Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold220
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: 3999181
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 12171 characters in sequence are not A, C, G, or T
File 7 of 19
Found at i:1529386 original size:15 final size:16
Alignment explanation
Indices: 1529366--1529408 Score: 61
Period size: 15 Copynumber: 2.7 Consensus size: 16
1529356 ATACATATTG
1529366 TATAAAAATTTT-AAA
1 TATAAAAATTTTAAAA
*
1529381 TATAAATATTTTAAAA
1 TATAAAAATTTTAAAA
1529397 TATTAAAAATTT
1 TA-TAAAAATTT
1529409 AGCGTCTGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 11 0.46
16 5 0.21
17 8 0.33
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TATAAAAATTTTAAAA
Found at i:1529409 original size:16 final size:15
Alignment explanation
Indices: 1529366--1529409 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
1529356 ATACATATTG
*
1529366 TATAAAAATTTTAAA
1 TATAAAAATTTAAAA
*
1529381 TATAAATATTTTAAAA
1 TATAAA-AATTTAAAA
1529397 TATTAAAAATTTA
1 TA-TAAAAATTTA
1529410 GCGTCTGCCA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
15 6 0.25
16 14 0.58
17 4 0.17
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TATAAAAATTTAAAA
Found at i:1529773 original size:17 final size:17
Alignment explanation
Indices: 1529753--1529820 Score: 50
Period size: 17 Copynumber: 3.8 Consensus size: 17
1529743 TTATATAAAT
1529753 TTTAATATATTTTTATA
1 TTTAATATATTTTTATA
*
1529770 TTTATTATATTTAAATTATA
1 TTTAATATATTT---TTATA
* *
1529790 TTTTATTTTATATTTTAT-
1 -TTTAATATAT-TTTTATA
1529808 TTTAAT-TATTTTT
1 TTTAATATATTTTT
1529821 TTAATATTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
15 4 0.09
16 3 0.07
17 16 0.37
19 4 0.09
20 5 0.12
21 9 0.21
22 2 0.05
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTAATATATTTTTATA
Found at i:1529785 original size:33 final size:30
Alignment explanation
Indices: 1529741--1529804 Score: 74
Period size: 33 Copynumber: 2.0 Consensus size: 30
1529731 TAATAATTAA
*
1529741 TATTATATAAATTTTAATATATTTTTATATT
1 TATTATATAAATTATAATATA-TTTTATATT
* *
1529772 TATTATATTTAAATTATATTTTATTTTATATT
1 TATTATA--TAAATTATAATATATTTTATATT
1529804 T
1 T
1529805 TATTTTAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
31 7 0.25
32 10 0.36
33 11 0.39
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (30 bp):
TATTATATAAATTATAATATATTTTATATT
Found at i:1529790 original size:28 final size:29
Alignment explanation
Indices: 1529740--1529830 Score: 91
Period size: 27 Copynumber: 3.2 Consensus size: 29
1529730 ATAATAATTA
* *
1529740 ATATTATA-TAAATTTTAA-TATATTTTT
1 ATATTATATTATATTTAAATTATATTTTT
1529767 ATATT-TATTATATTTAAATTATA-TTTT
1 ATATTATATTATATTTAAATTATATTTTT
* * * *
1529794 ATTTTATATTTTATTTTAATTATTTTTTT
1 ATATTATATTATATTTAAATTATATTTTT
1529823 AATATTAT
1 -ATATTAT
1529831 TCGGTACAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 7
0.79 0.11 0.11
Matches are distributed among these distances:
26 2 0.04
27 21 0.40
28 19 0.37
29 4 0.08
30 6 0.12
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (29 bp):
ATATTATATTATATTTAAATTATATTTTT
Found at i:1529831 original size:28 final size:27
Alignment explanation
Indices: 1529740--1529831 Score: 80
Period size: 28 Copynumber: 3.3 Consensus size: 27
1529730 ATAATAATTA
* *
1529740 ATATTATATAAATTTTAA-TATATTTTT
1 ATATTAT-TATATTTTAATTATTTTTTT
*
1529767 ATATTTATTATATTTAAATTATATTTTATT
1 ATA-TTATTATATTTTAATTAT-TTTT-TT
* *
1529797 TTA-TATTTTATTTTAATTATTTTTTT
1 ATATTATTATATTTTAATTATTTTTTT
1529823 AATATTATT
1 -ATATTATT
1529832 CGGTACAAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
26 2 0.04
27 17 0.33
28 26 0.50
29 3 0.06
30 4 0.08
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (27 bp):
ATATTATTATATTTTAATTATTTTTTT
Found at i:1535169 original size:2 final size:2
Alignment explanation
Indices: 1535162--1535198 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1535152 TTTGTCTTTT
1535162 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1535199 GACTGTCTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1537585 original size:21 final size:21
Alignment explanation
Indices: 1537559--1537618 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
1537549 TTTAAATTTT
1537559 TTTAATTTAATATATAAAAAA
1 TTTAATTTAATATATAAAAAA
* * *
1537580 TTTAA-TTATTATATTATAATA
1 TTTAATTTAATATA-TAAAAAA
1537601 TTTAAGTTTCAATATATA
1 TTTAA-TTT-AATATATA
1537619 TTGTCGTGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
20 7 0.23
21 15 0.48
23 4 0.13
24 5 0.16
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (21 bp):
TTTAATTTAATATATAAAAAA
Found at i:1538458 original size:2 final size:2
Alignment explanation
Indices: 1538451--1538490 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1538441 TGAACACAAT
1538451 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
1538491 ATACATTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1539006 original size:18 final size:20
Alignment explanation
Indices: 1538988--1539034 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
1538978 TATTTTATAA
*
1538988 ATTTAATTTAAAATATAAAT
1 ATTTAATATAAAATATAAAT
*
1539008 ATTTAATATAAAATA-ATAT
1 ATTTAATATAAAATATAAAT
1539027 -TTTAATAT
1 ATTTAATAT
1539035 TTTTAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 8 0.32
19 3 0.12
20 14 0.56
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATTTAATATAAAATATAAAT
Found at i:1543283 original size:24 final size:24
Alignment explanation
Indices: 1543255--1543304 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
1543245 GTCCTCATGT
1543255 ATAAACATATTGGTATGCACTATA
1 ATAAACATATTGGTATGCACTATA
1543279 ATAAACATATTGGTATGCACTATA
1 ATAAACATATTGGTATGCACTATA
1543303 AT
1 AT
1543305 TTTAACACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.34
Consensus pattern (24 bp):
ATAAACATATTGGTATGCACTATA
Found at i:1546848 original size:18 final size:18
Alignment explanation
Indices: 1546822--1546859 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1546812 ATTATATTTA
1546822 AAATATTAA-ATATTATAT
1 AAATATTAATATATTA-AT
*
1546840 AAATTTTAATATATTAAT
1 AAATATTAATATATTAAT
1546858 AA
1 AA
1546860 TTATAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
AAATATTAATATATTAAT
Found at i:1554476 original size:2 final size:2
Alignment explanation
Indices: 1554469--1554520 Score: 68
Period size: 2 Copynumber: 25.5 Consensus size: 2
1554459 TAAGCACATC
* * *
1554469 TA TA TA TA TA TA TA TA TA TA TA TA TC TA AA GTT 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
1554512 TA TA TA TA T
1 TA TA TA TA T
1554521 CTAAAGTCTA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1554506 original size:27 final size:27
Alignment explanation
Indices: 1554475--1554533 Score: 109
Period size: 27 Copynumber: 2.2 Consensus size: 27
1554465 CATCTATATA
*
1554475 TATATATATATATATATATCTAAAGTT
1 TATATATATATATATATATCTAAAGTC
1554502 TATATATATATATATATATCTAAAGTC
1 TATATATATATATATATATCTAAAGTC
1554529 TATAT
1 TATAT
1554534 TGATAACAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.47
Consensus pattern (27 bp):
TATATATATATATATATATCTAAAGTC
Found at i:1554795 original size:2 final size:2
Alignment explanation
Indices: 1554783--1554824 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
1554773 AGAGTTTTAC
*
1554783 AT AT AT GT 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
1554825 CTTCTCTGGT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1556143 original size:37 final size:42
Alignment explanation
Indices: 1556056--1556145 Score: 102
