Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397275.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_34.0, 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: 2955990
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 53928 characters in sequence are not A, C, G, or T
File 4 of 8
Found at i:1332481 original size:16 final size:16
Alignment explanation
Indices: 1332460--1332490 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1332450 ATCCTAGAAA
1332460 AATAAAGACAATATCT
1 AATAAAGACAATATCT
1332476 AATAAAGACAATATC
1 AATAAAGACAATATC
1332491 CAAAGAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.13, G:0.06, T:0.23
Consensus pattern (16 bp):
AATAAAGACAATATCT
Found at i:1336419 original size:12 final size:12
Alignment explanation
Indices: 1336400--1336446 Score: 71
Period size: 12 Copynumber: 4.0 Consensus size: 12
1336390 CAGAATAGTT
1336400 TCTTGCTGCCTC
1 TCTTGCTGCCTC
1336412 -CTTTGCTGCCTC
1 TC-TTGCTGCCTC
1336424 TCTTGCTGCCTC
1 TCTTGCTGCCTC
1336436 TCTTGCT-CCTC
1 TCTTGCTGCCTC
1336447 CAAAATCTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
11 5 0.15
12 27 0.82
13 1 0.03
ACGTcount: A:0.00, C:0.43, G:0.15, T:0.43
Consensus pattern (12 bp):
TCTTGCTGCCTC
Found at i:1343465 original size:17 final size:15
Alignment explanation
Indices: 1343435--1343477 Score: 68
Period size: 17 Copynumber: 2.7 Consensus size: 15
1343425 ATTTGGTTGA
1343435 AAATTAATTAAAACT
1 AAATTAATTAAAACT
1343450 AAATTCAATCTAAAACT
1 AAATT-AAT-TAAAACT
1343467 AAATTAATTAA
1 AAATTAATTAA
1343478 CAAAAATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
15 8 0.31
16 6 0.23
17 12 0.46
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.33
Consensus pattern (15 bp):
AAATTAATTAAAACT
Found at i:1347392 original size:20 final size:20
Alignment explanation
Indices: 1347367--1347420 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
1347357 TCTAGTTGTT
*
1347367 ATCTATCTATAGAT-GTGTCC
1 ATCTATCTATAGATCTTG-CC
*
1347387 ATCTATCGATAGATCTTGCC
1 ATCTATCTATAGATCTTGCC
*
1347407 ATTTATCTATAGAT
1 ATCTATCTATAGAT
1347421 ATTCTTTAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 27 0.93
21 2 0.07
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.41
Consensus pattern (20 bp):
ATCTATCTATAGATCTTGCC
Found at i:1351378 original size:41 final size:42
Alignment explanation
Indices: 1351333--1351418 Score: 95
Period size: 41 Copynumber: 2.1 Consensus size: 42
1351323 ACATATTGAG
**
1351333 TTATT-GGGTGAAACTATTGAGATATAAAATGTTATAATA-GC
1 TTATTAGGGTG-AACTATAAAGATATAAAATGTTATAATATGC
* * * *
1351374 TTATTAGGTTGGACTGTAAAGATATAATATGTTATAATATGC
1 TTATTAGGGTGAACTATAAAGATATAAAATGTTATAATATGC
1351416 TTA
1 TTA
1351419 GATTTATATT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
41 28 0.76
42 9 0.24
ACGTcount: A:0.37, C:0.05, G:0.19, T:0.40
Consensus pattern (42 bp):
TTATTAGGGTGAACTATAAAGATATAAAATGTTATAATATGC
Found at i:1352041 original size:23 final size:23
Alignment explanation
Indices: 1352001--1352050 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
1351991 ATGAGTAAAT
* *
1352001 ATAATAGAAATAAATAAATATAA
1 ATAATAGAAATAAATAAAAAAAA
*
1352024 ATAATA-ATATAAATTAAAAAAAA
1 ATAATAGAAATAAA-TAAAAAAAA
1352047 ATAA
1 ATAA
1352051 AAAACAACTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 6 0.26
23 17 0.74
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (23 bp):
ATAATAGAAATAAATAAAAAAAA
Found at i:1352514 original size:59 final size:59
Alignment explanation
Indices: 1352422--1352539 Score: 157
Period size: 59 Copynumber: 2.0 Consensus size: 59
1352412 ATATTCAACA
* * *
1352422 AAATTTAATCAGAACTATCAGGAGAAAACAAAAACATGATCATGGACAACCCTTGGAAT
1 AAATTTAAACAGAACTATCAGGAGAAAACAAAAACATGAACATGAACAACCCTTGGAAT
* ** *
1352481 AAATTTAAACAGGAA-TATCAGGCGGCAACAAAAACATGAACATGAACAACCCTTTGAAT
1 AAATTTAAACA-GAACTATCAGGAGAAAACAAAAACATGAACATGAACAACCCTTGGAAT
1352540 CAAAATACCT
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
59 48 0.94
60 3 0.06
ACGTcount: A:0.47, C:0.18, G:0.15, T:0.19
Consensus pattern (59 bp):
AAATTTAAACAGAACTATCAGGAGAAAACAAAAACATGAACATGAACAACCCTTGGAAT
Found at i:1353304 original size:2 final size:2
Alignment explanation
Indices: 1353297--1353324 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1353287 TATGCTTTAC
1353297 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
1353325 GCATATACAT
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:1359826 original size:12 final size:12
Alignment explanation
Indices: 1359811--1359859 Score: 64
Period size: 12 Copynumber: 4.1 Consensus size: 12
1359801 GAGATTTTTG
1359811 AGGCAGCAAGAA
1 AGGCAGCAAGAA
*
1359823 AGGCAGCAAGAG
1 AGGCAGCAAGAA
*
1359835 AGGCAGCAA-AGG
1 AGGCAGCAAGA-A
1359847 AGGCAGCAAGAA
1 AGGCAGCAAGAA
1359859 A
1 A
1359860 CTATTCTGGA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
11 1 0.03
12 31 0.94
13 1 0.03
ACGTcount: A:0.47, C:0.16, G:0.37, T:0.00
Consensus pattern (12 bp):
AGGCAGCAAGAA
Found at i:1359842 original size:24 final size:24
Alignment explanation
Indices: 1359810--1359857 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
1359800 AGAGATTTTT
1359810 GAGGCAGC-AAGAAAGGCAGCAAGA
1 GAGGCAGCAAAG-AAGGCAGCAAGA
*
1359834 GAGGCAGCAAAGGAGGCAGCAAGA
1 GAGGCAGCAAAGAAGGCAGCAAGA
1359858 AACTATTCTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 19 0.86
25 3 0.14
ACGTcount: A:0.44, C:0.17, G:0.40, T:0.00
Consensus pattern (24 bp):
GAGGCAGCAAAGAAGGCAGCAAGA
Found at i:1362780 original size:19 final size:21
Alignment explanation
Indices: 1362756--1362796 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1362746 ACATGTTGAC
1362756 TAGTT-AATT-TAAGTTATTT
1 TAGTTAAATTATAAGTTATTT
*
1362775 TAGTTAAATTATATGTTATTT
1 TAGTTAAATTATAAGTTATTT
1362796 T
1 T
1362797 GTCTTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 4 0.21
21 10 0.53
ACGTcount: A:0.32, C:0.00, G:0.10, T:0.59
Consensus pattern (21 bp):
TAGTTAAATTATAAGTTATTT
Found at i:1373621 original size:10 final size:10
Alignment explanation
Indices: 1373608--1373648 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
1373598 TTAACATTTT
1373608 TTAAAGTAAA
1 TTAAAGTAAA
**
1373618 TTAAACCAAA
1 TTAAAGTAAA
1373628 TTAAAGTAAAA
1 TTAAAGT-AAA
1373639 TTAAAGTAAA
1 TTAAAGTAAA
1373649 CTAGCTTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
10 16 0.62
11 10 0.38
ACGTcount: A:0.61, C:0.05, G:0.07, T:0.27
Consensus pattern (10 bp):
TTAAAGTAAA
Found at i:1381323 original size:21 final size:20
Alignment explanation
Indices: 1381279--1381327 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
1381269 CTTCTTAACC
*
1381279 TAAATTAAACCAAAATAAAG
1 TAAATTAAACCAAAACAAAG
* **
1381299 TAAAATTAAACTAAAACAACT
1 T-AAATTAAACCAAAACAAAG
1381320 TAAATTAA
1 TAAATTAA
1381328 CTATTCAACA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.63, C:0.10, G:0.02, T:0.24
Consensus pattern (20 bp):
TAAATTAAACCAAAACAAAG
Found at i:1383676 original size:21 final size:21
Alignment explanation
Indices: 1383650--1383689 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1383640 AGCTTTATAT
*
1383650 GTTGTCTTAATTAAGACAAAA
1 GTTGTCTGAATTAAGACAAAA
*
1383671 GTTGTCTGAATTTAGACAA
1 GTTGTCTGAATTAAGACAA
1383690 GCTAGATATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (21 bp):
GTTGTCTGAATTAAGACAAAA
Found at i:1385950 original size:243 final size:243
Alignment explanation
Indices: 1385501--1385985 Score: 654
Period size: 243 Copynumber: 2.0 Consensus size: 243
1385491 CAAATTCTAG
** *
1385501 AAATTAATTAAAGGAAACTTTTAATTAAAAATGCTAAACTAAGGAATAAAGGCCAAAAATTACTA
1 AAATTAATTAAAGGAAAAATTTAATTAAAAATGCTAAACTAAGGAATAAAGACCAAAAATTACTA
*
1385566 GAAAAGCATTTGATTGAAAGCGTACGATCATGGTATTCCTCAACAATTCATTTAGAACTAATCTC
66 GAAAAGCAGTTGATTGAAAGCGTACGATCATGGTATTCCTCAACAATTCATTTAGAACTAATCTC
* * * * *
1385631 TCTCTTTATACTTAAATTAATTGGTTGAATTGCTAGCCTAAAGTCTAAATTTATTTATAAGTGTT
131 TCTCTTTATACTTAAATCAATTGGTTGAATTGCTAGCCTAAAGTCCAAATTTATATACAAGTCTT
** * * * * * *
1385696 TGTTGAGATTCTTGTGCAAATACCTCTCATATTTAACTCACTACATGA
196 TGTCAAGATTCTTATACAAATACCTCACATAATCAACTCACAACATGA
* * * *
1385744 AAATTAATTAAA-GACAAAATTTAATTGACAATGCTAAACTACGGAATAAAGACTAAAAATTACT
1 AAATTAATTAAAGGA-AAAATTTAATTAAAAATGCTAAACTAAGGAATAAAGACCAAAAATTACT
* * * * *
1385808 AGAGAA-CTAGTTGATTGAAAGCTTAGGATCTTGGTATTTCCTCAACAATTCATTTGGAACTAAT
65 AGAAAAGC-AGTTGATTGAAAGCGTACGATCATGGTA-TTCCTCAACAATTCATTTAGAACTAAT
* *
1385872 CTCTCTCTTTATACTTAAATCAA-TGGCTTGAATTGCTAGTCTAGAGTCCAAA-TTATATACAAG
128 CTCTCTCTTTATACTTAAATCAATTGG-TTGAATTGCTAGCCTAAAGTCCAAATTTATATACAAG
1385935 TCTTTGTCAAGATTCTTATACAAATACCTCACATAATCAACTCACAACATG
192 TCTTTGTCAAGATTCTTATACAAATACCTCACATAATCAACTCACAACATG
1385986 TCTATGTGAA
Statistics
Matches: 210, Mismatches: 28, Indels: 8
0.85 0.11 0.03
Matches are distributed among these distances:
242 3 0.01
243 137 0.65
244 70 0.33
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (243 bp):
AAATTAATTAAAGGAAAAATTTAATTAAAAATGCTAAACTAAGGAATAAAGACCAAAAATTACTA
GAAAAGCAGTTGATTGAAAGCGTACGATCATGGTATTCCTCAACAATTCATTTAGAACTAATCTC
TCTCTTTATACTTAAATCAATTGGTTGAATTGCTAGCCTAAAGTCCAAATTTATATACAAGTCTT
TGTCAAGATTCTTATACAAATACCTCACATAATCAACTCACAACATGA
Found at i:1391436 original size:14 final size:14
Alignment explanation
Indices: 1391417--1391449 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1391407 CCAATAATGC
1391417 TAAAATAAAAAATA
1 TAAAATAAAAAATA
*
1391431 TAAAATAAAGAATA
1 TAAAATAAAAAATA
1391445 -AAAAT
1 TAAAAT
1391450 TACTAGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (14 bp):
TAAAATAAAAAATA
Found at i:1394642 original size:59 final size:59
Alignment explanation
Indices: 1394579--1394749 Score: 227
Period size: 59 Copynumber: 2.9 Consensus size: 59
1394569 CTTAATAGCG
* * *
1394579 AATCAATTCATGCTCAACAACCA-CTTAAACCAAGCTCAATAAACTCATGCTCGTTAGTA
1 AATCAAATCATGCTCAAC-AGCATCTTAAACCAAGCTCAATAAACTCATGCTCATTAGTA
* * * * * *
1394638 AATCAAATCATGCTCAATAGTATTTTAAACCAAGCTCTATAAACTGATGCTTATTAGTA
1 AATCAAATCATGCTCAACAGCATCTTAAACCAAGCTCAATAAACTCATGCTCATTAGTA
* *
1394697 AATCAAATCATGTTCAACAGCATCTTAGACCAAGCTCAATAAACTCATGCTCA
1 AATCAAATCATGCTCAACAGCATCTTAAACCAAGCTCAATAAACTCATGCTCA
1394750 ATTCTAGAAT
Statistics
Matches: 94, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
58 2 0.02
59 92 0.98
ACGTcount: A:0.39, C:0.23, G:0.09, T:0.28
Consensus pattern (59 bp):
AATCAAATCATGCTCAACAGCATCTTAAACCAAGCTCAATAAACTCATGCTCATTAGTA
Found at i:1395563 original size:31 final size:31
Alignment explanation
Indices: 1395488--1395563 Score: 89
Period size: 31 Copynumber: 2.5 Consensus size: 31
1395478 TTTCCTTATT
* * *
