Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A09
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: 77927517
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1491452 characters in sequence are not A, C, G, or T
File 5 of 250
Found at i:1337818 original size:51 final size:51
Alignment explanation
Indices: 1337759--1337860 Score: 195
Period size: 51 Copynumber: 2.0 Consensus size: 51
1337749 TCTTAAATTG
*
1337759 AAAATTTCTTTCAATTTATTAATTTAGATAATAATAAAAATTCATTCCCTT
1 AAAATTTCTTTCAATTTATTAATTTAGATAATAAAAAAAATTCATTCCCTT
1337810 AAAATTTCTTTCAATTTATTAATTTAGATAATAAAAAAAATTCATTCCCTT
1 AAAATTTCTTTCAATTTATTAATTTAGATAATAAAAAAAATTCATTCCCTT
1337861 CAATTTGGTC
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.42, C:0.12, G:0.02, T:0.44
Consensus pattern (51 bp):
AAAATTTCTTTCAATTTATTAATTTAGATAATAAAAAAAATTCATTCCCTT
Found at i:1339977 original size:21 final size:21
Alignment explanation
Indices: 1339953--1339995 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1339943 GCCCAGTTCC
*
1339953 AAAGAAGACTTGGGTTAAGTT
1 AAAGAAGACTTAGGTTAAGTT
*
1339974 AAAGAATACTTAGGTTAAGTT
1 AAAGAAGACTTAGGTTAAGTT
1339995 A
1 A
1339996 GGAAAGGGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.42, C:0.05, G:0.23, T:0.30
Consensus pattern (21 bp):
AAAGAAGACTTAGGTTAAGTT
Found at i:1340345 original size:104 final size:104
Alignment explanation
Indices: 1340165--1340376 Score: 307
Period size: 104 Copynumber: 2.0 Consensus size: 104
1340155 GCTATGTCTG
*
1340165 GGTTAAAAGTGATGACAAGGATTACCCGAATGAGTTTTAATGAAATGTATCTATCTATCAAGGGA
1 GGTTAAAAGTGATGACAAGGATTACCCGAATAAGTTTTAATGAAATGTATCTATCTATCAAGGGA
* * *
1340230 AAAAGGAGGCTGTAGTGTTTGGTTAGGCAAAGAATCTAA
66 AAAAGGAGGCTGCAGTGTCTGGCTAGGCAAAGAATCTAA
* * ** * * *
1340269 GGTTAAAAGTGATGATAATGATTACTTGAATAAGTTTTAATGAAATGTTTCTGTCTATCGAGGGA
1 GGTTAAAAGTGATGACAAGGATTACCCGAATAAGTTTTAATGAAATGTATCTATCTATCAAGGGA
* *
1340334 AAAAGGAGGCTGCAGTGTCTGGCTAGGTAAAGAATCTGA
66 AAAAGGAGGCTGCAGTGTCTGGCTAGGCAAAGAATCTAA
1340373 GGTT
1 GGTT
1340377 TAAATTGCCC
Statistics
Matches: 95, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
104 95 1.00
ACGTcount: A:0.34, C:0.09, G:0.27, T:0.30
Consensus pattern (104 bp):
GGTTAAAAGTGATGACAAGGATTACCCGAATAAGTTTTAATGAAATGTATCTATCTATCAAGGGA
AAAAGGAGGCTGCAGTGTCTGGCTAGGCAAAGAATCTAA
Found at i:1340729 original size:53 final size:54
Alignment explanation
Indices: 1340636--1340765 Score: 147
Period size: 53 Copynumber: 2.4 Consensus size: 54
1340626 CATGGTAAGT
* * *
1340636 AGACCATATTGTGTAAGGCCTAGCCATTTGCTATGGCATCATA-AGGAAAATGA
1 AGACCATATAGTGTAAGGCCTAGCCATTTGCTATGACATCATATAGGAAAACGA
* ** * *
1340689 ATACCATATAGTGTAAGGCCTAGCTGTTTGGC-ATGACATCATATGGGAATACGA
1 AGACCATATAGTGTAAGGCCTAGCCATTT-GCTATGACATCATATAGGAAAACGA
* *
1340743 AGACCACATAGTGTAAGACCTAG
1 AGACCATATAGTGTAAGGCCTAG
1340766 TCAGGGACTA
Statistics
Matches: 64, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
53 35 0.55
54 29 0.45
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (54 bp):
AGACCATATAGTGTAAGGCCTAGCCATTTGCTATGACATCATATAGGAAAACGA
Found at i:1348168 original size:443 final size:445
Alignment explanation
Indices: 1347333--1348208 Score: 1522
Period size: 443 Copynumber: 2.0 Consensus size: 445
1347323 CGTAACATAC
* * *
1347333 GGTTTTTGTTCCTACACATCAGTAACCTAACAATCTCGAGAAGACAAAAGAAAAATTATAATGTA
1 GGTTGTTGTTCCTACACATCAATAACCTAACAATCTCAAGAAGACAAAAGAAAAATTATAATGTA
*
1347398 AAAATTAAACTAAAAACAAAAATATAAAAATAAAATAAAAAAGGCTAAATTGATAAAAATCAAAT
66 AAAATTAAACT-AAAACAAAAATATAAAAATAAAATAAAAAAGGCTAAATTAATAAAAATCAAAT
*
1347463 GTTCCTAATATTTTAGTCCTCGACAACGGTGCCAAAAACTTGATGGTCACTAAACTAACTATAAA
130 GTTCCTAATATTTTAGTCCCCGACAACGGTGCCAAAAACTTGATGGTCACTAAACTAACTATAAA
* * *
1347528 TACGAAAAAGGCAAGTGCACCTATCGAACAATAGTATAGCTATGGTGAGTAGAGAATATTGTATG
195 TACGAAAAAGGCAAGTGCACCTATCGAACAATAGTATAGCTATGGTAAGTAGAGAATATCGTATC
* *
1347593 CACGAGGACTAAAAGTATTAATAATTACCGTTTTTCTATTATTTAGCCGACAATTTGGAGTGATG
260 CACGAGGACTAAAAGTATTAATAATTACCCTTTTTCCATTATTTAGCCGACAATTTGGAGTGATG
1347658 TGTTTTAATCTAAATTTACTAAACTAATTTAACTAAGAATGCAACTGAGAATAAATCAAAGAAAT
325 TGTTTTAATCTAAATTTACTAAACTAATTTAACTAAGAATGCAACTGAGAATAAATCAAAGAAAT
**
1347723 AATCGAATATTAACCAATGGGATAGACGATATCCAGGAAAGAAATAATCAACGTAA
390 AATCGAATATTAACCAATAAGATAGACGATATCCAGGAAAGAAATAATCAACGTAA
*
1347779 GGTTGTTGTTCCTAGACATCAATAACCTAACAATCTCAAGAAGACAAAAGAAAAATTATAATGTA
1 GGTTGTTGTTCCTACACATCAATAACCTAACAATCTCAAGAAGACAAAAGAAAAATTATAATGTA
* *
1347844 AAAATTAAACT-AAA-AAATATATAAAAATAAAATAAAAAAGGCTAAATTAATAAAAATCAAGTG
66 AAAATTAAACTAAAACAAAAATATAAAAATAAAATAAAAAAGGCTAAATTAATAAAAATCAAATG
1347907 TTCCTAATATTTTAGTCCCCGACAACGGTGCCAAAAACTTGATGGTCACTAAACTAACTATAAAT
131 TTCCTAATATTTTAGTCCCCGACAACGGTGCCAAAAACTTGATGGTCACTAAACTAACTATAAAT
1347972 ACGAAAAAGGCAAGTGCACCTATCGAACAATAGTATAGCTATGGTAAGTAGAGAATATCGTATCC
196 ACGAAAAAGGCAAGTGCACCTATCGAACAATAGTATAGCTATGGTAAGTAGAGAATATCGTATCC
* * *
1348037 ACGAGGACTAAGAGTATTAGTAATTACCCTTTTTCCATTATTTAGCTGACAATTTGGAGTGATGT
261 ACGAGGACTAAAAGTATTAATAATTACCCTTTTTCCATTATTTAGCCGACAATTTGGAGTGATGT
* * * *
1348102 GTTTTAATCTAAGTTTACTAAACTGATTTAACTAAGAATGCAACTGAGAATGAATCAAATAAATA
326 GTTTTAATCTAAATTTACTAAACTAATTTAACTAAGAATGCAACTGAGAATAAATCAAAGAAATA
*
1348167 ATCGAATATTAACCAATAAGATAGACGATTTCCAGGAAAGAA
391 ATCGAATATTAACCAATAAGATAGACGATATCCAGGAAAGAA
1348209 TCCACAATAT
Statistics
Matches: 407, Mismatches: 23, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
443 332 0.82
444 3 0.01
446 72 0.18
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.27
Consensus pattern (445 bp):
GGTTGTTGTTCCTACACATCAATAACCTAACAATCTCAAGAAGACAAAAGAAAAATTATAATGTA
AAAATTAAACTAAAACAAAAATATAAAAATAAAATAAAAAAGGCTAAATTAATAAAAATCAAATG
TTCCTAATATTTTAGTCCCCGACAACGGTGCCAAAAACTTGATGGTCACTAAACTAACTATAAAT
ACGAAAAAGGCAAGTGCACCTATCGAACAATAGTATAGCTATGGTAAGTAGAGAATATCGTATCC
ACGAGGACTAAAAGTATTAATAATTACCCTTTTTCCATTATTTAGCCGACAATTTGGAGTGATGT
GTTTTAATCTAAATTTACTAAACTAATTTAACTAAGAATGCAACTGAGAATAAATCAAAGAAATA
ATCGAATATTAACCAATAAGATAGACGATATCCAGGAAAGAAATAATCAACGTAA
Found at i:1361437 original size:31 final size:31
Alignment explanation
Indices: 1361402--1361463 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
1361392 GTAAGTTTGA
1361402 GTATGTTGGTAAGGCATCGTAAACTGTTGGG
1 GTATGTTGGTAAGGCATCGTAAACTGTTGGG
1361433 GTATGTTGGTAAGGCATCGTAAACTGTTGGG
1 GTATGTTGGTAAGGCATCGTAAACTGTTGGG
1361464 TTAAATAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.23, C:0.10, G:0.35, T:0.32
Consensus pattern (31 bp):
GTATGTTGGTAAGGCATCGTAAACTGTTGGG
Found at i:1367069 original size:30 final size:30
Alignment explanation
Indices: 1367006--1367071 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
1366996 AGAGAGCACA
* *
1367006 GCCGGAGAAGCCGTTCATCCTCTCCACGTC
1 GCCGCAGAAGCCGTTCATCCTCTCCACGAC
1367036 GCCGCAGAAGCCGTTCA-CCATCT-CATCGAC
1 GCCGCAGAAGCCGTTCATCC-TCTCCA-CGAC
1367066 GCCGCA
1 GCCGCA
1367072 AAAGTCGATC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 4 0.12
30 28 0.88
ACGTcount: A:0.20, C:0.41, G:0.23, T:0.17
Consensus pattern (30 bp):
GCCGCAGAAGCCGTTCATCCTCTCCACGAC
Found at i:1368860 original size:37 final size:37
Alignment explanation
Indices: 1368805--1368883 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
1368795 TTTGCTAGAG
*
1368805 ATAAAACACACCATGAACATTATAAGTGAATTTATTT
1 ATAAAACACACCAGGAACATTATAAGTGAATTTATTT
*
1368842 ATAAAA-AGCACCAGGAACATTGTAAGTGAATTTATTT
1 ATAAAACA-CACCAGGAACATTATAAGTGAATTTATTT
*
1368879 TTAAA
1 ATAAA
1368884 CAGATTTAAG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
36 1 0.03
37 37 0.97
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (37 bp):
ATAAAACACACCAGGAACATTATAAGTGAATTTATTT
Found at i:1371401 original size:51 final size:53
Alignment explanation
Indices: 1371301--1371449 Score: 141
Period size: 51 Copynumber: 2.9 Consensus size: 53
1371291 AAGTATATAT
* * * *
1371301 ATAATATAGACAAAAATATATGCATAATGTAGTATTGAAAGTATTTACATGGG
1 ATAATATAGACAAAAATATATGAATAATGTAGTATTAAAAATATATACATGGG
***
1371354 ATAATATA-A-AAAAATATATGAATAATGT-GATATTAAAAATATATACATAAA
1 ATAATATAGACAAAAATATATGAATAATGTAG-TATTAAAAATATATACATGGG
* *
1371405 ATATATATATATC--AAATATAT--ATAATATAGTATTAAAAATATATA
1 ATA-ATATAGA-CAAAAATATATGAATAATGTAGTATTAAAAATATATA
1371450 TAATACATAC
Statistics
Matches: 82, Mismatches: 8, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
50 1 0.01
51 57 0.70
52 7 0.09
53 17 0.21
ACGTcount: A:0.54, C:0.03, G:0.09, T:0.34
Consensus pattern (53 bp):
ATAATATAGACAAAAATATATGAATAATGTAGTATTAAAAATATATACATGGG
Found at i:1371412 original size:15 final size:15
Alignment explanation
Indices: 1371387--1371428 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
1371377 AATGTGATAT
1371387 TAAAA-ATATATACA
1 TAAAATATATATACA
*
1371401 TAAAATATATATATA
1 TAAAATATATATACA
*
1371416 TCAAATATATATA
1 TAAAATATATATA
1371429 ATATAGTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 5 0.20
15 20 0.80
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.36
Consensus pattern (15 bp):
TAAAATATATATACA
Found at i:1371448 original size:21 final size:20
Alignment explanation
Indices: 1371391--1371449 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 20
1371381 TGATATTAAA
*
1371391 AATATATA-CATAAA-ATAT
1 AATATATATCAAAAATATAT
*
1371409 -ATATATATCAAATATATAT
1 AATATATATCAAAAATATAT
*
1371428 AATATAGTATTAAAAATATAT
1 AATATA-TATCAAAAATATAT
1371449 A
1 A
1371450 TAATACATAC
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
17 7 0.21
18 4 0.12
19 4 0.12
20 5 0.15
21 13 0.39
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.37
Consensus pattern (20 bp):
AATATATATCAAAAATATAT
Found at i:1371555 original size:23 final size:23
Alignment explanation
Indices: 1371510--1371555 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1371500 AATACTTCAT
* *
1371510 AAATATATACATATATATGTTAA
1 AAATAAATACATATATATATTAA
1371533 AAATAAATACATAT-TAATATTAA
1 AAATAAATACATATAT-ATATTAA
1371556 GATGATGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 1 0.05
23 19 0.95
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (23 bp):
AAATAAATACATATATATATTAA
Found at i:1371654 original size:3 final size:3
Alignment explanation
Indices: 1371619--1371755 Score: 59
Period size: 3 Copynumber: 45.0 Consensus size: 3
1371609 CATATAAGTG
* * * *
1371619 TAA TAA TAG TAA TTA TAA TAC TAA TAC TAA TAA TAA -ATA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA
* * * *
1371664 TAG TAG TAA CAA TAAA TAA -AA TAA TAA TCA TAA -AA TTAA T-A TAAA
1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA -TAA TAA T-AA