Period size: 37 Copynumber: 2.3 Consensus size: 42
1556046 TATAATATTC
*
1556056 TAAATATAATATATAATATATTGAAATTTATATAAAAATATA
1 TAAATATAATATATAATATATTGAAATATATATAAAAATATA
* *
1556098 -ATATTATAA-ATATAAT-TA-T-AAA-ATATGTAAAAATATA
1 TA-AATATAATATATAATATATTGAAATATATATAAAAATATA
1556135 TAAATATAATA
1 TAAATATAATA
1556146 CACAGGCATA
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
37 19 0.46
38 5 0.12
39 1 0.02
40 2 0.05
41 8 0.20
42 6 0.15
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (42 bp):
TAAATATAATATATAATATATTGAAATATATATAAAAATATA
Found at i:1563115 original size:2 final size:2
Alignment explanation
Indices: 1563108--1563144 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
1563098 TTATCATGTG
* *
1563108 TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA GA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1563145 GTACACACTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
TA
Found at i:1563354 original size:2 final size:2
Alignment explanation
Indices: 1563347--1563376 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1563337 AGGAAAAGCA
1563347 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1563377 GTATAAAGCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1564335 original size:16 final size:16
Alignment explanation
Indices: 1564314--1564348 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
1564304 GTACACACGC
1564314 ATACATACATATATAT
1 ATACATACATATATAT
1564330 ATACATACATATATAT
1 ATACATACATATATAT
1564346 ATA
1 ATA
1564349 TATATAGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.37
Consensus pattern (16 bp):
ATACATACATATATAT
Found at i:1564338 original size:20 final size:20
Alignment explanation
Indices: 1564313--1564352 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1564303 AGTACACACG
1564313 CATACATACATATATATATA
1 CATACATACATATATATATA
*
1564333 CATACATATATATATATATA
1 CATACATACATATATATATA
1564353 TAGTTAGTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (20 bp):
CATACATACATATATATATA
Found at i:1564449 original size:2 final size:2
Alignment explanation
Indices: 1564432--1564470 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
1564422 CCTTAGCTTT
* *
1564432 TA TA TC TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1564471 TAAGAATAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1565463 original size:13 final size:14
Alignment explanation
Indices: 1565447--1565476 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
1565437 AAAATATTGG
1565447 ATTGAATC-ATTAA
1 ATTGAATCAATTAA
1565460 ATTGAATCAATTAA
1 ATTGAATCAATTAA
1565474 ATT
1 ATT
1565477 AAAAATTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (14 bp):
ATTGAATCAATTAA
Found at i:1565730 original size:17 final size:17
Alignment explanation
Indices: 1565692--1565745 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
1565682 TATATTTTTA
1565692 ATTAATAATTTA-TT-AT
1 ATTAAT-ATTTATTTAAT
1565708 ATTTAATATTTATTTAAT
1 A-TTAATATTTATTTAAT
*
1565726 ATTAAT-TTTTTTTAAGT
1 ATTAATATTTATTTAA-T
1565743 ATT
1 ATT
1565746 TAAAATTTGA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
16 14 0.42
17 16 0.48
18 3 0.09
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (17 bp):
ATTAATATTTATTTAAT
Found at i:1566453 original size:13 final size:13
Alignment explanation
Indices: 1566435--1566482 Score: 53
Period size: 13 Copynumber: 3.5 Consensus size: 13
1566425 GTTTTTTTCT
1566435 TTAAATTTAATAA
1 TTAAATTTAATAA
1566448 TTAAATTTATATAA
1 TTAAATTTA-ATAA
*
1566462 CTTAACTTGTAAT-A
1 -TTAAATT-TAATAA
1566476 TTAAATT
1 TTAAATT
1566483 CAATTAGTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
13 15 0.50
14 5 0.17
15 8 0.27
16 2 0.07
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (13 bp):
TTAAATTTAATAA
Found at i:1567199 original size:34 final size:34
Alignment explanation
Indices: 1567153--1567404 Score: 332
Period size: 34 Copynumber: 7.5 Consensus size: 34
1567143 GTAAAAACCA
*
1567153 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
1567187 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* *
1567221 CCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
1567255 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
*
1567289 CCATTTAATCAACAATGGTAAGCTACCAAATCT-
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
1567322 CCATTTAGTCAACAATGGCAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGG-TAACCTACCAAATCTC
* * *
1567356 CCATTTAATCAACAATGGTAAACTACTAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
1567389 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
1567405 TCTCCCACTT
Statistics
Matches: 194, Mismatches: 19, Indels: 11
0.87 0.08 0.05
Matches are distributed among these distances:
33 47 0.24
34 143 0.74
35 4 0.02
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:1567363 original size:67 final size:68
Alignment explanation
Indices: 1567153--1567404 Score: 373
Period size: 68 Copynumber: 3.7 Consensus size: 68
1567143 GTAAAAACCA
* * *
1567153 CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCAAAT
1 CCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAATCAACAATGGTAAACCACCAAAT
1567218 CAC
66 CAC
* * *
1567221 CCATTTAATCAATAATGGTAAGCTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAAAT
1 CCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAATCAACAATGGTAAACCACCAAAT
**
1567286 TTC
66 CAC
* *
1567289 CCATTTAATCAACAATGGTAAGCTACCAAATCT-CCATTTAGTCAACAATGGCAAACCACCAAAT
1 CCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAATCAACAATGGTAAACCACCAAAT
1567353 CAC
66 CAC
* * *
1567356 CCATTTAATCAACAATGGTAAACTACTAAATC-ACCATTTAATCAACAAT
1 CCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAATCAACAAT
1567405 TCTCCCACTT
Statistics
Matches: 165, Mismatches: 18, Indels: 3
0.89 0.10 0.02
Matches are distributed among these distances:
67 73 0.44
68 92 0.56
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (68 bp):
CCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAATCAACAATGGTAAACCACCAAAT
CAC
Found at i:1571963 original size:33 final size:34
Alignment explanation
Indices: 1571819--1572067 Score: 333
Period size: 34 Copynumber: 7.4 Consensus size: 34
1571809 GTAAAAACCA
* *
1571819 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAAACTACCAAATCTC
* * *
1571853 CCATTTAGTCAACAATGGTAAACCACCAAATCAC
1 CCATTTAATCAACAATGGTAAACTACCAAATCTC
* *
1571887 CCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAAACTACCAAATCTC
* *
1571921 CCATTTAATCAACAATGGTAAGCTACCAAAT-TT
1 CCATTTAATCAACAATGGTAAACTACCAAATCTC
*
1571954 CCATTTAATCAACAATGGTAAGCTACCAAATCT-
1 CCATTTAATCAACAATGGTAAACTACCAAATCTC
* * * *
1571987 CCATTTAGTCAACAATGGCAAACCACCAAATCAC
1 CCATTTAATCAACAATGGTAAACTACCAAATCTC
* *
1572021 CCATTTAATCAACAATGGTAAACTACTAAATC-A
1 CCATTTAATCAACAATGGTAAACTACCAAATCTC
1572054 CCATTTAATCAACA
1 CCATTTAATCAACA
1572068 TTTAATTTGA
Statistics
Matches: 191, Mismatches: 22, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
33 74 0.39
34 117 0.61
ACGTcount: A:0.41, C:0.27, G:0.08, T:0.25
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAAACTACCAAATCTC
Found at i:1572025 original size:67 final size:68
Alignment explanation
Indices: 1571819--1572067 Score: 360
Period size: 67 Copynumber: 3.7 Consensus size: 68
1571809 GTAAAAACCA
* * *
1571819 CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCAAAT
1 CCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAATCAACAATGGTAAACCACCAAAT
1571884 CAC
66 CAC
* * *
