Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008650.1 Hibiscus syriacus cultivar Beakdansim tig00111640_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1713193
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 6
Found at i:1529162 original size:28 final size:28
Alignment explanation
Indices: 1529095--1529155 Score: 104
Period size: 28 Copynumber: 2.2 Consensus size: 28
1529085 ATTTTTTATA
* *
1529095 TAATCTAATATAACTTAAACTAACAAAT
1 TAATATAATATAACTTAAACTAACAAAC
1529123 TAATATAATATAACTTAAACTAACAAAC
1 TAATATAATATAACTTAAACTAACAAAC
1529151 TAATA
1 TAATA
1529156 ATTTATACTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31
Consensus pattern (28 bp):
TAATATAATATAACTTAAACTAACAAAC
Found at i:1529165 original size:21 final size:21
Alignment explanation
Indices: 1529132--1529180 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
1529122 TTAATATAAT
1529132 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
1529153 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
1529174 ATTAACT
1 A-TAACT
1529181 AAATTTTGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:1529858 original size:30 final size:30
Alignment explanation
Indices: 1529818--1529971 Score: 220
Period size: 30 Copynumber: 5.1 Consensus size: 30
1529808 TTTGGCGAGC
1529818 TGGGCGTGCATGGAGGTCGTTGGGCGTGCA
1 TGGGCGTGCATGGAGGTCGTTGGGCGTGCA
* * *
1529848 TGGCCGTGCATGGAGGTCGTTGGACGTGCC
1 TGGGCGTGCATGGAGGTCGTTGGGCGTGCA
*
1529878 TGGGCATGCATGGAGGTCGTTGGGCGTGCA
1 TGGGCGTGCATGGAGGTCGTTGGGCGTGCA
1529908 TGGGCGTGCATGGAGGTCGTTGGGCGTGCA
1 TGGGCGTGCATGGAGGTCGTTGGGCGTGCA
** *
1529938 TGGGCGTTGC-TGGTAGGTCGCAGGGCATGCA
1 TGGGCG-TGCATGG-AGGTCGTTGGGCGTGCA
1529969 TGG
1 TGG
1529972 CGACCTACCA
Statistics
Matches: 111, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
30 91 0.82
31 20 0.18
ACGTcount: A:0.11, C:0.18, G:0.47, T:0.23
Consensus pattern (30 bp):
TGGGCGTGCATGGAGGTCGTTGGGCGTGCA
Found at i:1529913 original size:10 final size:10
Alignment explanation
Indices: 1529898--1529944 Score: 53
Period size: 10 Copynumber: 4.7 Consensus size: 10
1529888 TGGAGGTCGT
1529898 TGGGCGTGCA
1 TGGGCGTGCA
1529908 TGGGCGTGCA
1 TGGGCGTGCA
*
1529918 TGGAG-GT-CGT
1 TGG-GCGTGC-A
1529928 TGGGCGTGCA
1 TGGGCGTGCA
1529938 TGGGCGT
1 TGGGCGT
1529945 TGCTGGTAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
9 2 0.06
10 27 0.87
11 2 0.06
ACGTcount: A:0.09, C:0.17, G:0.51, T:0.23
Consensus pattern (10 bp):
TGGGCGTGCA
Found at i:1529992 original size:29 final size:29
Alignment explanation
Indices: 1529952--1530038 Score: 120
Period size: 29 Copynumber: 3.0 Consensus size: 29
1529942 CGTTGCTGGT
*
1529952 AGGTCGCAGGGCATGCATGGCGACCTACC
1 AGGTCGCAGGGCGTGCATGGCGACCTACC
* ***
1529981 AGGTCGCTGGGCGTGCATGGCGACCTGGT