** * * *
1371709 TAA TGTG TACA TGAA AAA TAA TAA TGA T-A TGA TAA TAA TAA TAA TAA
1 TAA T-AA TA-A T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1371756 AACGAAAAAA
Statistics
Matches: 100, Mismatches: 22, Indels: 24
0.68 0.15 0.16
Matches are distributed among these distances:
2 9 0.09
3 79 0.79
4 11 0.11
5 1 0.01
ACGTcount: A:0.58, C:0.04, G:0.06, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:1371677 original size:24 final size:24
Alignment explanation
Indices: 1371632--1371712 Score: 76
Period size: 24 Copynumber: 3.4 Consensus size: 24
1371622 TAATAGTAAT
* *
1371632 TATAATACTAATACTAATAATAAA
1 TATAATAATAATACTAACAATAAA
* *
1371656 TATAATAATAGTAGTAACAATAAA
1 TATAATAATAATACTAACAATAAA
* *
1371680 TAAAATAATAAT-CATAA-AATTAA
1 TATAATAATAATAC-TAACAATAAA
1371703 TATAAATAAT
1 TAT-AATAAT
1371713 GTGTACATGA
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
23 7 0.15
24 39 0.85
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.32
Consensus pattern (24 bp):
TATAATAATAATACTAACAATAAA
Found at i:1374502 original size:15 final size:14
Alignment explanation
Indices: 1374462--1374504 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
1374452 ATTTGTTAAA
*
1374462 ATTTAATTATTTGT
1 ATTTAATTATTTTT
*
1374476 ATTTATTATATTTTT
1 ATTTAAT-TATTTTT
1374491 ATTTGAATTATTTT
1 ATTT-AATTATTTT
1374505 GAATATTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 6 0.25
15 16 0.67
16 2 0.08
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (14 bp):
ATTTAATTATTTTT
Found at i:1377995 original size:20 final size:19
Alignment explanation
Indices: 1377970--1378007 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1377960 TACAAAATAA
*
1377970 TTCAAAATAATTTTTAAAAT
1 TTCAAAAT-ATTTATAAAAT
1377990 TTCAAAATATTTATAAAA
1 TTCAAAATATTTATAAAA
1378008 ACTCCAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (19 bp):
TTCAAAATATTTATAAAAT
Found at i:1378008 original size:20 final size:20
Alignment explanation
Indices: 1377970--1378008 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1377960 TACAAAATAA
*
1377970 TTCAAAATAATTTTTAAAAT
1 TTCAAAATAATTTTAAAAAT
1377990 TTCAAAAT-ATTTATAAAAA
1 TTCAAAATAATTT-TAAAAA
1378009 CTCCAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (20 bp):
TTCAAAATAATTTTAAAAAT
Found at i:1380725 original size:3 final size:3
Alignment explanation
Indices: 1380712--1380803 Score: 75
Period size: 3 Copynumber: 31.3 Consensus size: 3
1380702 AATGGGTAAA
* *
1380712 AAT AA- AAT AAT AAT AAT -AT AAT AGT AAT AAT AAT GAT AAT AAT AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * *
1380757 AGT AAT AAAT CAT AAT GAT AAT AAT GAT GAT AAT -AT AAGT AAT AAT
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT
1380803 A
1 A
1380804 TAAGTAAATA
Statistics
Matches: 71, Mismatches: 12, Indels: 12
0.75 0.13 0.13
Matches are distributed among these distances:
2 7 0.10
3 58 0.82
4 6 0.08
ACGTcount: A:0.60, C:0.01, G:0.08, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1380750 original size:23 final size:23
Alignment explanation
Indices: 1380717--1380810 Score: 84
Period size: 24 Copynumber: 4.0 Consensus size: 23
1380707 GTAAAAATAA
1380717 AATAATAATAAT-ATAATAGTAAT
1 AATAATAATAATAATAA-AGTAAT
*
1380740 AATAATGATAATAATAAAGTAAT
1 AATAATAATAATAATAAAGTAAT
* * * *
1380763 AAATCATAATGATAATAATGATGAT
1 -AATAATAATAATAATAAAG-TAAT
1380788 AAT-ATAAGTAATAATATAAGTAA
1 AATAATAA-TAATAATA-AAGTAA
1380811 ATACAGAGAG
Statistics
Matches: 57, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
23 21 0.37
24 31 0.54
25 5 0.09
ACGTcount: A:0.59, C:0.01, G:0.09, T:0.32
Consensus pattern (23 bp):
AATAATAATAATAATAAAGTAAT
Found at i:1380771 original size:21 final size:23
Alignment explanation
Indices: 1380717--1380779 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 23
1380707 GTAAAAATAA
*
1380717 AATAATAATAATATAATAGTAAT
1 AATAATCATAATATAATAGTAAT
*
1380740 AATAATGATAATAATAA-AGTAAT
1 AATAATCATAAT-ATAATAGTAAT
1380763 -A-AATCATAATGATAATA
1 AATAATCATAAT-ATAATA
1380780 ATGATGATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
21 12 0.34
22 2 0.06
23 17 0.49
24 4 0.11
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.32
Consensus pattern (23 bp):
AATAATCATAATATAATAGTAAT
Found at i:1380918 original size:3 final size:3
Alignment explanation
Indices: 1380910--1381009 Score: 67
Period size: 3 Copynumber: 33.0 Consensus size: 3
1380900 AGGTGGAAAA
* * * * *
1380910 AAT AAT AAT AAT AAT -AT ATT AAT AAG AAT AAA AAT ATAT ATT TAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT
* * * * * *
1380955 AAT AAC GAT AAAT AAT TAT AAT AAT GAT TAT GAT AAT AAT AAT AAT
1 AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
1381001 AAT AGT AAT
1 AAT AAT AAT
1381010 GGTAATAGCA
Statistics
Matches: 72, Mismatches: 22, Indels: 6
0.72 0.22 0.06
Matches are distributed among these distances:
2 2 0.03
3 65 0.90
4 5 0.07
ACGTcount: A:0.58, C:0.01, G:0.05, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:1381282 original size:18 final size:19
Alignment explanation
Indices: 1381246--1381295 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
1381236 AACAATAAAA
1381246 ATACA-ATATTAAAAGATGT
1 ATACATATA-TAAAAGATGT
*
1381265 ATATATATATAAAA-ATGT
1 ATACATATATAAAAGATGT
1381283 ATACATAATATAA
1 ATACAT-ATATAA
1381296 TATTAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 9 0.33
19 15 0.56
20 3 0.11
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.34
Consensus pattern (19 bp):
ATACATATATAAAAGATGT
Found at i:1381303 original size:24 final size:25
Alignment explanation
Indices: 1381265--1381400 Score: 84
Period size: 24 Copynumber: 5.4 Consensus size: 25
1381255 TAAAAGATGT
*
1381265 ATATATATATAAAAATGTATACATA
1 ATATATATATAAAAATATATACATA
* *
1381290 ATATA-ATATTAAAATATTTACATA
1 ATATATATATAAAAATATATACATA
* * *
1381314 GTATATACATAATAATA-ATA-ATA
1 ATATATATATAAAAATATATACATA
* *
1381337 ATA-ACTAT-TAATATTATATACATA
1 ATATA-TATATAAAAATATATACATA
*
1381361 TATACATATATCCATTAAAGATATATACATA
1 -AT--ATATAT--A-TAAAAATATATACATA
*
1381392 AGATATATA
1 ATATATATA
1381401 AATATATAAA
Statistics
Matches: 84, Mismatches: 15, Indels: 23
0.69 0.12 0.19
Matches are distributed among these distances:
22 8 0.10
23 10 0.12
24 25 0.30
25 15 0.18
26 1 0.01
27 4 0.05
28 7 0.08
30 1 0.01
31 13 0.15
ACGTcount: A:0.53, C:0.07, G:0.03, T:0.38
Consensus pattern (25 bp):
ATATATATATAAAAATATATACATA
Found at i:1381335 original size:44 final size:43
Alignment explanation
Indices: 1381227--1381364 Score: 116
Period size: 44 Copynumber: 3.1 Consensus size: 43
1381217 AGTATTAAGG
* * * * * * *
1381227 TATATGCATAACAATAAAAATACAATATTAAAAGATGTATATA
1 TATATACATAATAATAATAATATAATATTAAAATATATACATA
* * *
1381270 TATATA-AAAATGTATACATAATATAATATTAAAATATTTACATA
1 TATATACATAAT-AATA-ATAATATAATATTAAAATATATACATA
*
1381314 GTATATACATAATAATAATAATAATAACTATTAATATTATATACATA
1 -TATATACATAATAATAATAAT-ATAA-TATTAA-AATATATACATA
1381361 TATA
1 TATA
1381365 CATATATCCA
Statistics
Matches: 75, Mismatches: 13, Indels: 11
0.76 0.13 0.11
Matches are distributed among these distances:
42 3 0.04
43 8 0.11
44 27 0.36
45 13 0.17
46 14 0.19
47 10 0.13
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.36
Consensus pattern (43 bp):
TATATACATAATAATAATAATATAATATTAAAATATATACATA
Found at i:1381355 original size:36 final size:35
Alignment explanation
Indices: 1381282--1381364 Score: 100
Period size: 36 Copynumber: 2.4 Consensus size: 35
1381272 TATAAAAATG
*
1381282 TATACATAATATAATATTAAAATATTTACATAGTA
1 TATACATAATATAATAATAAAATATTTACATAGTA
*
1381317 TATACATAATAATAATAATAATAACTA-TTA-ATATTA
1 TATACATAAT-ATAATAATAA-AA-TATTTACATAGTA
1381353 TATACAT-ATATA
1 TATACATAATATA
1381365 CATATATCCA
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
34 3 0.07
35 12 0.28
36 21 0.49
37 5 0.12
38 2 0.05
ACGTcount: A:0.53, C:0.06, G:0.01, T:0.40
Consensus pattern (35 bp):
TATACATAATATAATAATAAAATATTTACATAGTA
Found at i:1382857 original size:20 final size:22
Alignment explanation
Indices: 1382832--1382885 Score: 67
Period size: 20 Copynumber: 2.5 Consensus size: 22
1382822 AAGAATACTA
1382832 TAATAATAATAATAT-GT-TAG
1 TAATAATAATAATATAGTATAG
*
1382852 TAATAATAACAATATAGTAATAG
1 TAATAATAATAATATAGT-ATAG
*
1382875 TAATAAAAATA
1 TAATAATAATA
1382886 GTACTAATGT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 14 0.50
21 2 0.07
23 12 0.43
ACGTcount: A:0.57, C:0.02, G:0.07, T:0.33
Consensus pattern (22 bp):
TAATAATAATAATATAGTATAG
Found at i:1383036 original size:3 final size:3
Alignment explanation
Indices: 1383015--1383101 Score: 86
Period size: 3 Copynumber: 28.0 Consensus size: 3
1383005 TAATGCTAAG
* *
1383015 ATA ATG ATA ATA GTA ATA ATA ATA ATA ATA ATA ATA ATA ATTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA
* * *
1383061 ATTCA ATA ATA GTA ATA ATG ACA ATA ATA GA-A ATA ATA ATA
1 A-T-A ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA
1383102 GTGTTTGAAT
Statistics
Matches: 69, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
2 1 0.01
3 60 0.87
4 6 0.09
5 2 0.03
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1388226 original size:5 final size:5
Alignment explanation
Indices: 1388216--1388247 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
1388206 TTGTGTGTTC
1388216 TTTAT TTTA- TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1388248 TCACAAATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:1388230 original size:9 final size:9
Alignment explanation
Indices: 1388216--1388246 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
1388206 TTGTGTGTTC
1388216 TTTATTTTA
1 TTTATTTTA
1388225 TTTATTTTA
1 TTTATTTTA
1388234 TTTTATTTTA
1 -TTTATTTTA
1388244 TTT
1 TTT
1388247 TTCACAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTATTTTA
Found at i:1393566 original size:19 final size:19
Alignment explanation
Indices: 1393531--1393568 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1393521 ATGTTTTTCC
*
1393531 TTCATTTTTTTTAATTTAT
1 TTCATTTTATTTAATTTAT
1393550 TTCATTTTAATTT-ATTTAT
1 TTCATTTT-ATTTAATTTAT
1393569 ATATTTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (19 bp):
TTCATTTTATTTAATTTAT
Found at i:1399829 original size:15 final size:15
Alignment explanation
Indices: 1399809--1399839 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1399799 TTGCATGTGG
*
1399809 AAAATAATATATTAA
1 AAAATAATACATTAA
1399824 AAAATAATACATTAA
1 AAAATAATACATTAA
1399839 A
1 A
1399840 TTAAAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (15 bp):
AAAATAATACATTAA
Found at i:1404846 original size:38 final size:38
