATATAAAAACACTAACATTAATATTTTTAAAAAATGTAGGAAATGTCGAAAATG
1 TGATAAACGATATAT-AAAACACTAACATT-A-ATTTTT-AAAAATGTAGGAAATGTCGAAAATG
1506660 TGTAGCATCAAAAGAGTGAACTACATAATTGAACACTTGAAAGAGAAGAACAA
62 TGTAGCATCAAAAGAGTGAACTACATAATTGAACACTTGAAAGAGAAGAACAA
1506713 AGTACATGTG
Statistics
Matches: 112, Mismatches: 1, Indels: 5
0.95 0.01 0.04
Matches are distributed among these distances:
113 15 0.13
114 13 0.12
115 1 0.01
116 6 0.05
117 39 0.35
118 38 0.34
ACGTcount: A:0.49, C:0.11, G:0.16, T:0.25
Consensus pattern (114 bp):
TGATAAACGATATATAAAACACTAACATTAATTTTTAAAAATGTAGGAAATGTCGAAAATGTGTA
GCATCAAAAGAGTGAACTACATAATTGAACACTTGAAAGAGAAGAACAA
Found at i:1507422 original size:72 final size:73
Alignment explanation
Indices: 1507338--1507498 Score: 204
Period size: 72 Copynumber: 2.2 Consensus size: 73
1507328 CTTAACCAGT
* * * *
1507338 TAAAATAAAATAGGCGATACCTATTCCGTT-AATCACCTACCAATTTGTTTAAAGG-TATTAATA
1 TAAAATAAAATAGGCGATACCTATTACATTAAAT-ACCTACC-AGTTGTTTAAAGGTTACTAATA
*
1507401 ATAT-AATGG
64 ATATAAACGG
*
1507410 TAAAATAAAATAGGCGCTACCTATTACATTAAAATACCTACCAGTTGTTTAAAGGTTACTAATAA
1 TAAAATAAAATAGGCGATACCTATTACATT-AAATACCTACCAGTTGTTTAAAGGTTACTAATAA
*
1507475 TGTAAACGG
65 TATAAACGG
1507484 TAAAAT-AAATAGGCG
1 TAAAATAAAATAGGCG
1507499 TAAATGCCAA
Statistics
Matches: 78, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
72 39 0.50
73 26 0.33
74 13 0.17
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (73 bp):
TAAAATAAAATAGGCGATACCTATTACATTAAATACCTACCAGTTGTTTAAAGGTTACTAATAAT
ATAAACGG
Found at i:1507780 original size:194 final size:194
Alignment explanation
Indices: 1507490--1507885 Score: 453
Period size: 194 Copynumber: 2.0 Consensus size: 194
1507480 ACGGTAAAAT
* * **
1507490 AAATAGGCGTAAATGCCAAGTACCGATACTTCTCATGTCTGTATCGATACTTTTATTCCAGTATA
1 AAATAGGCGTAAATACCAAGTACCGATACTTCTCATATAGGTATCGATACTTTTATTCCAGTAT-
* * * *
1507555 ATTCTCAACAGTTTGCACACAAATATATCGAT-ACATATGTAAATTATCTACACTTGGAA-TTCT
65 ATTCTCAACAATTTGCACACAAATATATCGATCACATATATAAAGTATCTACACTTAGAATTTC-
* *
1507618 GAAACCTATTACTTTAAAGTAATATGTTAATTAACAATGTAAACGGTAAAA-GTCTACCGGTATA
129 GAAACCTATTAC-TTAAAGTAATA-GGTAATTAACAATGTAAACGGTAAAATGTCTACCGATATA
*
1507682 TTG
192 ATG
* * *
1507685 ATAATAGGCGTAAATACCAAGTATCGATA-TTTTTATATAGGTAT-GATACTTTTATTCCAGTAT
1 A-AATAGGCGTAAATACCAAGTACCGATACTTCTCATATAGGTATCGATACTTTTATTCCAGTAT
* * * * ** *
1507748 -TTCTCAAACAATTTGTACGCAAAATGTATCGATGCACATATATAAAGTATTTGTACTTATAATT
65 ATTCTC-AACAATTTGCACAC-AAATATATCGAT-CACATATATAAAGTATCTACACTTAGAATT
* * * *
1507812 TCGGAACCTATTACTTAATGTAATAGGTAATTAACAATGTAAATGGTAAAATTTCTACCGATATA
127 TCGAAACCTATTACTTAAAGTAATAGGTAATTAACAATGTAAACGGTAAAATGTCTACCGATATA
1507877 ATG
192 ATG
1507880 AAATAG
1 AAATAG
1507886 ACATAAATGT
Statistics
Matches: 169, Mismatches: 25, Indels: 15
0.81 0.12 0.07
Matches are distributed among these distances:
192 5 0.03
193 11 0.07
194 59 0.35
195 35 0.21
196 56 0.33
197 3 0.02
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.35
Consensus pattern (194 bp):
AAATAGGCGTAAATACCAAGTACCGATACTTCTCATATAGGTATCGATACTTTTATTCCAGTATA
TTCTCAACAATTTGCACACAAATATATCGATCACATATATAAAGTATCTACACTTAGAATTTCGA
AACCTATTACTTAAAGTAATAGGTAATTAACAATGTAAACGGTAAAATGTCTACCGATATAATG
Found at i:1508137 original size:131 final size:130
Alignment explanation
Indices: 1507773--1508138 Score: 506
Period size: 131 Copynumber: 2.8 Consensus size: 130
1507763 TACGCAAAAT
* * * *
1507773 GTATCGATGCACATATATAAAGTATTTG-TACTTATAATTTCGGAACCTATTAC-TTAATGTAAT
1 GTATCGATACTCATATATAAAGTA-TTGATACTTATAATTTCGAAACCTATTACTTTAAAGTAAT
* *
1507836 AGGT-AATTAACAATGTAAATGGTAAA-ATTTCTACCGATATAATGAAATAGACATAAATGTCCA
65 AGGTAAATTAACAATGTAAATGGTAAACGTTTCTACCGGTATAATGAAATAGACATAAATGTCCA
1507899 A
130 A
* * * ** *
1507900 GCATTGATACTCATATACAAAGTATCAATACTTATAATTTCGAAACCTATTACTTTAAATTAATA
1 GTATCGATACTCATATATAAAGTATTGATACTTATAATTTCGAAACCTATTACTTTAAAGTAATA
* * * *
1507965 GGTAAATTAACAACGTACATGGTAAACGTTTCTACCAGTATAATGAAAATAGGCATAAATGTCCA
66 GGTAAATTAACAATGTAAATGGTAAACGTTTCTACCGGTATAATG-AAATAGACATAAATGTCCA