1 AGGTCGCAGGGCGTGCATGGCGACCTACC
*
1530010 AGGTCGCCGGGCGTGCATGGCGACCTACC
1 AGGTCGCAGGGCGTGCATGGCGACCTACC
1530039 CCCGGTACTG
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.15, C:0.30, G:0.39, T:0.16
Consensus pattern (29 bp):
AGGTCGCAGGGCGTGCATGGCGACCTACC
Found at i:1530029 original size:58 final size:60
Alignment explanation
Indices: 1529921--1530038 Score: 177
Period size: 58 Copynumber: 2.0 Consensus size: 60
1529911 GCGTGCATGG
* **
1529921 AGGTCGTTGGGCGTGCATGGGCGTTGCTGGTAGGTCGCAGGGCATGCATGGCGACCTACC
1 AGGTCGCTGGGCGTGCATGGGCGTACCTGGTAGGTCGCAGGGCATGCATGGCGACCTACC
* *
1529981 AGGTCGCTGGGCGTGCAT-GGCG-ACCTGGTAGGTCGCCGGGCGTGCATGGCGACCTACC
1 AGGTCGCTGGGCGTGCATGGGCGTACCTGGTAGGTCGCAGGGCATGCATGGCGACCTACC
1530039 CCCGGTACTG
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
58 32 0.60
59 4 0.08
60 17 0.32
ACGTcount: A:0.13, C:0.26, G:0.42, T:0.19
Consensus pattern (60 bp):
AGGTCGCTGGGCGTGCATGGGCGTACCTGGTAGGTCGCAGGGCATGCATGGCGACCTACC
Found at i:1530080 original size:62 final size:62
Alignment explanation
Indices: 1530008--1530131 Score: 248
Period size: 62 Copynumber: 2.0 Consensus size: 62
1529998 TGGCGACCTG
1530008 GTAGGTCGCCGGGCGTGCATGGCGACCTACCCCCGGTACTGTAGAGGACACTACTTTAGCAA
1 GTAGGTCGCCGGGCGTGCATGGCGACCTACCCCCGGTACTGTAGAGGACACTACTTTAGCAA
1530070 GTAGGTCGCCGGGCGTGCATGGCGACCTACCCCCGGTACTGTAGAGGACACTACTTTAGCAA
1 GTAGGTCGCCGGGCGTGCATGGCGACCTACCCCCGGTACTGTAGAGGACACTACTTTAGCAA
1530132 TTAATCTGGC
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.21, C:0.29, G:0.31, T:0.19
Consensus pattern (62 bp):
GTAGGTCGCCGGGCGTGCATGGCGACCTACCCCCGGTACTGTAGAGGACACTACTTTAGCAA
Found at i:1534537 original size:12 final size:12
Alignment explanation
Indices: 1534520--1534566 Score: 58
Period size: 12 Copynumber: 3.7 Consensus size: 12
1534510 TCGGTTTTTT
*
1534520 AACCGGATAAAA
1 AACCGGTTAAAA
1534532 AACCGGTTTGAAAAA
1 AACCGG-TT--AAAA
1534547 AACCGGTTAAAA
1 AACCGGTTAAAA
1534559 AACCGGTT
1 AACCGGTT
1534567 TTTATCCGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
12 18 0.58
13 1 0.03
14 2 0.06
15 10 0.32
ACGTcount: A:0.47, C:0.17, G:0.19, T:0.17
Consensus pattern (12 bp):
AACCGGTTAAAA
Found at i:1536389 original size:11 final size:11
Alignment explanation
Indices: 1536369--1536398 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
1536359 GATATAATGA
1536369 ATTT-GATATT
1 ATTTAGATATT
1536379 ATTTAGATATT
1 ATTTAGATATT
1536390 ATTTAGATA
1 ATTTAGATA
1536399 AACTCATCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.21
11 15 0.79
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (11 bp):
ATTTAGATATT
Found at i:1538089 original size:71 final size:71
Alignment explanation
Indices: 1537973--1538112 Score: 253
Period size: 71 Copynumber: 2.0 Consensus size: 71
1537963 AAATAATAGC