1395488 TTTCATTTCAATTCAATCTTTCAATATTTTA
1 TTTCTTTTCAATTTAATCCTTCAATATTTTA
* * * *
1395519 TTCCTTTTCAATTTAGTCCTTCAGTATTTTC
1 TTTCTTTTCAATTTAATCCTTCAATATTTTA
1395550 TTTCTTTTCAATTT
1 TTTCTTTTCAATTT
1395564 GTTCCTTTTT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.21, C:0.18, G:0.03, T:0.58
Consensus pattern (31 bp):
TTTCTTTTCAATTTAATCCTTCAATATTTTA
Found at i:1396105 original size:15 final size:15
Alignment explanation
Indices: 1396085--1396115 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1396075 CAAGTATCAA
1396085 TACTTTCTATTCTAG
1 TACTTTCTATTCTAG
1396100 TACTTTCTATTCTAG
1 TACTTTCTATTCTAG
1396115 T
1 T
1396116 TTTCAAGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.19, G:0.06, T:0.55
Consensus pattern (15 bp):
TACTTTCTATTCTAG
Found at i:1397870 original size:102 final size:102
Alignment explanation
Indices: 1397641--1397885 Score: 255
Period size: 102 Copynumber: 2.4 Consensus size: 102
1397631 GATAGCATGT
* * * *
1397641 TATTGGATGCAAGCTTTATCGCTTATTCTTTAGACATAGTTCATCATTCCTATTTCAACTATAAG
1 TATTGGATGCAAGCTTTATCGCTCATTCTTTAGACATAGTTCATCACTCATATTTCAACTACAAG
*** *
1397706 TTTTATCACTCATACTTTAGTTGCAATAATATTATGC
66 TTTTATCAAAAATACTTTAGATGCAATAATATTATGC
* * * * *
1397743 TATTGGTTGCAAGCTTGATCACTCATTCTTTGGCCATA-TGTCATCACTCATATTTCAA-TCACA
1 TATTGGATGCAAGCTTTATCGCTCATTCTTTAGACATAGT-TCATCACTCATATTTCAACT-ACA
* * * *
1397806 AGTTTTA-CTAAAAATATTTTGGATGTAATGATATTATGC
64 AGTTTTATC-AAAAATACTTTAGATGCAATAATATTATGC
* *
1397845 TATTGGATGCAAGCTTTATTGCTCATT-TCTTAGTCATAGTT
1 TATTGGATGCAAGCTTTATCGCTCATTCT-TTAGACATAGTT
1397886 AACATATGAA
Statistics
Matches: 115, Mismatches: 23, Indels: 10
0.78 0.16 0.07
Matches are distributed among these distances:
101 4 0.03
102 110 0.96
103 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.42
Consensus pattern (102 bp):
TATTGGATGCAAGCTTTATCGCTCATTCTTTAGACATAGTTCATCACTCATATTTCAACTACAAG
TTTTATCAAAAATACTTTAGATGCAATAATATTATGC
Found at i:1399327 original size:22 final size:22
Alignment explanation
Indices: 1399301--1399343 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1399291 ATGGATTATG
1399301 GGCCATTATCCATTTATCCTAT
1 GGCCATTATCCATTTATCCTAT
1399323 GGCCATTATCCATTTATCCTA
1 GGCCATTATCCATTTATCCTA
1399344 AATATGATGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.28, G:0.09, T:0.40
Consensus pattern (22 bp):
GGCCATTATCCATTTATCCTAT
Found at i:1403422 original size:11 final size:12
Alignment explanation
Indices: 1403404--1403430 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1403394 CACAAAATGT
1403404 AACTTTTTTGTA
1 AACTTTTTTGTA
1403416 AACTTTTTTGTA
1 AACTTTTTTGTA
1403428 AAC
1 AAC
1403431 CAATGCATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.30, C:0.11, G:0.07, T:0.52
Consensus pattern (12 bp):
AACTTTTTTGTA
Found at i:1403851 original size:43 final size:42
Alignment explanation
Indices: 1403756--1403853 Score: 108
Period size: 42 Copynumber: 2.3 Consensus size: 42
1403746 ACCTCACACG
* * *
1403756 TTTTCCTTCTTAGCTTGTTCTCTTATACATTATACATATACT
1 TTTTCCCTCTTACCTTATTCTCTTATACATTATACATATACT
* * * *
1403798 TGTTT-TCTCTTACCTTATTCTCTTATACCTTTTCACTTATACT
1 T-TTTCCCTCTTACCTTATTCTCTTATACATTAT-ACATATACT
1403841 TTTTCCCTCTTAC
1 TTTTCCCTCTTAC
1403854 TTGCTACTAA
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
42 26 0.58
43 19 0.42
ACGTcount: A:0.17, C:0.26, G:0.03, T:0.54
Consensus pattern (42 bp):
TTTTCCCTCTTACCTTATTCTCTTATACATTATACATATACT
Found at i:1404348 original size:39 final size:38
Alignment explanation
Indices: 1404294--1404389 Score: 106
Period size: 39 Copynumber: 2.4 Consensus size: 38
1404284 TTTACTCTTT
*
1404294 CCTATTCTTAACTTTACTCTA-CTGCTC-GCTTATTCACTA
1 CCTATTCTT-ACTTTACTCTACCT-CTCATC-TATTCACTA
* *
1404333 CCTATTCTTGACTTTATTCTACCTCTCATCTATTCTCTA
1 CCTATTCTT-ACTTTACTCTACCTCTCATCTATTCACTA
1404372 CCTATTCTTAGCTTTACT
1 CCTATTCTTA-CTTTACT
1404390 TGATTACTCA
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
38 1 0.02
39 45 0.92
40 3 0.06
ACGTcount: A:0.19, C:0.30, G:0.04, T:0.47
Consensus pattern (38 bp):
CCTATTCTTACTTTACTCTACCTCTCATCTATTCACTA
Found at i:1404695 original size:26 final size:26
Alignment explanation
Indices: 1404665--1404722 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
1404655 ACTCTTCATA
* *
1404665 TTCAAGTGTGAAACAAATGTTATTTT
1 TTCAAGTGTGAAAAAAATGTTAATTT
1404691 TTCAAGTGTGAAAAAAATGTTAATTT
1 TTCAAGTGTGAAAAAAATGTTAATTT
1404717 TTCAAG
1 TTCAAG
1404723 AAAGAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.38, C:0.07, G:0.16, T:0.40
Consensus pattern (26 bp):
TTCAAGTGTGAAAAAAATGTTAATTT
Found at i:1404731 original size:27 final size:26
Alignment explanation
Indices: 1404674--1404732 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
1404664 ATTCAAGTGT
* * ***
1404674 GAAACAAATGTTATTTTTTCAAGTGT
1 GAAAAAAATGTTAATTTTTCAAGAAA
1404700 GAAAAAAATGTTAATTTTTCAAGAAA
1 GAAAAAAATGTTAATTTTTCAAGAAA
1404726 GAAAAAA
1 GAAAAAA
1404733 TCAACACCAC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.49, C:0.05, G:0.14, T:0.32
Consensus pattern (26 bp):
GAAAAAAATGTTAATTTTTCAAGAAA
Found at i:1408306 original size:53 final size:53
Alignment explanation
Indices: 1408226--1408333 Score: 216
Period size: 53 Copynumber: 2.0 Consensus size: 53
1408216 CCAATTTTTT
1408226 TCTATTTAGCTTTCTTTACATATTTACAAATATAATATAAGGTTTGCACCTCA
1 TCTATTTAGCTTTCTTTACATATTTACAAATATAATATAAGGTTTGCACCTCA
1408279 TCTATTTAGCTTTCTTTACATATTTACAAATATAATATAAGGTTTGCACCTCA
1 TCTATTTAGCTTTCTTTACATATTTACAAATATAATATAAGGTTTGCACCTCA
1408332 TC
1 TC
1408334 AAGGTGTCAC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.31, C:0.18, G:0.07, T:0.44
Consensus pattern (53 bp):
TCTATTTAGCTTTCTTTACATATTTACAAATATAATATAAGGTTTGCACCTCA
Found at i:1409202 original size:29 final size:29
Alignment explanation
Indices: 1409157--1409220 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
1409147 AAAGGCCAAC
* * *
1409157 TTACACACCATGTTGAAAAAAAAAATTTG
1 TTACACACCATGCTGAAAAAAAAAAGTTA
*
1409186 TTACACACCGTGCTGAAAAAAAAAAGTTA
1 TTACACACCATGCTGAAAAAAAAAAGTTA
1409215 TTACAC
1 TTACAC
1409221 GTCATGTTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.47, C:0.17, G:0.11, T:0.25
Consensus pattern (29 bp):
TTACACACCATGCTGAAAAAAAAAAGTTA
Found at i:1409302 original size:128 final size:127
Alignment explanation
Indices: 1408916--1409306 Score: 403
Period size: 129 Copynumber: 3.1 Consensus size: 127
1408906 CAAAATCTCT
* ** * * *
1408916 AAAAAAAAAA-TTGTTACACATCATGTTGAAAATTAAAA-TTGTTACATGCCATGTTTAAGGTGT
1 AAAAAAAAAATTTGTTACACACCATGTTGAAAAAAAAAAGTTATTACACGTCATGTTTAAGGTGT
* * * * * * * * *
1408979 TTAACTCAAAAGGTTTATATGCTAGTGAAATACAAAGATAGAAACCAAGTTATACACCATGTT
66 TTAATTCAAGA-GTTTATGTCCTAATGAAATACAAAGATAGAGACCAAATTACACACCATGTG
* * * * * *
1409042 TAAAAAATAATATTGTTACACACTATTTTGAAAAAAAAATGTTATTACACATCATGTTTAAGGTG
1 AAAAAAAAAAT-TTGTTACACACCATGTTGAAAAAAAAAAGTTATTACACGTCATGTTTAAGGTG
* * * * *
1409107 TTTAACTCCAAGAGCTTT-TGTCCTATTGAAATACAAAGATAAAGGCCAACTTACACACCATGTT
65 TTTAA-TTCAAGAG-TTTATGTCCTAATGAAATACAAAGATAGAGACCAAATTACACACCATG-T
1409171 G
127 G
* * *
1409172 AAAAAAAAAATTTGTTACACACCGTGCTGAAAAAAAAAAGTTATTACACGTCATGTTTGAGGTG-
1 AAAAAAAAAATTTGTTACACACCATGTTGAAAAAAAAAAGTTATTACACGTCATGTTTAAGGTGT
* **
1409236 TTAATTTCAAGAGTTTATGTCCAAATGAAATACAAAGATAGAGACCAAATTACATGCCATGCTG
66 TTAA-TTCAAGAGTTTATGTCCTAATGAAATACAAAGATAGAGACCAAATTACACACCATG-TG
1409300 AAAAAAA
1 AAAAAAA
1409307 TAGTTATAAC
Statistics
Matches: 215, Mismatches: 43, Indels: 12
0.80 0.16 0.04
Matches are distributed among these distances:
126 8 0.04
127 3 0.01
128 79 0.37
129 108 0.50
130 17 0.08
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.30
Consensus pattern (127 bp):
AAAAAAAAAATTTGTTACACACCATGTTGAAAAAAAAAAGTTATTACACGTCATGTTTAAGGTGT
TTAATTCAAGAGTTTATGTCCTAATGAAATACAAAGATAGAGACCAAATTACACACCATGTG
Found at i:1409358 original size:227 final size:220
Alignment explanation
Indices: 1409074--1409511 Score: 490
Period size: 227 Copynumber: 2.0 Consensus size: 220
1409064 CTATTTTGAA
* * *
1409074 AAAAAAATGTTATTACACATCATGTTTAAGGTGTTTAACTCCAAGAGCTTTTGTCCTATTGAAAT
1 AAAAAAATGTTATTACACATCATGTTTAAGGTATTTAACTCCAAGAGCTTTTGTCCTAGTAAAAT
* * * *
1409139 ACAAAGATAAAGGCCAACTTACACACCATGTTGAAAAAAAAAATTTGTTACACACCGTGCTGAAA
66 ACAAAGATAAAGACCAACTTAAACACCATGTT--AAAAAAAAA--TATTACACACCATG-T--AA
* ** *
1409204 AAAAAAAGTTATTACACGTCATGTTT-GAGGTGTTAATTTC-AAGAGTTTATGTCCAAATGAAAT
124 AAAAAAAGTTATTACACGCCATGTTTAG-GGTGTTAAACTCTAACAGTTTATGTCCAAATGAAAT
1409267 ACAAAGATAGAGACCAAATTACATGCCATGCTG
188 ACAAAGATAGAGACCAAATTACATGCCATGCTG
*
1409300 AAAAAAATAGTTA-TA-ACATGCCATGTTTAAGGTATTTAACTTCAAGAG-TTTATGTCCTAGTA
1 AAAAAAAT-GTTATTACACAT--CATGTTTAAGGTATTTAACTCCAAGAGCTTT-TGTCCTAGTA
* * * ** * * * **
1409362 AAATACAAATATAGAGATCATGTTAAATACTATGTTAAAAAAAAATATTACACATCATGTTTAAA
62 AAATACAAAGATAAAGACCAACTTAAACACCATGTTAAAAAAAAATATTACACACCATGTAAAAA
* * * *
1409427 AAAAGTTATTATATGCCATGTTTAGGGTGTTAAACTCTAACAGTTTATGTCCTAGTGAAATACAA
127 AAAAGTTATTACACGCCATGTTTAGGGTGTTAAACTCTAACAGTTTATGTCCAAATGAAATACAA
*
1409492 AGATAGAGACCAAGTTACAT
192 AGATAGAGACCAAATTACAT
1409512 AGCTTATTGA
Statistics
Matches: 179, Mismatches: 27, Indels: 17
0.80 0.12 0.08
Matches are distributed among these distances:
220 33 0.18
221 44 0.25
222 1 0.01
223 11 0.06
225 13 0.07
226 13 0.07
227 64 0.36
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (220 bp):
AAAAAAATGTTATTACACATCATGTTTAAGGTATTTAACTCCAAGAGCTTTTGTCCTAGTAAAAT
ACAAAGATAAAGACCAACTTAAACACCATGTTAAAAAAAAATATTACACACCATGTAAAAAAAAA
GTTATTACACGCCATGTTTAGGGTGTTAAACTCTAACAGTTTATGTCCAAATGAAATACAAAGAT
AGAGACCAAATTACATGCCATGCTG
Found at i:1409366 original size:99 final size:99
Alignment explanation
Indices: 1409196--1409378 Score: 251
Period size: 99 Copynumber: 1.8 Consensus size: 99
1409186 TTACACACCG
* * * *
1409196 TGCTGAAAAAAAAAAGTTATTACACGTCATGTTTGAGGTGTTAATTTCAAGAGTTTATGTCCAAA
1 TGCTGAAAAAAAAAAGTTATAACACGCCATGTTTAAGGTGTTAACTTCAAGAGTTTATGTCCAAA
*
1409261 TGAAATACAAAGATAGAGACCAAATTACATGCCA
66 TAAAATACAAAGATAGAGACCAAATTACATGCCA
* * * *
1409295 TGCTG-AAAAAAATAGTTATAACATGCCATGTTTAAGGTATTTAACTTCAAGAGTTTATGTCCTA
1 TGCTGAAAAAAAAAAGTTATAACACGCCATGTTTAAGGT-GTTAACTTCAAGAGTTTATGTCCAA
* *
1409359 GTAAAATACAAATATAGAGA
65 ATAAAATACAAAGATAGAGA
1409379 TCATGTTAAA
Statistics
Matches: 72, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
98 28 0.39
99 44 0.61
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (99 bp):
TGCTGAAAAAAAAAAGTTATAACACGCCATGTTTAAGGTGTTAACTTCAAGAGTTTATGTCCAAA
TAAAATACAAAGATAGAGACCAAATTACATGCCA
Found at i:1409403 original size:99 final size:98