Alignment explanation
Indices: 1404788--1404864 Score: 120
Period size: 38 Copynumber: 2.0 Consensus size: 38
1404778 AATTGCCCCT
*
1404788 TTCTATTAAAAATTACATTCATTTCTACTATTAAAAAC
1 TTCTATTAAAAATTACATTCACTTCTACTATTAAAAAC
*
1404826 TTCTCTTAAAAATTTA-ATTCACTTCTACTATTAAAAAC
1 TTCTATTAAAAA-TTACATTCACTTCTACTATTAAAAAC
1404864 T
1 T
1404865 GCCATGACTG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 33 0.92
39 3 0.08
ACGTcount: A:0.40, C:0.17, G:0.00, T:0.43
Consensus pattern (38 bp):
TTCTATTAAAAATTACATTCACTTCTACTATTAAAAAC
Found at i:1419573 original size:25 final size:26
Alignment explanation
Indices: 1419545--1419606 Score: 74
Period size: 24 Copynumber: 2.4 Consensus size: 26
1419535 AAATATTTTC
*
1419545 AAAAAATAAATAT-TTAATTAATAAT
1 AAAAAATAAATATGATAATTAATAAT
*
1419570 -AAAATTAAATATGATAATTAATAAT
1 AAAAAATAAATATGATAATTAATAAT
1419595 AAATATAATAAA
1 AAA-A-AATAAA
1419607 ATTAAATATG
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
24 11 0.37
25 11 0.37
26 2 0.07
27 1 0.03
28 5 0.17
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (26 bp):
AAAAAATAAATATGATAATTAATAAT
Found at i:1419578 original size:24 final size:25
Alignment explanation
Indices: 1419546--1419602 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
1419536 AATATTTTCA
*
1419546 AAAAATAAATAT-TTAATTAATAAT
1 AAAAATAAATATGATAATTAATAAT
*
1419570 AAAATTAAATATGATAATTAATAAT
1 AAAAATAAATATGATAATTAATAAT
*
1419595 AAATATAA
1 AAAAATAA
1419603 TAAAATTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 11 0.39
25 17 0.61
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (25 bp):
AAAAATAAATATGATAATTAATAAT
Found at i:1419586 original size:15 final size:15
Alignment explanation
Indices: 1419568--1419616 Score: 53
Period size: 15 Copynumber: 3.0 Consensus size: 15
1419558 TTAATTAATA
1419568 ATAAAATTAAATATG
1 ATAAAATTAAATATG
*
1419583 ATAATTAATAATAAATATA
1 ATAA--AAT--TAAATATG
1419602 ATAAAATTAAATATG
1 ATAAAATTAAATATG
1419617 TTTAAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
15 11 0.39
17 6 0.21
19 11 0.39
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (15 bp):
ATAAAATTAAATATG
Found at i:1427185 original size:20 final size:20
Alignment explanation
Indices: 1427150--1427205 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
1427140 GCATCACAGA
*
1427150 TGCATAACAGGAGCACTAAA-G
1 TGCA-AACAGGGGCAC-AAATG
*
1427171 TGCAGACAGGGGCACAAATG
1 TGCAAACAGGGGCACAAATG
1427191 TGCAAACAGGGGCAC
1 TGCAAACAGGGGCAC
1427206 CGTAGTGCGA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 3 0.10
20 24 0.77
21 4 0.13
ACGTcount: A:0.38, C:0.21, G:0.30, T:0.11
Consensus pattern (20 bp):
TGCAAACAGGGGCACAAATG
Found at i:1428837 original size:26 final size:26
Alignment explanation
Indices: 1428807--1428857 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
1428797 ACCAATGAAC
*
1428807 CGGGGAATCAGCACTTAGCAACCCCT
1 CGGGGAATCAGCACATAGCAACCCCT
1428833 CGGGGAATCAGCACATAGCAACCCC
1 CGGGGAATCAGCACATAGCAACCCC
1428858 CTTTTCACAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.29, C:0.35, G:0.24, T:0.12
Consensus pattern (26 bp):
CGGGGAATCAGCACATAGCAACCCCT
Found at i:1428864 original size:104 final size:104
Alignment explanation
Indices: 1428670--1429040 Score: 638
Period size: 104 Copynumber: 3.6 Consensus size: 104
1428660 TAACCGTTAT
* * **
1428670 TGGTGGATCTCGCACTTAGCACCACCGCTGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATCACGCACATAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTC-GGGG
1428735 AATCAGCACATAGCAACCCCC-TTTCACATTTCAAAGATA
65 AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
* *
1428774 TGGTGGAT-ATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGG
1 TGGTGGATCA-CGCACATAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGG
1428838 AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
65 AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
1428878 TGGTGGATCACGCACATAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGA
1 TGGTGGATCACGCACATAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGA
1428943 ATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
66 ATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
**
1428982 TGGTGGATCACGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 TGGTGGATCACGCACATAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
1429041 TTATATACAA
Statistics
Matches: 256, Mismatches: 8, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
103 25 0.10
104 230 0.90
105 1 0.00
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.19
Consensus pattern (104 bp):
TGGTGGATCACGCACATAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGA
ATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
Found at i:1428940 original size:26 final size:26
Alignment explanation
Indices: 1428910--1428961 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
1428900 CACCAATGAA
*
1428910 TCGGGGAATCAGCACTTAGCAACCCC
1 TCGGGGAATCAGCACATAGCAACCCC
1428936 TCGGGGAATCAGCACATAGCAACCCC
1 TCGGGGAATCAGCACATAGCAACCCC
1428962 CTTTTCACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.29, C:0.35, G:0.23, T:0.13
Consensus pattern (26 bp):
TCGGGGAATCAGCACATAGCAACCCC
Found at i:1429400 original size:29 final size:29
Alignment explanation
Indices: 1429367--1429430 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
1429357 TAATCCACCA
1429367 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
1429396 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
1429426 CCCAA
1 CCCAA
1429431 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:1429404 original size:30 final size:30
Alignment explanation
Indices: 1429374--1429430 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
1429364 CCACCCAACT
1429374 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
1429403 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
1429431 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:1430940 original size:15 final size:15
Alignment explanation
Indices: 1430920--1430985 Score: 55
Period size: 14 Copynumber: 4.3 Consensus size: 15
1430910 ACTACAAAAC
1430920 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
1430935 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
1430954 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
*
1430969 A-TTAATATTAA-AT
1 ATTTATTATTAATAT
1430982 ATTT
1 ATTT
1430986 TCAATAATAT
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
13 3 0.07
14 11 0.26
15 10 0.24
16 1 0.02
17 7 0.17
18 1 0.02
19 9 0.21
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:1431092 original size:22 final size:22
Alignment explanation
Indices: 1431048--1431107 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
1431038 TTAAAATAAA
* *
1431048 ATTAAAAT-ATTAAGTA-ATTT
1 ATTAAAATAATAAATTATATTT
1431068 ATTAAAATAATAAATTATATTT
1 ATTAAAATAATAAATTATATTT
* * *
1431090 ATTATATTAATAAGTTAT
1 ATTAAAATAATAAATTAT
1431108 TATAAGACTA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
20 8 0.24
21 6 0.18
22 19 0.58
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (22 bp):
ATTAAAATAATAAATTATATTT
Found at i:1438487 original size:6 final size:6
Alignment explanation
Indices: 1438478--1438502 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1438468 AATTCTGCTC
1438478 CTTTTA CTTTTA CTTTTA CTTTTA C
1 CTTTTA CTTTTA CTTTTA CTTTTA C
1438503 ACACTGTGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.20, G:0.00, T:0.64
Consensus pattern (6 bp):
CTTTTA
Found at i:1440745 original size:11 final size:10
Alignment explanation
Indices: 1440718--1440788 Score: 53
Period size: 10 Copynumber: 7.2 Consensus size: 10
1440708 GACTAAAAAA
1440718 AATATTT-A-
1 AATATTTAAT
1440726 AATAATTTAAT
1 AAT-ATTTAAT
*
1440737 AATATTTTAT
1 AATATTTAAT
*
1440747 AACTTTTTAA-
1 AA-TATTTAAT
1440757 AA-ATTTAAT
1 AATATTTAAT
1440766 GAA-ATTTAAT
1 -AATATTTAAT
1440776 AATAATTTAAT
1 AAT-ATTTAAT
1440787 AA
1 AA
1440789 GGTTACATGT
Statistics
Matches: 51, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
8 8 0.16
9 6 0.12
10 20 0.39
11 17 0.33
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (10 bp):
AATATTTAAT
Found at i:1440784 original size:29 final size:30
Alignment explanation
Indices: 1440720--1440785 Score: 75
Period size: 29 Copynumber: 2.2 Consensus size: 30
1440710 CTAAAAAAAA
*
1440720 TATTTAAATAATTTAATAATATTTTATAAC
1 TATTTAAATAATTTAATAATATTTAATAAC
*
1440750 TTTTTAAA-AATTTAATGAA-ATTTAATAA-
1 TATTTAAATAATTTAAT-AATATTTAATAAC
1440778 TAATTTAA
1 T-ATTTAA
1440786 TAAGGTTACA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
28 1 0.03
29 21 0.68
30 9 0.29
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (30 bp):
TATTTAAATAATTTAATAATATTTAATAAC
Found at i:1441610 original size:3 final size:3
Alignment explanation
Indices: 1441604--1441634 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1441594 GGAGCTGCTG
1441604 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1441635 AGATGATGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:1442142 original size:3 final size:3
Alignment explanation
Indices: 1442134--1442186 Score: 63
Period size: 3 Copynumber: 17.7 Consensus size: 3
1442124 TGAGAAGCCA
* * *
1442134 AAG AAG AAG ATG AAG AAA AAG AAG AGG AAG AAG AAG AAG AA- AACG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA-G
1442179 AAG AAG AA
1 AAG AAG AA
1442187 AGTGGAAATA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
2 2 0.05
3 38 0.90
4 2 0.05
ACGTcount: A:0.66, C:0.02, G:0.30, T:0.02
Consensus pattern (3 bp):
AAG
Found at i:1456343 original size:46 final size:46
Alignment explanation
Indices: 1456276--1456370 Score: 156
Period size: 46 Copynumber: 2.1 Consensus size: 46
1456266 TCTCCATACC
*
1456276 CTTAATATGTTTCTCTAGAACTTTTAGCCACTAGAGAAAAATGCAT
1 CTTAATATGTTTCTCTAGAACTTTCAGCCACTAGAGAAAAATGCAT
*
1456322 CTTAATATGTTTCTCCT-GAACTTTCAGCCACTAGAGAACAATGCAT
1 CTTAATATGTTTCT-CTAGAACTTTCAGCCACTAGAGAAAAATGCAT
1456368 CTT
1 CTT
1456371 TCTCACCCAA
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
46 44 0.96
47 2 0.04
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.35
Consensus pattern (46 bp):
CTTAATATGTTTCTCTAGAACTTTCAGCCACTAGAGAAAAATGCAT
Found at i:1467168 original size:33 final size:29
Alignment explanation
Indices: 1467131--1467195 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 29
1467121 TATTATATAA
*
1467131 TTATATTAAAATTTTAAAATTAATAATAAATAT
1 TTATA-TAAAATTAT-AAATTAA-AATAAAT-T
*
1467164 TTATATGAAATTATAAATTAAAATAAATT
1 TTATATAAAATTATAAATTAAAATAAATT
1467193 TTA