1508030 A
130 A
*
1508031 GTATCGATACTCATATATAAAATATTGATACTTATAATTTCGAAACCTATTACTTTAAAGTAATA
1 GTATCGATACTCATATATAAAGTATTGATACTTATAATTTCGAAACCTATTACTTTAAAGTAATA
* * *
1508096 GGTAAATTAACAATGTATATGGTAAACGTTTTTATCGGTATAA
66 GGTAAATTAACAATGTAAATGGTAAACGTTTCTACCGGTATAA
1508139 GTATTGATCC
Statistics
Matches: 206, Mismatches: 28, Indels: 6
0.86 0.12 0.03
Matches are distributed among these distances:
126 1 0.00
127 43 0.21
128 12 0.06
129 20 0.10
130 15 0.07
131 115 0.56
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.34
Consensus pattern (130 bp):
GTATCGATACTCATATATAAAGTATTGATACTTATAATTTCGAAACCTATTACTTTAAAGTAATA
GGTAAATTAACAATGTAAATGGTAAACGTTTCTACCGGTATAATGAAATAGACATAAATGTCCAA
Found at i:1508558 original size:23 final size:23
Alignment explanation
Indices: 1508510--1508558 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
1508500 CCCATCAGAT
*
1508510 TTAAAAAGGCGCTACTTATTACG
1 TTAAAAAGGCGCTACCTATTACG
* *
1508533 TTAAATAA-GCGCTACCTGTTATG
1 TTAAA-AAGGCGCTACCTATTACG
1508556 TTA
1 TTA
1508559 TTATGGTTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 20 0.91
24 2 0.09
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (23 bp):
TTAAAAAGGCGCTACCTATTACG
Found at i:1510363 original size:23 final size:23
Alignment explanation
Indices: 1510336--1510418 Score: 96
Period size: 23 Copynumber: 3.6 Consensus size: 23
1510326 ATAAATTGAA
*
1510336 CCGAAGTG-CCACATAAAAATGTC
1 CCGAAG-GACCACATAGAAATGTC
*
1510359 CCGAAGGACCACATAGATATGTC
1 CCGAAGGACCACATAGAAATGTC
* * *
1510382 TCAAAGGACCACGTAGAAATGTC
1 CCGAAGGACCACATAGAAATGTC
*
1510405 CCGAATGACCACAT
1 CCGAAGGACCACAT
1510419 GGAATTATCC
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
22 1 0.02
23 48 0.98
ACGTcount: A:0.37, C:0.27, G:0.19, T:0.17
Consensus pattern (23 bp):
CCGAAGGACCACATAGAAATGTC
Found at i:1510542 original size:16 final size:16
Alignment explanation
Indices: 1510521--1510574 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
1510511 TTTACACATT
1510521 TCACATATTCATATAA
1 TCACATATTCATATAA
1510537 TCACATAGTTCA-AT-A
1 TCACATA-TTCATATAA
* **
1510552 TTACATAGACATATAA
1 TCACATATTCATATAA
1510568 TCACATA
1 TCACATA
1510575 AGTCCTTGTC
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
14 2 0.06
15 9 0.29
16 16 0.52
17 4 0.13
ACGTcount: A:0.44, C:0.19, G:0.04, T:0.33
Consensus pattern (16 bp):
TCACATATTCATATAA
Found at i:1516653 original size:21 final size:22
Alignment explanation
Indices: 1516626--1516675 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 22
1516616 CGATGTTCCC
*
1516626 TGGTATCGATAC-CCTTCACATA
1 TGGTATCGATACACCTAC-CATA
1516648 -GGTATCGATACACCTACCATA
1 TGGTATCGATACACCTACCATA
1516669 TGGTATC
1 TGGTATC
1516676 AGTATTGTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 15 0.60
22 10 0.40
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.30
Consensus pattern (22 bp):
TGGTATCGATACACCTACCATA
Found at i:1518013 original size:30 final size:32
Alignment explanation
Indices: 1517951--1518015 Score: 80
Period size: 30 Copynumber: 2.1 Consensus size: 32
1517941 AACATCATAT
*
1517951 ATTTAAACAACAGAATATATATAAAATCATGC
1 ATTTAAACAACAGAATACATATAAAATCATGC
* * *
1517983 ATTTAACCAACA-AA-ACATATAACATTATGC
1 ATTTAAACAACAGAATACATATAAAATCATGC
1518013 ATT
1 ATT
1518016 GTTCATTCTG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 16 0.55
31 2 0.07
32 11 0.38
ACGTcount: A:0.51, C:0.15, G:0.05, T:0.29
Consensus pattern (32 bp):
ATTTAAACAACAGAATACATATAAAATCATGC
Found at i:1518299 original size:64 final size:67
Alignment explanation
Indices: 1518151--1518282 Score: 205
Period size: 66 Copynumber: 1.9 Consensus size: 67
1518141 GCATATATGC
1518151 ATATATATATATATATAT-ATCACAAAAACATCATTCATTCTCATTCTCATTATCATATCATTAC
1 ATATATATATATATATATCATCACAAAAACATCATTCATTCTCATTCTCATTATCATATCATTAC
1518215 AT
66 AT
*
1518217 ATATATATATATATATATCATCA-AAAAACATTTTCATTCATTCTCATTATCATTATCATTATCA
1 ATATATATATATATATATCATCACAAAAACA---TCATTCATTCTCATTCTCATTATCA-TATCA
1518281 TT
62 TT
1518283 TACTATTCAT
Statistics