* *
1537973 ACGGACCTGCAACGTAAAATTGCCTGAGAACTCAAATAATCAAGAAGACAATATGTCAAAAGAAG
1 ACGGACCTGCAAAGTAAAATTGCCTGACAACTCAAATAATCAAGAAGACAATATGTCAAAAGAAG
1538038 TCTATT
66 TCTATT
*
1538044 ACGGACCTGCAAAGTAAAATTGCTTGACAACTCAAATAATCAAGAAGACAATATGTCAAAAGAAG
1 ACGGACCTGCAAAGTAAAATTGCCTGACAACTCAAATAATCAAGAAGACAATATGTCAAAAGAAG
1538109 TCTA
66 TCTA
1538113 CAGGAAAAAG
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
71 66 1.00
ACGTcount: A:0.45, C:0.18, G:0.16, T:0.21
Consensus pattern (71 bp):
ACGGACCTGCAAAGTAAAATTGCCTGACAACTCAAATAATCAAGAAGACAATATGTCAAAAGAAG
TCTATT
Found at i:1539451 original size:21 final size:21
Alignment explanation
Indices: 1539411--1539451 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1539401 TAGTAAAAAT
* **
1539411 TATTTAAAACATTATTATTTA
1 TATTTAAAACATCAAAATTTA
1539432 TATTTAAAACATCAAAATTT
1 TATTTAAAACATCAAAATTT
1539452 TTTAACATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.46
Consensus pattern (21 bp):
TATTTAAAACATCAAAATTTA
Found at i:1539550 original size:21 final size:21
Alignment explanation
Indices: 1539476--1539552 Score: 75
Period size: 21 Copynumber: 3.4 Consensus size: 21
1539466 TAAAGTGCCT
1539476 AATAATAACAAAACCGGTATAA
1 AATAATAACAAAACCGGTA-AA
*
1539498 AA-AATAACAAAACAGGTAAAA
1 AATAATAACAAAACCGGT-AAA
1539519 CTCCCAATAATAACAAAACCGGTAAA
1 -----AATAATAACAAAACCGGTAAA
1539545 AATAATAA
1 AATAATAA
1539553 TGTTTTCGAT
Statistics
Matches: 46, Mismatches: 2, Indels: 15
0.73 0.03 0.24
Matches are distributed among these distances:
21 24 0.52
22 3 0.07
26 5 0.11
27 14 0.30
ACGTcount: A:0.61, C:0.16, G:0.08, T:0.16
Consensus pattern (21 bp):
AATAATAACAAAACCGGTAAA
Found at i:1542482 original size:20 final size:22
Alignment explanation
Indices: 1542449--1542489 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
1542439 AAAATTGTAT
*
1542449 ATTTTTAAACTTTTTT-TTTTA
1 ATTTTCAAACTTTTTTATTTTA
1542470 ATTTTCAAA-TTTTTTATTTT
1 ATTTTCAAACTTTTTTATTTT
1542490 TTAGATTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (22 bp):
ATTTTCAAACTTTTTTATTTTA
Found at i:1557646 original size:7 final size:7
Alignment explanation
Indices: 1557634--1557672 Score: 53
Period size: 7 Copynumber: 5.4 Consensus size: 7
1557624 TGATGCTGTC
1557634 TATTTAT
1 TATTTAT
1557641 TATTTAT
1 TATTTAT
1557648 TATTTAT
1 TATTTAT
1557655 TATTAATAT
1 TATT--TAT
1557664 TA-TTAT
1 TATTTAT
1557670 TAT
1 TAT
1557673 AAATAAACTG
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
6 5 0.17
7 18 0.62
8 1 0.03
9 5 0.17
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (7 bp):
TATTTAT
Found at i:1560493 original size:13 final size:13
Alignment explanation
Indices: 1560475--1560499 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1560465 ATTAAGTTAT
1560475 AATTAATAAATAC