1 TTA
1467196 AAACATTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 4 0.13
30 7 0.23
31 7 0.23
32 7 0.23
33 5 0.17
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.45
Consensus pattern (29 bp):
TTATATAAAATTATAAATTAAAATAAATT
Found at i:1468330 original size:16 final size:14
Alignment explanation
Indices: 1468299--1468337 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
1468289 TTATTTATTA
1468299 AATTAATTTTAATT
1 AATTAATTTTAATT
1468313 AATTAAATTTTCAATT
1 AATT-AATTTT-AATT
*
1468329 AAATAATTT
1 AATTAATTT
1468338 CTTAACTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 4 0.18
15 11 0.50
16 7 0.32
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (14 bp):
AATTAATTTTAATT
Found at i:1472292 original size:25 final size:25
Alignment explanation
Indices: 1472259--1472314 Score: 105
Period size: 25 Copynumber: 2.3 Consensus size: 25
1472249 GGTAGAAAAG
1472259 AAGC-ATTCATTAAAGTCGTTCTTC
1 AAGCTATTCATTAAAGTCGTTCTTC
1472283 AAGCTATTCATTAAAGTCGTTCTTC
1 AAGCTATTCATTAAAGTCGTTCTTC
1472308 AAGCTAT
1 AAGCTAT
1472315 CCCAACTTAC
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 4 0.13
25 27 0.87
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (25 bp):
AAGCTATTCATTAAAGTCGTTCTTC
Found at i:1474011 original size:82 final size:82
Alignment explanation
Indices: 1473881--1474044 Score: 328
Period size: 82 Copynumber: 2.0 Consensus size: 82
1473871 ACAGAGGAGG
1473881 GAACTCATACCTGAGAGGAGAAGAACTGAAGCCACACAATAGAATCAGAGAGAATATGGCCAAAA
1 GAACTCATACCTGAGAGGAGAAGAACTGAAGCCACACAATAGAATCAGAGAGAATATGGCCAAAA
1473946 AACTCAGACTGAGGAAA
66 AACTCAGACTGAGGAAA
1473963 GAACTCATACCTGAGAGGAGAAGAACTGAAGCCACACAATAGAATCAGAGAGAATATGGCCAAAA
1 GAACTCATACCTGAGAGGAGAAGAACTGAAGCCACACAATAGAATCAGAGAGAATATGGCCAAAA
1474028 AACTCAGACTGAGGAAA
66 AACTCAGACTGAGGAAA
1474045 TGTTTGGGAG
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
82 82 1.00
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.12
Consensus pattern (82 bp):
GAACTCATACCTGAGAGGAGAAGAACTGAAGCCACACAATAGAATCAGAGAGAATATGGCCAAAA
AACTCAGACTGAGGAAA
Found at i:1478172 original size:28 final size:28
Alignment explanation
Indices: 1478127--1478192 Score: 68
Period size: 28 Copynumber: 2.4 Consensus size: 28
1478117 GCAAGCTGAA
*
1478127 AAGAAAG-AAGATATGTGTACTGA-ATAAG
1 AAGAAAGAAAGATAAGTGT--TGATATAAG
1478155 AAGAAAGAAAGA-AAGTGTTGATATAAG
1 AAGAAAGAAAGATAAGTGTTGATATAAG
1478182 AGAGAAA-AAAG
1 A-AGAAAGAAAG
1478193 GCGGGCGATA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
26 3 0.09
27 10 0.29
28 17 0.50
29 4 0.12
ACGTcount: A:0.56, C:0.02, G:0.26, T:0.17
Consensus pattern (28 bp):
AAGAAAGAAAGATAAGTGTTGATATAAG
Found at i:1479195 original size:21 final size:24
Alignment explanation
Indices: 1479151--1479202 Score: 65
Period size: 21 Copynumber: 2.3 Consensus size: 24
1479141 TATGTACATA
*
1479151 ACATATACTTAGTAATAATGTTGG
1 ACATATACTTAGTAATAATATTGG
1479175 ACATATAC-TA-T-ATAATATTGG
1 ACATATACTTAGTAATAATATTGG
*
1479196 AAATATA
1 ACATATA
1479203 TACACAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 15 0.58
22 1 0.04
23 2 0.08
24 8 0.31
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.37
Consensus pattern (24 bp):
ACATATACTTAGTAATAATATTGG
Found at i:1479689 original size:26 final size:25
Alignment explanation
Indices: 1479660--1479714 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 25
1479650 AAATATGCAT
*
1479660 ACAATATTACAAA-ATATATATAACTA
1 ACAATATTA-AAATATATACATAAC-A
1479686 ACAATATTAAAATATATACATAACA
1 ACAATATTAAAATATATACATAACA
1479711 ACAA
1 ACAA
1479715 AAGTATGATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 8 0.30
26 19 0.70
ACGTcount: A:0.60, C:0.13, G:0.00, T:0.27
Consensus pattern (25 bp):
ACAATATTAAAATATATACATAACA
Found at i:1482106 original size:75 final size:75
Alignment explanation
Indices: 1481983--1482150 Score: 237
Period size: 75 Copynumber: 2.2 Consensus size: 75
1481973 AGTAGAAATT
* * * *
1481983 AAAAACAGAATTTGAAAATACCTCAGCGTGTCCTGAGACTCAACTCACCTCTCGCAATATGAATT
1 AAAAATAGAATTTGAAAATACCTCAGCGTGCCCCGAGACCCAACTCACCTCTCGCAATATGAATT
1482048 GATTTTTTTG
66 GATTTTTTTG
* * * * *
1482058 AAAAATAGAAATTGAAATTACCTCAGCGTGCCCCGAGGCCCAACTCACCTCTCGTAATATGAGTT
1 AAAAATAGAATTTGAAAATACCTCAGCGTGCCCCGAGACCCAACTCACCTCTCGCAATATGAATT
1482123 GATTTTTTTG
66 GATTTTTTTG
* *
1482133 CAAAGTAGAATTTGAAAA
1 AAAAATAGAATTTGAAAA
1482151 ACAGAAATTG
Statistics
Matches: 80, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
75 80 1.00
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (75 bp):
AAAAATAGAATTTGAAAATACCTCAGCGTGCCCCGAGACCCAACTCACCTCTCGCAATATGAATT
GATTTTTTTG
Found at i:1482289 original size:88 final size:87
Alignment explanation
Indices: 1482055--1482825 Score: 872
Period size: 89 Copynumber: 8.9 Consensus size: 87
1482045 ATTGATTTTT
* * * * * *
1482055 TTGAAAAATAGAAATTGAAATTACCTCAGCGTGCCCCGAGGCCCAACTCACCTCTCGTAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
* ** *
1482120 GTTGATTTTTTTGCAAAGTAGAAT
66 GTTGA--TTTTTGAAAAACAGAAA
*
1482144 TTGAAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
**
1482209 GTTGATTTTTGAAAAGTAGAAA
66 GTTGATTTTTGAAAAACAGAAA
* * *
1482231 TTG-AAAACAGAAATTGAAATTACCTCAGCGTGTGAGCC-AAGGCTCAACTCACCTCTCGCAATG
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGT---CCTGAGGCTCAACTCACCTCTCGCAATA
* * *
1482294 TGAGTTGATTTTTGAAAAATATAGA
63 TGAGTTGATTTTTGAAAAACAGAAA
*
1482319 TTGGAAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCACAATAT
1 TT-G-AAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATAT
* *
1482384 GAGTTGA---TTCAAAAACAGACA
64 GAGTTGATTTTTGAAAAACAGAAA
* * *
1482405 TT-AAGAACAAAAATTGAAAATACCTCAGCGTGTCCTAAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
* * * *
1482469 GTTGATCTTTGAAAAATATAGA
66 GTTGATTTTTGAAAAACAGAAA
*
1482491 TTGGAAAAAACAAAAATTGAAAATA-CTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATAT
1 TT-G-AAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATAT
* *
1482555 GAGTTGA---TTCAAAAACAGACA
64 GAGTTGATTTTTGAAAAACAGAAA
*
1482576 TT-AAGAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
1482640 GTTGATTTTTTG-AAAACATG-AA
66 GTTGA-TTTTTGAAAAACA-GAAA
* * * * * * *
1482662 TTAAAAAAACATAAATTGAAGATACCTCAGTATGTGAGCC-GAAGCTCAACTCACTTCTCGCAAT
1 TT-GAAAAACAGAAATTGAAAATACCTCAG--CGTG-TCCTGAGGCTCAACTCACCTCTCGCAAT
1482726 ATGAGTTGATTTTTG-AAAACAG-AA
62 ATGAGTTGATTTTTGAAAAACAGAAA
** * * * *
1482750 TTGAAAAACAGAAATTGAAGTTACCTCAGTGTGCCCTGAGGCTCAACTCACTTCTCACAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
1482815 GTTGACTTTTT
66 GTTGA-TTTTT
1482826 TTCTCTTTTT
Statistics
Matches: 605, Mismatches: 51, Indels: 55
0.85 0.07 0.08
Matches are distributed among these distances:
82 18 0.03
83 109 0.18
84 2 0.00
85 47 0.08
86 68 0.11
87 45 0.07
88 122 0.20
89 129 0.21
90 34 0.06
91 31 0.05
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (87 bp):
TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
GTTGATTTTTGAAAAACAGAAA
Found at i:1482592 original size:171 final size:169
Alignment explanation
Indices: 1481931--1482825 Score: 1010
Period size: 171 Copynumber: 5.2 Consensus size: 169
1481921 CATGTGACCC
* * * * *
1481931 GAGGCTCAACTCATCTCTCGCAATATGAGTTGATTTTTGAAAAGTAGAAATT--AAAAACAGAAT
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATATAGATTGAAAAAACAGAAA
* * ****
1481994 TTGAAAATACCTCAGCGTGTCCTGAGACTCAACTCACCTCTCGCAATATGAATTGATT---TTTT
66 TTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTCAAAAAC
* * * *
1482056 TG-A--AAAATAGAAATTGAAATTACCTCAGCGTGCCCC
131 AGAATTAAAACAGAAATTGAAATTACCTCAGCGTGTCCT
* * * * *
1482092 GAGGCCCAACTCACCTCTCGTAATATGAGTTGATTTTTTTGCAAAGTAGA-ATTTG-AAAAACAG
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAATATAGA-TTGAAAAAACAG
* *
1482155 AAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG
63 AAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA---TTC
**
1482220 AAAAGTAGAAATTGAAAACAGAAATTGAAATTACCTCAGCGTGTGAGCC-
125 AAAAACAG-AATT-AAAACAGAAATTGAAATTACCTCAGCGTGT---CCT
* *
1482269 AAGGCTCAACTCACCTCTCGCAATGTGAGTTGATTTTTGAAAAATATAGATTGGAAAAAACAGAA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATATAGATT-GAAAAAACAGAA
*
1482334 ATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCACAATATGAGTTGATTCAAAAA
65 ATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTCAAAAA
* *
1482399 CAGACATTAAGAACAAAAATTGAAAATACCTCAGCGTGTCCT
130 CAGA-ATTAA-AACAGAAATTGAAATTACCTCAGCGTGTCCT
* * *
1482441 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATCTTTGAAAAATATAGATTGGAAAAAACAAAA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATATAGATT-GAAAAAACAGAA
1482506 ATTGAAAATA-CTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTCAAAAA
65 ATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTCAAAAA
*
1482570 CAGACATTAAGAACAGAAATTGAAAATACCTCAGCGTGTCCT
130 CAGA-ATTAA-AACAGAAATTGAAATTACCTCAGCGTGTCCT
* * *
1482612 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTG-AAAACAT-GAATTAAAAAAACATA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAATATAG-ATTGAAAAAACAGA
* * * * *
1482675 AATTGAAGATACCTCAGTATGTGAGCC-GAAGCTCAACTCACTTCTCGCAATATGAGTTGATTTT
64 AATTGAAAATACCTCAG--CGTG-TCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TT
** * * *
1482739 TGAAAACAGAATTGAAAAACAGAAATTGAAGTTACCTCAGTGTGCCCT
124 CAAAAACAGAATT--AAAACAGAAATTGAAATTACCTCAGCGTGTCCT
* *
1482787 GAGGCTCAACTCACTTCTCACAATATGAGTTGACTTTTT
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTT
1482826 TTCTCTTTTT
Statistics
Matches: 648, Mismatches: 52, Indels: 54
0.86 0.07 0.07
Matches are distributed among these distances:
161 30 0.05
162 1 0.00
163 16 0.02
164 63 0.10
167 2 0.00
170 22 0.03
171 142 0.22
172 78 0.12
173 37 0.06
174 42 0.06
175 115 0.18
176 4 0.01
177 94 0.15
178 2 0.00
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (169 bp):
GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATATAGATTGAAAAAACAGAAA
TTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTCAAAAAC
AGAATTAAAACAGAAATTGAAATTACCTCAGCGTGTCCT
Found at i:1491192 original size:4 final size:4
Alignment explanation
Indices: 1491138--1491173 Score: 72
Period size: 4 Copynumber: 9.0 Consensus size: 4
1491128 TGGGATATGC
1491138 AATG AATG AATG AATG AATG AATG AATG AATG AATG
1 AATG AATG AATG AATG AATG AATG AATG AATG AATG
1491174 CATAAATGTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (4 bp):
AATG
Found at i:1494909 original size:21 final size:24
Alignment explanation
Indices: 1494865--1494916 Score: 65
Period size: 21 Copynumber: 2.3 Consensus size: 24
1494855 TATGTACATA
*