Matches: 60, Mismatches: 1, Indels: 6
0.90 0.01 0.09
Matches are distributed among these distances:
66 25 0.42
67 4 0.07
69 24 0.40
70 7 0.12
ACGTcount: A:0.40, C:0.17, G:0.00, T:0.43
Consensus pattern (67 bp):
ATATATATATATATATATCATCACAAAAACATCATTCATTCTCATTCTCATTATCATATCATTAC
AT
Found at i:1518506 original size:23 final size:23
Alignment explanation
Indices: 1518405--1518506 Score: 69
Period size: 23 Copynumber: 4.4 Consensus size: 23
1518395 CACGGAAGTG
* *
1518405 CCACATAGAAATGTCCCGAAGGA
1 CCACGTAGAAATGTCCCAAAGGA
* ** * *
1518428 TCATATATATATGTCCCAAAGGA
1 CCACGTAGAAATGTCCCAAAGGA
* * *
1518451 CCACGTAGAAATATCTCAAAAGA
1 CCACGTAGAAATGTCCCAAAGGA
*** *
1518474 CCATACAGAATTGTCCCAAAGGA
1 CCACGTAGAAATGTCCCAAAGGA
*
1518497 CCGCGTAGAA
1 CCACGTAGAA
1518507 CCCTCGACTC
Statistics
Matches: 55, Mismatches: 24, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
23 55 1.00
ACGTcount: A:0.40, C:0.24, G:0.18, T:0.19
Consensus pattern (23 bp):
CCACGTAGAAATGTCCCAAAGGA
Found at i:1518598 original size:16 final size:15
Alignment explanation
Indices: 1518577--1518614 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1518567 CATTTACATT
1518577 TCACATA-TTCATATAA
1 TCACATAGTTCA-AT-A
1518593 TCACATAGTTCAATA
1 TCACATAGTTCAATA
1518608 TCACATA
1 TCACATA
1518615 AATATCACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 8 0.38
16 9 0.43
17 4 0.19
ACGTcount: A:0.42, C:0.21, G:0.03, T:0.34
Consensus pattern (15 bp):
TCACATAGTTCAATA
Found at i:1520283 original size:22 final size:23
Alignment explanation
Indices: 1520257--1520302 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
1520247 ACCGGTAGAG
*
1520257 AGTATCGGTACCATAGT-AGGGT
1 AGTATCGATACCATAGTAAGGGT
*
1520279 AGTATCGATACCATGGTAAGGGT
1 AGTATCGATACCATAGTAAGGGT
1520302 A
1 A
1520303 TCGTTACCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.30, C:0.13, G:0.30, T:0.26
Consensus pattern (23 bp):
AGTATCGATACCATAGTAAGGGT
Found at i:1520333 original size:95 final size:96
Alignment explanation
Indices: 1520180--1520369 Score: 258
Period size: 95 Copynumber: 2.0 Consensus size: 96
1520170 ATACCGAGAA
* * *
1520180 GGTAGTATCGATACCATGATAAGGGGTATTGATACCATGAAACATCGAATCTAATTTTGGTATCC
1 GGTAGTATCGATACCATGATAAGGGGTATCGATACCAAGAAACATCGAACCTAATTTTGGTATCC
*
1520245 ATACCGG-TAGAGAGTATCGGTACCATAGTAG
66 ATACCGGAAAG-GAGTATCGGTACCATAGTAG
* * * * *
1520276 GGTAGTATCGATACCATGGTAA-GGGTATCGTTACCAAGCAACATCGAACCTATTTTTGGTATCG
1 GGTAGTATCGATACCATGATAAGGGGTATCGATACCAAGAAACATCGAACCTAATTTTGGTATCC
* *
1520340 ATACCTGAAAGGGGTATCGGTACCATAGTA
66 ATACCGGAAAGGAGTATCGGTACCATAGTA
1520370 TAGAAGTATC
Statistics
Matches: 82, Mismatches: 11, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
95 59 0.72
96 23 0.28
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (96 bp):
GGTAGTATCGATACCATGATAAGGGGTATCGATACCAAGAAACATCGAACCTAATTTTGGTATCC
ATACCGGAAAGGAGTATCGGTACCATAGTAG
Found at i:1520399 original size:95 final size:95
Alignment explanation
Indices: 1520183--1520400 Score: 208
Period size: 95 Copynumber: 2.3 Consensus size: 95
1520173 CCGAGAAGGT
* * * * * * * *
1520183 AGTATCGATACCATGATAAGGGGTATTGATACCATGAAACATCGAATCTAATTTTGGTATCCATA
1 AGTATCGATACCAGGGTAA-GAGTATCGTTACCAAGCAACATCGAACCTAATTTTGGTATCCATA
** * *
1520248 CCGGTAGAGAGTATCGGTACCATAGTAGGGT
65 CCGAAAGAGAGTATCGGTACCATAGTAGAGA
* * * *
1520279 AGTATCGATACCATGGTAAGGGTATCGTTACCAAGCAACATCGAACCTATTTTTGGTATCGATAC
1 AGTATCGATACCAGGGTAAGAGTATCGTTACCAAGCAACATCGAACCTAATTTTGGTATCCATAC
* *
1520344 CTGAAAG-GGGTATCGGTACCATAGTATAGA
66 C-GAAAGAGAGTATCGGTACCATAGTAGAGA
*
1520374 AGTATC-AGTACTAGGGT-AGTAGTATCG
1 AGTATCGA-TACCAGGGTAAG-AGTATCG
1520401 GTACTGTGGA
Statistics
Matches: 102, Mismatches: 17, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
94 3 0.03
95 78 0.76
96 21 0.21
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (95 bp):
AGTATCGATACCAGGGTAAGAGTATCGTTACCAAGCAACATCGAACCTAATTTTGGTATCCATAC
CGAAAGAGAGTATCGGTACCATAGTAGAGA
Found at i:1521146 original size:68 final size:68
Alignment explanation
Indices: 1521038--1521494 Score: 698