1 AATTAATAAATAC
1560488 AATTAATAAATA
1 AATTAATAAATA
1560500 TTTATTCAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
AATTAATAAATAC
Found at i:1560628 original size:73 final size:73
Alignment explanation
Indices: 1560524--1560815 Score: 223
Period size: 73 Copynumber: 3.9 Consensus size: 73
1560514 AAAAAAAAAT
** * * ** *
1560524 TAAATTATAACTAATAAATAAAAGTTCAGAATGATTTTTTCATTAA-AATAAA-TAAATATATAT
1 TAAATTATAGTTAAGAAATAAAAATAAAGAAT-ATTTTTTCATTAATAA-AAATTAAAAATATAT
* *
1560587 ATAAATGTTG
64 AAAAATGTTA
* * *
1560597 TAAATTGTAGTTAAGAGATAAAAACT-AAGAATATTTATTCATTAATAAAAATTAAAAATATATA
1 TAAATTATAGTTAAGAAATAAAAA-TAAAGAATATTTTTTCATTAATAAAAATTAAAAATATATA
1560661 AAAATGTTA
65 AAAATGTTA
* * * *
1560670 TAAATTATAGTTAATAAATAAAAATAAAGAATCATTTCTTCCATTAACAAAAAGATTAGAAATAT
1 TAAATTATAGTTAAGAAATAAAAATAAAGAAT-ATTT-TTTCATTAA-TAAAA-ATTAAAAATAT
* **
1560735 AAAAAAATAATA
62 ATAAAAATGTTA
* * * * * * * *
1560747 TAAATCATAATTAATAAGTACAAATTAAGAATTATGTTTCCATTAATAAAAATATAAAAAT-TAA
1 TAAATTATAGTTAAGAAATAAAAATAAAGAA-TATTTTTTCATTAATAAAAAT-TAAAAATAT-A
1560811 TAAAA
63 TAAAA
1560816 TCATATTTAA
Statistics
Matches: 178, Mismatches: 30, Indels: 20
0.78 0.13 0.09
Matches are distributed among these distances:
72 16 0.09
73 70 0.39
74 8 0.04
75 22 0.12
76 13 0.07
77 48 0.27
78 1 0.01
ACGTcount: A:0.55, C:0.05, G:0.06, T:0.34
Consensus pattern (73 bp):
TAAATTATAGTTAAGAAATAAAAATAAAGAATATTTTTTCATTAATAAAAATTAAAAATATATAA
AAATGTTA
Found at i:1561765 original size:21 final size:21
Alignment explanation
Indices: 1561740--1561783 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1561730 AATTTAGTTA
1561740 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
1561761 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
1561782 AT
1 AT
1561784 ATATTATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:1562335 original size:19 final size:18
Alignment explanation
Indices: 1562281--1562336 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 18
1562271 ATAATTTTCG
*
1562281 TTTAAAAAA-ATTTTGTA
1 TTTAAAAAATATTTTGTT
1562298 TTT-AAAAATATTTAGTGTT
1 TTTAAAAAATATTT--TGTT
1562317 TTTAAAAAAATATTTTGTT
1 TTT-AAAAAATATTTTGTT
1562336 T
1 T
1562337 AATTTATATT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
16 5 0.15
17 7 0.21
19 11 0.33
21 10 0.30
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (18 bp):
TTTAAAAAATATTTTGTT
Found at i:1563550 original size:26 final size:26
Alignment explanation
Indices: 1563496--1564100 Score: 228
Period size: 26 Copynumber: 24.2 Consensus size: 26
1563486 GACTATGATT
1563496 TAATAATGATTTAATAAT-A--ATT-
1 TAATAATGATTTAATAATAATCATTA
*
1563518 TAATAATGATTTAGTAATAATCATTA
1 TAATAATGATTTAATAATAATCATTA
*
1563544 TAATAATGATTTAAT-A-AA-GATT-
1 TAATAATGATTTAATAATAATCATTA
* * *