1494865 ACATATACTTAGTAATAATGTTGG
1 ACATATACTTAGTAATAATATTGG
1494889 ACATATAC-TA-T-ATAATATTGG
1 ACATATACTTAGTAATAATATTGG
*
1494910 AAATATA
1 ACATATA
1494917 TACACAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 15 0.58
22 1 0.04
23 2 0.08
24 8 0.31
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.37
Consensus pattern (24 bp):
ACATATACTTAGTAATAATATTGG
Found at i:1497403 original size:22 final size:22
Alignment explanation
Indices: 1497347--1497403 Score: 55
Period size: 22 Copynumber: 2.5 Consensus size: 22
1497337 TATAAGTAAT
1497347 ATATATATTATA-AGAATAATGC
1 ATATATA-TATACAGAATAATGC
* *
1497369 ATGTATGTCATACA-AATATATGC
1 ATATATAT-ATACAGAATA-ATGC
1497392 ATATATATATAC
1 ATATATATATAC
1497404 GTACCAAAGG
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
21 1 0.04
22 16 0.57
23 11 0.39
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.37
Consensus pattern (22 bp):
ATATATATATACAGAATAATGC
Found at i:1497455 original size:3 final size:3
Alignment explanation
Indices: 1497447--1497484 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
1497437 AATAGGAAGA
*
1497447 AAT AAT AAT AAT AAT GAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1497485 ATTTATTAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1499148 original size:87 final size:84
Alignment explanation
Indices: 1499057--1499389 Score: 223
Period size: 86 Copynumber: 3.9 Consensus size: 84
1499047 ATTTTAATCC
* * *
1499057 GCTCCACTGTAACTTCAGGGAGATAGGATAGTG-TCTTCAATCTGCTCCGCTGTAATCTCAGGGA
1 GCTCCACTGTAACTTCAGGGAGATAAGAT-CTGATCTTCAATCTGCTCCACTGTAATCTCAGGGA
* *
1499121 GATAAGATTTCTGGCCT-CGATCT
65 AATAAGA--CCTGG--TGCGATCT
* * * * *
1499144 GCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTTTTAGTCTGTTCCACTGTAATCTCAGGG
1 GCTCCACTGTAACTTCAGGGAGATAAGATCTG--ATCTTCAATCTGCTCCACTGTAATCTCAGGG
1499209 AAATAAGACCTGGTGCGATCT
64 AAATAAGACCTGGTGCGATCT
* * * *
1499230 GCTCTACTGTAACTTCAGAGAGATAAGATC----CTTTAATCCGCTCCACTGTAA-CTTCAGGGA
1 GCTCCACTGTAACTTCAGGGAGATAAGATCTGATCTTCAATCTGCTCCACTGTAATC-TCAGGGA
* * * ** * *
1499290 GATAGGATTACTATATTCAATCT
65 AATAAGA--CCT-GGTGCGATCT
* *** * *
1499313 GCTCCGCTGTAA-TCTCAGGGAGATAAGATCTGCAATTCTTTGGTCTGTTCCACCGTAATCTCAG
1 GCTCCACTGTAACT-TCAGGGAGATAAGATCTG--A-TCTTCAATCTGCTCCACTGTAATCTCAG
*
1499377 GGGAATAAGACCT
62 GGAAATAAGACCT
1499390 TTTATAATGA
Statistics
Matches: 193, Mismatches: 36, Indels: 33
0.74 0.14 0.13
Matches are distributed among these distances:
79 1 0.01
80 29 0.15
82 3 0.02
83 31 0.16
85 1 0.01
86 35 0.18
87 31 0.16
88 2 0.01
89 32 0.17
90 27 0.14
91 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (84 bp):
GCTCCACTGTAACTTCAGGGAGATAAGATCTGATCTTCAATCTGCTCCACTGTAATCTCAGGGAA
ATAAGACCTGGTGCGATCT
Found at i:1499154 original size:44 final size:43
Alignment explanation
Indices: 1499052--1499341 Score: 145
Period size: 44 Copynumber: 6.8 Consensus size: 43
1499042 CCTTTATTTT
* * * * *
1499052 AATCCGCTCCACTGTAACTTCAGGGAGATAGGA-TAGTGTCTTC
1 AATCTGCTCCACTGTAAC-TCAGGGAGATAAGATTACTGGCCTC
* *
1499095 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTCTGGCCTC
1 AATCTGCTCCACTGTAA-CTCAGGGAGATAAGATTACTGGCCTC
* *** *
1499139 GATCTGCTCCACTGTAACCTCAGGGAGATAAGA-T-CTGAAATTTTT
1 AATCTGCTCCACTGTAA-CTCAGGGAGATAAGATTACTG---GCCTC
* * * *
1499184 AGTCTGTTCCACTGTAATCTCAGGGAAATAAGA--CCTGG--TGC
1 AATCTGCTCCACTGTAA-CTCAGGGAGATAAGATTACTGGCCT-C
* * * * *
1499225 GATCTGCTCTACTGTAACTTCAGAGAGATAAGA-T-C---CTTT
1 AATCTGCTCCACTGTAAC-TCAGGGAGATAAGATTACTGGCCTC
* * ****
1499264 AATCCGCTCCACTGTAACTTCAGGGAGATAGGATTACTATATTC
1 AATCTGCTCCACTGTAAC-TCAGGGAGATAAGATTACTGGCCTC
*
1499308 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGAT
1 AATCTGCTCCACTGTAA-CTCAGGGAGATAAGAT
1499342 CTGCAATTCT
Statistics
Matches: 192, Mismatches: 38, Indels: 33
0.73 0.14 0.13
Matches are distributed among these distances:
39 28 0.15
40 4 0.02
41 27 0.14
42 3 0.02
43 29 0.15
44 68 0.35
45 33 0.17
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.29
Consensus pattern (43 bp):
AATCTGCTCCACTGTAACTCAGGGAGATAAGATTACTGGCCTC
Found at i:1499253 original size:86 final size:87
Alignment explanation
Indices: 1499097--1499386 Score: 229
Period size: 86 Copynumber: 3.4 Consensus size: 87
1499087 GTGTCTTCAA
* * *
1499097 TCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTCTGGCCTCGATCTGCTCCACTGTAACCTCAG
1 TCTGCTCCACTGTAATCTCAGGGAAATAAGA-TCCTGG-CTCGATCTGCTCCACTGTAACCTCAG
*
1499162 GGAGATAAGATCTGAAATTTTTAG
64 AGAGATAAGATCTGAAATTTTTAG
* * *
1499186 TCTGTTCCACTGTAATCTCAGGGAAATAAGA-CCTGG-TGCGATCTGCTCTACTGTAACTTCAGA
1 TCTGCTCCACTGTAATCTCAGGGAAATAAGATCCTGGCT-CGATCTGCTCCACTGTAACCTCAGA
* *
1499249 GAGATAAGATC------CTTTAA
65 GAGATAAGATCTGAAATTTTTAG
* * * * *** * * *
1499266 TCCGCTCCACTGTAA-CTTCAGGGAGATAGGATTACTATATTCAATCTGCTCCGCTGTAATCTCA
1 TCTGCTCCACTGTAATC-TCAGGGAAATAAGA-TCCT-GGCTCGATCTGCTCCACTGTAACCTCA
* * *
1499330 GGGAGATAAGATCTGCAATTCTTTGG
63 GAGAGATAAGATCTGAAATT-TTTAG
* * *
1499356 TCTGTTCCACCGTAATCTCAGGGGAATAAGA
1 TCTGCTCCACTGTAATCTCAGGGAAATAAGA
1499387 CCTTTTATAA
Statistics
Matches: 156, Mismatches: 31, Indels: 27
0.73 0.14 0.13
Matches are distributed among these distances:
79 1 0.01
80 29 0.19
82 2 0.01
83 30 0.19
84 1 0.01
85 1 0.01
86 33 0.21
87 4 0.03
89 28 0.18
90 26 0.17
91 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (87 bp):
TCTGCTCCACTGTAATCTCAGGGAAATAAGATCCTGGCTCGATCTGCTCCACTGTAACCTCAGAG
AGATAAGATCTGAAATTTTTAG
Found at i:1500590 original size:1 final size:1
Alignment explanation
Indices: 1500584--1500608 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
1500574 CAAAGTCCCC
1500584 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
1500609 AGGAAGCAAA
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:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1512098 original size:3 final size:3
Alignment explanation
Indices: 1512090--1512127 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
1512080 AATAGGAAGA
*
1512090 AAT AAT AAT AAT AAT GAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1512128 ATTTATTAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1514181 original size:12 final size:12
Alignment explanation
Indices: 1514164--1514202 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
1514154 ACTAACAATC
1514164 ATTTATTAATAT
1 ATTTATTAATAT
1514176 ATTTATATAAATAT
1 ATTTAT-T-AATAT
*
1514190 ATTTTTTAATAT
1 ATTTATTAATAT
1514202 A
1 A
1514203 AAATATTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
12 12 0.50
13 2 0.08
14 10 0.42
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATTTATTAATAT
Found at i:1523006 original size:16 final size:15
Alignment explanation
Indices: 1522971--1523014 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
1522961 AGACTTAAAT
1522971 TTTTAAATTCAAAAA
1 TTTTAAATTCAAAAA
* *
1522986 ATTTAAGATTTAAAAA
1 TTTTAA-ATTCAAAAA
1523002 TTTTAAATT-AAAA
1 TTTTAAATTCAAAA
1523015 GTAGGATTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
14 4 0.16
15 8 0.32
16 13 0.52
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (15 bp):
TTTTAAATTCAAAAA
Found at i:1525623 original size:27 final size:27
Alignment explanation
Indices: 1525581--1525634 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
1525571 TGCTGTTAGC
* *
1525581 CCCAATACCCAAAGGGTCGTGGGCAAT
1 CCCAATACCCAAAGGGTCATGGACAAT
**
1525608 CCCAATACCCTGAGGGTCATGGACAAT
1 CCCAATACCCAAAGGGTCATGGACAAT
1525635 TATTTTACCG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.30, C:0.30, G:0.24, T:0.17
Consensus pattern (27 bp):
CCCAATACCCAAAGGGTCATGGACAAT
Found at i:1529134 original size:130 final size:129
Alignment explanation
Indices: 1528858--1529347 Score: 418
Period size: 130 Copynumber: 3.8 Consensus size: 129
1528848 TGAAAACCTA
* ** * * *
1528858 AAGGAATATTCGATTGTTTTG-ACTAAA-CGAGAAATCACAACCCAGCACGATAGGGCATGATTC
1 AAGG-ATATTCGATTATTTTGAAC-AAATCG-GAAATTGCAACCCAACACGTTAGGGCACGATTC
* * * * * * * * * ***
1528921 C-CGAATCGTCAAACACCGAGTATTGCCTCCGTTTTAAAGGATTTTTAGAAGAGC-CGAGTGAAA
63 CGCGAATCGCCAAACATCAAATATCGTCTTCGTTTTAGA-GA-TTTTAAAAGA-CACGAACAAAA
1528984 TTTTG
125 TTTTG
* * * *
1528989 AAGGGATATTTGATTATTTTAAAC-AATCGGGAAATTGCTACCCAACACGTTAGGGCACGATCCC
1 AA-GGATATTCGATTATTTTGAACAAATC-GGAAATTGCAACCCAACACGTTAGGGCACGATTCC
* * * * *
1529053 GCGAATTGCCAAATATCACATATCGCCTTCGTTTTAGAGATTTTAAAAGACACGAGCAAAATTTT
64 GCGAATCGCCAAACATCAAATATCGTCTTCGTTTTAGAGATTTTAAAAGACACGAACAAAATTTT
*
1529118 A
129 G
1529119 AAGTGATATTCGATTATTTTGAACAAAT-GCGAAATTGCAACCCAACACGTTAGGGCACGATTCC
1 AAG-GATATTCGATTATTTTGAACAAATCG-GAAATTGCAACCCAACACGTTAGGGCACGATTCC
* * * * * * * * ** *
1529183 GCGAATGGCCAAACATCAAATCTCATCTTCATTTAAGGGATTTTAAAAGATATGAATGAAATTTC
64 GCGAATCGCCAAACATCAAATATCGTCTTCGTTTTAGAGATTTTAAAAGACACGAACAAAATTTT
1529248 G
129 G
* * *
1529249 AAGGAAAATTCGATTATTTTGAGCAAATAC-GAAATTGCAACCCAACACCTTAGGGCACGATTCC
1 AAGG-ATATTCGATTATTTTGAACAAAT-CGGAAATTGCAACCCAACACGTTAGGGCACGATTCC
* * *
1529313 GTGAATCGCCGAACATCAAATTTCGTCTTCGTTTT
64 GCGAATCGCCAAACATCAAATATCGTCTTCGTTTT
1529348 GAAGAATTTT
Statistics
Matches: 293, Mismatches: 54, Indels: 25
0.79 0.15 0.07
Matches are distributed among these distances:
129 4 0.01
130 209 0.71
131 48 0.16
132 32 0.11
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (129 bp):
AAGGATATTCGATTATTTTGAACAAATCGGAAATTGCAACCCAACACGTTAGGGCACGATTCCGC
GAATCGCCAAACATCAAATATCGTCTTCGTTTTAGAGATTTTAAAAGACACGAACAAAATTTTG
Found at i:1532317 original size:44 final size:44
Alignment explanation
Indices: 1532269--1532730 Score: 721
Period size: 44 Copynumber: 10.5 Consensus size: 44
1532259 GTTCTTTGTA
* *
1532269 AATACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCCACC
1 AATACAGAGATGCCAAATCTGCTATCTTCGATCTGCTCTCCGCC
* *
1532313 AATACAGAGATGCCAAATCTGCTATCTTCAATCTGCTCTCTGCC
1 AATACAGAGATGCCAAATCTGCTATCTTCGATCTGCTCTCCGCC
* *
1532357 AATACAGAGATGCCAAATCTGCTATCTTTGATCTGCTCTCCACC
1 AATACAGAGATGCCAAATCTGCTATCTTCGATCTGCTCTCCGCC
* *
1532401 AATACAGAGATGCCAAATCTACGATCTTCGATCTGCTCTCCGCC
1 AATACAGAGATGCCAAATCTGCTATCTTCGATCTGCTCTCCGCC
* * * * *
1532445 AATACAGAGATGCCAAATCTGCTATTTTCGACCTGTTCACCGCT
1 AATACAGAGATGCCAAATCTGCTATCTTCGATCTGCTCTCCGCC
1532489 AATACAGAGATGCCAAATCTGC-ATTCTTCGATCTGCTCTCCGCC
1 AATACAGAGATGCCAAATCTGCTA-TCTTCGATCTGCTCTCCGCC
*
1532533 AATACAGAGATGCCAAATCTG-TGACCTTCGATCTGCTCTCCGCC
1 AATACAGAGATGCCAAATCTGCT-ATCTTCGATCTGCTCTCCGCC
* *
1532577 AATACAGAGATGCCAAATCTACTATCTTCGATCTGTTCTCCGCC
1 AATACAGAGATGCCAAATCTGCTATCTTCGATCTGCTCTCCGCC
*
1532621 AATACAGAGATGTCAAATCTGCTATCTTCGATCTGCTCTCCGCC
1 AATACAGAGATGCCAAATCTGCTATCTTCGATCTGCTCTCCGCC