Period size: 68 Copynumber: 6.7 Consensus size: 68
1521028 GATTAAGAAT
* * *
1521038 CCTAACTGTGTATTTGATAGAAATGTGTAATTTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTG
1 CCTAACTGTGCATTTGACAGAAATGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTG
*
1521103 AGT
66 AGG
* *
1521106 CCTAAATGTGCATTTGACAGAAATGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCTTGG
1 CCTAACTGTGCATTTGACAGAAATGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTG
1521171 AGG
66 AGG
* * *
1521174 CCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCTAGTTAGATGAAAGGCTAAGTACCTTTG
1 CCTAACTGTGCATTTGACAGAAATGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTG
1521239 AGG
66 AGG
* *
1521242 CCTAACTGTGCATTTGATAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTG
1 CCTAACTGTGCATTTGACAGAAATGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTG
1521307 AGG
66 AGG
*
1521310 CCTAACTGTGCATTTGACAGAAATGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGTCTTTG
1 CCTAACTGTGCATTTGACAGAAATGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTG
1521375 AGG
66 AGG
* * * * * *
1521378 CCTAACTGTGCGTTTGACATAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGTCTTTA
1 CCTAACTGTGCATTTGACAGAAATGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTG
1521443 AGG
66 AGG
* ** ** *
1521446 CCTAACTGTGCAATTGGTAGAAATGTACCAATTATGCCAGTTAGATGAA
1 CCTAACTGTGCATTTGACAGAAATGTGTCATTTATGCCAGTTAGATGAA
1521495 CAATTTAATA
Statistics
Matches: 359, Mismatches: 30, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
68 359 1.00
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.31
Consensus pattern (68 bp):
CCTAACTGTGCATTTGACAGAAATGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTG
AGG
Found at i:1521583 original size:81 final size:81
Alignment explanation
Indices: 1521445--1521680 Score: 382
Period size: 81 Copynumber: 2.9 Consensus size: 81
1521435 TGTCTTTAAG
**
1521445 GCCTAACTGTGCAATTGGTAGAAATGTACCAATTATGCCAGTTAGATGAACAATTTAATACCGTT
1 GCCTAACTGTGCAATTGGTAGAAATGTACCAATTATGCCAGTTAGATGAACGGTTTAATACCGTT
1521510 GAGTAAAAGAATAATA
66 GAGTAAAAGAATAATA
* *
1521526 GCCTAATTGTGCAATTGGTAGAAATGTACCAATTATGCCAGGTAGATGAACGGTTTAATACCGTT
1 GCCTAACTGTGCAATTGGTAGAAATGTACCAATTATGCCAGTTAGATGAACGGTTTAATACCGTT
* *
1521591 GAGTAAAGGAATAATG
66 GAGTAAAAGAATAATA
* * *
1521607 GCCTAACTGTGCAATTGGTAGAAATGTGCCAATTATGCCAGTTAGATGAACGGTTAAACACCGTT
1 GCCTAACTGTGCAATTGGTAGAAATGTACCAATTATGCCAGTTAGATGAACGGTTTAATACCGTT
1521672 GAGTGAAAA
66 GAGT-AAAA
1521681 CGAAAGGTTA
Statistics
Matches: 142, Mismatches: 12, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
81 139 0.98
82 3 0.02
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (81 bp):
GCCTAACTGTGCAATTGGTAGAAATGTACCAATTATGCCAGTTAGATGAACGGTTTAATACCGTT
GAGTAAAAGAATAATA
Found at i:1521700 original size:28 final size:28
Alignment explanation
Indices: 1521658--1521724 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 28
1521648 TTAGATGAAC
* * *
1521658 GGTTAAACACCGTTGAGTGAAAACGAAA
1 GGTTAAACACTGTTGAGTAAAAACAAAA
1521686 GGTTAAACACTGTTGAGTAAAAACAAAA
1 GGTTAAACACTGTTGAGTAAAAACAAAA
1521714 GGTTAAACACT
1 GGTTAAACACT
1521725 TTTTAAAGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.45, C:0.13, G:0.21, T:0.21
Consensus pattern (28 bp):
GGTTAAACACTGTTGAGTAAAAACAAAA
Found at i:1535091 original size:19 final size:19
Alignment explanation
Indices: 1535057--1535093 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1535047 ATTGAAATTG
* *
1535057 AAAATTTTATATTTTTCAT
1 AAAATTTTAAAATTTTCAT
1535076 AAAATTTTAAAATTTTCA
1 AAAATTTTAAAATTTTCA
1535094 GTTACAACCG
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:0.43, C:0.05, G:0.00, T:0.51
Consensus pattern (19 bp):
AAAATTTTAAAATTTTCAT
Found at i:1535971 original size:20 final size:21
Alignment explanation
Indices: 1535946--1535984 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1535936 TATAAATTTG
*
1535946 TATAACTTTTTA-GTTTAACA
1 TATAACATTTTAGGTTTAACA
1535966 TATAACATTTTAGGTTTAA
1 TATAACATTTTAGGTTTAA