1571887 CCATTTAATCAATAATGGTAAGCTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAAAT
1 CCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAATCAACAATGGTAAACCACCAAAT
**
1571952 -TT
66 CAC
* *
1571954 CCATTTAATCAACAATGGTAAGCTACCAAATCT-CCATTTAGTCAACAATGGCAAACCACCAAAT
1 CCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAATCAACAATGGTAAACCACCAAAT
1572018 CAC
66 CAC
* * *
1572021 CCATTTAATCAACAATGGTAAACTACTAAATC-ACCATTTAATCAACA
1 CCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAATCAACA
1572068 TTTAATTTGA
Statistics
Matches: 161, Mismatches: 18, Indels: 5
0.88 0.10 0.03
Matches are distributed among these distances:
66 27 0.17
67 75 0.47
68 59 0.37
ACGTcount: A:0.41, C:0.27, G:0.08, T:0.25
Consensus pattern (68 bp):
CCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAATCAACAATGGTAAACCACCAAAT
CAC
Found at i:1573967 original size:9 final size:9
Alignment explanation
Indices: 1573953--1573982 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
1573943 ATTCGAATTA
1573953 AATATTTTT
1 AATATTTTT
1573962 AATATTTTT
1 AATATTTTT
1573971 -ATATTTTT
1 AATATTTTT
1573979 AATA
1 AATA
1573983 AAATGTCAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
AATATTTTT
Found at i:1574486 original size:2 final size:2
Alignment explanation
Indices: 1574479--1574508 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1574469 TTCAACGAGC
1574479 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
1574509 TACAATCATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1576104 original size:4 final size:4
Alignment explanation
Indices: 1576095--1576125 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
1576085 TCCTATACTT
*
1576095 ATAC ATAC ATAC ATAC ATAC ATAC ATGC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1576126 TATATATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.48, C:0.23, G:0.03, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:1577195 original size:27 final size:27
Alignment explanation
Indices: 1577141--1577195 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
1577131 AGAAGTTCGG
* *
1577141 TGAGTATCAAACTTTTTCTGAAAGGGA
1 TGAGTATCAAACTTTTTCTCAAAAGGA
*
1577168 TGAGTATCAAACTTTTTGTCAAAAGGA
1 TGAGTATCAAACTTTTTCTCAAAAGGA
1577195 T
1 T
1577196 TGAATTAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.35
Consensus pattern (27 bp):
TGAGTATCAAACTTTTTCTCAAAAGGA
Found at i:1581342 original size:4 final size:4
Alignment explanation
Indices: 1581335--1581362 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
1581325 TTTTTATATA
1581335 TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG
1581363 GGAAAATAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:1582636 original size:14 final size:14
Alignment explanation
Indices: 1582613--1582644 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1582603 CATCCCCAAA
1582613 AGTTACTTCTTTTT
1 AGTTACTTCTTTTT
*
1582627 AGTTATTTCTTTTT
1 AGTTACTTCTTTTT
1582641 AGTT
1 AGTT
1582645 GTTTTTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.16, C:0.09, G:0.09, T:0.66
Consensus pattern (14 bp):
AGTTACTTCTTTTT
Found at i:1582798 original size:2 final size:2
Alignment explanation
Indices: 1582779--1582818 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
1582769 CCCTTGTAGA
* * *
1582779 AT AT AT AG AT CT AC 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
1582819 GCGCTCCTTG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1582968 original size:2 final size:2
Alignment explanation
Indices: 1582963--1582993 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1582953 ACGCTAATAC
1582963 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 A
1582994 GTGTGTGTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1584031 original size:14 final size:13
Alignment explanation
Indices: 1583999--1584049 Score: 61
Period size: 14 Copynumber: 3.9 Consensus size: 13
1583989 ATAACCTTCA
1583999 TTATTTTAATT-T
1 TTATTTTAATTAT
1584011 TTA-TTTAATTAT
1 TTATTTTAATTAT
*
1584023 TTATCTTTAATTAA
1 TTAT-TTTAATTAT
1584037 TTATCTTTAATTA
1 TTAT-TTTAATTA
1584050 ATTTGACCTC
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
11 7 0.20
12 7 0.20
14 21 0.60
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (13 bp):
TTATTTTAATTAT
Found at i:1584050 original size:14 final size:14
Alignment explanation
Indices: 1584014--1584052 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
1584004 TTAATTTTTA
*
1584014 TTTAATTATTTATC
1 TTTAATTAATTATC
1584028 TTTAATTAATTATC
1 TTTAATTAATTATC
1584042 TTTAATTAATT
1 TTTAATTAATT
1584053 TGACCTCTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (14 bp):
TTTAATTAATTATC
Found at i:1585657 original size:14 final size:15
Alignment explanation
Indices: 1585629--1585671 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
1585619 ATTAAAAAAT
1585629 TATTATAAATATTAA
1 TATTATAAATATTAA
*
1585644 TATT-TAAATTTTAA
1 TATTATAAATATTAA
1585658 GT-TTATAAATATTA
1 -TATTATAAATATTA
1585672 TTTTTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (15 bp):
TATTATAAATATTAA
Found at i:1588750 original size:14 final size:15
Alignment explanation
Indices: 1588731--1588764 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
1588721 GGTATTTGGG
1588731 TTTTT-CTTTTTTTT
1 TTTTTCCTTTTTTTT
1588745 TTTTTCCTTTTTTTT
1 TTTTTCCTTTTTTTT
1588760 TTTTT
1 TTTTT
1588765 TGCTTTTCGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (15 bp):
TTTTTCCTTTTTTTT
Found at i:1588758 original size:16 final size:16
Alignment explanation
Indices: 1588737--1588771 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
1588727 TGGGTTTTTC
1588737 TTTTTTTTTTTTTCCT
1 TTTTTTTTTTTTTCCT
*
1588753 TTTTTTTTTTTTTGCT
1 TTTTTTTTTTTTTCCT
1588769 TTT
1 TTT
1588772 CGGATTAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.00, C:0.09, G:0.03, T:0.89
Consensus pattern (16 bp):
TTTTTTTTTTTTTCCT
Found at i:1588771 original size:9 final size:8
Alignment explanation
Indices: 1588731--1588771 Score: 50
Period size: 7 Copynumber: 5.2 Consensus size: 8
1588721 GGTATTTGGG
1588731 TTTTTCTT
1 TTTTTCTT
1588739 TTTTT-TT
1 TTTTTCTT
*
1588746 TTTTCCTT
1 TTTTTCTT
1588754 TTTTT-TT
1 TTTTTCTT
1588761 TTTTTGCTT
1 TTTTT-CTT
1588770 TT
1 TT
1588772 CGGATTAGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
7 13 0.46
8 11 0.39
9 4 0.14
ACGTcount: A:0.00, C:0.10, G:0.02, T:0.88
Consensus pattern (8 bp):
TTTTTCTT
Found at i:1589625 original size:2 final size:2
Alignment explanation
Indices: 1589618--1589650 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
1589608 ACACCTTCGC
1589618 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
1589651 TTAATCAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1593268 original size:18 final size:19
Alignment explanation
Indices: 1593242--1593300 Score: 66
Period size: 18 Copynumber: 3.1 Consensus size: 19
1593232 ATTTCGAAAA
* *
1593242 ATTTATATATTTTTATTAT
1 ATTTATATATTATAATTAT
1593261 ATTT-TATATTATAATTAT
1 ATTTATATATTATAATTAT
* *
1593279 ATTTAAAATATTATATTTAT
1 ATTT-ATATATTATAATTAT
1593299 AT
1 AT
1593301 AATTTTTAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
18 16 0.47
19 4 0.12
20 14 0.41
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTATATATTATAATTAT
Found at i:1593332 original size:18 final size:19
Alignment explanation
Indices: 1593244--1593332 Score: 52
Period size: 18 Copynumber: 5.1 Consensus size: 19
1593234 TTCGAAAAAT
*
1593244 TTATAT-ATTTTTATTATA
1 TTATATAATTTATATTATA
*
1593262 TTTTAT-A-TTATAATTATA
1 TTATATAATTTAT-ATTATA