1563566 T--TAAT-ATTTAATGATTTGATGATT-
1 TAATAATGATTTAAT-A-ATAATCATTA
*
1563590 TAATAATGATTTGATAATAATCATTA
1 TAATAATGATTTAATAATAATCATTA
* *
1563616 TAGTAATGATTTAGTAATAATCATTA
1 TAATAATGATTTAATAATAATCATTA
* *
1563642 TAATAATGATGT--T-ATAATGATT-
1 TAATAATGATTTAATAATAATCATTA
* * * *
1563664 T--TAAT-ATTTGATGATTTGATGATT-
1 TAATAATGATTTAAT-A-ATAATCATTA
* *
1563688 TAGTAATGATTTGATAATAATCATTA
1 TAATAATGATTTAATAATAATCATTA
* *
1563714 TAATAATGATTTAGTAAAAATCATTA
1 TAATAATGATTTAATAATAATCATTA
* *
1563740 TAATAATAATTTAATAATAATGATT-
1 TAATAATGATTTAATAATAATCATTA
*
1563765 TAATAAT-ATCATT-ATAATAATGATTTAA
1 TAATAATGAT--TTAATAATAATCA-TT-A
* *
1563793 TAATAATGATTTAATAATGAT-TTTAA
1 TAATAATGATTTAATAATAATCATT-A
* * * *
1563819 TATTTGATGATTTAGTAATGAT--TTGA
1 TA-ATAATGATTTAATAATAATCATT-A
* *
1563845 TAATAATCA-TT-ATAATAATGATTTAA
1 TAATAATGATTTAATAATAATCA-TT-A
* * * *
1563871 TAATAATCATGATAATAATGAT-TTTA
1 TAATAATGAT-TTAATAATAATCATTA
* *
1563897 TAATAAT--TTTAATATTTAATGATTTGA
1 TAATAATGATTTAATA-ATAATCA-TT-A
* *
1563924 TAATAATCA-TT-ATAATAATGATTTA
1 TAATAATGATTTAATAATAATCA-TTA
* *
1563949 GTAATAATCA-TT-ATAATAATGATTTAA
1 -TAATAATGATTTAATAATAATCA-TT-A
*
1563976 TAATAATGA--TAATAATGAT--TTAA
1 TAATAATGATTTAATAATAATCATT-A
*
1563999 TAATAATCATTATAATAATAAT--TTAA
1 TAATAATGATT-TAATAATAATCATT-A
*
1564025 TAATAATGA--TAATAATGAT--TTAA
1 TAATAATGATTTAATAATAATCATT-A
* *
1564048 TAATAATCA-TT-ATAATAATGATT-
1 TAATAATGATTTAATAATAATCATTA
* *
1564071 TAATAATGATTTTATAATAATGATT-
1 TAATAATGATTTAATAATAATCATTA
1564096 TAATA
1 TAATA
1564101 CTAATTATTA
Statistics
Matches: 472, Mismatches: 58, Indels: 103
0.75 0.09 0.16
Matches are distributed among these distances:
19 10 0.02
20 8 0.02
21 1 0.00
22 19 0.04
23 72 0.15
24 27 0.06
25 58 0.12
26 206 0.44
27 45 0.10
28 17 0.04
29 9 0.02
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.44
Consensus pattern (26 bp):
TAATAATGATTTAATAATAATCATTA
Found at i:1563664 original size:98 final size:97
Alignment explanation
Indices: 1563490--1564124 Score: 465
Period size: 98 Copynumber: 6.5 Consensus size: 97
1563480 GAGATAGACT
1563490 ATGATTTAATAATGATTTAATAATAAT--TTA-ATAATGATTTAGTAATAATCATTATAATAATG
1 ATGATTTAATAATGATTTAATAATAATCATTATATAATGATTTAGTAATAATCATTATAATAATG
* *
1563552 ATTTAATAAAGATTTTAATATTTAATGATTTG
66 ATTTAATAATGATTTTAATATTTAATGATTTA
*
1563584 ATGATTTAATAATGATTTGATAATAATCATTATAGTAATGATTTAGTAATAATCATTATAATAAT
1 ATGATTTAATAATGATTTAATAATAATCATTATA-TAATGATTTAGTAATAATCATTATAATAAT
* *
1563649 GATGTT-ATAATGATTTTAATATTTGATGATTTG
65 GAT-TTAATAATGATTTTAATATTTAATGATTTA
* * *
1563682 ATGATTTAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAAAAATCATTATAATAAT
1 ATGATTTAATAATGATTTAATAATAATCATTAT-ATAATGATTTAGTAATAATCATTATAATAAT
* * * * * *
1563747 AATTTAATAATAATGATTTAATAATATCATTATAATA