1535985 AACGACTGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.49
Consensus pattern (21 bp):
TATAACATTTTAGGTTTAACA
Found at i:1536536 original size:66 final size:63
Alignment explanation
Indices: 1536465--1536594 Score: 233
Period size: 66 Copynumber: 2.0 Consensus size: 63
1536455 AATAATACAC
1536465 ATCACATTAATAGAACTAATAAAAAAAGAAAATTTACTCATTCATCCAAAATATTTTAATGATTT
1 ATCACATTAATAGAACTAATAAAAAAAG-AAATTTACT-ATTCATCC-AAATATTTTAATGATTT
1536530 T
63 T
1536531 ATCACATTAATAGAACTAATAAAAAAAGAAATTTACTATTCATCCAAATATTTTAATGATTTT
1 ATCACATTAATAGAACTAATAAAAAAAGAAATTTACTATTCATCCAAATATTTTAATGATTTT
1536594 A
1 A
1536595 ATAATTATAT
Statistics
Matches: 64, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
63 19 0.30
64 8 0.12
65 9 0.14
66 28 0.44
ACGTcount: A:0.48, C:0.12, G:0.05, T:0.35
Consensus pattern (63 bp):
ATCACATTAATAGAACTAATAAAAAAAGAAATTTACTATTCATCCAAATATTTTAATGATTTT
Found at i:1537267 original size:42 final size:42
Alignment explanation
Indices: 1537186--1537301 Score: 216
Period size: 42 Copynumber: 2.8 Consensus size: 42
1537176 TTCCCGAATT
*
1537186 CCGTGTTTGTTTCACGT-ATTCGTTTTCCGGAAAATGTTTTC
1 CCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTTTTC
1537227 CCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTTTTC
1 CCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTTTTC
1537269 CCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1 CCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1537302 TGTAATTCAT
Statistics
Matches: 73, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
41 17 0.23
42 56 0.77
ACGTcount: A:0.16, C:0.21, G:0.20, T:0.44
Consensus pattern (42 bp):
CCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTTTTC
Found at i:1537532 original size:23 final size:22
Alignment explanation
Indices: 1537494--1537549 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
1537484 TATTAAAATA
*
1537494 TTTAA-AATATATTATTAATA-T
1 TTTAATAATATAATATT-ATACT
1537515 TTATAATAATATAATATTATACT
1 TT-TAATAATATAATATTATACT
*
1537538 TTTAATATTATA
1 TTTAATAATATA
1537550 TAAAATAATC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
21 2 0.07
22 15 0.50
23 13 0.43
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
TTTAATAATATAATATTATACT
Found at i:1537608 original size:24 final size:26
Alignment explanation
Indices: 1537576--1537644 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 26
1537566 TTATAATAAT
*
1537576 ATAAGATATTATATTTT-TAT-TTTA
1 ATAATATATTATATTTTATATATTTA
*
1537600 ATAATATATAATAAATTTTTTATATATTTA
1 ATAATATAT--T--ATATTTTATATATTTA
1537630 ATGAATATATTATAT
1 AT-AATATATTATAT
1537645 ATATTTCAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 11
0.71 0.06 0.22
Matches are distributed among these distances:
24 8 0.23
26 1 0.03
27 3 0.09
28 6 0.17
29 4 0.11
30 6 0.17
31 7 0.20
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (26 bp):
ATAATATATTATATTTTATATATTTA
Found at i:1537611 original size:53 final size:51
Alignment explanation
Indices: 1537494--1537619 Score: 134
Period size: 51 Copynumber: 2.5 Consensus size: 51
1537484 TATTAAAATA
* * *
1537494 TTTAA-AATATATTATTAATATTTATAATAATATAATATTATACTTTTAAT
1 TTTAATAATATATAATAAATTTTTATAATAATATAATATTATACTTTTAAT
* * *
1537544 ATTATATAA-A-ATAATCAATTTATTATAATAATATAAGATATTATA-TTTTTAT
1 TTTA-ATAATATATAATAAATTT-TTATAATAATAT-A-ATATTATACTTTTAAT
1537596 TTTAATAATATATAATAAATTTTT
1 TTTAATAATATATAATAAATTTTT
1537620 TATATATTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 12
0.77 0.09 0.15
Matches are distributed among these distances:
50 11 0.18
51 18 0.29
52 15 0.24
53 18 0.29
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.51
Consensus pattern (51 bp):
TTTAATAATATATAATAAATTTTTATAATAATATAATATTATACTTTTAAT
Found at i:1537617 original size:26 final size:28
Alignment explanation
Indices: 1537562--1537650 Score: 74
Period size: 29 Copynumber: 3.0 Consensus size: 28
1537552 AAATAATCAA
1537562 TTTATTATAATAATATAAGATATTATATT
1 TTTATTATAATAATATAAGATA-TATATT
* *
1537591 TTTATTTTAATAATATATA-ATAAAT-TT