1593280 TT-TA-AA---ATATTATA
1 TTATATAATTTATATTATA
* **
1593294 TTTATATAATTTTTAACATA
1 -TTATATAATTTATATTATA
1593314 TTA-ATAATTTATATTATA
1 TTATATAATTTATATTATA
1593332 T
1 T
1593333 AAATTTTAAT
Statistics
Matches: 55, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
14 6 0.11
15 4 0.07
16 2 0.04
17 8 0.15
18 27 0.49
19 3 0.05
20 5 0.09
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.58
Consensus pattern (19 bp):
TTATATAATTTATATTATA
Found at i:1593333 original size:32 final size:33
Alignment explanation
Indices: 1593281--1593351 Score: 92
Period size: 32 Copynumber: 2.2 Consensus size: 33
1593271 ATAATTATAT
*
1593281 TTAAAATATTATATTTATATAATTTTTAACATA
1 TTAAAATATTATATTTATATAAATTTTAACATA
*
1593314 TTAATAAT-TTATA-TTATATAAATTTTAATATA
1 TTAA-AATATTATATTTATATAAATTTTAACATA
1593346 TATAAA
1 T-TAAA
1593352 TTCATAACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
32 19 0.56
33 12 0.35
34 3 0.09
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (33 bp):
TTAAAATATTATATTTATATAAATTTTAACATA
Found at i:1593340 original size:16 final size:16
Alignment explanation
Indices: 1593275--1593353 Score: 53
Period size: 16 Copynumber: 5.0 Consensus size: 16
1593265 TATATTATAA
*
1593275 TTATATT-TA-AAATA
1 TTATATTATATAAATT
*
1593289 TTATATTTATATAATTT
1 TTATA-TTATATAAATT
1593306 TTAACATATTA-AT-AA-T
1 TT---ATATTATATAAATT
1593322 TTATATTATATAAATT
1 TTATATTATATAAATT
1593338 TTA-ATATATATAAATT
1 TTATAT-TATATAAATT
1593354 CATAACATAT
Statistics
Matches: 52, Mismatches: 3, Indels: 18
0.71 0.04 0.25
Matches are distributed among these distances:
13 6 0.12
14 7 0.13
15 6 0.12
16 19 0.37
17 6 0.12
18 2 0.04
19 3 0.06
20 3 0.06
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (16 bp):
TTATATTATATAAATT
Found at i:1593372 original size:8 final size:8
Alignment explanation
Indices: 1593361--1593417 Score: 53
Period size: 8 Copynumber: 6.6 Consensus size: 8
1593351 ATTCATAACA
1593361 TATTTATT
1 TATTTATT
1593369 TATTTATT
1 TATTTATT
1593377 TATTTATT
1 TATTTATT
1593385 ATATTATATTT
1 -TATT-TA-TT
*
1593396 TAATTATT
1 TATTTATT
1593404 T-TTATATT
1 TATT-TATT
1593412 ATATTT
1 -TATTT
1593418 TTATAACATA
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
7 1 0.02
8 23 0.56
9 8 0.20
10 7 0.17
11 2 0.05
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (8 bp):
TATTTATT
Found at i:1593382 original size:16 final size:17
Alignment explanation
Indices: 1593361--1593417 Score: 64
Period size: 17 Copynumber: 3.3 Consensus size: 17
1593351 ATTCATAACA
1593361 TATTTATTTATT-TATT
1 TATTTATTTATTATATT
1593377 TATTTATTATATTATATTT
1 TATTTATT-TATTATA-TT
*
1593396 TAATTATTT-TTATATT
1 TATTTATTTATTATATT
1593412 ATATTT
1 -TATTT
1593418 TTATAACATA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
16 10 0.29
17 13 0.37
18 3 0.09
19 9 0.26
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TATTTATTTATTATATT
Found at i:1593401 original size:11 final size:12
Alignment explanation
Indices: 1593371--1593418 Score: 59
Period size: 11 Copynumber: 4.2 Consensus size: 12
1593361 TATTTATTTA
1593371 TTTAT-TTAT-T
1 TTTATATTATAT
1593381 TATTATATTATAT
1 T-TTATATTATAT
1593394 TTTA-ATTAT-T
1 TTTATATTATAT
1593404 TTTATATTATAT
1 TTTATATTATAT
1593416 TTT
1 TTT
1593419 TATAACATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
10 6 0.18
11 14 0.42
12 11 0.33
13 2 0.06
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (12 bp):
TTTATATTATAT
Found at i:1593408 original size:22 final size:23
Alignment explanation
Indices: 1593371--1593418 Score: 80
Period size: 22 Copynumber: 2.1 Consensus size: 23
1593361 TATTTATTTA
*
1593371 TTTATTTATTTATTATATTATAT
1 TTTAATTATTTATTATATTATAT
1593394 TTTAATTATTT-TTATATTATAT
1 TTTAATTATTTATTATATTATAT
1593416 TTT
1 TTT
1593419 TATAACATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 14 0.58
23 10 0.42
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (23 bp):
TTTAATTATTTATTATATTATAT
Found at i:1594603 original size:2 final size:2
Alignment explanation
Indices: 1594596--1594632 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1594586 AATATCCTTT
1594596 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1594633 CAATCAAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1595631 original size:14 final size:13
Alignment explanation
Indices: 1595614--1595651 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
1595604 AAAACGAAAT
1595614 TAATAAAATAATAC
1 TAATAAAA-AATAC
*
1595628 TAAT-AAAAATAT
1 TAATAAAAAATAC
1595640 TAATAAAAAATA
1 TAATAAAAAATA
1595652 AAATATATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
12 8 0.36
13 10 0.45
14 4 0.18
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (13 bp):
TAATAAAAAATAC
Found at i:1596468 original size:2 final size:2
Alignment explanation
Indices: 1596463--1596498 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1596453 TTTTTTCTGC
1596463 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1596499 TACATCATAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1598016 original size:20 final size:22
Alignment explanation
Indices: 1597984--1598031 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 22
1597974 AAAATTTTGA
1597984 TAAAA-AATATTTAAATTT-TT
1 TAAAATAATATTTAAATTTCTT
*
1598004 TAAAATAAT-TTTATATTTCGTT
1 TAAAATAATATTTAAATTTC-TT
1598026 TAAAAT
1 TAAAAT
1598032 TGAAATAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 13 0.54
21 3 0.12
22 8 0.33
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (22 bp):
TAAAATAATATTTAAATTTCTT
Found at i:1598169 original size:16 final size:17
Alignment explanation
Indices: 1598142--1598178 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
1598132 TTAAATTAAT
1598142 TTATAATAAAAT-AAGTA
1 TTATAATAAAATCAA-TA
1598159 TTATAAT-AAATCAATA
1 TTATAATAAAATCAATA
1598175 TTAT
1 TTAT
1598179 GTACTTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (17 bp):
TTATAATAAAATCAATA
Found at i:1600104 original size:44 final size:44
Alignment explanation
Indices: 1600036--1600154 Score: 157
Period size: 44 Copynumber: 2.7 Consensus size: 44
1600026 ATGCTAACAA
* *
1600036 CGATCAAGTGAGTGTCGAACACCCAGTTGGATCCAAGGATTAAC
1 CGATCAAGTGAGTGTCGAAGACCCAGTAGGATCCAAGGATTAAC
* * *
1600080 CGGTCAAGTGAGTGTCGAAGACCCAGTAGGATCCAAGGTTTAAT
1 CGATCAAGTGAGTGTCGAAGACCCAGTAGGATCCAAGGATTAAC
* * * *
1600124 TGATCAAGCGAGTGGCGAAGACCGAGTAGGA
1 CGATCAAGTGAGTGTCGAAGACCCAGTAGGA
1600155 AATAAGTGCA
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 65 1.00
ACGTcount: A:0.31, C:0.19, G:0.30, T:0.19
Consensus pattern (44 bp):
CGATCAAGTGAGTGTCGAAGACCCAGTAGGATCCAAGGATTAAC
Found at i:1603578 original size:1 final size:1
Alignment explanation
Indices: 1603572--1603596 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
1603562 ATTTTACTGA
1603572 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
1603597 AAAAAAAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:1605473 original size:2 final size:2
Alignment explanation
Indices: 1605466--1605492 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1605456 CAAACCCAAA
1605466 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
1605493 ATGTTTTATA
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:1611864 original size:22 final size:23
Alignment explanation
Indices: 1611826--1611869 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
1611816 TATTATTTTA
1611826 AATTACAAAATTAATTTTAAATT
1 AATTACAAAATTAATTTTAAATT
*
1611849 AATTA-AAATTTAATTTTAAAT
1 AATTACAAAATTAATTTTAAAT