*
1532665 AATACAGAGATGCCAAATCTACTATCTTCGATCTGCTCTCCGCC
1 AATACAGAGATGCCAAATCTGCTATCTTCGATCTGCTCTCCGCC
*
1532709 AATACAGAGACGCCAAATCTGC
1 AATACAGAGATGCCAAATCTGC
1532731 AGGATTTACC
Statistics
Matches: 379, Mismatches: 35, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
43 1 0.00
44 376 0.99
45 2 0.01
ACGTcount: A:0.27, C:0.31, G:0.15, T:0.27
Consensus pattern (44 bp):
AATACAGAGATGCCAAATCTGCTATCTTCGATCTGCTCTCCGCC
Found at i:1544732 original size:130 final size:130
Alignment explanation
Indices: 1544488--1544840 Score: 420
Period size: 130 Copynumber: 2.7 Consensus size: 130
1544478 GAGCCGAGTG
* * * * *
1544488 AAATTTTGAAGGGATATTTGATTATTTTAAAC-AATCGGGAAATTGCTACCCAACACGTTAAGGC
1 AAATTTTGAAGGGATATTCGATTATTTTGAACAAAT-GCGAAATTGCAACCCAACACGTTAGGGC
* * * * * * * *
1544552 ACGATCCCGCGAATTGCCAAATATCACATATCGCCTTCGTTTTAGAGATTTTAAAAGACATGAGC
65 ACGATTCCGCGAATCGCCAAACATCAAATATCACCTTCATTTAAGAGATTTTAAAAGACATGAAC
1544617 A
130 A
* *
1544618 AAATTTTAAAGTGATATTCGATTATTTTGAACAAATGCGAAATTGCAACCCAACACGTTAGGGCA
1 AAATTTTGAAGGGATATTCGATTATTTTGAACAAATGCGAAATTGCAACCCAACACGTTAGGGCA
* * * * * * **
1544683 CGATTCCGCGAATGGCCAAACATCAAATCTCATCTTTATTTAAGGGATTTTAAAAGATATGAATG
66 CGATTCCGCGAATCGCCAAACATCAAATATCACCTTCATTTAAGAGATTTTAAAAGACATGAACA
* * * *
1544748 AAATTTCGAAGGGAAATTCGATTATTTTGAGCAAATACGAAATTGCAACCCAACACGTTAGGGCA
1 AAATTTTGAAGGGATATTCGATTATTTTGAACAAATGCGAAATTGCAACCCAACACGTTAGGGCA
* * *
1544813 CGACTCCGTGAATCGCCGAACATCAAAT
66 CGATTCCGCGAATCGCCAAACATCAAAT
1544841 TTCGTCTTCA
Statistics
Matches: 190, Mismatches: 32, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
130 187 0.98
131 3 0.02
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (130 bp):
AAATTTTGAAGGGATATTCGATTATTTTGAACAAATGCGAAATTGCAACCCAACACGTTAGGGCA
CGATTCCGCGAATCGCCAAACATCAAATATCACCTTCATTTAAGAGATTTTAAAAGACATGAACA
Found at i:1550222 original size:23 final size:23
Alignment explanation
Indices: 1550196--1550239 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1550186 CTGATGGACA
*
1550196 GTAAGCTCTATTGAACTGAAACG
1 GTAAGCTCTAATGAACTGAAACG
*
1550219 GTAAGCTCTAATGAGCTGAAA
1 GTAAGCTCTAATGAACTGAAA
1550240 ATAGTAAGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (23 bp):
GTAAGCTCTAATGAACTGAAACG
Found at i:1550251 original size:24 final size:24
Alignment explanation
Indices: 1550193--1550261 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 24
1550183 GAGCTGATGG
* *
1550193 ACAGTAAGCTCTATTGAACTG-AA
1 ACAGTAAGCTCTAATGAGCTGAAA
*
1550216 ACGGTAAGCTCTAATGAGCTGAAA
1 ACAGTAAGCTCTAATGAGCTGAAA
* * *
1550240 ATAGTAAGCTCTTACGAGCTGA
1 ACAGTAAGCTCTAATGAGCTGA
1550262 TATATAGGCA
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
23 18 0.47
24 20 0.53
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.25
Consensus pattern (24 bp):
ACAGTAAGCTCTAATGAGCTGAAA
Found at i:1553192 original size:27 final size:27
Alignment explanation
Indices: 1553154--1553209 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
1553144 TATATACTGC
1553154 TTCGACTCTTCATTTTTCTTTTTCTTT
1 TTCGACTCTTCATTTTTCTTTTTCTTT
1553181 TTCGACTCTTCATTTTTCTTTTTCTTT
1 TTCGACTCTTCATTTTTCTTTTTCTTT
1553208 TT
1 TT
1553210 AACATTTATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.07, C:0.21, G:0.04, T:0.68
Consensus pattern (27 bp):
TTCGACTCTTCATTTTTCTTTTTCTTT
Found at i:1553198 original size:15 final size:15
Alignment explanation
Indices: 1553154--1553198 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
1553144 TATATACTGC
1553154 TTCGACTCTTCATTT
1 TTCGACTCTTCATTT
* *
1553169 TTC--TTTTTC-TTT
1 TTCGACTCTTCATTT
1553181 TTCGACTCTTCATTT
1 TTCGACTCTTCATTT
1553196 TTC
1 TTC
1553199 TTTTTCTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 6
0.70 0.12 0.18
Matches are distributed among these distances:
12 6 0.26
13 4 0.17
14 4 0.17
15 9 0.39
ACGTcount: A:0.09, C:0.24, G:0.04, T:0.62
Consensus pattern (15 bp):
TTCGACTCTTCATTT
Found at i:1562471 original size:19 final size:19
Alignment explanation
Indices: 1562449--1562487 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1562439 TTTTAAATAG
*
1562449 ATACACATGTATTAATAAT
1 ATACACATGTATAAATAAT
1562468 ATACACATGTATAAATAAT
1 ATACACATGTATAAATAAT
1562487 A
1 A
1562488 AATAAGTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.51, C:0.10, G:0.05, T:0.33
Consensus pattern (19 bp):
ATACACATGTATAAATAAT
Found at i:1562914 original size:15 final size:15
Alignment explanation
Indices: 1562891--1562938 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
1562881 TATCAAATTT
1562891 ATATTGATTGAAATC
1 ATATTGATTGAAATC
* * *
1562906 ATTTTGATTGAATTT
1 ATATTGATTGAAATC
1562921 ATATTGATTGAAAT-
1 ATATTGATTGAAATC
1562935 ATAT
1 ATAT
1562939 ATTATATATA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
14 4 0.14
15 24 0.86
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (15 bp):
ATATTGATTGAAATC
Found at i:1563462 original size:23 final size:23
Alignment explanation
Indices: 1563434--1563491 Score: 107
Period size: 23 Copynumber: 2.5 Consensus size: 23
1563424 TAATATTCCG
1563434 GGTGTGTTTGGGTTGGATATTCT
1 GGTGTGTTTGGGTTGGATATTCT
1563457 GGTGTGTTTGGGTTGGATATTCT
1 GGTGTGTTTGGGTTGGATATTCT
*
1563480 AGTGTGTTTGGG
1 GGTGTGTTTGGG
1563492 AAGAATCCGC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.09, C:0.03, G:0.41, T:0.47
Consensus pattern (23 bp):
GGTGTGTTTGGGTTGGATATTCT
Found at i:1563617 original size:18 final size:19
Alignment explanation
Indices: 1563596--1563636 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
1563586 AATGAAATGA
1563596 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
1563614 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
1563633 GAAA
1 GAAA
1563637 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:1569519 original size:28 final size:29
Alignment explanation
Indices: 1569479--1569534 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
1569469 TACTAAATAT
*
1569479 ATATATATATTTT-TTTTTATTTTTAATC
1 ATATATATATTTTATTTTTAATTTTAATC
*
1569507 ATATTTATATTTTATTTTTAATTTTAAT
1 ATATATATATTTTATTTTTAATTTTAAT
1569535 ATAATCACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 12 0.48
29 13 0.52
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (29 bp):
ATATATATATTTTATTTTTAATTTTAATC
Found at i:1569523 original size:23 final size:22
Alignment explanation
Indices: 1569485--1569528 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
1569475 ATATATATAT
*
1569485 ATATTTTTTTTTATTTTTAATC
1 ATATTTTATTTTATTTTTAATC
1569507 ATATTTATATTTTATTTTTAAT
1 ATATTT-TATTTTATTTTTAAT
1569529 TTTAATATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.70
Consensus pattern (22 bp):
ATATTTTATTTTATTTTTAATC
Found at i:1571980 original size:23 final size:23
Alignment explanation
Indices: 1571931--1571981 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
1571921 TTCACACAAG
*
1571931 TGCGCCATGGTTGCGGGCTCCCG
1 TGCGCCATGGTTGCGGGCTCCCA
**
1571954 TGCGCCATGGTTGCGGGCTGTCA
1 TGCGCCATGGTTGCGGGCTCCCA
1571977 TGCGC
1 TGCGC
1571982 AACCCATGAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.06, C:0.31, G:0.39, T:0.24
Consensus pattern (23 bp):
TGCGCCATGGTTGCGGGCTCCCA
Found at i:1573918 original size:18 final size:17
Alignment explanation
Indices: 1573897--1573933 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
1573887 AATTTCATTT
1573897 ATTTTAAATATTTTATAA
1 ATTTTAAATATTTT-TAA
*
1573915 ATTTTTAATATTTTTAA
1 ATTTTAAATATTTTTAA
1573932 AT
1 AT
1573934 ATATAAAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTTTAAATATTTTTAA
Found at i:1579599 original size:27 final size:28
Alignment explanation
Indices: 1579556--1579608 Score: 65
Period size: 27 Copynumber: 1.9 Consensus size: 28
1579546 AAAAATTCAA
* *
1579556 AAAAAATTATAACTAAATATTTAAAAAT
1 AAAAAATTATAACTAAAAATTCAAAAAT
1579584 AAAAAA-TATATA-TAAAAATTCAAAA
1 AAAAAATTATA-ACTAAAAATTCAAAA
1579609 GTTATTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
27 15 0.68
28 7 0.32
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (28 bp):
AAAAAATTATAACTAAAAATTCAAAAAT
Found at i:1584624 original size:22 final size:22
Alignment explanation
Indices: 1584596--1584646 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
1584586 AGCACACGGT
1584596 CGTGTGGTGGCTCGAGTGAGGC
1 CGTGTGGTGGCTCGAGTGAGGC
*
1584618 CGTGTGGTGGCTCGATTGAGGC
1 CGTGTGGTGGCTCGAGTGAGGC
1584640 CGTGTGG
1 CGTGTGG
1584647 GCCACACGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.08, C:0.18, G:0.49, T:0.25
Consensus pattern (22 bp):
CGTGTGGTGGCTCGAGTGAGGC
Found at i:1586243 original size:14 final size:14
Alignment explanation
Indices: 1586220--1586258 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1586210 GTTAAGTTTG
1586220 TTTTAAAAAATAAT
1 TTTTAAAAAATAAT
* *
1586234 TTTTAGAAAATAAG
1 TTTTAAAAAATAAT
*
1586248 TTTAAAAAAAT
1 TTTTAAAAAAT
1586259 TTGCACAATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (14 bp):
TTTTAAAAAATAAT
Found at i:1588361 original size:26 final size:26
Alignment explanation
Indices: 1588332--1588415 Score: 66
Period size: 26 Copynumber: 3.2 Consensus size: 26
1588322 AAATCTATGT
*
1588332 TTTTATAGATATTTTATAATTATTTA
1 TTTTATAAATATTTTATAATTATTTA
* * *
1588358 TTTTTTATAAT-TTTAATATTTATTGTAA
1 TTTTATA-AATATTTTATAATTATT-T-A
* *
1588386 TTTT-TAAATATTTT-TAATGATTTT
1 TTTTATAAATATTTTATAATTATTTA
1588410 TTTTAT
1 TTTTAT
1588416 TTTTTATAAT
Statistics
Matches: 45, Mismatches: 8, Indels: 11
0.70 0.12 0.17
Matches are distributed among these distances:
24 4 0.09
25 2 0.04
26 26 0.58
27 8 0.18
28 5 0.11
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (26 bp):
TTTTATAAATATTTTATAATTATTTA
Found at i:1590947 original size:22 final size:22
Alignment explanation
Indices: 1590906--1590964 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
1590896 GTTTTAAGAA
* *
1590906 TTGTTTTAGTA-TCATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
1590927 TTGTTTTAATATTTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
* *
1590949 GT-TTTTAA-ATATATTT
1 TTGTTTTAATATTTATTT
1590965 GATTTATTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 7 0.21
21 16 0.48
22 10 0.30
ACGTcount: A:0.24, C:0.02, G:0.07, T:0.68
Consensus pattern (22 bp):
TTGTTTTAATATTTATTTTTAT
Found at i:1590963 original size:20 final size:22
Alignment explanation
Indices: 1590919--1590964 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
1590909 TTTTAGTATC
* *
1590919 ATTTTTATTTGTTTTAATATTT
1 ATTTTTATGTGTTTTAATATAT
1590941 ATTTTTATGT-TTTTAA-ATAT
1 ATTTTTATGTGTTTTAATATAT
1590961 ATTT
1 ATTT