1 TTTATTATAATAATATA-AGATATATATT
**
1537618 TTTATATATTTAATGAATATATTATATATATT
1 TTTAT-TA--TAAT-AATATAAGATATATATT
1537650 T
1 T
1537651 CAATAATATT
Statistics
Matches: 48, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
27 7 0.15
28 3 0.06
29 19 0.40
30 5 0.10
31 11 0.23
32 3 0.06
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (28 bp):
TTTATTATAATAATATAAGATATATATT
Found at i:1537623 original size:53 final size:51
Alignment explanation
Indices: 1537514--1537623 Score: 134
Period size: 53 Copynumber: 2.1 Consensus size: 51
1537504 ATTATTAATA
*
1537514 TTTATAATAATATAATATTATACTTTTAATATTATATAAAATAATCAATTT
1 TTTATAATAATATAATATTATACTTTTAATATTATATAAAATAATAAATTT
* * *
1537565 ATTATAATAATATAAGATATTATA-TTTTTATTTTA-ATAATATATAATAAATTT
1 TTTATAATAATAT-A-ATATTATACTTTTAATATTATATAA-A-ATAATAAATTT
1537618 TTTATA
1 TTTATA
1537624 TATTTAATGA
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
51 16 0.32
52 11 0.22
53 23 0.46
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (51 bp):
TTTATAATAATATAATATTATACTTTTAATATTATATAAAATAATAAATTT
Found at i:1537626 original size:20 final size:20
Alignment explanation
Indices: 1537603--1537648 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
1537593 TATTTTAATA
* *
1537603 ATATATAATAAATTTTTTAT
1 ATATATAATAAATATATTAT
* *
1537623 ATATTTAATGAATATATTAT
1 ATATATAATAAATATATTAT
1537643 ATATAT
1 ATATAT
1537649 TTCAATAATA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
ATATATAATAAATATATTAT
Found at i:1537888 original size:20 final size:20
Alignment explanation
Indices: 1537810--1537879 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
1537800 TCATAAAACG
1537810 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
1537830 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
1537850 TTTTACAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
1537870 TTTTCCAGAA
1 TTTTCCAGAA
1537880 TTCAAATTCC
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:1537888 original size:40 final size:40
Alignment explanation
Indices: 1537810--1537888 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
1537800 TCATAAAACG
* **
1537810 TTTTCCAGAAATGTAATTCATTTTCCAGAAATGTAATTCA
1 TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
*
1537850 TTTTACAGAAATGTAATTCATTTTCCAGAATTCAAATTC
1 TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTC
1537889 CAGTAATTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (40 bp):
TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
Found at i:1537898 original size:15 final size:15
Alignment explanation
Indices: 1537862--1537943 Score: 112
Period size: 15 Copynumber: 5.5 Consensus size: 15
1537852 TTACAGAAAT
**
1537862 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
1537877 G-AATTCAAATTCCA
1 GTAATTCAAATTCCA
**
1537891 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
*
1537906 GTAATTCAAATTCTA
1 GTAATTCAAATTCCA
1537921 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
1537936 GTAATTCA
1 GTAATTCA
1537944 TTTTCTGGAA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
14 12 0.21
15 46 0.79
ACGTcount: A:0.35, C:0.18, G:0.07, T:0.39
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:1537914 original size:30 final size:30
Alignment explanation
Indices: 1537862--1537943 Score: 130
Period size: 30 Copynumber: 2.8 Consensus size: 30
1537852 TTACAGAAAT
1537862 GTAATTCATTTTCCAG-AATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
*
1537891 GTAATTCATTTTCCAGTAATTCAAATTCTA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
**
1537921 GTAATTCAAATTCCAGTAATTCA
1 GTAATTCATTTTCCAGTAATTCA
1537944 TTTTCTGGAA
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 16 0.33
30 33 0.67
ACGTcount: A:0.35, C:0.18, G:0.07, T:0.39
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:1545711 original size:3 final size:3
Alignment explanation
Indices: 1545703--1545732 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
1545693 ATCCCATCCT
*