1611870 ATAAAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (23 bp):
AATTACAAAATTAATTTTAAATT
Found at i:1612144 original size:19 final size:21
Alignment explanation
Indices: 1612112--1612160 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
1612102 ATAATAATAA
1612112 TTTATAT-ATGT-AAATTTAT
1 TTTATATAATGTAAAATTTAT
1612131 TTTATATAAT-TAAAATTTAT
1 TTTATATAATGTAAAATTTAT
*
1612151 ATTATTATAA
1 TTTA-TATAA
1612161 AATTATTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 8 0.31
20 13 0.50
21 5 0.19
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (21 bp):
TTTATATAATGTAAAATTTAT
Found at i:1612170 original size:15 final size:17
Alignment explanation
Indices: 1612141--1612172 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
1612131 TTTATATAAT
1612141 TAAAATTTATATTATTA
1 TAAAATTTATATTATTA
1612158 TAAAA-TTAT-TTATTA
1 TAAAATTTATATTATTA
1612173 ATTTAATGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TAAAATTTATATTATTA
Found at i:1612175 original size:34 final size:34
Alignment explanation
Indices: 1612099--1612175 Score: 88
Period size: 34 Copynumber: 2.3 Consensus size: 34
1612089 AGTATTAGTA
* *
1612099 TATATAA-TAATAATTTATATATGTAAATTTATTT
1 TATATAATTAA-AATTTATATATATAAAATTATTT
1612133 TATATAATTAAAATTTATATTATTATAAAATTA-TT
1 TATATAATTAAAATTTATA-TA-TATAAAATTATTT
1612168 TAT-TAATT
1 TATATAATT
1612176 TAATGTTTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
34 20 0.53
35 10 0.26
36 8 0.21
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.53
Consensus pattern (34 bp):
TATATAATTAAAATTTATATATATAAAATTATTT
Found at i:1613523 original size:57 final size:57
Alignment explanation
Indices: 1613450--1613669 Score: 291
Period size: 57 Copynumber: 3.9 Consensus size: 57
1613440 TCATAATACT
* *
1613450 CATTAGTAATGTCATTGTGAAGAGGAAAACACCGGAAGGACCAAGTCCTGTTCCTCC
1 CATTAGTAATATCATTGTGAAGAGGAAAACACCGGGAGGACCAAGTCCTGTTCCTCC
* *
1613507 CATTAGTAATGTCATTGTGAAGAGGATAACACCGGGAGGACCAAGTCCTGTTCCTCC
1 CATTAGTAATATCATTGTGAAGAGGAAAACACCGGGAGGACCAAGTCCTGTTCCTCC
* * * * * *
1613564 CATTAATAATATCATCGT-AAAAAGAGAAACACCAGGAGGGCCAA-TCCCTGTTCCTCC
1 CATTAGTAATATCATTGTGAAGAGGA-AAACACCGGGAGGACCAAGT-CCTGTTCCTCC
* * *
1613621 CATTAGTAATATCATTATGAAGAGGAAAACACCGGGAGGGCCAAATCCT
1 CATTAGTAATATCATTGTGAAGAGGAAAACACCGGGAGGACCAAGTCCT
1613670 ATTCATAATG
Statistics
Matches: 143, Mismatches: 16, Indels: 8
0.86 0.10 0.05
Matches are distributed among these distances:
56 6 0.04
57 131 0.92
58 6 0.04
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.22
Consensus pattern (57 bp):
CATTAGTAATATCATTGTGAAGAGGAAAACACCGGGAGGACCAAGTCCTGTTCCTCC
Found at i:1613884 original size:17 final size:19
Alignment explanation
Indices: 1613848--1613884 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1613838 TAAAATTATT
*
1613848 TTCTAAATTATTTATGAAG
1 TTCTAAAATATTTATGAAG
1613867 TTCTAAAAT-TTTAT-AAG
1 TTCTAAAATATTTATGAAG
1613884 T
1 T
1613885 GAAATAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 4 0.24
18 5 0.29
19 8 0.47
ACGTcount: A:0.38, C:0.05, G:0.08, T:0.49
Consensus pattern (19 bp):
TTCTAAAATATTTATGAAG
Found at i:1616591 original size:17 final size:17
Alignment explanation
Indices: 1616565--1616597 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1616555 TTTTATAATC
1616565 TTTGAAATAATTTTAAA
1 TTTGAAATAATTTTAAA
*
1616582 TTTGATATAATTTTAA
1 TTTGAAATAATTTTAA
1616598 TAATTTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (17 bp):
TTTGAAATAATTTTAAA
Found at i:1616612 original size:21 final size:21
Alignment explanation
Indices: 1616586--1616658 Score: 96
Period size: 21 Copynumber: 3.5 Consensus size: 21
1616576 TTTAAATTTG
*
1616586 ATATAATTTTAATAATTTTTT
1 ATATAATTTTAATAATTTTTA
*
1616607 ATATAATTTTAATAATGTTTCA
1 ATATAATTTTAATAAT-TTTTA
*
1616629 A-ATAATTTTGATAA-TTTTA
1 ATATAATTTTAATAATTTTTA
1616648 ATATAATTTTA
1 ATATAATTTTA
1616659 CAAGAATTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
19 5 0.11
20 8 0.18
21 28 0.62
22 4 0.09
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (21 bp):
ATATAATTTTAATAATTTTTA
Found at i:1616616 original size:11 final size:11
Alignment explanation
Indices: 1616506--1616657 Score: 51
Period size: 11 Copynumber: 14.5 Consensus size: 11
1616496 GAATTTAGGT
1616506 ATTTTTATATA
1 ATTTTTATATA
* *
1616517 ATTTTAACTTTATT
1 ATTTT---TATATA
*
1616531 ATTTTTATATG
1 ATTTTTATATA
*
1616542 A-TTTT-TGTA
1 ATTTTTATATA
*
1616551 ATTTTTTTATA
1 ATTTTTATATA
* *
1616562 ATCTTTGAAATA
1 AT-TTTTATATA
1616574 A--TTT-TA-A
1 ATTTTTATATA
*
1616581 A-TTTGATATA
1 ATTTTTATATA
1616591 A-TTTTA-ATA
1 ATTTTTATATA
1616600 ATTTTTTATATA
1 A-TTTTTATATA
1616612 A-TTTTA-ATA
1 ATTTTTATATA
* *
1616621 ATGTTTCAAATA
1 AT-TTTTATATA
*
1616633 A-TTTT-GATA
1 ATTTTTATATA
*
1616642 ATTTTAATATA
1 ATTTTTATATA
1616653 ATTTT
1 ATTTT
1616658 ACAAGAATTT
Statistics
Matches: 105, Mismatches: 19, Indels: 34
0.66 0.12 0.22
Matches are distributed among these distances:
7 2 0.02
8 3 0.03
9 19 0.18
10 25 0.24
11 32 0.30
12 15 0.14
14 9 0.09
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.59
Consensus pattern (11 bp):
ATTTTTATATA
Found at i:1616658 original size:11 final size:11
Alignment explanation
Indices: 1616586--1616709 Score: 70
Period size: 11 Copynumber: 11.7 Consensus size: 11
1616576 TTTAAATTTG
1616586 ATATAATTTTA
1 ATATAATTTTA
* *
1616597 ATA-ATTTTTT
1 ATATAATTTTA
1616607 ATATAATTTT-
1 ATATAATTTTA
1616617 A-ATAATGTTTCA
1 ATATAAT-TTT-A
1616629 A-ATAATTTT-
1 ATATAATTTTA
*
1616638 -GATAATTTTA
1 ATATAATTTTA
1616648 ATATAATTTTA
1 ATATAATTTTA
*
1616659 CA-AGAATTTTA
1 -ATATAATTTTA
1616670 ATA-AGATTTTA
1 ATATA-ATTTTA
* *
1616681 A-ATAGTTTTG
1 ATATAATTTTA
*
1616691 ATA-ATTTTTA
1 ATATAATTTTA
1616701 ATAATAATT
1 AT-ATAATT
1616710 AAAATAAATT
Statistics
Matches: 89, Mismatches: 10, Indels: 27
0.71 0.08 0.21
Matches are distributed among these distances:
9 13 0.15
10 27 0.30
11 39 0.44
12 10 0.11
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.52
Consensus pattern (11 bp):
ATATAATTTTA
Found at i:1616722 original size:52 final size:51
Alignment explanation
Indices: 1616588--1616723 Score: 141
Period size: 52 Copynumber: 2.6 Consensus size: 51
1616578 TAAATTTGAT
** * *
1616588 ATAATTTTAATAATTTTTTATATAATTTTAATAATGTTTCAAATAATTTTG
1 ATAATTTTAATAATAATTAAAATAATTTTAATAATGTTTCAAATAATTTTG
* * * *
1616639 ATAATTTTAAT-ATAATTTTACAAGAATTTTAATAA-GATTTTAAATAGTTTTG
1 ATAATTTTAATAATAA--TTAAAATAATTTTAATAATG-TTTCAAATAATTTTG
*
1616691 ATAATTTTTAATAATAATTAAAATAAATTTAAT
1 ATAA-TTTTAATAATAATTAAAATAATTTTAAT
1616724 TTCATTTGCT
Statistics
Matches: 69, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
50 2 0.03
51 12 0.17
52 44 0.64
53 7 0.10
54 4 0.06
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.50
Consensus pattern (51 bp):
ATAATTTTAATAATAATTAAAATAATTTTAATAATGTTTCAAATAATTTTG
Found at i:1616816 original size:14 final size:14
Alignment explanation
Indices: 1616797--1616844 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
1616787 AACATATCTA
1616797 ATATTAAATTATAT
1 ATATTAAATTATAT
* *
1616811 ATATTAAAATAAAT
1 ATATTAAATTATAT
*
1616825 AATATTAACTTAT-T
1 -ATATTAAATTATAT
1616839 ATATTA
1 ATATTA
1616845 TTCACCTAAG
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
13 6 0.21
14 13 0.46
15 9 0.32
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (14 bp):
ATATTAAATTATAT
Found at i:1621257 original size:17 final size:16
Alignment explanation
Indices: 1621230--1621265 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
1621220 ATTATATTTT
*
1621230 TATATTTATATTTAAA