1590965 GATTTATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.32
21 6 0.27
22 9 0.41
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (22 bp):
ATTTTTATGTGTTTTAATATAT
Found at i:1590981 original size:26 final size:24
Alignment explanation
Indices: 1590935--1590982 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
1590925 ATTTGTTTTA
*
1590935 ATATTTATTTTTATGTTTTTAAAT
1 ATATTTATTTTTATATTTTTAAAT
1590959 ATATTTGATTTATTATATTTTTAA
1 ATATTT-ATTT-TTATATTTTTAA
1590983 TTTTTTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.29
25 4 0.19
26 11 0.52
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (24 bp):
ATATTTATTTTTATATTTTTAAAT
Found at i:1591266 original size:25 final size:25
Alignment explanation
Indices: 1591237--1591286 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
1591227 TACTCAACCA
1591237 AAACTTTATTTAATTTTATTATTTT
1 AAACTTTATTTAATTTTATTATTTT
1591262 AAACTTTATTTAATTTTATTATTTT
1 AAACTTTATTTAATTTTATTATTTT
1591287 CCGTTAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (25 bp):
AAACTTTATTTAATTTTATTATTTT
Found at i:1601447 original size:32 final size:30
Alignment explanation
Indices: 1601395--1601453 Score: 73
Period size: 32 Copynumber: 1.9 Consensus size: 30
1601385 TAATCAAGTA
*
1601395 AATTAATTGATTTTTTAATTAAATAAATTT
1 AATTAATTGATTTTTAAATTAAATAAATTT
* *
1601425 AATTAGTTGAATTTTCTAAATTAATTAAA
1 AATTAATTG-ATTTT-TAAATTAAATAAA
1601454 GGAAAATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 8 0.33
31 5 0.21
32 11 0.46
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (30 bp):
AATTAATTGATTTTTAAATTAAATAAATTT
Found at i:1605622 original size:22 final size:23
Alignment explanation
Indices: 1605597--1605642 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
1605587 ATTTAAATAT
*
1605597 AAAAAATAAA-TAAATATACTTA
1 AAAAAATAAAGGAAATATACTTA
*
1605619 AAAAAATAAAGGAAATATATTTA
1 AAAAAATAAAGGAAATATACTTA
1605642 A
1 A
1605643 TGCACTATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.26
Consensus pattern (23 bp):
AAAAAATAAAGGAAATATACTTA
Found at i:1605756 original size:20 final size:19
Alignment explanation
Indices: 1605704--1605757 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
1605694 AGTGAAAGAT
1605704 TTATAAATAAATACTAATAA
1 TTATAAATAAATA-TAATAA
* ** *
1605724 TTTTATTTCAATATAATTAA
1 TTATAAATAAATATAA-TAA
1605744 TTATAAATAAATAT
1 TTATAAATAAATAT
1605758 TAAAACTCCG
Statistics
Matches: 25, Mismatches: 8, Indels: 2
0.71 0.23 0.06
Matches are distributed among these distances:
19 3 0.12
20 22 0.88
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (19 bp):
TTATAAATAAATATAATAA
Found at i:1609373 original size:15 final size:15
Alignment explanation
Indices: 1609355--1609409 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 15
1609345 AAAAAGTATA
*
1609355 TAATTTTAGTTTCAT
1 TAATTGTAGTTTCAT
*
1609370 TAATTGTA-TAT-A-
1 TAATTGTAGTTTCAT
*
1609382 TAATTTTAGTTTCAT
1 TAATTGTAGTTTCAT
1609397 TAATTGTAGTTTC
1 TAATTGTAGTTTC
1609410 TTATTCCACA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
12 7 0.22
13 3 0.09
14 3 0.09
15 19 0.59
ACGTcount: A:0.29, C:0.05, G:0.09, T:0.56
Consensus pattern (15 bp):
TAATTGTAGTTTCAT
Found at i:1609388 original size:27 final size:27
Alignment explanation
Indices: 1609351--1609404 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
1609341 AATTAAAAAG
1609351 TATATAATTTTAGTTTCATTAATTGTA
1 TATATAATTTTAGTTTCATTAATTGTA
1609378 TATATAATTTTAGTTTCATTAATTGTA
1 TATATAATTTTAGTTTCATTAATTGTA
1609405 GTTTCTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.56
Consensus pattern (27 bp):
TATATAATTTTAGTTTCATTAATTGTA
Found at i:1609446 original size:26 final size:26
Alignment explanation
Indices: 1609396--1609447 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
1609386 TTTAGTTTCA
*
1609396 TTAATTGTAGTTTCTTATTCCACAAG
1 TTAATTGTAGTTTCTTATGCCACAAG
*
1609422 TTAATTTTAGTTTCTTA-GCCTACAAG
1 TTAATTGTAGTTTCTTATGCC-ACAAG
1609448 AATAAAACCC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 2 0.09
26 21 0.91
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.46
Consensus pattern (26 bp):
TTAATTGTAGTTTCTTATGCCACAAG
Found at i:1610843 original size:15 final size:15
Alignment explanation
Indices: 1610823--1610853 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1610813 ATAAAAGCAC
*
1610823 TTAATTTTAGTTTCT
1 TTAATTATAGTTTCT
1610838 TTAATTATAGTTTCT
1 TTAATTATAGTTTCT
1610853 T
1 T
1610854 ATTCTACAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.06, G:0.06, T:0.65
Consensus pattern (15 bp):
TTAATTATAGTTTCT
Found at i:1616482 original size:2 final size:2
Alignment explanation
Indices: 1616475--1616503 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1616465 AATTTTCAAA
1616475 AG 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 AG A
1616504 AAAGTAGAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1620163 original size:25 final size:25
Alignment explanation
Indices: 1620128--1620178 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
1620118 TCATCTATAT
*
1620128 TTACTTGATTGATATGAAGATTTTG
1 TTACTTAATTGATATGAAGATTTTG
1620153 TTACTTAATTGATATGAAGATTTTG
1 TTACTTAATTGATATGAAGATTTTG
1620178 T
1 T
1620179 GACTAACATG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.29, C:0.04, G:0.18, T:0.49
Consensus pattern (25 bp):
TTACTTAATTGATATGAAGATTTTG
Found at i:1624906 original size:31 final size:31
Alignment explanation
Indices: 1624871--1624932 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
1624861 GCTTGCTCTT
*
1624871 GGATATATGACAGTCGCAATTAACTTTAAAC
1 GGATATATGACAGACGCAATTAACTTTAAAC
1624902 GGATATATGACAGACGCAATTAACTTTAAAC
1 GGATATATGACAGACGCAATTAACTTTAAAC
1624933 CTTACCTGCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.27
Consensus pattern (31 bp):
GGATATATGACAGACGCAATTAACTTTAAAC
Found at i:1632070 original size:18 final size:18
Alignment explanation
Indices: 1632026--1632072 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
1632016 CATGATATAC
1632026 ATAACATATATATAAAACA
1 ATAACATA-ATATAAAACA
*
1632045 ATAA-ATAATATGAAAATA
1 ATAACATAATAT-AAAACA
1632063 A-AACATAATA
1 ATAACATAATA
1632073 AAGATTATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 6 0.24
18 15 0.60
19 4 0.16
ACGTcount: A:0.66, C:0.06, G:0.02, T:0.26
Consensus pattern (18 bp):
ATAACATAATATAAAACA
Found at i:1632270 original size:19 final size:19
Alignment explanation
Indices: 1632188--1632271 Score: 55
Period size: 19 Copynumber: 4.2 Consensus size: 19
1632178 ATGTGAAAAT
* *
1632188 ATAATAATATATAAAAAGAT
1 ATAA-AATATATAATAAGAA
*
1632208 GTAAAATA-ATAATTTAAGGATA
1 ATAAAATATATAA--TAA-GA-A
* *
1632230 ATAATATATATAATAAGTA
1 ATAAAATATATAATAAGAA
1632249 ATAAAATATATAATTAA-AA
1 ATAAAATATATAA-TAAGAA
1632268 ATAA
1 ATAA
1632272 TACTCATAAT
Statistics
Matches: 50, Mismatches: 8, Indels: 13
0.70 0.11 0.18
Matches are distributed among these distances:
18 4 0.08
19 22 0.44
20 9 0.18
21 5 0.10
22 6 0.12
23 4 0.08
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (19 bp):
ATAAAATATATAATAAGAA
Found at i:1632272 original size:41 final size:41
Alignment explanation
Indices: 1632148--1632273 Score: 100
Period size: 41 Copynumber: 3.0 Consensus size: 41
1632138 AACAATATAT
* *
1632148 ATATGTATAAGTAATTAAT-AAATATAATATATGTGAAAATATAATA
1 ATATATATAA-TAAGTAATAAAATAT-ATA-AT-T-AAAA-ATAATA
* **
1632194 ATATATA-AA-AAG-ATGTAAAATA-ATAATTTAAGGATAATA
1 ATATATATAATAAGTA-ATAAAATATATAA-TTAAAAATAATA
1632233 ATATATATAATAAGTAATAAAATATATAATTAAAAATAATA
1 ATATATATAATAAGTAATAAAATATATAATTAAAAATAATA
1632274 CTCATAATAA
Statistics
Matches: 65, Mismatches: 8, Indels: 19
0.71 0.09 0.21
Matches are distributed among these distances:
39 13 0.20
40 4 0.06
41 22 0.34
42 10 0.15
43 3 0.05
44 5 0.08
45 2 0.03
46 6 0.09
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (41 bp):
ATATATATAATAAGTAATAAAATATATAATTAAAAATAATA
Found at i:1632353 original size:19 final size:19
Alignment explanation
Indices: 1632329--1632366 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1632319 AAAATAAACA
*
1632329 AATAATACAATATATATAG
1 AATAATACAATAAATATAG
*
1632348 AATAATATAATAAATATAG
1 AATAATACAATAAATATAG
1632367 GACTAAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.32
Consensus pattern (19 bp):
AATAATACAATAAATATAG
Found at i:1634021 original size:83 final size:83
Alignment explanation
Indices: 1633891--1634715 Score: 1330
Period size: 83 Copynumber: 10.1 Consensus size: 83
1633881 ATGTTAAATT
* *
1633891 ATCTTGAGTCTGCTTGAGAACATTTGAGAGTCATATCTGCAATGTCCTCGATTTGTTCCTTGTAA
1 ATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAACGTCCTCGATTTGTTCCTTGTAA
1633956 GCACAAGGATGCCAAACC
66 GCACAAGGATGCCAAACC
*
1633974 ATCTTGAGTCTGTTTGAGGACATTTGAGAGTCATATCTGCAACGTCCTCGATTTGTTCCTTGTAA
1 ATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAACGTCCTCGATTTGTTCCTTGTAA
1634039 GCACAAGGATGCCAAACC
66 GCACAAGGATGCCAAACC
* *
1634057 ATCTTGAGTCTGTTTGAGGACATTTGAGAGTCATATCTACAACGTCCTCGATTTGTTCCTTGTAA
1 ATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAACGTCCTCGATTTGTTCCTTGTAA
1634122 GCACAAGGATGCCAAACC
66 GCACAAGGATGCCAAACC
* *
1634140 ATCTT-AATCTGTTTGAGAACATTTGAGAGTCATATCTGCAACATCCTCGATTTGTTCCTTGTAA
1 ATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAACGTCCTCGATTTGTTCCTTGTAA
*
1634204 GCACAAGGATGCCAAATC
66 GCACAAGGATGCCAAACC
* * *
1634222 ATCTTGAGTCTG--T-------TTTGAGAGTCATATCTGCTATGTCCTTGATTTGTTCCTTGTAA
1 ATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAACGTCCTCGATTTGTTCCTTGTAA
*
1634278 GCACAAGGATGCTAAACC
66 GCACAAGGATGCCAAACC
* * *
1634296 ATCTTGAGTCTGTTTGAGGACATTTGAGAGTCATATCTGCAACATCCTCGATTTCTTCCTTGTAA
1 ATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAACGTCCTCGATTTGTTCCTTGTAA
1634361 GCACAAGGATGCCAAACC
66 GCACAAGGATGCCAAACC
*
1634379 ATCTTGAGTCTGTTTGAGGACATTT-AGAGTCATATCTGCAACGTCCTCGATTTGTTCCTTGTAA
1 ATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAACGTCCTCGATTTGTTCCTTGTAA
1634443 GCACAAGGATGCCAAACC
66 GCACAAGGATGCCAAACC
* *
1634461 ATCTTGAATCTATTTGAGAACATTTGAGAGTCATATCTGCAACGTCCTCGATTTGTTCCTTGTAA
1 ATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAACGTCCTCGATTTGTTCCTTGTAA
*
1634526 GCACAAGGATGCCAAATC
66 GCACAAGGATGCCAAACC
* *
1634544 ATCTTGAGTCTATTTGAGAACGTTTGAGAGTCATATCTGCAACGTCCTCGATTTGTTCCTTGTAA
1 ATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAACGTCCTCGATTTGTTCCTTGTAA
*
1634609 GCACAAGGATGCCAAATC
66 GCACAAGGATGCCAAACC
* * * *
1634627 ATCTTGAGTCTATTTGAGAACGTTTGAGAGTCATATCTGCTATGTCCTCGATTTGTTCCTTGTAA
1 ATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAACGTCCTCGATTTGTTCCTTGTAA