1545703 TTA TTA TTA TTA TTG TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1545733 ATGCCCCCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1546554 original size:59 final size:58
Alignment explanation
Indices: 1546447--1546574 Score: 163
Period size: 59 Copynumber: 2.2 Consensus size: 58
1546437 TAAATGTAGA
* *
1546447 TTTGCCCCTAAACTATACTCTTTTTACCGAAATGCTCCCTAAATTACTTTCAAGATGT
1 TTTGCCCCTAAACTATACTCTTTTTACCGAAATACTCCCTAAAATACTTTCAAGATGT
* * *
1546505 TTTGCCCCTAAACTATA-TAATTTTTTTCCG-AATAACTCCCTAAAATACTTTTAAGATGT
1 TTTGCCCCTAAACTATACT--CTTTTTACCGAAAT-ACTCCCTAAAATACTTTCAAGATGT
1546564 TTTG-CCCTAAA
1 TTTGCCCCTAAA
1546575 GTTTTCAAAC
Statistics
Matches: 62, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
57 1 0.02
58 27 0.44
59 34 0.55
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.39
Consensus pattern (58 bp):
TTTGCCCCTAAACTATACTCTTTTTACCGAAATACTCCCTAAAATACTTTCAAGATGT
Found at i:1547827 original size:19 final size:19
Alignment explanation
Indices: 1547780--1547817 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1547770 AAATAATCTA
1547780 AAATGAATAAAATTGTCTG
1 AAATGAATAAAATTGTCTG
1547799 AAATGAATAAAATTGTCTG
1 AAATGAATAAAATTGTCTG
1547818 TTATTTATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.05, G:0.16, T:0.32
Consensus pattern (19 bp):
AAATGAATAAAATTGTCTG
Found at i:1550278 original size:50 final size:51
Alignment explanation
Indices: 1550113--1550278 Score: 146
Period size: 50 Copynumber: 3.3 Consensus size: 51
1550103 TTTTGGGTTT
1550113 CAGTATCGATATCATATATGGTATC-AGTACCATTTTAGCATTCTGTTTTGA
1 CAGTATCGATATCATATATGGTATCGA-TACCATTTTAGCATTCTGTTTTGA
* * * * * ** * *
1550164 CAGTATCGATACTTCCTCAGTA--GTATCGGTACTACTTCATTATTTTGGGTTT--
1 CAGTATCGATA--TCAT-A-TATGGTATCGATACCATTTTAGCATTCT-GTTTTGA
*
1550216 CAGTATCGATATCATATATGGTATCGATACCATTTTAGCATTCTATTTTGA
1 CAGTATCGATATCATATATGGTATCGATACCATTTTAGCATTCTGTTTTGA
1550267 CAGTATC-ATATC
1 CAGTATCGATATC
1550279 GGTATCGGTA
Statistics
Matches: 86, Mismatches: 19, Indels: 21
0.68 0.15 0.17
Matches are distributed among these distances:
48 2 0.02
49 4 0.05
50 25 0.29
51 18 0.21
52 11 0.13
53 19 0.22
54 5 0.06
55 2 0.02
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.41
Consensus pattern (51 bp):
CAGTATCGATATCATATATGGTATCGATACCATTTTAGCATTCTGTTTTGA
Found at i:1553836 original size:30 final size:29
Alignment explanation
Indices: 1553795--1553857 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 29
1553785 GAATGTGCCA
* *
1553795 AATTGGCCCATTAGGGCAACCAGATAATTT
1 AATTAGCCCATTAGGGCAACCAAATAA-TT
*
1553825 AATTAGCCCATTAGGGCACCCAAATAATT
1 AATTAGCCCATTAGGGCAACCAAATAATT
1553854 AATT
1 AATT
1553858 TGGGATCTAC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 6 0.20
30 24 0.80
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.27
Consensus pattern (29 bp):
AATTAGCCCATTAGGGCAACCAAATAATT
Found at i:1556303 original size:50 final size:51
Alignment explanation
Indices: 1556143--1556392 Score: 134
Period size: 50 Copynumber: 4.8 Consensus size: 51
1556133 CTGCCTTAGC
* * *
1556143 AGTATCGATACTGCTTCATTATTTTAGGTTTCAGTATCGATATCATATATG
1 AGTATCGATACTACTTTATTATTTTGGGTTTCAGTATCGATATCATATATG
* * ** * * * * * * *
1556194 -GTATTCGACACCA-TTCTAGCATTCT-GTTTTGACAGTATTGGTACTTCCT-CATC
1 AGTA-TCGATACTACTT-TATTATTTTGGGTTT--CAGTATCGATA--TCATATATG
*
1556247 AGTATCGGTACTACTTTATTATTTTGGGTTTCAGTATCGATATCATATATG
1 AGTATCGATACTACTTTATTATTTTGGGTTTCAGTATCGATATCATATATG
* * * * * ** * *
1556298 -GTATCGATACTATTTTAGTATATT-GTTTTGACAGTATCGGTATTGTCTCTG
1 AGTATCGATACTACTTTATTATTTTGGGTTT--CAGTATCGATATCATATATG
* * *
1556349 CAATATCGATACTGCTTCATTATTTTGGGTTTCAGTATCGATAT
1 -AGTATCGATACTACTTTATTATTTTGGGTTTCAGTATCGATAT
1556393 ACGTATCGAT
Statistics
Matches: 141, Mismatches: 43, Indels: 29
0.66 0.20 0.14
Matches are distributed among these distances:
49 4 0.03
50 32 0.23
51 28 0.20
52 29 0.21
53 32 0.23
54 16 0.11
ACGTcount: A:0.24, C:0.16, G:0.17, T:0.44
Consensus pattern (51 bp):
AGTATCGATACTACTTTATTATTTTGGGTTTCAGTATCGATATCATATATG
Found at i:1556315 original size:207 final size:204