1 TATATTTATATGTAAA
1621246 TATATATTATATGTAAA
1 TATAT-TTATATGTAAA
1621263 TAT
1 TAT
1621266 TAAATCAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TATATTTATATGTAAA
Found at i:1623156 original size:42 final size:42
Alignment explanation
Indices: 1623109--1623194 Score: 145
Period size: 42 Copynumber: 2.0 Consensus size: 42
1623099 TTCATACACA
* *
1623109 ATAAAATCTGAAGATATTTATCAGCTAATTTTTATGATTGCC
1 ATAAAATCTGAAGATATTTATCAGCTAATATATATGATTGCC
*
1623151 ATAAAATCTGAAGATATTTATCGGCTAATATATATGATTGCC
1 ATAAAATCTGAAGATATTTATCAGCTAATATATATGATTGCC
1623193 AT
1 AT
1623195 GACTTTATGG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.38
Consensus pattern (42 bp):
ATAAAATCTGAAGATATTTATCAGCTAATATATATGATTGCC
Found at i:1623833 original size:2 final size:2
Alignment explanation
Indices: 1623826--1623852 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1623816 TCTATTTCTT
1623826 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1623853 TATCTTACCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1624858 original size:17 final size:17
Alignment explanation
Indices: 1624834--1624874 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
1624824 AAAAATATAA
1624834 AAAT-TAAACATA-TATT
1 AAATATAAA-ATATTATT
1624850 AAATATAAAATATTATT
1 AAATATAAAATATTATT
*
1624867 AAAAATAA
1 AAATATAA
1624875 TATAAATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 7 0.32
17 15 0.68
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (17 bp):
AAATATAAAATATTATT
Found at i:1624880 original size:28 final size:29
Alignment explanation
Indices: 1624819--1624908 Score: 93
Period size: 28 Copynumber: 3.3 Consensus size: 29
1624809 CGATTATATA
* *
1624819 ATATTAAAAAT-ATAA-AA-ATTAAACAT
1 ATATTAAATATAATAATAATATTAAAAAT
*
1624845 ATATTAAATATAA-AATATTATTAAAAAT
1 ATATTAAATATAATAATAATATTAAAAAT
*
1624873 A-ATATAAATATAATAATAATA-TATAAAT
1 ATAT-TAAATATAATAATAATATTAAAAAT
1624901 ATATTAAA
1 ATATTAAA
1624909 ATTTATATAA
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
26 12 0.23
27 4 0.08
28 29 0.55
29 8 0.15
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (29 bp):
ATATTAAATATAATAATAATATTAAAAAT
Found at i:1624906 original size:39 final size:39
Alignment explanation
Indices: 1624851--1624926 Score: 118
Period size: 39 Copynumber: 1.9 Consensus size: 39
1624841 ACATATATTA
1624851 AATATAAAATATTATTAAAAATAATATAAATATAATAAT
1 AATATAAAATATTATTAAAAATAATATAAATATAATAAT
* *
1624890 AATATATAAATA-TATTAAAATTTATATAAATATAATA
1 AATATA-AAATATTATTAAAAATAATATAAATATAATA
1624927 CTTTAAATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
39 29 0.85
40 5 0.15
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (39 bp):
AATATAAAATATTATTAAAAATAATATAAATATAATAAT
Found at i:1626281 original size:2 final size:2
Alignment explanation
Indices: 1626274--1626310 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1626264 CCAAAGTAAA
1626274 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 A
1626311 AAAGAAAAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1626590 original size:7 final size:7
Alignment explanation
Indices: 1626580--1626610 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
1626570 TTAAATTTTT
1626580 AAATAAA
1 AAATAAA
1626587 AAATAAA
1 AAATAAA
1626594 AAATAAA
1 AAATAAA
1626601 AAATAAA
1 AAATAAA
1626608 AAA
1 AAA
1626611 ATTAATATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (7 bp):
AAATAAA
Found at i:1627174 original size:13 final size:13
Alignment explanation
Indices: 1627156--1627186 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1627146 TATTTTTTAA
1627156 AATATTTATATCT
1 AATATTTATATCT
*
1627169 AATATTTATCTCT
1 AATATTTATATCT
1627182 AATAT
1 AATAT
1627187 ATATTCGAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.52
Consensus pattern (13 bp):
AATATTTATATCT
Found at i:1627839 original size:21 final size:21
Alignment explanation
Indices: 1627813--1627853 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1627803 ATATTGAGTT
*
1627813 CAGCATCCGAATGAATGTCTG
1 CAGCATCAGAATGAATGTCTG
1627834 CAGCATCAGAATGAATGTCT
1 CAGCATCAGAATGAATGTCT
1627854 CTGTTTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.24
Consensus pattern (21 bp):
CAGCATCAGAATGAATGTCTG
Found at i:1629138 original size:11 final size:11
Alignment explanation
Indices: 1629124--1629158 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
1629114 TTTATTTTCA
1629124 TATATTTATAT
1 TATATTTATAT
1629135 TATATTTATA-
1 TATATTTATAT
1629145 T-TATTTATAT
1 TATATTTATAT
1629155 TATA
1 TATA
1629159 ATCATATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 8 0.36
10 2 0.09
11 12 0.55
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
TATATTTATAT
Found at i:1629165 original size:20 final size:20
Alignment explanation
Indices: 1629121--1629166 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
1629111 ATTTTTATTT
*
1629121 TCATA-TATTTATATTATAT
1 TCATATTATTTATATTATAA
*
1629140 TTATATTATTTATATTATAA
1 TCATATTATTTATATTATAA
1629160 TCATATT
1 TCATATT
1629167 TAAAATAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (20 bp):
TCATATTATTTATATTATAA
Found at i:1630229 original size:13 final size:12
Alignment explanation
Indices: 1630206--1630244 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
1630196 GACATTAATT
1630206 TAATTAATAAAA
1 TAATTAATAAAA
1630218 TAATTAAATAAAA
1 TAATT-AATAAAA
*
1630231 TTATT-ATAAAA
1 TAATTAATAAAA
1630242 TAA
1 TAA
1630245 AAATTATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 8 0.33
12 5 0.21
13 11 0.46
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
TAATTAATAAAA
Found at i:1634592 original size:29 final size:29
Alignment explanation
Indices: 1634550--1634610 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
1634540 ATGTAAACTA
1634550 ATTACCTAGTCCGTCCGAAAAGAAAAATG
1 ATTACCTAGTCCGTCCGAAAAGAAAAATG
1634579 ATTACCTAGTCCGTCCGAAAAGAAAAATG
1 ATTACCTAGTCCGTCCGAAAAGAAAAATG
1634608 ATT
1 ATT
1634611 TTTATCACAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.41, C:0.20, G:0.16, T:0.23
Consensus pattern (29 bp):
ATTACCTAGTCCGTCCGAAAAGAAAAATG
Found at i:1635253 original size:10 final size:10
Alignment explanation
Indices: 1635238--1635268 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1635228 GGTGAGACTA
*
1635238 ATTACTTGTT
1 ATTACTTATT
1635248 ATTACTTATT
1 ATTACTTATT
1635258 ATTACTTATT
1 ATTACTTATT
1635268 A
1 A
1635269 GTGATTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.29, C:0.10, G:0.03, T:0.58
Consensus pattern (10 bp):
ATTACTTATT
Found at i:1639316 original size:2 final size:2
Alignment explanation
Indices: 1639309--1639339 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1639299 GACCTCACAA
*
1639309 AT AT AT AT AT AT AC 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 A
1639340 AGCTGTGACT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1645873 original size:15 final size:15
Alignment explanation
Indices: 1645853--1645882 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1645843 TAAATAATAA
1645853 ATACAATATTCAAAT
1 ATACAATATTCAAAT
*
1645868 ATACAATATTTAAAT
1 ATACAATATTCAAAT
1645883 TTATAAAAAT
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:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (15 bp):
ATACAATATTCAAAT
Found at i:1649214 original size:33 final size:35
Alignment explanation
Indices: 1649167--1649231 Score: 100
Period size: 33 Copynumber: 1.9 Consensus size: 35
1649157 AATGAAAAAT
1649167 TATTTAATTAAATATT-TATT-ATTTAAAAAACTA
1 TATTTAATTAAATATTGTATTAATTTAAAAAACTA