Alignment explanation
Indices: 1409196--1409406 Score: 233
Period size: 99 Copynumber: 2.1 Consensus size: 98
1409186 TTACACACCG
* * * *
1409196 TGCTGAAAAAAAAAAGTTATTACACGTCATGTTTGAGGTGTTAATTTCAAGAGTTTATGTCCAAA
1 TGCT-AAAAAAAAAAGTTATAACACGCCATGTTTAAGGTGTTAACTTCAAGAGTTTATGTCCAAA
* * *
1409261 TGAAATACAAAGATAGAGACCAAATTACATGCCA
65 TAAAATACAAAGATAGAGACCAAATTAAATACCA
* * * * * *
1409295 TGCTGAAAAAAATAGTTATAACATGCCATGTTTAAGGTATTTAACTTCAAGAGTTTATGTCCTAG
1 TGCTAAAAAAAAAAGTTATAACACGCCATGTTTAAGGT-GTTAACTTCAAGAGTTTATGTCCAAA
* * ** *
1409360 TAAAATACAAATATAGAGATCATGTTAAATACTA
65 TAAAATACAAAGATAGAGACCAAATTAAATACCA
*
1409394 TGTTAAAAAAAAA
1 TGCTAAAAAAAAA
1409407 TATTACACAT
Statistics
Matches: 90, Mismatches: 21, Indels: 2
0.80 0.19 0.02
Matches are distributed among these distances:
98 28 0.31
99 62 0.69
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.30
Consensus pattern (98 bp):
TGCTAAAAAAAAAAGTTATAACACGCCATGTTTAAGGTGTTAACTTCAAGAGTTTATGTCCAAAT
AAAATACAAAGATAGAGACCAAATTAAATACCA
Found at i:1409481 original size:122 final size:126
Alignment explanation
Indices: 1409300--1409636 Score: 364
Period size: 128 Copynumber: 2.7 Consensus size: 126
1409290 TGCCATGCTG
* *
1409300 AAAAAAATAGTTATAACATGCCATGTTTAAGGTATTTAACT-TCAAGAGTTTATGTCCTAGTAAA
1 AAAAAAA-AGTTATTACATGCCATGTTTAAGGTGTTTAACTCT-AAGAGTTTATGTCCTAGTAAA
* * * * *
1409364 ATACAAATATAGAGATCATGTTAAATA-C-TA-TGTTAAAAAAAAA-TATTACACATCATGTTT
64 ATACAAAGATAGAGACCAAGTTAAATAGCTTATTG-AAAAAAAAAAGTATTACACACCATGTTT
* * * * *
1409424 -AAAAAAAGTTATTATATGCCATGTTTAGGGTGTTAAACTCTAACAGTTTATGTCCTAGTGAAAT
1 AAAAAAAAGTTATTACATGCCATGTTTAAGGTGTTTAACTCTAAGAGTTTATGTCCTAGTAAAAT
* * *
1409488 ACAAAGATAGAGACCAAGTTACATAGCTTATTGAAAAAAAAAAGTTGTTGCACACCATGTTT
66 ACAAAGATAGAGACCAAGTTAAATAGCTTATTGAAAAAAAAAAG-TATTACACACCATGTTT
* * * * * *
1409550 AAAAAAAAAATTATTACATGTCATGTTTAAGGTGTTTAACTCCAAGAGTTTATTTACC-AATGAA
1 -AAAAAAAAGTTATTACATGCCATGTTTAAGGTGTTTAACTCTAAGAGTTTATGT-CCTAGTAAA
**
1409614 ATACAAAGATAGAGGTCAAGTTA
64 ATACAAAGATAGAGACCAAGTTA
1409637 CATGTCATGT
Statistics
Matches: 178, Mismatches: 26, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
122 70 0.39
123 8 0.04
124 11 0.06
125 2 0.01
126 14 0.08
128 71 0.40
129 2 0.01
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.32
Consensus pattern (126 bp):
AAAAAAAAGTTATTACATGCCATGTTTAAGGTGTTTAACTCTAAGAGTTTATGTCCTAGTAAAAT
ACAAAGATAGAGACCAAGTTAAATAGCTTATTGAAAAAAAAAAGTATTACACACCATGTTT
Found at i:1409600 original size:128 final size:124
Alignment explanation
Indices: 1409300--1409639 Score: 391
Period size: 122 Copynumber: 2.7 Consensus size: 124
1409290 TGCCATGCTG
* * * * *
1409300 AAAAAAATAGTTATAACATGCCATGTTTAAGGTATTTAACTTCAAGAGTTTATGTCCTAGTAAAA
1 AAAAAAAAAGTTATTACATGCCATGTTTAAGGTGTTTAACTCCAAGAGTTTATGTCCTAGTGAAA
* * * * *
1409365 TACAAATATAGAGATCATGTTAAATACTATGTTAAAAAAAAATATTACACATCATGTTT
66 TACAAAGATAGAGATCAAGTTACATACTATGTAAAAAAAAAATATTACACACCATGTTT
* * * * *
1409424 --AAAAAAAGTTATTATATGCCATGTTTAGGGTGTTAAACTCTAACAGTTTATGTCCTAGTGAAA
1 AAAAAAAAAGTTATTACATGCCATGTTTAAGGTGTTTAACTCCAAGAGTTTATGTCCTAGTGAAA
* * *
1409487 TACAAAGATAGAGACCAAGTTACATAGCTTAT-TGAAAAAAAAAAGTTGTTGCACACCATGTTT
66 TACAAAGATAGAGATCAAGTTACATA-C-TATGT-AAAAAAAAAA--TATTACACACCATGTTT
* * * *
1409550 AAAAAAAAAATTATTACATGTCATGTTTAAGGTGTTTAACTCCAAGAGTTTATTTACC-AATGAA
1 AAAAAAAAAGTTATTACATGCCATGTTTAAGGTGTTTAACTCCAAGAGTTTATGT-CCTAGTGAA
*
1409614 ATACAAAGATAGAGGTCAAGTTACAT
65 ATACAAAGATAGAGATCAAGTTACAT
1409640 GTCATGTCTA
Statistics
Matches: 179, Mismatches: 29, Indels: 12
0.81 0.13 0.05
Matches are distributed among these distances:
122 75 0.42
123 2 0.01
124 12 0.07
126 14 0.08
128 74 0.41
129 2 0.01
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.32
Consensus pattern (124 bp):
AAAAAAAAAGTTATTACATGCCATGTTTAAGGTGTTTAACTCCAAGAGTTTATGTCCTAGTGAAA
TACAAAGATAGAGATCAAGTTACATACTATGTAAAAAAAAAATATTACACACCATGTTT
Found at i:1409614 original size:349 final size:354
Alignment explanation
Indices: 1408959--1409645 Score: 838
Period size: 349 Copynumber: 1.9 Consensus size: 354
1408949 TAAAATTGTT
* * *
1408959 ACATGCCATGTTTAAGGTGTTTAACTCAAAAGGTTTATATGCTAGTGAAATACAAAGATAGAAAC
1 ACATGCCATGTTTAAGGTATTTAACTCAAAAGGTTTATATCCTAGTAAAATACAAAGATAGAAAC
* *
1409024 CAAGTTATACACCATGTTTAAAAAATAATATTGTTACACACTATTTTGAAAAAAAAATGTTATTA
66 CAAGTTAAACACCATGTTTAAAAAATAATATTATTACACACTATTTT--AAAAAAAATGTTATTA
* * * * *
1409089 CACATCATGTTTAAGGTGTTTAACTCCAAGAGCTTTTGTCCTATTGAAATACAAAGATAAAGGCC
129 CACACCATGTTTAAGGTGTTAAACTCCAACAGCTTTTGTCCTAGTGAAATACAAAGATAAAGACC
* * *
1409154 AACTTACACACCATGTTGAAAAAAAAAATTTGTTACACACCGTGCTGAAAAAAAAAAGTTATTAC
194 AACTTACACACCATATTGAAAAAAAAAAGTTGTTACACACCATGCTGAAAAAAAAAAGTTATTAC
* * *
1409219 ACGTCATGTTTGAGGTGTTAATTTCAAGAGTTTATGTCCAAATGAAATACAAAGATAGAGACCAA
259 ACGTCATGTTTAAGGTGTTAACTCCAAGAGTTTATGTCCAAATGAAATACAAAGATAGAGACCAA
1409284 ATTACATGCCATGCTGAAAAAAATAGTTATA
324 ATTACATGCCATGCTGAAAAAAATAGTTATA
* * * *
1409315 ACATGCCATGTTTAAGGTATTTAACTTCAAGA-GTTTATGTCCTAGTAAAATACAAATATAGAGA
1 ACATGCCATGTTTAAGGTATTTAAC-TCAAAAGGTTTATATCCTAGTAAAATACAAAGATAGAAA
* * * *
1409379 TCATGTTAAATACTATG-TTAAAAAA-AA-A-TATTACACA-TCATGTTT-AAAAAAA-GTTATT
65 CCAAGTTAAACACCATGTTTAAAAAATAATATTATTACACACT-AT-TTTAAAAAAAATGTTATT
* ** * * *
1409437 ATATGCCATGTTTAGGGTGTTAAACTCTAACAG-TTTATGTCCTAGTGAAATACAAAGATAGAGA
128 ACACACCATGTTTAAGGTGTTAAACTCCAACAGCTTT-TGTCCTAGTGAAATACAAAGATAAAGA
* * * * * * *
1409501 CCAAGTTACATAGCTTATTGAAAAAAAAAAGTTGTTGCACACCATGTTTAAAAAAAAAA-TTATT
192 CCAACTTACACACCATATTGAAAAAAAAAAGTTGTTACACACCATGCTGAAAAAAAAAAGTTATT
* * *
1409565 ACATGTCATGTTTAAGGTGTTTAACTCCAAGAGTTTATTTACC-AATGAAATACAAAGATAGAGG
257 ACACGTCATGTTTAAGGTG-TTAACTCCAAGAGTTTATGT-CCAAATGAAATACAAAGATAGAGA
* * *
1409629 TCAAGTTACATGTCATG
320 CCAAATTACATGCCATG
1409646 TCTACACCAT
Statistics
Matches: 282, Mismatches: 43, Indels: 19
0.82 0.12 0.06
Matches are distributed among these distances:
348 25 0.09
349 155 0.55
350 9 0.03
351 1 0.00
352 10 0.04
353 4 0.01
354 2 0.01
355 8 0.03
356 63 0.22
357 5 0.02
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (354 bp):
ACATGCCATGTTTAAGGTATTTAACTCAAAAGGTTTATATCCTAGTAAAATACAAAGATAGAAAC
CAAGTTAAACACCATGTTTAAAAAATAATATTATTACACACTATTTTAAAAAAAATGTTATTACA
CACCATGTTTAAGGTGTTAAACTCCAACAGCTTTTGTCCTAGTGAAATACAAAGATAAAGACCAA
CTTACACACCATATTGAAAAAAAAAAGTTGTTACACACCATGCTGAAAAAAAAAAGTTATTACAC
GTCATGTTTAAGGTGTTAACTCCAAGAGTTTATGTCCAAATGAAATACAAAGATAGAGACCAAAT
TACATGCCATGCTGAAAAAAATAGTTATA
Found at i:1410048 original size:75 final size:74
Alignment explanation
Indices: 1409900--1410051 Score: 191
Period size: 75 Copynumber: 2.0 Consensus size: 74
1409890 GATGGCGATG
* * * *
1409900 ATTGTAAAATTAGAAAGTGTTGGATGGCAAGAGAAAGAAATAGAGAGCACAGCAAATGAATGTCA
1 ATTGTAAAATTAGAAAGAGATGGATGGCAAGAGAAAGAAATAGAGAGCACAGCAAATGAAAGCCA
* *
1409965 GAGTGAGAA
66 CAGAGAGAA
* *
1409974 ATTGATAAAATTATAAAGAGATGGATGGCAAGAGAAAGAAATCAGA-AGCA-TGACAAATGAAAG
1 ATTG-TAAAATTAGAAAGAGATGGATGGCAAGAGAAAGAAAT-AGAGAGCACAG-CAAATGAAAG
1410037 CCACAGAGAGAA
63 CCACAGAGAGAA
1410049 ATT
1 ATT
1410052 AGGGGAAAAA
Statistics
Matches: 67, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
74 5 0.07
75 59 0.88
76 3 0.04
ACGTcount: A:0.49, C:0.08, G:0.26, T:0.18
Consensus pattern (74 bp):
ATTGTAAAATTAGAAAGAGATGGATGGCAAGAGAAAGAAATAGAGAGCACAGCAAATGAAAGCCA
CAGAGAGAA
Found at i:1412200 original size:68 final size:68
Alignment explanation
Indices: 1412120--1412257 Score: 213
Period size: 68 Copynumber: 2.0 Consensus size: 68
1412110 GTGTGTGTGT
* *
1412120 ATATATATATATATATATATAGTATTTCAGGCCTGCTAATTCATCTTTTGGACCACTTCTAATTT
1 ATATATATATATATATATATAGTATTTCAGCCCTGCTAATTCATCTTTAGGACCACTTCTAATTT
1412185 ATA
66 ATA
* * * * *
1412188 ATATATATATATATATATATGGTATTTCTGCCCTGTTTATTCATCTTTAGGACCACTTTTAATTT
1 ATATATATATATATATATATAGTATTTCAGCCCTGCTAATTCATCTTTAGGACCACTTCTAATTT
1412253 ATA
66 ATA
1412256 AT
1 AT
1412258 CGTCTTACAC
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
68 63 1.00
ACGTcount: A:0.31, C:0.14, G:0.09, T:0.46
Consensus pattern (68 bp):
ATATATATATATATATATATAGTATTTCAGCCCTGCTAATTCATCTTTAGGACCACTTCTAATTT
ATA
Found at i:1412445 original size:15 final size:15
Alignment explanation
Indices: 1412416--1412444 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1412406 GTCTATAACA
1412416 AAATTAATTAATTTT
1 AAATTAATTAATTTT
1412431 AAATTAA-TAATTTT
1 AAATTAATTAATTTT
1412445 TTATACAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
AAATTAATTAATTTT
Found at i:1412793 original size:94 final size:94
Alignment explanation
Indices: 1412632--1412806 Score: 248
Period size: 94 Copynumber: 1.9 Consensus size: 94
1412622 ATGTAGGAAC
* * * * *
1412632 CTTTAAATCATATACTTGGGAGGACTAGGGATTCATTAACTAAAAGTAAGGCTAGGTCCTCTCTT
1 CTTTAAATCATATACTTCGCAAGACTAAGGATTCATTAACTAAAAGCAAGGCTAGGTCCTCTCTT
1412697 TTGTTTACACAAAAAAGAAAAATCGTAAG
66 TTGTTTACACAAAAAAGAAAAATCGTAAG
1412726 CTTTAAATCATATAAC-TCGCAAGACTAAGGATTCATTAGA-TAAAAGCAAGGCTAGGTTCC-CT
1 CTTTAAATCATAT-ACTTCGCAAGACTAAGGATTCATTA-ACTAAAAGCAAGGCTAGG-TCCTCT
*
1412788 CTTTTGTTTCCACAAAAAA
63 CTTTTGTTTACACAAAAAA
1412807 TTTAAGATTC
Statistics
Matches: 72, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
94 66 0.92
95 6 0.08
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Consensus pattern (94 bp):
CTTTAAATCATATACTTCGCAAGACTAAGGATTCATTAACTAAAAGCAAGGCTAGGTCCTCTCTT
TTGTTTACACAAAAAAGAAAAATCGTAAG
Found at i:1417444 original size:31 final size:31
Alignment explanation
Indices: 1417406--1417467 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
1417396 AGACCCGTTC
* * *
1417406 CCCCTTCCATTAGCTCCCCTTCTCCCATTTG
1 CCCCTTCCATCAGCACCACTTCTCCCATTTG
*
1417437 CCCCTTCCATCGGCACCACTTCTCCCATTTG
1 CCCCTTCCATCAGCACCACTTCTCCCATTTG
1417468 ATCATTTCTC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.11, C:0.48, G:0.08, T:0.32
Consensus pattern (31 bp):
CCCCTTCCATCAGCACCACTTCTCCCATTTG
Found at i:1419092 original size:347 final size:347
Alignment explanation
Indices: 1418311--1419096 Score: 921
Period size: 347 Copynumber: 2.3 Consensus size: 347
1418301 TTTCCACTAT
*
1418311 TTAAGGTGTTAATGAGTTAATTAAATAATTTAGTTAATTAAGTAATGTAAAGTGTTAGTAATTAA
1 TTAAGGTGTTAATGA-TTAATTAAATAATTTAGTT-ATTAAGTAATGTAATGTGTTAGTAATTAA
* * *
1418376 GAAATTAATTAAATAAGAAATATTATATAATACTTTATTTATTTAAATTAATTAAGGTTTGAGGG
64 GAAATTAATTAAATTAGTAA-ATTATATAATACTTTATTTATTTAAATTAATTAAGGTTTAAGGG
* *
1418441 AAGTAACTATCACATAATTTAACTAATTAAAAAGAATCATGTATTAGTAATTAAGCAATTAATTA
128 AAGTAACTATCACACAATTTAACTAATTAAAAAGAATCATGTATTAGTAATTAAGCAATGAATTA
* * * *