65 GATTTAATAATGAT--TTTAAT-ATTTAATGAT-TTA
* * * *
1563784 ATGATTTAATAATAATGATTTAATAATGAT-TTTAATATTTGATGATTTAGTAATGAT--TTGAT
1 ATGA-TT--TAATAATGATTTAATAATAATCATT-ATA--TAATGATTTAGTAATAATCATT-AT
* * *
1563846 AATAATCATTATAATAATGA-TTT-A-A--TAAT-A-ATC
59 AATAATGATT-TAATAATGATTTTAATATTTAATGATTTA
* *
1563879 ATGA--TAATAATGATTTTATAATAAT-TTTAATATTTAATGATTT-GATAATAATCATTATAAT
1 ATGATTTAATAATGATTTAATAATAATCATT-ATA--TAATGATTTAG-TAATAATCATTATAAT
* * * *
1563940 AATGATTTAGTAATAATCATT-ATA-ATAATGATTTA
62 AATGATTTAATAATGAT-TTTAATATTTAATGATTTA
* * * *
1563975 ATAATAATGATAATAATGATTTAATAATAATCATTATAATAAT-AATT--TAATAATAATGATAA
1 ATGAT--T--TAATAATGATTTAATAATAATCATTAT-ATAATGATTTAGTAATAATCATTATAA
* * *
1564037 TAATGATTTAATAATAATCATT-ATA-ATAATGATTTAATA
61 TAATGATTTAATAATGAT-TTTAATATTTAATGA-TT--TA
* *
1564076 ATGATTTTATAATAATGATTTAATACTAATTATTATTAATAATGATTTA
1 ATGA--TT-TAATAATGATTTAATAATAATCATTA-T-ATAATGATTTA
1564125 TTATTAATAT
Statistics
Matches: 453, Mismatches: 44, Indels: 79
0.79 0.08 0.14
Matches are distributed among these distances:
89 1 0.00
90 49 0.11
91 11 0.02
92 5 0.01
93 1 0.00
94 30 0.07
95 7 0.02
96 7 0.02
97 4 0.01
98 175 0.39
99 5 0.01
100 35 0.08
101 24 0.05
102 31 0.07
103 9 0.02
104 5 0.01
105 31 0.07
106 23 0.05
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (97 bp):
ATGATTTAATAATGATTTAATAATAATCATTATATAATGATTTAGTAATAATCATTATAATAATG
ATTTAATAATGATTTTAATATTTAATGATTTA
Found at i:1563830 original size:16 final size:18
Alignment explanation
Indices: 1563809--1563845 Score: 51
Period size: 16 Copynumber: 2.1 Consensus size: 18
1563799 TGATTTAATA
1563809 ATGATTT-TAAT-ATTTG
1 ATGATTTATAATGATTTG
1563825 ATGATTTAGTAATGATTTG
1 ATGATTTA-TAATGATTTG
1563844 AT
1 AT
1563846 AATAATCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.39
18 4 0.22
19 7 0.39
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.51
Consensus pattern (18 bp):
ATGATTTATAATGATTTG
Found at i:1563987 original size:6 final size:6
Alignment explanation
Indices: 1563923--1564066 Score: 73
Period size: 6 Copynumber: 24.8 Consensus size: 6
1563913 TAATGATTTG
* * * * * * * *
1563923 ATAATA ATCATT ATAATA ATGAT- TTAGTA ATAATC ATTATA ATAATG
1 ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA
* * * * * *
1563970 AT-TTA ATAATA ATGATA ATAATG AT-TTA ATAATA ATCATT ATAATA
1 ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA
* * * * * *
1564016 ATAAT- TTAATA ATAATG ATAATA ATGAT- TTAATA ATAATC ATTATA
1 ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA
1564062 ATAAT
1 ATAAT
1564067 GATTTAATAA
Statistics
Matches: 93, Mismatches: 40, Indels: 10
0.65 0.28 0.07
Matches are distributed among these distances:
5 15 0.16
6 78 0.84
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (6 bp):