1649200 TATTTAA-TATAATATTGTATTAATTTAAAAAA
1 TATTTAATTA-AATATTGTATTAATTTAAAAAA
1649232 ATTATAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
32 2 0.07
33 13 0.45
34 4 0.14
35 10 0.34
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (35 bp):
TATTTAATTAAATATTGTATTAATTTAAAAAACTA
Found at i:1649230 original size:34 final size:32
Alignment explanation
Indices: 1649152--1649230 Score: 85
Period size: 33 Copynumber: 2.5 Consensus size: 32
1649142 ATATCTATAG
*
1649152 GTATTAA-TGAAAAATTATTTAATTAAATATT
1 GTATTAATTTAAAAATTATTTAATTAAATATT
1649183 -TATT-ATTTAAAAAACTATATTTAA-TATAATATT
1 GTATTAATTT-AAAAA-T-TATTTAATTA-AATATT
1649216 GTATTAATTTAAAAA
1 GTATTAATTTAAAAA
1649231 AATTATAATA
Statistics
Matches: 40, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
29 1 0.03
30 5 0.12
31 5 0.12
32 3 0.08
33 13 0.32
34 9 0.22
35 4 0.10
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.46
Consensus pattern (32 bp):
GTATTAATTTAAAAATTATTTAATTAAATATT
Found at i:1649561 original size:39 final size:38
Alignment explanation
Indices: 1649516--1649592 Score: 111
Period size: 38 Copynumber: 2.0 Consensus size: 38
1649506 TTATTTATTT
* *
1649516 ATAAATATAAATAAATTTTATATTTTATATTT-AATTTAA
1 ATAAATATAAAT-AATATTA-ATATTATATTTAAATTTAA
1649555 ATAAATATAAATAATATTAATATTATATTTAAATTTAA
1 ATAAATATAAATAATATTAATATTATATTTAAATTTAA
1649593 TCTGAGTTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
37 10 0.29
38 13 0.37
39 12 0.34
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (38 bp):
ATAAATATAAATAATATTAATATTATATTTAAATTTAA
Found at i:1649743 original size:2 final size:2
Alignment explanation
Indices: 1649731--1649765 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
1649721 GGGATAATAA
* *
1649731 AT AT AT GT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1649766 GTTTCTTTAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1653547 original size:5 final size:5
Alignment explanation
Indices: 1653520--1653561 Score: 59
Period size: 5 Copynumber: 8.4 Consensus size: 5
1653510 CTAAGATACT
*
1653520 TTATA TTTATA TTA-A TTAAA TTATA TTATA TTATA TTATA TT
1 TTATA -TTATA TTATA TTATA TTATA TTATA TTATA TTATA TT
1653562 TTCAATATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
4 4 0.12
5 25 0.74
6 5 0.15
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TTATA
Found at i:1653604 original size:17 final size:17
Alignment explanation
Indices: 1653578--1653626 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
1653568 ATTTTATTTT
*
1653578 TATATAATTTTTAATGTA
1 TATAAAATTTTTAAT-TA
* *
1653596 T-TAATATTTTAAATTA
1 TATAAAATTTTTAATTA
1653612 TATAAAATTTTTAAT
1 TATAAAATTTTTAAT
1653627 ATTTATATAT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
16 3 0.12
17 21 0.84
18 1 0.04
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (17 bp):
TATAAAATTTTTAATTA
Found at i:1653604 original size:33 final size:32
Alignment explanation
Indices: 1653565--1653652 Score: 86
Period size: 34 Copynumber: 2.6 Consensus size: 32
1653555 TTATATTTTC
*
1653565 AATATTTTATTTTTATATAATTTTTAATGTATT
1 AATATTTTATTTTTATATAATTTTTAATAT-TT
* * *
1653598 AATATTTTAAATTATATAAAATTTTTAATATTT
1 AATATTTT-ATTTTTATATAATTTTTAATATTT
1653631 ATATATTTCTATTATATTATAT
1 A-ATATTT-TATT-T-TTATAT
1653653 TTTAATTATA
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
33 11 0.26
34 26 0.60
35 2 0.05
36 4 0.09
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (32 bp):
AATATTTTATTTTTATATAATTTTTAATATTT
Found at i:1653638 original size:17 final size:17
Alignment explanation
Indices: 1653576--1653669 Score: 54
Period size: 17 Copynumber: 5.4 Consensus size: 17
1653566 ATATTTTATT
*
1653576 TTTATATAATTTTTAATG
1 TTTATAT-ATTTTTAATA
1653594 TATTA-ATA-TTTTAA-A
1 T-TTATATATTTTTAATA
*
1653609 TTATATAAAATTTTTAATA
1 TT-TAT-ATATTTTTAATA
* *
1653628 TTTATATATTTCTATTA
1 TTTATATATTTTTAATA
1653645 TATTATAT-TTTAATT-ATA
1 T-TTATATATTT--TTAATA
1653663 TTTATAT
1 TTTATAT
1653670 TATCATATTT
Statistics
Matches: 60, Mismatches: 7, Indels: 19
0.70 0.08 0.22
Matches are distributed among these distances:
14 1 0.02
15 3 0.05
16 6 0.10
17 22 0.37
18 21 0.35
19 7 0.12
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (17 bp):
TTTATATATTTTTAATA
Found at i:1653653 original size:16 final size:17
Alignment explanation
Indices: 1653625--1653670 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
1653615 AAAATTTTTA
*
1653625 ATATTTATATATTTCTATT
1 ATATTTATAT-TTT-AATT
1653644 ATA-TTATATTTTAATT
1 ATATTTATATTTTAATT
1653660 ATATTTATATT
1 ATATTTATATT
1653671 ATCATATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 6 0.24
17 10 0.40
18 6 0.24
19 3 0.12
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (17 bp):
ATATTTATATTTTAATT
Found at i:1657329 original size:2 final size:2
Alignment explanation
Indices: 1657322--1657365 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
1657312 TCTAAACTTG
* *
1657322 CT CT CT CT GT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CC CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1657364 CT
1 CT
1657366 GCTTTTCTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.02, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1661167 original size:3 final size:3
Alignment explanation
Indices: 1661159--1661187 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1661149 ATTGTTAGAA
1661159 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1661188 ATGTCCGACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1663765 original size:28 final size:29
Alignment explanation
Indices: 1663710--1663774 Score: 75
Period size: 28 Copynumber: 2.3 Consensus size: 29
1663700 ATAATTAAAA
1663710 ATAAATATATAAATTTGTTAAAATTTA-T
1 ATAAATATATAAATTTGTTAAAATTTATT
*
1663738 ATAAATTTATAATATTT-TT-AAATATTATT
1 ATAAATATATAA-ATTTGTTAAAAT-TTATT
1663767 AT-AATATA
1 ATAAATATA
1663775 AACATAATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
27 4 0.12
28 21 0.66
29 7 0.22
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (29 bp):
ATAAATATATAAATTTGTTAAAATTTATT
Found at i:1664610 original size:2 final size:2
Alignment explanation
Indices: 1664603--1664633 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1664593 ATTGGTGGCT
1664603 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1664634 TGCCACTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1665715 original size:22 final size:22
Alignment explanation
Indices: 1665689--1665731 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1665679 GCCTTCTGTC
1665689 ACTTTACCTACCGCTTTGTTCA
1 ACTTTACCTACCGCTTTGTTCA
* * *
1665711 ACTTTGCCTGCCTCTTTGTTC
1 ACTTTACCTACCGCTTTGTTC
1665732 TCACTATCTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.12, C:0.33, G:0.12, T:0.44
Consensus pattern (22 bp):
ACTTTACCTACCGCTTTGTTCA
Found at i:1672048 original size:19 final size:19
Alignment explanation
Indices: 1672010--1672062 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 19
1672000 TAAAAATAAA
*
1672010 TATTTTTAAATATATTTTATTT
1 TATTTTT-AA-AT-TTTTATAT
1672032 TATTTTTAAATTTTTATAT
1 TATTTTTAAATTTTTATAT
* *
1672051 AATTTTTTAATT
1 TATTTTTAAATT
1672063 AAATTTGTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 17 0.61
20 2 0.07
21 2 0.07
22 7 0.25
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TATTTTTAAATTTTTATAT
Found at i:1673088 original size:22 final size:22
Alignment explanation
Indices: 1673063--1673115 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
1673053 ATTTTTAATA
*