1418506 TAGTTGTAAATATAGTAAATTTTGAAACTATTTAAATTAATTAAGTTTTAATAATTTAATGAAAT
193 TAATTATAAATATAGTAAATTTTGAAACTATTTAAATTAATTAAGTTTTAATAAATTAATAAAAT
* ** * *
1418571 GATTTATTTACAAAAATGAAAAAATGTTTTTGTAATTAAGAAATTAATTAAATTTGTAATATTAT
258 AATTTATCGACAAAAATGAAAAAATGTTTTTGTAACTAAGAAATTAATTAAATTAGTAATATTAT
* *
1418636 TTAATTTAAAAGATATTTAAGTTAA
323 TTAAATTAAAAGATATTTAAATTAA
** * * * * * *
1418661 TTAAGGTGTTAATGGGCTAATTAAATAATTTAGGGTATTAAATAATGCAATTTGTTGGTACTTAA
1 TTAAGGTGTTAAT-GATTAATTAAATAATTTA-GTTATTAAGTAATGTAATGTGTTAGTAATTAA
* * * * *
1418726 GAAATTAATTAAGTTAGTAAGATTATATAATA-TTTGATTTCTTTTAATTAATTAGGGTTTAATG
64 GAAATTAATTAAATTAGTAA-ATTATATAATACTTT-ATTTATTTAAATTAATTAAGGTTTAAGG
* * *
1418790 GAATTAA-T-T-ACACAATTTAACTAGTTAAAAAGAATCATGTATTAGTAATTACGCAATGAATT
127 GAAGTAACTATCACACAATTTAACTAATTAAAAAGAATCATGTATTAGTAATTAAGCAATGAATT
* *
1418852 A-AATTAATAAATGTAGTCAAA-TTT-AAACTTATTT-AATTAATTAAGGTTTTATTAAATTAAT
192 ATAATT-ATAAATATAGT-AAATTTTGAAAC-TATTTAAATTAATTAA-GTTTTAATAAATTAAT
* * **
1418913 AAAATAATTTATCGA-AGCAAATGAAAAGATGTTTTAT-TAACTAAGCTATTAATTAAATTAGTA
253 AAAATAATTTATCGACA-AAAATGAAAAAATGTTTT-TGTAACTAAGAAATTAATTAAATTAGTA
1418976 ATATTATTTAAATTAAAA-ACTATTTAAATTAA
316 ATATTATTTAAATTAAAAGA-TATTTAAATTAA
* ** * * *
1419008 TTAAGGTGCTAATGCATTAACCAAATAATTTAGTTATTTAAGTTACGTAATGTGTTCGTAATTAA
1 TTAAGGTGTTAATG-ATTAATTAAATAATTTAGTTA-TTAAGTAATGTAATGTGTTAGTAATTAA
*
1419073 GCAAA-TAAATAAATTAGTAAATTA
64 G-AAATTAATTAAATTAGTAAATTA
1419097 AGTAAAATTT
Statistics
Matches: 368, Mismatches: 55, Indels: 30
0.81 0.12 0.07
Matches are distributed among these distances:
346 27 0.07
347 218 0.59
348 8 0.02
349 4 0.01
350 108 0.29
351 3 0.01
ACGTcount: A:0.44, C:0.04, G:0.11, T:0.40
Consensus pattern (347 bp):
TTAAGGTGTTAATGATTAATTAAATAATTTAGTTATTAAGTAATGTAATGTGTTAGTAATTAAGA
AATTAATTAAATTAGTAAATTATATAATACTTTATTTATTTAAATTAATTAAGGTTTAAGGGAAG
TAACTATCACACAATTTAACTAATTAAAAAGAATCATGTATTAGTAATTAAGCAATGAATTATAA
TTATAAATATAGTAAATTTTGAAACTATTTAAATTAATTAAGTTTTAATAAATTAATAAAATAAT
TTATCGACAAAAATGAAAAAATGTTTTTGTAACTAAGAAATTAATTAAATTAGTAATATTATTTA
AATTAAAAGATATTTAAATTAA
Found at i:1422758 original size:20 final size:20
Alignment explanation
Indices: 1422733--1422791 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
1422723 ATTAAGAATT
1422733 TTTAGGCTA-AAATAGTTCAA
1 TTTAGGCTATAAATAGTT-AA
*
1422753 TTTAGG-TATAATTAGGTTAA
1 TTTAGGCTATAAATA-GTTAA
*
1422773 GTTAGGCTATAAATAGTTA
1 TTTAGGCTATAAATAGTTA
1422792 GCTTAACAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
19 2 0.06
20 21 0.64
21 10 0.30
ACGTcount: A:0.37, C:0.05, G:0.19, T:0.39
Consensus pattern (20 bp):
TTTAGGCTATAAATAGTTAA
Found at i:1437644 original size:35 final size:35
Alignment explanation
Indices: 1437605--1437675 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
1437595 TTTACTTATA
*
1437605 ATTAATCTTCTAGTTTTGATTACTTGAATAAAATT
1 ATTAATCTTCTAGTTTTGATGACTTGAATAAAATT
1437640 ATTAATCTTCTAGTTTTGATGACTTGAATAAAATT
1 ATTAATCTTCTAGTTTTGATGACTTGAATAAAATT
1437675 A
1 A
1437676 GTCTATCATA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.35, C:0.08, G:0.10, T:0.46
Consensus pattern (35 bp):
ATTAATCTTCTAGTTTTGATGACTTGAATAAAATT
Found at i:1440488 original size:144 final size:145
Alignment explanation
Indices: 1440207--1440488 Score: 410
Period size: 144 Copynumber: 2.0 Consensus size: 145
1440197 AGAATGGTTG
* * *
1440207 TATTTAATTTGATTTCATTTACGTGGGTCCGAATTATTTAATGTAATAATGTTTGTTTGATTTCT
1 TATTTAATTTGATTTCATTTACGTGAGTCCGAATTATTTAATGTAATAATATTTGTTTAATTTCT
* * *
1440272 TTAATAAAAAATATGAATCTTGTCTTTCAATAAAGAAATATTCATGTCACATTCACACATTAGAC
66 TTAATAAAAAATATGAATCTCGTCTTTCAAAAAAGAAAAATTCATGTCACATTCACACATTAGAC
1440337 GGCCTTTATTAATAT
131 GGCCTTTATTAATAT
* *
1440352 TATTTAATTTGATTTCGTTTATGTGAGTCCGAATTATTTAATGTAATAATATTAAT-TTTAATTT
1 TATTTAATTTGATTTCATTTACGTGAGTCCGAATTATTTAATGTAATAATATT--TGTTTAATTT
* * *
1440416 -TTTAAT-AAAAATTTGTATCTCGTGTTTCAAAAAAGAAAAATTCATGTCACATTCACACATTAG
64 CTTTAATAAAAAATATGAATCTCGTCTTTCAAAAAAGAAAAATTCATGTCACATTCACACATTA-
1440479 GA-GGCCTTTA
128 GACGGCCTTTA
1440489 ATGATATCAC
Statistics
Matches: 123, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
144 58 0.47
145 57 0.46
146 7 0.06
147 1 0.01
ACGTcount: A:0.34, C:0.11, G:0.12, T:0.43
Consensus pattern (145 bp):
TATTTAATTTGATTTCATTTACGTGAGTCCGAATTATTTAATGTAATAATATTTGTTTAATTTCT
TTAATAAAAAATATGAATCTCGTCTTTCAAAAAAGAAAAATTCATGTCACATTCACACATTAGAC
GGCCTTTATTAATAT
Found at i:1447129 original size:17 final size:17
Alignment explanation
Indices: 1447107--1447142 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
1447097 GAACAAATAT
1447107 GGAGGTCAATAAGAGTA
1 GGAGGTCAATAAGAGTA
1447124 GGAGGTCAATAAGAGTA
1 GGAGGTCAATAAGAGTA
1447141 GG
1 GG
1447143 CACTGCACCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.39, C:0.06, G:0.39, T:0.17
Consensus pattern (17 bp):
GGAGGTCAATAAGAGTA
Found at i:1449921 original size:57 final size:57
Alignment explanation
Indices: 1449823--1449978 Score: 156
Period size: 57 Copynumber: 2.7 Consensus size: 57
1449813 TCTTGTCTTT
* * * * *
1449823 AATTAAGAC-AAAAATATTTTATCTTGTTTAAATTCTA-ACAAATCTATTTTCTTATCTA
1 AATTAAGACAAAAAATATTTT-T-TTGTCTAAATT-AAGACAAATATATTTTATGATCTA
* * *
1449881 GATTATGACAAAAAATA-TTTTTTGTCTTAAATTAAGACAAATATATTTTATGGTCTA
1 AATTAAGACAAAAAATATTTTTTTGTC-TAAATTAAGACAAATATATTTTATGATCTA
* * *
1449938 AATTAAGACCAAACATATTTTTTTGTCTAAATTAAGCCAAA
1 AATTAAGACAAAAAATATTTTTTTGTCTAAATTAAGACAAA
1449979 CACGTTAAAG
Statistics
Matches: 81, Mismatches: 13, Indels: 9
0.79 0.13 0.09
Matches are distributed among these distances:
56 5 0.06
57 50 0.62
58 19 0.23
59 7 0.09
ACGTcount: A:0.41, C:0.11, G:0.07, T:0.41
Consensus pattern (57 bp):
AATTAAGACAAAAAATATTTTTTTGTCTAAATTAAGACAAATATATTTTATGATCTA
Found at i:1449939 original size:28 final size:28
Alignment explanation
Indices: 1449823--1449978 Score: 127
Period size: 29 Copynumber: 5.4 Consensus size: 28
1449813 TCTTGTCTTT
*
1449823 AATTAAGACAAAAATATTTTATCTTGTTTA
1 AATTAAGACAAAAATATTTTA--TTGTCTA
* ** * *
1449853 AATTCTA-ACAAATCTATTTTCTTATCTA
1 AATT-AAGACAAAAATATTTTATTGTCTA
* *
1449881 GATTATGACAAAAAATATTTT-TTGTCTTA
1 AATTAAGAC-AAAAATATTTTATTGTC-TA
* *
1449910 AATTAAGACAAATATATTTTATGGTCTA
1 AATTAAGACAAAAATATTTTATTGTCTA
* *
1449938 AATTAAGACCAAACATATTTTTTTGTCTA
1 AATTAAGA-CAAAAATATTTTATTGTCTA
*
1449967 AATTAAGCCAAA
1 AATTAAGACAAA
1449979 CACGTTAAAG
Statistics
Matches: 100, Mismatches: 20, Indels: 14
0.75 0.15 0.10
Matches are distributed among these distances:
28 38 0.38
29 46 0.46
30 15 0.15
31 1 0.01
ACGTcount: A:0.41, C:0.11, G:0.07, T:0.41
Consensus pattern (28 bp):
AATTAAGACAAAAATATTTTATTGTCTA
Found at i:1456177 original size:57 final size:57
Alignment explanation
Indices: 1456111--1456218 Score: 162
Period size: 57 Copynumber: 1.9 Consensus size: 57
1456101 TATAGATACG
* * * *
1456111 AAAACATATTTGGTCTTAATTTAGACAAGAAAATATGTTTGTCTTAATTTAAAATCA
1 AAAAAATATTTGGTCTTAATCTAGACAAGAAAACATATTTGTCTTAATTTAAAATCA
* *
1456168 AAAAAATATTTTGTCTTAATCTAGACAAGAAAACGTATTTGTCTTAATTTA
1 AAAAAATATTTGGTCTTAATCTAGACAAGAAAACATATTTGTCTTAATTTA
1456219 GGCAAGATAA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
57 45 1.00
ACGTcount: A:0.42, C:0.09, G:0.10, T:0.39
Consensus pattern (57 bp):
AAAAAATATTTGGTCTTAATCTAGACAAGAAAACATATTTGTCTTAATTTAAAATCA
Found at i:1456209 original size:28 final size:28
Alignment explanation
Indices: 1456085--1456235 Score: 137
Period size: 28 Copynumber: 5.3 Consensus size: 28
1456075 TGACGCCTTT
* * * * *
1456085 AACATGTTTGTTTTAATATAGATACGAA
1 AACATATTTGTCTTAATTTAGACAAGAA
1456113 AACATATTTGGTCTTAATTTAGACAAGAA
1 AACATATTT-GTCTTAATTTAGACAAGAA
* * *
1456142 AATATGTTTGTCTTAATTTAAAATCAA-AA
1 AACATATTTGTCTTAATTT-AGA-CAAGAA
*
1456171 AA-ATATTTTGTCTTAATCTAGACAAGAA
1 AACATA-TTTGTCTTAATTTAGACAAGAA
* *
1456199 AACGTATTTGTCTTAATTTAGGCAAGATA
1 AACATATTTGTCTTAATTTAGACAAGA-A
1456228 AA-ATATTT
1 AACATATTT
1456236 TTATCTTAAT
Statistics
Matches: 101, Mismatches: 15, Indels: 14
0.78 0.12 0.11
Matches are distributed among these distances:
27 3 0.03
28 50 0.50
29 45 0.45
30 3 0.03
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (28 bp):
AACATATTTGTCTTAATTTAGACAAGAA
Found at i:1456231 original size:57 final size:56
Alignment explanation
Indices: 1456111--1456245 Score: 146
Period size: 57 Copynumber: 2.4 Consensus size: 56
1456101 TATAGATACG
* * * * * *
1456111 AAAACATATTTGGTCTTAATTTAGACAAGAAAATATGTTTGTCTTAATTTAAAATCA
1 AAAAAATATTTTGTCTTAATCTAGACAAGAAAACATATTTGTCTTAATTT-AAAGCA
* *
1456168 AAAAAATATTTTGTCTTAATCTAGACAAGAAAACGTATTTGTCTTAATTT-AGGCA
1 AAAAAATATTTTGTCTTAATCTAGACAAGAAAACATATTTGTCTTAATTTAAAGCA
*
1456223 AGATAAAATATTTTTATCTTAAT
1 A-A-AAAATA-TTTTGTCTTAAT
1456246 GAAAGACAAG
Statistics
Matches: 66, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
55 4 0.06
56 1 0.02
57 50 0.76
58 11 0.17
ACGTcount: A:0.41, C:0.09, G:0.10, T:0.39
Consensus pattern (56 bp):
AAAAAATATTTTGTCTTAATCTAGACAAGAAAACATATTTGTCTTAATTTAAAGCA
Found at i:1456402 original size:17 final size:17
Alignment explanation
Indices: 1456380--1456414 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1456370 ATAACATTAA
1456380 AATAA-GAGTTTTTATTT
1 AATAAGGAG-TTTTATTT
1456397 AATAAGGAGTTTTATTT
1 AATAAGGAGTTTTATTT
1456414 A
1 A
1456415 TCAAAAACTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.82
18 3 0.18
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (17 bp):
AATAAGGAGTTTTATTT
Found at i:1461500 original size:21 final size:22
Alignment explanation
Indices: 1461470--1461525 Score: 73
Period size: 21 Copynumber: 2.6 Consensus size: 22
1461460 CTTTTTCTTG
1461470 TTCC-TCCTTTTTCCCTTTCTC
1 TTCCTTCCTTTTTCCCTTTCTC
1461491 -TCCTTCCTTTCTT-CCTTTCTC
1 TTCCTTCCTTT-TTCCCTTTCTC
*
1461512 TTCCTTCTTTTTTC
1 TTCCTTCCTTTTTC
1461526 TTCTTCTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
20 3 0.10
21 16 0.53
22 11 0.37
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (22 bp):
TTCCTTCCTTTTTCCCTTTCTC
Found at i:1461527 original size:14 final size:13
Alignment explanation
Indices: 1461499--1461547 Score: 53
Period size: 14 Copynumber: 3.6 Consensus size: 13
1461489 TCTCCTTCCT
* *
1461499 TTCTTCCTTTCTC
1 TTCTTCTTTTTTC
1461512 TTCCTTCTTTTTTC
1 TT-CTTCTTTTTTC
*
1461526 TTCTTCTTTTTCTT
1 TTCTTCTTTTT-TC
1461540 TTCTTCTT
1 TTCTTCTT
1461548 GGTAGTGGAC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
13 11 0.35
14 20 0.65
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (13 bp):
TTCTTCTTTTTTC
Found at i:1461530 original size:17 final size:17
Alignment explanation