ATAATA
Found at i:1564036 original size:20 final size:22
Alignment explanation
Indices: 1563950--1564105 Score: 114
Period size: 23 Copynumber: 6.5 Consensus size: 22
1563940 AATGATTTAG
* *
1563950 TAATAATCATTATAATAATGATT
1 TAATAATAATGATAATAA-GATT
1563973 TAATAATAATGATAATAATGATT
1 TAATAATAATGATAATAA-GATT
* *
1563996 TAATAATAATCATTATAATAATAATT
1 TAATAAT-A--ATGATAATAA-GATT
1564022 TAATAATAATGATAATAATGATT
1 TAATAATAATGATAATAA-GATT
*
1564045 TAATAATAATCATTATAATAATGATT
1 TAATAAT-A--ATGATAATAA-GATT
* *
1564071 TAATAATGATTTTATAATAATGATT
1 TAATAAT-A-ATGATAATAA-GATT
*
1564096 TAATACTAAT
1 TAATAATAAT
1564106 TATTATTAAT
Statistics
Matches: 115, Mismatches: 12, Indels: 12
0.83 0.09 0.09
Matches are distributed among these distances:
23 49 0.43
24 3 0.03
25 21 0.18
26 42 0.37
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (22 bp):
TAATAATAATGATAATAAGATT
Found at i:1564141 original size:14 final size:14
Alignment explanation
Indices: 1564037--1564143 Score: 59
Period size: 14 Copynumber: 8.1 Consensus size: 14
1564027 ATAATGATAA
* *
1564037 TAATGATTTAATAA
1 TAATGATTTATTAT
* *
1564051 TAATCA-TTA-TAA
1 TAATGATTTATTAT
1564063 TAATGATTTA--A-
1 TAATGATTTATTAT
*
1564074 TAATGATTT-TATAA
1 TAATGATTTAT-TAT
* *
1564088 TAATGATTTAATAC
1 TAATGATTTATTAT
* *
1564102 TAATTA-TTATTAA
1 TAATGATTTATTAT
1564115 TAATGATTTATTAT
1 TAATGATTTATTAT
1564129 TAAT-ATTTAATTAT
1 TAATGATTT-ATTAT
1564143 T
1 T
1564144 TGATACTAAT
Statistics
Matches: 76, Mismatches: 9, Indels: 16
0.75 0.09 0.16
Matches are distributed among these distances:
11 9 0.12
12 9 0.12
13 21 0.28
14 37 0.49
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.50
Consensus pattern (14 bp):
TAATGATTTATTAT
Found at i:1564142 original size:17 final size:17
Alignment explanation
Indices: 1564102--1564143 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
1564092 GATTTAATAC
1564102 TAATTATTATTAATAAT
1 TAATTATTATTAATAAT
* * *
1564119 GATTTATTATTAATATT
1 TAATTATTATTAATAAT
1564136 TAATTATT
1 TAATTATT
1564144 TGATACTAAT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (17 bp):
TAATTATTATTAATAAT
Found at i:1564144 original size:21 final size:22
Alignment explanation
Indices: 1564115--1564172 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 22
1564105 TTATTATTAA
* *
1564115 TAATGATTTATTATTAAT-ATT
1 TAATTATTTATTACTAATGATT
1564136 TAATTATTTGA-TACTAATGATT
1 TAATTATTT-ATTACTAATGATT
*
1564158 T-ATTAATTATTACTA
1 TAATTATTTATTACTA
1564173 GTAATGAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
20 1 0.03
21 25 0.81
22 5 0.16
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.53
Consensus pattern (22 bp):
TAATTATTTATTACTAATGATT
Found at i:1566480 original size:11 final size:11
Alignment explanation