1673063 ATTTTTTATATAATT-TATATTT
1 ATTTTTTATAAAATTAT-TATTT
** *
1673085 ATTTAATATAAAATTATTTTTT
1 ATTTTTTATAAAATTATTATTT
1673107 ATTTTTTAT
1 ATTTTTTAT
1673116 TTAAATAAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
22 23 0.96
23 1 0.04
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (22 bp):
ATTTTTTATAAAATTATTATTT
Found at i:1673270 original size:18 final size:18
Alignment explanation
Indices: 1673222--1673271 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
1673212 ATAAATATTG
1673222 AATAAATTTAAAATTTTA
1 AATAAATTTAAAATTTTA
* * ***
1673240 AGTATACGAAAAATTTTA
1 AATAAATTTAAAATTTTA
1673258 AATAAATTTAAAAT
1 AATAAATTTAAAAT
1673272 ATCTAATTAT
Statistics
Matches: 22, Mismatches: 10, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (18 bp):
AATAAATTTAAAATTTTA
Found at i:1673882 original size:2 final size:2
Alignment explanation
Indices: 1673875--1673906 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1673865 TTAATTACAA
1673875 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
1673907 TATCACAGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1674920 original size:22 final size:22
Alignment explanation
Indices: 1674895--1674936 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1674885 TTAAATATAA
*
1674895 TTTACTTTTTATCTACATAAAG
1 TTTACTTTTTAACTACATAAAG
* *
1674917 TTTATTTTTTAACTTCATAA
1 TTTACTTTTTAACTACATAA
1674937 GTGATGTTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.31, C:0.12, G:0.02, T:0.55
Consensus pattern (22 bp):
TTTACTTTTTAACTACATAAAG
Found at i:1674938 original size:21 final size:21
Alignment explanation
Indices: 1674891--1674938 Score: 53
Period size: 22 Copynumber: 2.3 Consensus size: 21
1674881 ATTTTTAAAT
*
1674891 ATAA-TTTACTTTTTATCTAC
1 ATAAGTTTACTTTTTAACTAC
* *
1674911 ATAAAGTTTATTTTTTAACTTC
1 AT-AAGTTTACTTTTTAACTAC
1674933 ATAAGT
1 ATAAGT
1674939 GATGTTAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 2 0.09
21 6 0.26
22 15 0.65
ACGTcount: A:0.33, C:0.10, G:0.04, T:0.52
Consensus pattern (21 bp):
ATAAGTTTACTTTTTAACTAC
Found at i:1675219 original size:2 final size:2
Alignment explanation
Indices: 1675214--1675252 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1675204 TGTGTGTGTG
*
1675214 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1675253 TAATGTGAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1675620 original size:2 final size:2
Alignment explanation
Indices: 1675613--1675639 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1675603 CTGCCTTCAA
1675613 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1675640 AAATAATATT
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1676232 original size:12 final size:12
Alignment explanation
Indices: 1676193--1676247 Score: 51
Period size: 12 Copynumber: 4.6 Consensus size: 12
1676183 TATATAATAC
*
1676193 ATAAAAGATAAT
1 ATAAAATATAAT
*
1676205 -TAAATTATTAAT
1 ATAAAATA-TAAT
1676217 -TAAAATATAAT
1 ATAAAATATAAT
*
1676228 ATAAAATATGAT
1 ATAAAATATAAT
1676240 ACTAAAAT
1 A-TAAAAT
1676248 TTTAAATTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
11 9 0.25
12 21 0.58
13 6 0.17
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.35
Consensus pattern (12 bp):
ATAAAATATAAT
Found at i:1677063 original size:23 final size:23
Alignment explanation
Indices: 1677033--1677088 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
1677023 TTATTAAAAA
1677033 TTTA-AAAATAAATA-TATTATT
1 TTTATAAAATAAATATTATTATT
*
1677054 TTTAATAAAAT-ATTATTATTATT
1 TTT-ATAAAATAAATATTATTATT
1677077 TTTATAATAATA
1 TTTATAA-AATA
1677089 TATAAAATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
21 3 0.10
22 8 0.28
23 18 0.62
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TTTATAAAATAAATATTATTATT
Found at i:1677122 original size:30 final size:30
Alignment explanation
Indices: 1677079--1677152 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 30
1677069 TTATTATTTT
* * *
1677079 TATAATAATATATAAAATTATATAATATTAA
1 TATATTAA-ATATAAAATTATATAAAAATAA
* *
1677110 TATATTAAATATAAATTTATTTAAAAATAA
1 TATATTAAATATAAAATTATATAAAAATAA
* *
1677140 TAAATTAATTATA
1 TATATTAAATATA
1677153 TTTTTTCATC
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
30 29 0.81
31 7 0.19
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (30 bp):
TATATTAAATATAAAATTATATAAAAATAA
Found at i:1677838 original size:14 final size:14
Alignment explanation
Indices: 1677815--1677846 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1677805 GCTGATAATT
*
1677815 AGAGGGGAAGATAG
1 AGAGGCGAAGATAG
1677829 AGAGGCGAAGATAG
1 AGAGGCGAAGATAG
1677843 AGAG
1 AGAG
1677847 AGAGAACCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.44, C:0.03, G:0.47, T:0.06
Consensus pattern (14 bp):
AGAGGCGAAGATAG
Found at i:1678888 original size:3 final size:3
Alignment explanation
Indices: 1678880--1678904 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1678870 ACCTAGTTCA
1678880 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
1678905 TTTTGTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:1680315 original size:23 final size:23
Alignment explanation
Indices: 1680270--1680315 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
1680260 CAGGGAGAAA
* *
1680270 ACATCTTTCACAGATTGCTAGTT
1 ACATCTTTCACAGATTCCAAGTT
1680293 ACATCTTTCACAGATTCCAAGTT
1 ACATCTTTCACAGATTCCAAGTT
1680316 TTATATATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.28, C:0.24, G:0.11, T:0.37
Consensus pattern (23 bp):
ACATCTTTCACAGATTCCAAGTT
Found at i:1682417 original size:2 final size:2
Alignment explanation
Indices: 1682410--1682437 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1682400 AAATTTTTAC
1682410 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
1682438 TTCAAAAGAA
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:1684800 original size:12 final size:12
Alignment explanation
Indices: 1684783--1684807 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1684773 AAGAAAGGAC
1684783 CACTCTCTCTCT
1 CACTCTCTCTCT
1684795 CACTCTCTCTCT
1 CACTCTCTCTCT
1684807 C
1 C
1684808 TTAATTTCAT
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:0.08, C:0.52, G:0.00, T:0.40
Consensus pattern (12 bp):
CACTCTCTCTCT
Found at i:1685295 original size:23 final size:24
Alignment explanation
Indices: 1685267--1685316 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 24
1685257 TTAAAATTTT
1685267 ATATTTATGTTGTA-TTTAAATA-A
1 ATATTTAT-TTGTATTTTAAATATA
*
1685290 ATATTTATTTTTATTTTAAATATA
1 ATATTTATTTGTATTTTAAATATA
1685314 ATA
1 ATA
1685317 AAAATATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 4 0.17
23 16 0.67
24 4 0.17
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (24 bp):
ATATTTATTTGTATTTTAAATATA
Found at i:1691452 original size:62 final size:62
Alignment explanation
Indices: 1691380--1691516 Score: 197
Period size: 62 Copynumber: 2.2 Consensus size: 62
1691370 GAGCACATTT
* * * *
1691380 TAGTCTATTTTCCACGGTGTTGTTACACTTGTTTAATTTTACATTTTA-AGGAGCATAAAAAA
1 TAGTCCATTTTCCACGCTATTGTTACACTTGTTTAATTTCACA-TTTACAGGAGCATAAAAAA
* *
1691442 TAGTCCATTTTCCTCTCTATTGTTACACTTGTTTAATTTCACATTTACAGGAGCATAAAAAA
1 TAGTCCATTTTCCACGCTATTGTTACACTTGTTTAATTTCACATTTACAGGAGCATAAAAAA
1691504 -AGTCCATTTTCCA
1 TAGTCCATTTTCCA
1691517 ACAGTTGCAA
Statistics
Matches: 67, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
61 16 0.24
62 51 0.76
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.41
Consensus pattern (62 bp):
TAGTCCATTTTCCACGCTATTGTTACACTTGTTTAATTTCACATTTACAGGAGCATAAAAAA
Done.