Indices: 1461499--1461547 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
1461489 TCTCCTTCCT
*
1461499 TTCTTCCTTTC-TCTTCC
1 TTCTTCTTTTCTTCTT-C
1461516 TTCTT-TTTTCTTCTTC
1 TTCTTCTTTTCTTCTTC
*
1461532 TTTTTCTTTTCTTCTT
1 TTCTTCTTTTCTTCTT
1461548 GGTAGTGGAC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 9 0.32
17 19 0.68
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (17 bp):
TTCTTCTTTTCTTCTTC
Found at i:1462089 original size:40 final size:40
Alignment explanation
Indices: 1462045--1462122 Score: 115
Period size: 40 Copynumber: 1.9 Consensus size: 40
1462035 TATAAAAGAC
1462045 ACCAAT-TATGACAAGGTTGAAAA-CTCCATTAAGGTGAATT
1 ACCAATCT-TGACAAGGTTGAAAATC-CCATTAAGGTGAATT
*
1462085 ACCAATCTTGGCAAGGTTGAAAATCCCATTAAGGTGAA
1 ACCAATCTTGACAAGGTTGAAAATCCCATTAAGGTGAA
1462123 AAATAGCCAA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
40 33 0.94
41 2 0.06
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.26
Consensus pattern (40 bp):
ACCAATCTTGACAAGGTTGAAAATCCCATTAAGGTGAATT
Found at i:1465194 original size:36 final size:35
Alignment explanation
Indices: 1465112--1465340 Score: 260
Period size: 35 Copynumber: 6.5 Consensus size: 35
1465102 CTTAATTTTT
* *
1465112 AATTTAATCAATTAGGCCCAATAATTTAATTAAAC
1 AATTTAATCAATTAGGCCCAATAACTTCATTAAAC
** * *
1465147 AATTTAATCAATTAGGTACAAAAACTTGATTAAAC
1 AATTTAATCAATTAGGCCCAATAACTTCATTAAAC
1465182 AAATTTAATCAATTAGGCCCAATAACTTCATTAAAC
1 -AATTTAATCAATTAGGCCCAATAACTTCATTAAAC
1465218 AATTTAATCAATTAGGCCCAATAACTTCATTAAAC
1 AATTTAATCAATTAGGCCCAATAACTTCATTAAAC
* * ****
1465253 AAATTTAATCAATTAGGCCAAATAACTTAATTGTTT
1 -AATTTAATCAATTAGGCCCAATAACTTCATTAAAC
* ** * * * *
1465289 AATTTAATTAATTAGATCTAATGACTTAATTAAAT
1 AATTTAATCAATTAGGCCCAATAACTTCATTAAAC
*
1465324 AATTTAATGAATTAGGC
1 AATTTAATCAATTAGGC
1465341 ACAACTTAAT
Statistics
Matches: 166, Mismatches: 26, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
35 106 0.64
36 60 0.36
ACGTcount: A:0.45, C:0.13, G:0.07, T:0.35
Consensus pattern (35 bp):
AATTTAATCAATTAGGCCCAATAACTTCATTAAAC
Found at i:1465293 original size:71 final size:71
Alignment explanation
Indices: 1465112--1465367 Score: 295
Period size: 71 Copynumber: 3.6 Consensus size: 71
1465102 CTTAATTTTT
* * * *
1465112 AATTTAATCAATTAGGCCCAATAATTTAATTAAACAATTTAATCAATTAGGTACAAAAACTTGAT
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATCAATTAGGTCCAATAACTTAAT
1465177 TAAACA
66 TAAACA
* * *
1465183 AATTTAATCAATTAGGCCCAATAACTTCATTAAACAATTTAATCAATTAGGCCCAATAACTTCAT
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATCAATTAGGTCCAATAACTTAAT
1465248 TAAACA
66 TAAACA
* **** * * * *
1465254 AATTTAATCAATTAGGCCAAATAACTTAATTGTTTAATTTAATTAATTAGATCTAATGACTTAAT
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATCAATTAGGTCCAATAACTTAAT
*
1465319 TAAA-T
66 TAAACA
* * *
1465324 AATTTAATGAATTAGG--C-ACAACTTAATTAAACAGCTTTAATCAA
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAACA-ATTTAATCAA
1465368 ATGCTTGAGA
Statistics
Matches: 156, Mismatches: 28, Indels: 5
0.83 0.15 0.03
Matches are distributed among these distances:
67 11 0.07
68 8 0.05
70 15 0.10
71 122 0.78
ACGTcount: A:0.45, C:0.14, G:0.07, T:0.34
Consensus pattern (71 bp):
AATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATCAATTAGGTCCAATAACTTAAT
TAAACA
Found at i:1465293 original size:106 final size:106
Alignment explanation
Indices: 1465112--1465367 Score: 288
Period size: 106 Copynumber: 2.4 Consensus size: 106
1465102 CTTAATTTTT
* *
1465112 AATTTAATCAATTAGGCCCAATAATTTAATTAAACAATTTAATCAATTAGGTACAAAAACTTGAT
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATCAATTAGGTACAAAAACTTAAT
* *
1465177 TAAACAAATTTAATCAATTAGGCCCAATAACTTCATTAAAC
66 TAAACAAATTTAATCAATTAGACCCAATAACTTAATTAAAC
* *
1465218 AATTTAATCAATTAGGCCCAATAACTTCATTAAACAAATTTAATCAATTAGG-CCAAATAACTTA
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAAC-AATTTAATCAATTAGGTACAAA-AACTTA
**** * * * * *
1465282 ATT-GTTTAATTTAATTAATTAGATCTAATGACTTAATTAAAT
64 ATTAAACAAATTTAATCAATTAGACCCAATAACTTAATTAAAC
* * *
1465324 AATTTAATGAATTAGG--C-ACAACTTAATTAAACAGCTTTAATCAA
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAACA-ATTTAATCAA
1465368 ATGCTTGAGA
Statistics
Matches: 128, Mismatches: 19, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
102 1 0.01
103 22 0.17
104 1 0.01
106 80 0.62
107 24 0.19
ACGTcount: A:0.45, C:0.14, G:0.07, T:0.34
Consensus pattern (106 bp):
AATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATCAATTAGGTACAAAAACTTAAT
TAAACAAATTTAATCAATTAGACCCAATAACTTAATTAAAC
Found at i:1467194 original size:14 final size:14
Alignment explanation
Indices: 1467175--1467202 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1467165 TCAATATTCA
1467175 ACCTTTTGATCAAT
1 ACCTTTTGATCAAT
1467189 ACCTTTTGATCAAT
1 ACCTTTTGATCAAT
1467203 TGAACATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.21, G:0.07, T:0.43
Consensus pattern (14 bp):
ACCTTTTGATCAAT
Found at i:1488245 original size:21 final size:21
Alignment explanation
Indices: 1488221--1488271 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
1488211 ACTTAGGTAA
1488221 CACTAAAGGAACTAGTTAATG
1 CACTAAAGGAACTAGTTAATG
1488242 CACTAAAGGAACTAGTTAATG
1 CACTAAAGGAACTAGTTAATG
1488263 CACTAAAGG
1 CACTAAAGG
1488272 GTTTGGAACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.20, T:0.22
Consensus pattern (21 bp):
CACTAAAGGAACTAGTTAATG
Found at i:1502036 original size:25 final size:25
Alignment explanation
Indices: 1501993--1502040 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
1501983 ATGTAAATTG
*
1501993 TAATGTTTTATACGCTTTAATTTAT
1 TAATGTTTTATACGATTTAATTTAT
1502018 TAATGTTTTATATC-ATTTAATTT
1 TAATGTTTTATA-CGATTTAATTT
1502041 CTTTTTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 20 0.95
26 1 0.05
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.58
Consensus pattern (25 bp):
TAATGTTTTATACGATTTAATTTAT
Found at i:1508351 original size:64 final size:65
Alignment explanation
Indices: 1508245--1508398 Score: 188
Period size: 64 Copynumber: 2.4 Consensus size: 65
1508235 GAATGTTGGA
* * *
1508245 ACCACGTGTGGAATATTA-CCTCACA-CTGTGTGAAATGCCATCATCCA-TCATACTAGAAGCAT
1 ACCACGTGTGGAAT-GTAGCCTCACATC-ATGTGAAATACCATCATCCATTCATACTAGAAGCAT
1508307 TC
64 TC
* * * *
1508309 ACCATGTGTGGAATGTAGCCTCACATCATGTGAAATACCATCATCCATTTATACTATATGCATTC
1 ACCACGTGTGGAATGTAGCCTCACATCATGTGAAATACCATCATCCATTCATACTAGAAGCATTC
* *
1508374 GCCACGTGTGGAATGTTGCCTCACA
1 ACCACGTGTGGAATGTAGCCTCACA
1508399 CTGTGTGAAA
Statistics
Matches: 77, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
63 2 0.03
64 38 0.49
65 37 0.48
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (65 bp):
ACCACGTGTGGAATGTAGCCTCACATCATGTGAAATACCATCATCCATTCATACTAGAAGCATTC
Found at i:1508395 original size:65 final size:64
Alignment explanation
Indices: 1508245--1508408 Score: 204
Period size: 65 Copynumber: 2.5 Consensus size: 64
1508235 GAATGTTGGA
* * * *
1508245 ACCACGTGTGGAATATTACCTCACACTGTGTGAAATGCCATCATCCATCATACTAGAAGCATTC
1 ACCACGTGTGGAATGTTGCCTCACACTATGTGAAATACCATCATCCATCATACTAGAAGCATTC
* * * * *
1508309 ACCATGTGTGGAATGTAGCCTCACA-TCATGTGAAATACCATCATCCATTTATACTATATGCATT
1 ACCACGTGTGGAATGTTGCCTCACACT-ATGTGAAATACCATCATCCA-TCATACTAGAAGCATT
1508373 C
64 C
* *
1508374 GCCACGTGTGGAATGTTGCCTCACACTGTGTGAAA
1 ACCACGTGTGGAATGTTGCCTCACACTATGTGAAA
1508409 ATGCTAGAAA
Statistics
Matches: 84, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
63 1 0.01
64 39 0.46
65 43 0.51
66 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (64 bp):
ACCACGTGTGGAATGTTGCCTCACACTATGTGAAATACCATCATCCATCATACTAGAAGCATTC
Found at i:1510531 original size:74 final size:74
Alignment explanation
Indices: 1510442--1510588 Score: 267
Period size: 74 Copynumber: 2.0 Consensus size: 74
1510432 GGTAGTTATG
**
1510442 GTTCATTTGTGATGAATTTTAATTTTAATAGGATTTATCCTACTTTGGTTGAACTATTAAACATG
1 GTTCATTTGTGATGAATTTTAATTCAAATAGGATTTATCCTACTTTGGTTGAACTATTAAACATG
1510507 TTAGAATTA
66 TTAGAATTA
*
1510516 GTTCATTTGTGATGAATTTTAATTCAAATAGGATTTATCCTACTTTGGTTGAACTTTTAAACATG
1 GTTCATTTGTGATGAATTTTAATTCAAATAGGATTTATCCTACTTTGGTTGAACTATTAAACATG
1510581 TTAGAATT
66 TTAGAATT
1510589 GACTGAAAAT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
74 70 1.00
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.46
Consensus pattern (74 bp):
GTTCATTTGTGATGAATTTTAATTCAAATAGGATTTATCCTACTTTGGTTGAACTATTAAACATG
TTAGAATTA
Found at i:1518181 original size:26 final size:24
Alignment explanation
Indices: 1518144--1518195 Score: 59
Period size: 26 Copynumber: 2.1 Consensus size: 24
1518134 TGCTCTAAAC
* * *
1518144 TTATCTGATGTAGACGTACACTTG
1 TTATCTGATGTAAAAGTAAACTTG
1518168 TTATCATGTATGTAAAAGTAAACTTG
1 TTATC-TG-ATGTAAAAGTAAACTTG
1518194 TT
1 TT
1518196 CACTTATTAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 5 0.22
25 2 0.09
26 16 0.70
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.40
Consensus pattern (24 bp):
TTATCTGATGTAAAAGTAAACTTG
Found at i:1518443 original size:5 final size:5
Alignment explanation
Indices: 1518433--1518466 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
1518423 TTAGTATAAT
*
1518433 TTTTC TTTTC TTTTC TTTTC ATTTC TTTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
1518467 GTTACCTGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTTC
Found at i:1528699 original size:2 final size:2
Alignment explanation
Indices: 1528692--1528725 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1528682 TTGTGTAGAC
1528692 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
1528726 CACACACACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1537996 original size:21 final size:20
Alignment explanation
Indices: 1537971--1538012 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
1537961 AATTAATTAA
1537971 TTTAAATGAATCATATTCAAT
1 TTTAAATGAATCA-ATTCAAT
* *
1537992 TTTAAATTAATTAATTCAAT
1 TTTAAATGAATCAATTCAAT
1538012 T
1 T
1538013 CCATAGATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (20 bp):
TTTAAATGAATCAATTCAAT
Found at i:1539074 original size:2 final size:2
Alignment explanation
Indices: 1539067--1539104 Score: 53
Period size: 2 Copynumber: 19.5 Consensus size: 2
1539057 TATCATTAAT
1539067 TA TA TA TA TA -A TA TCA TA TA T- TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA T
1539105 TTAATTTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 2 0.06
2 29 0.88
3 2 0.06
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1539081 original size:21 final size:21
Alignment explanation
Indices: 1539057--1539119 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 21