Alignment explanation
Indices: 1555909--1556392 Score: 652
Period size: 207 Copynumber: 2.4 Consensus size: 204
1555899 GGCTTGACCG
* * * * *
1555909 TTGTTTTGACATTATCGGGTATTACCTC-AGCAGTATCGGTACTACTTCATTATTTTGGGTTTCA
1 TTGTTTTGACAGTATC-GGTACTGCCTCTAGCAGTATCGATACTGCTTCATTATTTTGGGTTTCA
* * * * * *
1555973 GCACCGATATCATATATGGTATTTGTACCATTTTAGCATTTTGTTTTGACAATATAGGTACTTCC
65 GTATCGATATCATATATGGTATTCGCACCATTCTAGCATTCTGTTTTGACAATATAGGTACTTCC
*
1556038 TCAGCAGTATCGATACTACATTATTTTGGGTTTCAGTATCGATGTCATATATGATATCGATACCA
130 TCAGCAGTATCGATACTACATTATTTTGGGTTTCAGTATCGATATCATATATGATATCGATACCA
1556103 TTTTAGCAT-
195 TTTTAGCATA
* * * *
1556112 TATGTTTTGATAGTATTGGTGCTGCCT-TAGCAGTATCGATACTGCTTCATTATTTTAGGTTTCA
1 T-TGTTTTGACAGTATCGGTACTGCCTCTAGCAGTATCGATACTGCTTCATTATTTTGGGTTTCA
* *
1556176 GTATCGATATCATATATGGTATTCGACACCATTCTAGCATTCTGTTTTGACAGTATTGGTACTTC
65 GTATCGATATCATATATGGTATTCG-CACCATTCTAGCATTCTGTTTTGACAATATAGGTACTTC
* * *
1556241 CTCATCAGTATCGGTACTACTTTATTATTTTGGGTTTCAGTATCGATATCATATATGGTATCGAT
129 CTCAGCAGTATCGATACTAC---ATTATTTTGGGTTTCAGTATCGATATCATATATGATATCGAT
* *
1556306 ACTATTTTAGTATA
191 ACCATTTTAGCATA
* * *
1556320 TTGTTTTGACAGTATCGGTATTGTCTCT-GCAATATCGATACTGCTTCATTATTTTGGGTTTCAG
1 TTGTTTTGACAGTATCGGTACTGCCTCTAGCAGTATCGATACTGCTTCATTATTTTGGGTTTCAG
1556384 TATCGATAT
66 TATCGATAT
1556393 ACGTATCGAT
Statistics
Matches: 243, Mismatches: 30, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
203 63 0.26
204 64 0.26
207 114 0.47
208 2 0.01
ACGTcount: A:0.24, C:0.16, G:0.17, T:0.43
Consensus pattern (204 bp):
TTGTTTTGACAGTATCGGTACTGCCTCTAGCAGTATCGATACTGCTTCATTATTTTGGGTTTCAG
TATCGATATCATATATGGTATTCGCACCATTCTAGCATTCTGTTTTGACAATATAGGTACTTCCT
CAGCAGTATCGATACTACATTATTTTGGGTTTCAGTATCGATATCATATATGATATCGATACCAT
TTTAGCATA
Found at i:1556376 original size:103 final size:102
Alignment explanation
Indices: 1555909--1556392 Score: 561
Period size: 103 Copynumber: 4.7 Consensus size: 102
1555899 GGCTTGACCG
* * *
1555909 TTGTTTTGACATTATCGGGTATTACCTCAGCAGTATCGGTACTACTTCATTATTTTGGGTTTCAG
1 TTGTTTTGACAGTATC-GGTATT-CCTCTGCAGTATCGATACTACTTCATTATTTTGGGTTTCAG
* * *
1555974 CACCGATATCATATATGGTATTTG-TACCATTTTAGCATT
64 TATCGATATCATATATGGTATTCGATACCATTTTAGCA-T
* * *
1556013 TTGTTTTGACAATATAGGTACTTCCTCAGCAGTATCGATACTA---CATTATTTTGGGTTTCAGT
1 TTGTTTTGACAGTATCGGTA-TTCCTCTGCAGTATCGATACTACTTCATTATTTTGGGTTTCAGT
* *
1556075 ATCGATGTCATATATGATA-TCGATACCATTTTAGCAT
65 ATCGATATCATATATGGTATTCGATACCATTTTAGCAT
* * * * * *
1556112 TATGTTTTGATAGTATTGGTGCTGCCT-TAGCAGTATCGATACTGCTTCATTATTTTAGGTTTCA
1 T-TGTTTTGACAGTATCGGT-ATTCCTCT-GCAGTATCGATACTACTTCATTATTTTGGGTTTCA
* *
1556176 GTATCGATATCATATATGGTATTCGACACCATTCTAGCAT
63 GTATCGATATCATATATGGTATTCGATACCATTTTAGCAT
* * *
1556216 TCTGTTTTGACAGTATTGGTACTTCCTCAT-CAGTATCGGTACTACTTTATTATTTTGGGTTTCA
1 T-TGTTTTGACAGTATCGGTA-TTCCTC-TGCAGTATCGATACTACTTCATTATTTTGGGTTTCA
* *
1556280 GTATCGATATCATATATGGTA-TCGATACTATTTTAGTAT
63 GTATCGATATCATATATGGTATTCGATACCATTTTAGCAT
* * *
1556319 ATTGTTTTGACAGTATCGGTATTGTCTCTGCAATATCGATACTGCTTCATTATTTTGGGTTTCAG
1 -TTGTTTTGACAGTATCGGTATT-CCTCTGCAGTATCGATACTACTTCATTATTTTGGGTTTCAG
1556384 TATCGATAT
64 TATCGATAT
1556393 ACGTATCGAT
Statistics
Matches: 327, Mismatches: 38, Indels: 31
0.83 0.10 0.08
Matches are distributed among these distances:
99 4 0.01
100 80 0.24
102 3 0.01
103 133 0.41
104 106 0.32
106 1 0.00
ACGTcount: A:0.24, C:0.16, G:0.17, T:0.43
Consensus pattern (102 bp):
TTGTTTTGACAGTATCGGTATTCCTCTGCAGTATCGATACTACTTCATTATTTTGGGTTTCAGTA
TCGATATCATATATGGTATTCGATACCATTTTAGCAT
Found at i:1556441 original size:20 final size:20
Alignment explanation
Indices: 1556395--1556444 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
1556385 ATCGATATAC
* * *
1556395 GTATCGATATTGTTTTAGCA
1 GTATCGGTACTGTTATAGCA
1556415 GTATCGGTACTGTTATAGCA
1 GTATCGGTACTGTTATAGCA
1556435 GTATCGGTAC
1 GTATCGGTAC
1556445 AACAATATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.24, C:0.14, G:0.24, T:0.38
Consensus pattern (20 bp):
GTATCGGTACTGTTATAGCA
Done.