*
1634692 GCACAAGGATGCCAAATC
66 GCACAAGGATGCCAAACC
1634710 ATCTTG
1 ATCTTG
1634716 GATCTGCTTC
Statistics
Matches: 699, Mismatches: 32, Indels: 22
0.93 0.04 0.03
Matches are distributed among these distances:
74 67 0.10
76 1 0.00
81 1 0.00
82 154 0.22
83 476 0.68
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (83 bp):
ATCTTGAGTCTGTTTGAGAACATTTGAGAGTCATATCTGCAACGTCCTCGATTTGTTCCTTGTAA
GCACAAGGATGCCAAACC
Found at i:1634498 original size:322 final size:325
Alignment explanation
Indices: 1633913--1634715 Score: 1362
Period size: 322 Copynumber: 2.5 Consensus size: 325
1633903 CTTGAGAACA
1633913 TTTGAGAGTCATATCTGCAATGTCCTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCT
1 TTTGAGAGTCATATCTGCAATGTCCTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCT
1633978 TGAGTCTGTTTGAGGACATTTGAGAGTCATATCTGCAACGTCCTCGATTTGTTCCTTGTAAGCAC
66 TGAGTCTGTTTGAGGACATTTGAGAGTCATATCTGCAACGTCCTCGATTTGTTCCTTGTAAGCAC
1634043 AAGGATGCCAAACCATCTTGAGTCTGTTTGAGGACATTTGAGAGTCATATCTACAACGTCCTCGA
131 AAGGATGCCAAACCATCTTGAGTCTGTTTGAGGACATTTGAGAGTCATATCTACAACGTCCTCGA
*
1634108 TTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTAATCTGTTTGAGAACATTTGAGAGTCAT
196 TTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTAATCTATTTGAGAACATTTGAGAGTCAT
*
1634173 ATCTGCAACATCCTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAATCATCTTGAGTC-T-G-T
261 ATCTGCAACATCCTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAATCATCTTGAGTCTTAGAG
* * *
1634235 TTTGAGAGTCATATCTGCTATGTCCTTGATTTGTTCCTTGTAAGCACAAGGATGCTAAACCATCT
1 TTTGAGAGTCATATCTGCAATGTCCTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCT
* *
1634300 TGAGTCTGTTTGAGGACATTTGAGAGTCATATCTGCAACATCCTCGATTTCTTCCTTGTAAGCAC
66 TGAGTCTGTTTGAGGACATTTGAGAGTCATATCTGCAACGTCCTCGATTTGTTCCTTGTAAGCAC
*
1634365 AAGGATGCCAAACCATCTTGAGTCTGTTTGAGGACATTT-AGAGTCATATCTGCAACGTCCTCGA
131 AAGGATGCCAAACCATCTTGAGTCTGTTTGAGGACATTTGAGAGTCATATCTACAACGTCCTCGA
1634429 TTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTGAATCTATTTGAGAACATTTGAGAGTCA
196 TTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTT-AATCTATTTGAGAACATTTGAGAGTCA
*
1634494 TATCTGCAACGTCCTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAATCATCTTGAGTCTATTT
260 TATCTGCAACATCCTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAATCATCTTGAGTC---TT
1634559 GAGAACG
322 -AG-A-G
* *
1634566 TTTGAGAGTCATATCTGCAACGTCCTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAATCATCT
1 TTTGAGAGTCATATCTGCAATGTCCTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCT
* * * * *
1634631 TGAGTCTATTTGAGAACGTTTGAGAGTCATATCTGCTATGTCCTCGATTTGTTCCTTGTAAGCAC
66 TGAGTCTGTTTGAGGACATTTGAGAGTCATATCTGCAACGTCCTCGATTTGTTCCTTGTAAGCAC
*
1634696 AAGGATGCCAAATCATCTTG
131 AAGGATGCCAAACCATCTTG
1634716 GATCTGCTTC
Statistics
Matches: 449, Mismatches: 22, Indels: 11
0.93 0.05 0.02
Matches are distributed among these distances:
321 61 0.14
322 249 0.55
326 1 0.00
328 1 0.00
331 137 0.31
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (325 bp):
TTTGAGAGTCATATCTGCAATGTCCTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCT
TGAGTCTGTTTGAGGACATTTGAGAGTCATATCTGCAACGTCCTCGATTTGTTCCTTGTAAGCAC
AAGGATGCCAAACCATCTTGAGTCTGTTTGAGGACATTTGAGAGTCATATCTACAACGTCCTCGA
TTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTTAATCTATTTGAGAACATTTGAGAGTCAT
ATCTGCAACATCCTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAATCATCTTGAGTCTTAGAG
Found at i:1634643 original size:166 final size:166
Alignment explanation
Indices: 1634235--1634715 Score: 802
Period size: 165 Copynumber: 2.9 Consensus size: 166
1634225 TTGAGTCTGT
* * * *
1634235 TTTGAGAGTCATATCTGCTATGTCCTTGATTTGTTCCTTGTAAGCACAAGGATGCTAAACCATCT
1 TTTGAGAGTCATATCTGCAACGTCCTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCT
* * * *
1634300 TGAGTCTGTTTGAGGACATTTGAGAGTCATATCTGCAACATCCTCGATTTCTTCCTTGTAAGCAC
66 TGAGTCTATTTGAGAACATTTGAGAGTCATATCTGCAACGTCCTCGATTTGTTCCTTGTAAGCAC
* * *
1634365 AAGGATGCCAAACCATCTTGAGTCTGTTTGAGGACA
131 AAGGATGCCAAATCATCTTGAGTCTATTTGAGAACA
1634401 TTT-AGAGTCATATCTGCAACGTCCTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCT
1 TTTGAGAGTCATATCTGCAACGTCCTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCT
*
1634465 TGAATCTATTTGAGAACATTTGAGAGTCATATCTGCAACGTCCTCGATTTGTTCCTTGTAAGCAC
66 TGAGTCTATTTGAGAACATTTGAGAGTCATATCTGCAACGTCCTCGATTTGTTCCTTGTAAGCAC
*
1634530 AAGGATGCCAAATCATCTTGAGTCTATTTGAGAACG
131 AAGGATGCCAAATCATCTTGAGTCTATTTGAGAACA
*
1634566 TTTGAGAGTCATATCTGCAACGTCCTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAATCATCT
1 TTTGAGAGTCATATCTGCAACGTCCTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCT
* * *
1634631 TGAGTCTATTTGAGAACGTTTGAGAGTCATATCTGCTATGTCCTCGATTTGTTCCTTGTAAGCAC
66 TGAGTCTATTTGAGAACATTTGAGAGTCATATCTGCAACGTCCTCGATTTGTTCCTTGTAAGCAC
1634696 AAGGATGCCAAATCATCTTG
131 AAGGATGCCAAATCATCTTG
1634716 GATCTGCTTC
Statistics
Matches: 296, Mismatches: 18, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
165 152 0.51
166 144 0.49
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (166 bp):
TTTGAGAGTCATATCTGCAACGTCCTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCT
TGAGTCTATTTGAGAACATTTGAGAGTCATATCTGCAACGTCCTCGATTTGTTCCTTGTAAGCAC
AAGGATGCCAAATCATCTTGAGTCTATTTGAGAACA
Found at i:1645562 original size:100 final size:101
Alignment explanation
Indices: 1645389--1645589 Score: 395
Period size: 100 Copynumber: 2.0 Consensus size: 101
1645379 TAAGACAAGA
1645389 GATAATCAATTACACGGCTTGACTCTCTTAAACGTCCCCAGCAGAGTCGCCAAGCTATCGAAACC
1 GATAATCAATTACACGGCTTGACTCTCTTAAACGTCCCCAGCAGAGTCGCCAAGCTATCGAAACC
1645454 ATTTTCAAATTCTA-TTTGGAAAATGGGAATCGATT
66 ATTTTCAAATTCTATTTTGGAAAATGGGAATCGATT
1645489 GATAATCAATTACACGGCTTGACTCTCTTAAACGTCCCCAGCAGAGTCGCCAAGCTATCGAAACC
1 GATAATCAATTACACGGCTTGACTCTCTTAAACGTCCCCAGCAGAGTCGCCAAGCTATCGAAACC
1645554 ATTTTCAAATTCTATTTTGGAAAATGGGAATCGATT
66 ATTTTCAAATTCTATTTTGGAAAATGGGAATCGATT
1645590 TTAAAAAACG
Statistics
Matches: 100, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
100 79 0.79
101 21 0.21
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (101 bp):
GATAATCAATTACACGGCTTGACTCTCTTAAACGTCCCCAGCAGAGTCGCCAAGCTATCGAAACC
ATTTTCAAATTCTATTTTGGAAAATGGGAATCGATT
Found at i:1647020 original size:20 final size:20
Alignment explanation
Indices: 1646984--1647021 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1646974 GGAAAATAAT
*
1646984 ATATATAATAAGTAATAACA
1 ATATATAATAAGAAATAACA
1647004 ATATATAATTAA-AAATAA
1 ATATATAA-TAAGAAATAA
1647022 TACTCATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.81
21 3 0.19
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.32
Consensus pattern (20 bp):
ATATATAATAAGAAATAACA
Found at i:1649338 original size:19 final size:19
Alignment explanation
Indices: 1649313--1649403 Score: 125
Period size: 19 Copynumber: 4.9 Consensus size: 19
1649303 ATAATCTTCA
1649313 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
*
1649332 GTGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
1649351 ATGATA--CAATCTTAGAT
1 ATGATATGCAATCTTAGAT
*
1649368 ATGAT-TCCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
* *
1649386 TTGATATACAATCTTAGA
1 ATGATATGCAATCTTAGA
1649404 AGATATGATT
Statistics
Matches: 65, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
17 16 0.25
18 15 0.23
19 34 0.52
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.37
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:1649353 original size:14 final size:15
Alignment explanation
Indices: 1649334--1649385 Score: 52
Period size: 17 Copynumber: 3.2 Consensus size: 15
1649324 TCTTAGATGT
1649334 GATATG-CAATCTTA
1 GATATGACAATCTTA
1649348 GATATGATACAATCTTA
1 GATATG--ACAATCTTA
1649365 GATATGATTCCAATCTTA
1 GATATGA---CAATCTTA
1649383 GAT
1 GAT
1649386 TTGATATACA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
14 6 0.19
15 1 0.03
17 14 0.44
18 11 0.34
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (15 bp):
GATATGACAATCTTA
Found at i:1649413 original size:40 final size:35
Alignment explanation
Indices: 1649321--1649403 Score: 112
Period size: 36 Copynumber: 2.3 Consensus size: 35
1649311 CAATGATATG
* *
1649321 CAATCTTAGATGTGATATGCAATCTTAGATATGATA
1 CAATCTTAGATATGAT-TCCAATCTTAGATATGATA
*
1649357 CAATCTTAGATATGATTCCAATCTTAGATTTGATATA
1 CAATCTTAGATATGATTCCAATCTTAGATATG--ATA
1649394 CAATCTTAGA
1 CAATCTTAGA
1649404 AGATATGATT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
35 14 0.33
36 15 0.36
37 13 0.31
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.37
Consensus pattern (35 bp):
CAATCTTAGATATGATTCCAATCTTAGATATGATA
Found at i:1658573 original size:17 final size:17
Alignment explanation
Indices: 1658553--1658585 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1658543 GATTAATGTT
1658553 TGGCACTGATTTTCTTA
1 TGGCACTGATTTTCTTA
1658570 TGGCACTGATTTTCTT
1 TGGCACTGATTTTCTT
1658586 GTGATGGAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.15, C:0.18, G:0.18, T:0.48
Consensus pattern (17 bp):
TGGCACTGATTTTCTTA
Found at i:1663076 original size:23 final size:23
Alignment explanation
Indices: 1663038--1663100 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
1663028 TTTTTCACTT
* *
1663038 AAATTTTTTAGAATTTTTTTTAAA
1 AAATTTATTA-AATTTTTTTCAAA
* *
1663062 AAATTTATTATATTTTTTTCGAA
1 AAATTTATTAAATTTTTTTCAAA
*
1663085 AATTTTATTAAATTTT
1 AAATTTATTAAATTTT
1663101 CTTAAAATAT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 24 0.73
24 9 0.27
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.59
Consensus pattern (23 bp):
AAATTTATTAAATTTTTTTCAAA
Found at i:1663949 original size:15 final size:16
Alignment explanation
Indices: 1663931--1663966 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
1663921 ATTATTTTTG
1663931 TTTTTATTTTTATT-T
1 TTTTTATTTTTATTAT
*
1663946 TTTTTATTTTTGTTAT
1 TTTTTATTTTTATTAT
1663962 TTTTT
1 TTTTT
1663967 TCTTTTTTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.11, C:0.00, G:0.03, T:0.86
Consensus pattern (16 bp):
TTTTTATTTTTATTAT
Found at i:1663953 original size:27 final size:26
Alignment explanation
Indices: 1663922--1663974 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 26
1663912 TATTTATCTA
*
1663922 TTATTTTTGTTTTTATTTTTATTTTTT
1 TTATTTTTGTTATT-TTTTTATTTTTT
*
1663949 TTATTTTTGTTATTTTTTTCTTTTTT
1 TTATTTTTGTTATTTTTTTATTTTTT
1663975 GGATGTTCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 11 0.46
27 13 0.54
ACGTcount: A:0.09, C:0.02, G:0.04, T:0.85
Consensus pattern (26 bp):
TTATTTTTGTTATTTTTTTATTTTTT
Done.