1539047 ATATAATTTG
1539057 TATCATTAATTATATATATAA
1 TATCATTAATTATATATATAA
1539078 TATCA-TATATTATATATATATA
1 TATCATTA-ATTATATATATA-A
*
1539100 TAT-ATTTAATT-TATACATAA
1 TATCA-TTAATTATATATATAA
1539120 ACATTACTAC
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
20 3 0.08
21 25 0.68
22 7 0.19
23 2 0.05
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (21 bp):
TATCATTAATTATATATATAA
Found at i:1539215 original size:206 final size:210
Alignment explanation
Indices: 1538884--1539289 Score: 563
Period size: 206 Copynumber: 1.9 Consensus size: 210
1538874 ATAAATATAC
* * * * *
1538884 TATATATACATATATTTAATTTAGACATAAATATTATTATAACTTATAATAGACTTTATTTATAC
1 TATATATACATATATTTAATTTAGACATAAACATTACTACAACTTATAATAAACTTTATCTATAC
* *
1538949 CATTACACTTAATAACTTTATTAGTTATCACTTTTGATTTTATAACATATCATTTATAATTAGTT
66 CATTACACTTAATAACTTTATTAGCTATCACTTTTAATTTTATAACATATCATTTATAATTAGTT
* * * * *
1539014 ATTATTTATAT-AATTTGATATGAACAT-TT-TAACATATAATTTGTATCATTAAT-T-ATATAT
131 ATTATTTATATAAATTTAATA-CAAAATATTATAACATATAAGTTATATCATTAATATCATATAT
1539074 ATAATATCATATATTA
195 ATAATATCATATATTA
* * * *
1539090 TATATATATATATATTTAATTTATACATAAACATTACTACAACTTATAATAAATTTTATCTATAT
1 TATATATACATATATTTAATTTAGACATAAACATTACTACAACTTATAATAAACTTTATCTATAC
* * **
1539155 GATTACACTTAATAAGTTTATTAGCTATCA-TTTTAAATTTTATAACATATTGTTTATAATTAGT
66 CATTACACTTAATAACTTTATTAGCTATCACTTTT-AATTTTATAACATATCATTTATAATTAGT
1539219 TATTATTTATATAAAATTTAATACAAAATATTATAACATATAAGTTATATCATTAATATCATATA
130 TATTATTTATAT-AAATTTAATACAAAATATTATAACATATAAGTTATATCATTAATATCATATA
1539284 TATAAT
194 TATAAT
1539290 TATGAAAGAA
Statistics
Matches: 173, Mismatches: 20, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
205 4 0.02
206 121 0.70
207 4 0.02
208 10 0.06
209 22 0.13
210 1 0.01
211 11 0.06
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.47
Consensus pattern (210 bp):
TATATATACATATATTTAATTTAGACATAAACATTACTACAACTTATAATAAACTTTATCTATAC
CATTACACTTAATAACTTTATTAGCTATCACTTTTAATTTTATAACATATCATTTATAATTAGTT
ATTATTTATATAAATTTAATACAAAATATTATAACATATAAGTTATATCATTAATATCATATATA
TAATATCATATATTA
Found at i:1540754 original size:90 final size:90
Alignment explanation
Indices: 1540601--1540781 Score: 362
Period size: 90 Copynumber: 2.0 Consensus size: 90
1540591 GAAATAAAGG
1540601 ACGGATTTATGAATCATACATGTTTACAAGTGCATGGTAATAAAATACTCTCCCTTTTGGCTTAT
1 ACGGATTTATGAATCATACATGTTTACAAGTGCATGGTAATAAAATACTCTCCCTTTTGGCTTAT
1540666 TCCCTTCCATATATTCACTCATAGA
66 TCCCTTCCATATATTCACTCATAGA
1540691 ACGGATTTATGAATCATACATGTTTACAAGTGCATGGTAATAAAATACTCTCCCTTTTGGCTTAT
1 ACGGATTTATGAATCATACATGTTTACAAGTGCATGGTAATAAAATACTCTCCCTTTTGGCTTAT
1540756 TCCCTTCCATATATTCACTCATAGA
66 TCCCTTCCATATATTCACTCATAGA
1540781 A
1 A
1540782 TCTATGTATC
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
90 91 1.00
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.36
Consensus pattern (90 bp):
ACGGATTTATGAATCATACATGTTTACAAGTGCATGGTAATAAAATACTCTCCCTTTTGGCTTAT
TCCCTTCCATATATTCACTCATAGA
Found at i:1546488 original size:2 final size:2
Alignment explanation
Indices: 1546481--1546519 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1546471 ACGATAAAGA
1546481 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1546520 AACAATTCTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1555229 original size:2 final size:2
Alignment explanation
Indices: 1555222--1555255 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1555212 TGCATAAATA
1555222 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
1555256 GCACTCACTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1555985 original size:106 final size:103
Alignment explanation
Indices: 1555843--1556258 Score: 393
Period size: 106 Copynumber: 4.0 Consensus size: 103
1555833 TGTGTATCAT
* * * * * * *
1555843 ATACAATTTGATATCTTATATCAAGTAGGTATAAACTCCAATTAACGTCAAATATATATTAAATG
1 ATACAATTTGATATATTATATCAAATAGGCATAAACTCCCACTAAC-TAAAATATATATTAAGTG
1555908 AGTATAATTCTAATATATCATCTCATAACAAGATTATTATA
65 -GTATAA-TCTAATATATCATCTCATAACAAGATTATTATA
* * *
1555949 AGT-CAATTTGATATATTATATCAAATAGGCATAAACTTCTACTAACCAAAAATATATATTAAGT
1 A-TACAATTTGATATATTATATCAAATAGGCATAAACTCCCACTAA-CTAAAATATATATTAAGT
* * *
1556013 GGATATAATC--CTA-A-CATGTTAT-AC---ATTATTATA
64 GG-TATAATCTAATATATCATCTCATAACAAGATTATTATA
* *
1556046 ATACAATTTGATA-ACTTATATTAAATAGCCATAAACTCCCACTAATCTAAAATATATATTAAGT
1 ATACAATTTGATATA-TTATATCAAATAGGCATAAACTCCCACTAA-CTAAAATATATATTAAGT
* * * *
1556110 GGGTATAAATGTAAAATGTTATCTCATAACAAGATTATTATA
64 -GGTAT-AATCTAATATATCATCTCATAACAAGATTATTATA
* * * ** *
1556152 ATGCAATTTAATATCTTATATCAAATAATCATAAACTCCCACTAATCAAAAATATATATTAAGTT
1 ATACAATTTGATATATTATATCAAATAGGCATAAACTCCCACTAA-CTAAAATATATATTAAG-T
* * *
1556217 GGTATGAATCTAACATGTTATCTCATAACAAGATTATTATA
64 GGTAT-AATCTAATATATCATCTCATAACAAGATTATTATA
1556258 A
1 A
1556259 CAACTATAGT
Statistics
Matches: 258, Mismatches: 35, Indels: 34
0.79 0.11 0.10
Matches are distributed among these distances:
96 2 0.01
97 66 0.26
98 5 0.02
100 3 0.01
101 6 0.02
102 6 0.02
103 4 0.02
105 3 0.01
106 160 0.62
107 3 0.01
ACGTcount: A:0.44, C:0.13, G:0.08, T:0.36
Consensus pattern (103 bp):
ATACAATTTGATATATTATATCAAATAGGCATAAACTCCCACTAACTAAAATATATATTAAGTGG
TATAATCTAATATATCATCTCATAACAAGATTATTATA
Found at i:1556204 original size:203 final size:203
Alignment explanation
Indices: 1555843--1556237 Score: 528
Period size: 203 Copynumber: 1.9 Consensus size: 203
1555833 TGTGTATCAT
* * ** * *
1555843 ATACAATTTGATATCTTATATCAAGTAGGTATAAACTCCAATTAACGTCAAATATATATTAAATG
1 ATACAATTTGATAACTTATATCAAATAGCCATAAACTCCAACTAACGTAAAATATATATTAAATG
* * *
1555908 AGTATAATTCTAATATATCATCTCATAACAAGATTATTATAAGTCAATTTGATATATTATATCAA
66 AGTATAAATCTAAAATATCATCTCATAACAAGATTATTATAAGTCAATTTAATATATTATATCAA
* * *
1555973 ATAGGCATAAACTTCTACTAACCAAAAATATATATTAAG-TGGATAT-AATCCTAACATGTTATA
131 ATAAGCATAAACTCCCACTAACCAAAAATATATATTAAGTTGG-TATGAAT-CTAACATGTTATA
1556036 CATTATTATA
194 CATTATTATA
* * *
1556046 ATACAATTTGATAACTTATATTAAATAGCCATAAACTCCCACTAATC-TAAAATATATATTAAGT
1 ATACAATTTGATAACTTATATCAAATAGCCATAAACTCCAACTAA-CGTAAAATATATATTAAAT
* * * * *
1556110 GGGTATAAATGTAAAATGTTATCTCATAACAAGATTATTATAA-TGCAATTTAATATCTTATATC
65 GAGTATAAATCTAAAATATCATCTCATAACAAGATTATTATAAGT-CAATTTAATATATTATATC
* *
1556174 AAATAATCATAAACTCCCACTAATCAAAAATATATATTAAGTTGGTATGAATCTAACATGTTAT
129 AAATAAGCATAAACTCCCACTAACCAAAAATATATATTAAGTTGGTATGAATCTAACATGTTAT
1556238 CTCATAACAA
Statistics
Matches: 166, Mismatches: 22, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
202 1 0.01
203 158 0.95
204 7 0.04
ACGTcount: A:0.44, C:0.13, G:0.08, T:0.36
Consensus pattern (203 bp):
ATACAATTTGATAACTTATATCAAATAGCCATAAACTCCAACTAACGTAAAATATATATTAAATG
AGTATAAATCTAAAATATCATCTCATAACAAGATTATTATAAGTCAATTTAATATATTATATCAA
ATAAGCATAAACTCCCACTAACCAAAAATATATATTAAGTTGGTATGAATCTAACATGTTATACA
TTATTATA
Found at i:1563612 original size:28 final size:28
Alignment explanation
Indices: 1563581--1563634 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
1563571 ATATTACAAA
* *
1563581 CAAATAAATTATACCAAATATAAATATG
1 CAAATAAATTACACCAAACATAAATATG
*
1563609 CAAATAAATTACATCAAACATAAATA
1 CAAATAAATTACACCAAACATAAATA
1563635 AAGTTTCAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.59, C:0.13, G:0.02, T:0.26
Consensus pattern (28 bp):
CAAATAAATTACACCAAACATAAATATG
Found at i:1573393 original size:22 final size:22
Alignment explanation
Indices: 1573368--1573409 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1573358 TTAAATATAA
1573368 TATATATATAA-TATATGATATT
1 TATATATATAATTA-ATGATATT
1573390 TATATATATAATTAATGATA
1 TATATATATAATTAATGATA
1573410 CAAATTATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (22 bp):
TATATATATAATTAATGATATT
Found at i:1573603 original size:207 final size:208
Alignment explanation
Indices: 1573176--1573604 Score: 509
Period size: 207 Copynumber: 2.1 Consensus size: 208
1573166 CTTCTTTCAT
* * ** *
1573176 AATTATATATATGATATTAATGTATAACTTATATGTTATAATATTTTGTATTAAATTTTATATAA
1 AATTATATATAT-ATATTAATGTACAAATTATATGTTATAATATTTCATATCAAA-TTTATATAA
* *
1573241 ATAATAACTAATTATAAACAATATGTTATAAAATTTAAAATGATAGCTAATAAACTTATTAAGTG
64 ATAATAACTAATTATAAACAATATGTTATAAAATTCAAAATGATAACTAATAAACTTATTAAGTG
* * * *
1573306 TAATCATATAGATAAAAATTTATTATAAGTTGTAGTAATGTTTATGTATAAATTAAATATAATAT
129 TAATCATATAGATAAAAATCTATTATAAGTTATAATAATATTTATGTATAAATTAAATATAATAT
1573371 ATATATAATATATGA
194 ATATATAATATATGA
*
1573386 TATT-TATATATATAATTAATGATACAAATTATATGTTA-AA-ATGTTCATATCAAA-TTATATA
1 AATTATATATATAT-ATTAATG-TACAAATTATATGTTATAATAT-TTCATATCAAATTTATATA
** *
1573447 AATAATAACTAATTATAAATGATATGTTATAAAA-TCAAAAGTGATAACTAATAAAGTTATTAAG
63 AATAATAACTAATTATAAACAATATGTTATAAAATTCAAAA-TGATAACTAATAAACTTATTAAG
** * *
1573511 TGTAATGGTATA-AT-AAAGTCTA-TATAAGTTATAATAATATTTATGTCTAAATTAAATAT-AT
127 TGTAATCATATAGATAAAAATCTATTATAAGTTATAATAATATTTATGTATAAATTAAATATAAT
* *
1573572 GTATATTAGTATATTTAT-A
192 ATATA-TA-TA-ATATATGA
1573591 CAATTATATATATA
1 -AATTATATATATA
1573605 CTCATTACAT
Statistics
Matches: 188, Mismatches: 22, Indels: 21
0.81 0.10 0.09
Matches are distributed among these distances:
203 6 0.03
204 35 0.19
205 9 0.05
206 15 0.08
207 78 0.41
208 4 0.02
209 24 0.13
210 17 0.09
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.42
Consensus pattern (208 bp):
AATTATATATATATATTAATGTACAAATTATATGTTATAATATTTCATATCAAATTTATATAAAT
AATAACTAATTATAAACAATATGTTATAAAATTCAAAATGATAACTAATAAACTTATTAAGTGTA
ATCATATAGATAAAAATCTATTATAAGTTATAATAATATTTATGTATAAATTAAATATAATATAT
ATATAATATATGA
Found at i:1580576 original size:29 final size:29
Alignment explanation
Indices: 1580543--1580612 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
1580533 AATAATATGA
*
1580543 ATACTTTTTAACT-TACTAAAAGTAGATGG
1 ATACTTTTTAA-TGCACTAAAAGTAGATGG
* * * *
1580572 ATACTTTGTAATGCATTAGAAGTGGATGG
1 ATACTTTTTAATGCACTAAAAGTAGATGG
1580601 ATACTTTTTAAT
1 ATACTTTTTAAT
1580613 CCAGTAGAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 1 0.03
29 33 0.97
ACGTcount: A:0.34, C:0.09, G:0.17, T:0.40
Consensus pattern (29 bp):
ATACTTTTTAATGCACTAAAAGTAGATGG
Found at i:1580620 original size:29 final size:29
Alignment explanation
Indices: 1580562--1580621 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
1580552 AACTTACTAA
* *
1580562 AAGTAGATGGATACTTTGTAATGCATTAG
1 AAGTAGATGGATACTTTGTAATCCAGTAG
* *
1580591 AAGTGGATGGATACTTTTTAATCCAGTAG
1 AAGTAGATGGATACTTTGTAATCCAGTAG
1580620 AA
1 AA
1580622 AAGGATAGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.35, C:0.08, G:0.23, T:0.33
Consensus pattern (29 bp):
AAGTAGATGGATACTTTGTAATCCAGTAG
Found at i:1580627 original size:29 final size:29
Alignment explanation
Indices: 1580567--1580636 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
1580557 ACTAAAAGTA
* * * **
1580567 GATGGATACTTTGTAATGCATTAGAAGTG
1 GATGGATACTTTTTAATCCAGTAGAAAAG
1580596 GATGGATACTTTTTAATCCAGTAGAAAAG
1 GATGGATACTTTTTAATCCAGTAGAAAAG
*
1580625 GATAGATA-TTTT
1 GATGGATACTTTT
1580637 AACTCACAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
28 4 0.11
29 31 0.89
ACGTcount: A:0.34, C:0.07, G:0.23, T:0.36
Consensus pattern (29 bp):
GATGGATACTTTTTAATCCAGTAGAAAAG
Found at i:1580684 original size:22 final size:23
Alignment explanation
Indices: 1580656--1580698 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
1580646 AAAATAAATA
1580656 GATACTTTTAA-CCACCAAGATG
1 GATACTTTTAATCCACCAAGATG
*
1580678 GATACTTTTAATCCATCAAGA
1 GATACTTTTAATCCACCAAGA
1580699 GAAGATATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.37, C:0.21, G:0.12, T:0.30
Consensus pattern (23 bp):
GATACTTTTAATCCACCAAGATG
Found at i:1580748 original size:2 final size:2
Alignment explanation
Indices: 1580743--1580777 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1580733 TAAAAAAATA
1580743 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1580778 GAAAATACGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1582928 original size:36 final size:36
Alignment explanation
Indices: 1582888--1582956 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
1582878 GATTCCAAAG
* **
1582888 ATAAAATCA-TAGAAAAAGAAAATGTGCAAATATTCA
1 ATAAAATCAGAAG-AAAAGAAAATAAGCAAATATTCA
1582924 ATAAAATCAGAAGAAAAGAAAATAAGCAAATAT
1 ATAAAATCAGAAGAAAAGAAAATAAGCAAATAT
1582957 ACAAGATGGT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
36 27 0.93
37 2 0.07
ACGTcount: A:0.62, C:0.07, G:0.12, T:0.19
Consensus pattern (36 bp):
ATAAAATCAGAAGAAAAGAAAATAAGCAAATATTCA
Found at i:1584417 original size:15 final size:14
Alignment explanation
Indices: 1584399--1584437 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
1584389 CGTATTTAAC
1584399 TATTTATA-TTTTA
1 TATTTATATTTTTA
1584412 TATATTATATTTTTA
1 TAT-TTATATTTTTA
1584427 TATTTAATATT
1 TATTT-ATATT
1584438 ACAAGTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 3 0.13
14 7 0.30
15 13 0.57
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TATTTATATTTTTA
Found at i:1590193 original size:27 final size:27
Alignment explanation
Indices: 1590165--1590252 Score: 104
Period size: 27 Copynumber: 3.3 Consensus size: 27
1590155 ATAAAAAATT
** * *
1590165 ATATTAAAAATGCAGTTGTTATATGTT
1 ATATTAAAAATTTAGTTATTATATGTC
* * *
1590192 ATGTTGAAAATTTAGTTATTACATGTC
1 ATATTAAAAATTTAGTTATTATATGTC
*
1590219 ATATTAAAAATTTAATTATTATATGTC
1 ATATTAAAAATTTAGTTATTATATGTC
1590246 ATATTAA
1 ATATTAA
1590253 TTGAAAAAAT
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.45
Consensus pattern (27 bp):
ATATTAAAAATTTAGTTATTATATGTC
Found at i:1595941 original size:87 final size:88
Alignment explanation
Indices: 1595824--1595986 Score: 229
Period size: 87 Copynumber: 1.9 Consensus size: 88
1595814 GGTTTTAGTG
* * ** * * *
1595824 TGTCACCACATTTGGGTATTTTAGGGCAATTTGTGTAACAAGTCAATAATTATAGTGATTGGCGT
1 TGTCACCACATTTGGATATTTTAGGACAATTCATGTAACAAGACAACAATTATAGTGATTGACGT
1595889 GTCACGACATGGCATGGTTGGCA
66 GTCACGACATGGCATGGTTGGCA
* *
1595912 TGTCACCACA-TTGGATATTTTAGGACAATTCATGTAACAAGACAACAATTCTAGTGATTGATGT
1 TGTCACCACATTTGGATATTTTAGGACAATTCATGTAACAAGACAACAATTATAGTGATTGACGT
*
1595976 GTCATGACATG
66 GTCACGACATG
1595987 CCTCAGTGTT
Statistics
Matches: 65, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
87 55 0.85
88 10 0.15
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33
Consensus pattern (88 bp):
TGTCACCACATTTGGATATTTTAGGACAATTCATGTAACAAGACAACAATTATAGTGATTGACGT
GTCACGACATGGCATGGTTGGCA
Found at i:1596039 original size:31 final size:31
Alignment explanation
Indices: 1596001--1596137 Score: 143
Period size: 31 Copynumber: 4.4 Consensus size: 31
1595991 AGTGTTGACA
* *
1596001 TGTAACAATATTTGACTCGGTATGCTTCGCG
1 TGTAACAATATTTGACTTGGTATGCTTAGCG
* *
1596032 TGTAACAATGTTTGACTTGGTATGATTAGCG
1 TGTAACAATATTTGACTTGGTATGCTTAGCG
* * * * *
1596063 CGTAACAACATTTTACTTAGTATG-TATAGCA
1 TGTAACAATATTTGACTTGGTATGCT-TAGCG
* *
1596094 TGTAACAACAATTT-ACTTGGTATGCATAGCG
1 TGTAACAA-TATTTGACTTGGTATGCTTAGCG
1596125 TGTAACAATATTT
1 TGTAACAATATTT
1596138 ATTTCTTTCT
Statistics
Matches: 87, Mismatches: 16, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
30 5 0.06
31 78 0.90
32 4 0.05
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.36
Consensus pattern (31 bp):
TGTAACAATATTTGACTTGGTATGCTTAGCG
Found at i:1600766 original size:25 final size:25
Alignment explanation
Indices: 1600731--1600779 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
1600721 TTGAATTTCT
*
1600731 TTTCTTCTTTTCT-TCTTTCTTTTTA
1 TTTCTTATTTT-TGTCTTTCTTTTTA
*
1600756 TTTCTTATTTTTGTGTTTCTTTTT
1 TTTCTTATTTTTGTCTTTCTTTTT
1600780 CCTAAAGCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.04, C:0.14, G:0.04, T:0.78
Consensus pattern (25 bp):
TTTCTTATTTTTGTCTTTCTTTTTA
Found at i:1610786 original size:15 final size:15
Alignment explanation
Indices: 1610735--1610788 Score: 65
Period size: 15 Copynumber: 3.7 Consensus size: 15
1610725 GGATAAAAAA
1610735 TGATAAATGATATTT
1 TGATAAATGATATTT
* * *
1610750 TGATTAATAATA-AT
1 TGATAAATGATATTT
*
1610764 TAATAAATGATATTT
1 TGATAAATGATATTT
1610779 TGATAAATGA
1 TGATAAATGA
1610789 AAATATTAAA
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
14 10 0.33
15 20 0.67
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (15 bp):
TGATAAATGATATTT
Found at i:1618368 original size:2 final size:2
Alignment explanation
Indices: 1618361--1618392 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1618351 TGATTTGTTC
*
1618361 AT AT AT AT AT CT 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
1618393 CAATGCCAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1619318 original size:53 final size:53
Alignment explanation
Indices: 1619248--1619356 Score: 182
Period size: 53 Copynumber: 2.1 Consensus size: 53
1619238 CATAGAGCCC
*
1619248 TTTAATCCATATCTTATAGCTGTGGTTATCATTGTGGGGGCTTTGGGTTCCCA
1 TTTAATCCATATATTATAGCTGTGGTTATCATTGTGGGGGCTTTGGGTTCCCA
* * *
1619301 TTTAATCTATATATTATAGCTGTGGTTATCATTGTGGGGTCTTTTGGTTCCCA
1 TTTAATCCATATATTATAGCTGTGGTTATCATTGTGGGGGCTTTGGGTTCCCA
1619354 TTT
1 TTT
1619357 TTGTTTAAAG
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.17, C:0.15, G:0.22, T:0.46
Consensus pattern (53 bp):
TTTAATCCATATATTATAGCTGTGGTTATCATTGTGGGGGCTTTGGGTTCCCA
Found at i:1621157 original size:20 final size:21
Alignment explanation
Indices: 1621132--1621172 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1621122 AAGGATCTTT
*
1621132 CACATC-AAATTCTGAATGAA
1 CACATCAAAATGCTGAATGAA
1621152 CACATCAAAATGCTGAATGAA
1 CACATCAAAATGCTGAATGAA
1621173 GAATTGTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.46, C:0.20, G:0.12, T:0.22
Consensus pattern (21 bp):
CACATCAAAATGCTGAATGAA
Found at i:1624345 original size:22 final size:21
Alignment explanation
Indices: 1624320--1624370 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
1624310 TAAATACCTC
* *
1624320 TATTGATGATGATATTAATGGT
1 TATTGATG-TGATATGAATGGG
*
1624342 TATTGATTGTGTTATGAATGGG
1 TATTGA-TGTGATATGAATGGG
1624364 TATTGAT
1 TATTGAT
1624371 TATGGAAACC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 1 0.04
22 22 0.88
23 2 0.08
ACGTcount: A:0.27, C:0.00, G:0.25, T:0.47
Consensus pattern (21 bp):
TATTGATGTGATATGAATGGG
Found at i:1640497 original size:9 final size:9
Alignment explanation
Indices: 1640483--1640510 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
1640473 GTCGTGCTCA
1640483 CTCCATTTC
1 CTCCATTTC
1640492 CTCCATTTC
1 CTCCATTTC
1640501 CTCCATTTC
1 CTCCATTTC
1640510 C
1 C
1640511 ATTATTGTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.11, C:0.46, G:0.00, T:0.43
Consensus pattern (9 bp):
CTCCATTTC
Found at i:1651749 original size:2 final size:2
Alignment explanation
Indices: 1651742--1651768 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1651732 AGGTCTGCAA
1651742 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
1651769 TTGCTCTTAA
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:1651950 original size:16 final size:16
Alignment explanation
Indices: 1651931--1651964 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1651921 TTTTTAAAAA
1651931 AAAAAAGGGGAAAGTG
1 AAAAAAGGGGAAAGTG
**
1651947 AAAAGCGGGGAAAGTG
1 AAAAAAGGGGAAAGTG
1651963 AA
1 AA
1651965 GGAAGTAAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.38, T:0.06
Consensus pattern (16 bp):
AAAAAAGGGGAAAGTG
Found at i:1655862 original size:19 final size:20
Alignment explanation
Indices: 1655792--1655863 Score: 71
Period size: 19 Copynumber: 3.6 Consensus size: 20
1655782 TTATTTAATA
*
1655792 ATTTATATATTTAATTATTAT
1 ATTTA-ATATTTTATTATTAT
*
1655813 A--TAAAATTTTATATATTAT
1 ATTTAATATTTTAT-TATTAT
1655832 ATTTAACT-TTTTATT-TTAT
1 ATTTAA-TATTTTATTATTAT
1655851 ATTTAATATTTTA
1 ATTTAATATTTTA
1655864 AATTTAAATA
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
18 8 0.19
19 24 0.56
20 1 0.02
21 10 0.23
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (20 bp):
ATTTAATATTTTATTATTAT
Found at i:1656945 original size:30 final size:30
Alignment explanation
Indices: 1656881--1656946 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 30
1656871 CAATTAAGTT
* *
1656881 TTTATATTTTTATGTTGAGCTAAATAACTT
1 TTTATATTTTTATGTTCAGCTAAATAACTC
*
1656911 TTTATATTTTTATTTTCAG-TCAAATTAAC-C
1 TTTATATTTTTATGTTCAGCT-AAA-TAACTC
1656941 TTTATA
1 TTTATA
1656947 ATTAATTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
29 1 0.03
30 26 0.84
31 4 0.13
ACGTcount: A:0.30, C:0.09, G:0.06, T:0.55
Consensus pattern (30 bp):
TTTATATTTTTATGTTCAGCTAAATAACTC
Found at i:1663847 original size:27 final size:27
Alignment explanation
Indices: 1663815--1663868 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
1663805 AGGAATTAGG
1663815 AATTAGCACAATTATA-GAGATTTTATT
1 AATTAGCACAATTATAGGA-ATTTTATT
*
1663842 AATTAGCACAATTTTAGGAATTTTATT
1 AATTAGCACAATTATAGGAATTTTATT
1663869 CTTTTCCTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 23 0.92
28 2 0.08
ACGTcount: A:0.39, C:0.07, G:0.11, T:0.43
Consensus pattern (27 bp):
AATTAGCACAATTATAGGAATTTTATT
Found at i:1666711 original size:49 final size:50
Alignment explanation
Indices: 1666657--1666826 Score: 166
Period size: 55 Copynumber: 3.2 Consensus size: 50
1666647 CATTTCTTAA
*
1666657 ATATATTTTTAATGTCATATATTTTATTTTTATTTATTATTATAATATTTT
1 ATATATTTTTAATATCATATATTTTATTTTTATTTATTATTATAATA-TTT
*
1666708 ATATTTTATTTTTAATAT-ATTTATATTTTATTATTAATTT-TTATATAATATCATATCTT
1 ATA---TATTTTTAATATCA--TATATTTTATT-TTTATTTATTAT-T-ATA--ATAT-TT
*
1666767 CAATATATTTTTAATATCATATATTTTATTTTTATTTATTATTATAAT-CTT
1 --ATATATTTTTAATATCATATATTTTATTTTTATTTATTATTATAATATTT
1666818 ATATATTTT
1 ATATATTTT
1666827 ATTTTTATTT
Statistics
Matches: 100, Mismatches: 4, Indels: 32
0.74 0.03 0.24
Matches are distributed among these distances:
49 9 0.09
51 5 0.05
53 3 0.03
54 11 0.11
55 18 0.18
56 14 0.14
57 18 0.18
58 13 0.13
59 6 0.06
61 3 0.03
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.63
Consensus pattern (50 bp):
ATATATTTTTAATATCATATATTTTATTTTTATTTATTATTATAATATTT
Found at i:1666730 original size:22 final size:21
Alignment explanation
Indices: 1666681--1666753 Score: 89
Period size: 22 Copynumber: 3.5 Consensus size: 21
1666671 TCATATATTT
1666681 TATTTT-TA-TTTATTATTATAA
1 TATTTTATATTTTATT-TT-TAA
1666702 TATTTTATATTTTATTTTTAA
1 TATTTTATATTTTATTTTTAA
*
1666723 TATATTTATATTTTATTATTAA
1 TAT-TTTATATTTTATTTTTAA
1666745 T-TTTTATAT
1 TATTTTATAT
1666754 AATATCATAT
Statistics
Matches: 48, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
20 7 0.15
21 13 0.27
22 22 0.46
23 6 0.12
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (21 bp):
TATTTTATATTTTATTTTTAA
Found at i:1666756 original size:112 final size:113
Alignment explanation
Indices: 1666604--1666833 Score: 399
Period size: 112 Copynumber: 2.0 Consensus size: 113
1666594 AAAATATAAG
*
1666604 TTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAA
1 TTTAATATATTTATA-TTTTTATTATTAATTTTTATATAATATCATATCTTAAATATATTTTTAA
* *
1666669 TGTCATATATTTTATTTTTATTTATTATTATAATATTTTATATTTTATT
65 TATCATATATTTTATTTTTATTTATTATTATAATATTATATATTTTATT
*
1666718 TTTAATATATTTATA-TTTTATTATTAATTTTTATATAATATCATATCTTCAATATATTTTTAAT
1 TTTAATATATTTATATTTTTATTATTAATTTTTATATAATATCATATCTTAAATATATTTTTAAT
*
1666782 ATCATATATTTTATTTTTATTTATTATTATAATCTTATATATTTTATT
66 ATCATATATTTTATTTTTATTTATTATTATAATATTATATATTTTATT
1666830 TTTA
1 TTTA
1666834 TTTCTTTAAT
Statistics
Matches: 111, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
112 96 0.86
114 15 0.14
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (113 bp):
TTTAATATATTTATATTTTTATTATTAATTTTTATATAATATCATATCTTAAATATATTTTTAAT
ATCATATATTTTATTTTTATTTATTATTATAATATTATATATTTTATT
Found at i:1666856 original size:33 final size:33
Alignment explanation
Indices: 1666785--1666870 Score: 102
Period size: 33 Copynumber: 2.6 Consensus size: 33
1666775 TTTTAATATC
*
1666785 ATATATTTTATTTTTATTTATTATTATAATCTT
1 ATATATTTTATTTTTATTTATTAATATAATCTT
* *
1666818 ATATATTTTATTTTTATTTCTTTAATAT-ATTTT
1 ATATATTTTATTTTTATTT-ATTAATATAATCTT
* *
1666851 TTATATTATATATTTTATTT
1 ATATATTTTAT-TTTTATTT
1666871 TAATTTATTT
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
33 32 0.70
34 14 0.30
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (33 bp):
ATATATTTTATTTTTATTTATTAATATAATCTT
Found at i:1666955 original size:33 final size:34
Alignment explanation
Indices: 1666906--1666981 Score: 108
Period size: 33 Copynumber: 2.4 Consensus size: 34
1666896 AATGTTAATT
1666906 TTTTATATT-T-TATTTTATTTT-A-ATTTTTTA
1 TTTTATATTATATATTTTATTTTAATATTTTTTA
1666936 TTCTTATATTATATATTTTATTTTAATATTTTTTA
1 TT-TTATATTATATATTTTATTTTAATATTTTTTA
1666971 TTTTA-ATTATA
1 TTTTATATTATA
1666982 ACATTATAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
30 2 0.05
31 7 0.17
32 1 0.02
33 17 0.41
34 4 0.10
35 10 0.24
ACGTcount: A:0.28, C:0.01, G:0.00, T:0.71
Consensus pattern (34 bp):
TTTTATATTATATATTTTATTTTAATATTTTTTA
Found at i:1666964 original size:15 final size:15
Alignment explanation
Indices: 1666916--1666977 Score: 56
Period size: 15 Copynumber: 3.9 Consensus size: 15
1666906 TTTTATATTT
1666916 TATTTTATTTTAAT-
1 TATTTTATTTTAATA
1666930 T-TTTTATTCTTATATTATA
1 TATTTTA-T-TT-TA--ATA
1666949 TATTTTATTTTAATA
1 TATTTTATTTTAATA
*
1666964 TTTTTTATTTTAAT
1 TATTTTATTTTAAT
1666978 TATAACATTA
Statistics
Matches: 40, Mismatches: 1, Indels: 13
0.74 0.02 0.24
Matches are distributed among these distances:
13 5 0.12
14 2 0.05
15 18 0.45
16 2 0.05
17 2 0.05
18 4 0.10
19 2 0.05
20 5 0.12
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (15 bp):
TATTTTATTTTAATA
Found at i:1669589 original size:14 final size:15
Alignment explanation
Indices: 1669561--1669590 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1669551 AATCAATAGG
1669561 TATTTTATAATTAAA
1 TATTTTATAATTAAA
1669576 TATTTTAT-ATTAAA
1 TATTTTATAATTAAA
1669590 T
1 T
1669591 TTGATAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TATTTTATAATTAAA
Found at i:1669959 original size:13 final size:14
Alignment explanation
Indices: 1669920--1669961 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
1669910 TAGAAAAAAA
*
1669920 AATTATGTTAATTAT
1 AATTAT-TTAATCAT
1669935 AATTATTTAATCAT
1 AATTATTTAATCAT
*
1669949 ATTTA-TTAATCAT
1 AATTATTTAATCAT
1669962 GCTGTATGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 8 0.32
14 11 0.44
15 6 0.24
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.52
Consensus pattern (14 bp):
AATTATTTAATCAT
Found at i:1670119 original size:18 final size:16
Alignment explanation
Indices: 1670087--1670121 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 16
1670077 TGTATTCATA
1670087 TTTAATTTTATTATAT
1 TTTAATTTTATTATAT
1670103 TTTATATTTTAATTATAT
1 TTTA-ATTTT-ATTATAT
1670121 T
1 T
1670122 AATATGATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 5 0.29
18 8 0.47
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TTTAATTTTATTATAT
Found at i:1670967 original size:15 final size:15
Alignment explanation
Indices: 1670946--1670987 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
1670936 AAAATTTTAA
*
1670946 AAATTATTAATATTT
1 AAATTATTAATAATT
*
1670961 TAATTA-TAATAATT
1 AAATTATTAATAATT
*
1670975 AAATTATAAATAA
1 AAATTATTAATAA
1670988 ATGATTAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AAATTATTAATAATT
Found at i:1671409 original size:27 final size:27
Alignment explanation
Indices: 1671358--1671409 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
1671348 AATTAATATT
* *
1671358 TAAATTATTAATATTTTGGATAAATTA
1 TAAATTATTAATATTTTGAAAAAATTA
*
1671385 TAAATTATTAATATTTTTAAAAAAT
1 TAAATTATTAATATTTTGAAAAAAT
1671410 AAAATAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (27 bp):
TAAATTATTAATATTTTGAAAAAATTA
Found at i:1673521 original size:19 final size:18
Alignment explanation
Indices: 1673499--1673535 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
1673489 TAATATTTAA
1673499 AAAAATTTATAAAAAAATT
1 AAAAATTTA-AAAAAAATT
*
1673518 AAAAATTTAAATAAAATT
1 AAAAATTTAAAAAAAATT
1673536 TTTTTTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
AAAAATTTAAAAAAAATT
Found at i:1675370 original size:24 final size:24
Alignment explanation
Indices: 1675329--1675394 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
1675319 ATGACTGATA
* *
1675329 TTTTAATTAATGATAATTAATTAAT
1 TTTTAATT-ATAAAAATTAATTAAT
*
1675354 TTTTAATTATAAAAATTTATTAAT
1 TTTTAATTATAAAAATTAATTAAT
* *
1675378 ATTT--TTAAAAAAATTAA
1 TTTTAATTATAAAAATTAA
1675395 AAAAACCTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
22 11 0.31
24 16 0.46
25 8 0.23
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (24 bp):
TTTTAATTATAAAAATTAATTAAT
Found at i:1675382 original size:25 final size:26
Alignment explanation
Indices: 1675326--1675382 Score: 73
Period size: 24 Copynumber: 2.3 Consensus size: 26
1675316 ATGATGACTG
* *
1675326 ATATTTTAATTAATGATAATTAATTA
1 ATATTTTAATTAATAAAAATTAATTA
*
1675352 AT-TTTTAATT-ATAAAAATTTATTA
1 ATATTTTAATTAATAAAAATTAATTA
1675376 ATATTTT
1 ATATTTT
1675383 TAAAAAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 13 0.48
25 12 0.44
26 2 0.07
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (26 bp):
ATATTTTAATTAATAAAAATTAATTA
Found at i:1677523 original size:31 final size:29
Alignment explanation
Indices: 1677488--1677564 Score: 84
Period size: 28 Copynumber: 2.6 Consensus size: 29
1677478 AATAATTAAT
**
1677488 TATAAAAATTTATTTGATTTAAAATAAAAAA
1 TATAAAAATTTATTT-AAATAAAAT-AAAAA
* * *
1677519 TATAAATATTTAATTAAATATAATAAAAA
1 TATAAAAATTTATTTAAATAAAATAAAAA
1677548 -ATAAAAATTTATTTAAA
1 TATAAAAATTTATTTAAA
1677565 ATTTTTTGAA
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
28 15 0.38
29 5 0.13
30 6 0.15
31 13 0.33
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (29 bp):
TATAAAAATTTATTTAAATAAAATAAAAA
Found at i:1677528 original size:27 final size:27
Alignment explanation
Indices: 1677498--1677566 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 27
1677488 TATAAAAATT
*
1677498 TATTTGATTTAAAATAA-AAAATATAAA
1 TATTT-ATTTAAAATAATAAAAAATAAA
*
1677525 TATTTAATTAAATATAATAAAAAATAAA
1 TATTTATTTAAA-ATAATAAAAAATAAA
*
1677553 AATTTATTTAAAAT
1 TATTTATTTAAAAT
1677567 TTTTTGAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
26 6 0.17
27 11 0.31
28 19 0.53
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (27 bp):
TATTTATTTAAAATAATAAAAAATAAA
Found at i:1678022 original size:22 final size:22
Alignment explanation
Indices: 1677997--1678041 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
1677987 TATCTCAAAA
1677997 TTATTTTTTTA-TTTTTGAATAT
1 TTATTTTTTTACTTTTTG-ATAT
1678019 TTATTTTTTTACTTTTTGATAT
1 TTATTTTTTTACTTTTTGATAT
1678041 T
1 T
1678042 AAAAATTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.20, C:0.02, G:0.04, T:0.73
Consensus pattern (22 bp):
TTATTTTTTTACTTTTTGATAT
Found at i:1678164 original size:16 final size:18
Alignment explanation
Indices: 1678129--1678167 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
1678119 TAGGATTTGA
1678129 TAAAAATAATATATTAAT
1 TAAAAATAATATATTAAT
*
1678147 TAAAAA-AAT-TATTCAT
1 TAAAAATAATATATTAAT
1678163 TAAAA
1 TAAAA
1678168 TAACAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 11 0.55
17 3 0.15
18 6 0.30
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (18 bp):
TAAAAATAATATATTAAT
Found at i:1678787 original size:18 final size:20
Alignment explanation
Indices: 1678751--1678788 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1678741 TAAGTAATAA
1678751 TATTTGAAAAAATCATTAAAT
1 TATTTGAAAAAAT-ATTAAAT
1678772 TATTT-AAAAAAT-TTAAA
1 TATTTGAAAAAATATTAAA
1678789 ATAAAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 5 0.29
20 7 0.41
21 5 0.29
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (20 bp):
TATTTGAAAAAATATTAAAT
Done.