Indices: 1566466--1566504 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
1566456 TTAAACTATT
1566466 CTTTAATATAA
1 CTTTAATATAA
*
1566477 CTTTAACTAT-T
1 CTTTAA-TATAA
1566488 CTTTAATATAA
1 CTTTAATATAA
1566499 CTTTAA
1 CTTTAA
1566505 CTAATAAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.38, C:0.13, G:0.00, T:0.49
Consensus pattern (11 bp):
CTTTAATATAA
Found at i:1566485 original size:30 final size:30
Alignment explanation
Indices: 1566451--1566537 Score: 91
Period size: 30 Copynumber: 3.2 Consensus size: 30
1566441 TTCCTTAAAC
1566451 AACTATTAAACTATTCTTT-A-AT-A---T
1 AACTATTAAACTATTCTTTAATATAACTTT
1566475 AACT-TT-AACTATTCTTTAATATAACTTT
1 AACTATTAAACTATTCTTTAATATAACTTT
* * *
1566503 AACTAATAAACTATTATTTAATATAACTTA
1 AACTATTAAACTATTCTTTAATATAACTTT
1566533 AACTA
1 AACTA
1566538 AAAAACTAAT
Statistics
Matches: 52, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
22 11 0.21
23 3 0.06
24 6 0.12
25 1 0.02
28 5 0.10
29 1 0.02
30 25 0.48
ACGTcount: A:0.44, C:0.13, G:0.00, T:0.44
Consensus pattern (30 bp):
AACTATTAAACTATTCTTTAATATAACTTT
Found at i:1566487 original size:22 final size:22
Alignment explanation
Indices: 1566459--1566507 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
1566449 ACAACTATTA
1566459 AACTATTCTTTAATATAACTTT
1 AACTATTCTTTAATATAACTTT
1566481 AACTATTCTTTAATATAACTTT
1 AACTATTCTTTAATATAACTTT
1566503 AACTA
1 AACTA
1566508 ATAAACTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.39, C:0.14, G:0.00, T:0.47
Consensus pattern (22 bp):
AACTATTCTTTAATATAACTTT
Found at i:1566524 original size:15 final size:16
Alignment explanation
Indices: 1566480--1566530 Score: 61
Period size: 15 Copynumber: 3.3 Consensus size: 16
1566470 AATATAACTT
*
1566480 TAACTATTCTTTAATA
1 TAACTATTATTTAATA
**
1566496 TAACT-TTAACTAATA
1 TAACTATTATTTAATA
1566511 -AACTATTATTTAATA
1 TAACTATTATTTAATA
1566526 TAACT
1 TAACT
1566531 TAAACTAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
14 4 0.14
15 15 0.54
16 9 0.32
ACGTcount: A:0.43, C:0.12, G:0.00, T:0.45
Consensus pattern (16 bp):
TAACTATTATTTAATA
Found at i:1566538 original size:30 final size:30
Alignment explanation
Indices: 1566481--1566545 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
1566471 ATATAACTTT
* * *
1566481 AACTATTCTTTAATATAACTTTAACTAATA
1 AACTATTATTTAATATAACTTAAACTAAAA
1566511 AACTATTATTTAATATAACTTAAACTAAAA
1 AACTATTATTTAATATAACTTAAACTAAAA
1566541 AACTA
1 AACTA
1566546 ATTAACTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.38
Consensus pattern (30 bp):
AACTATTATTTAATATAACTTAAACTAAAA
Found at i:1566552 original size:52 final size:52
Alignment explanation
Indices: 1566451--1566552 Score: 116
Period size: 52 Copynumber: 2.0 Consensus size: 52
1566441 TTCCTTAAAC
* * * *****
1566451 AACTATTAAACTATTCTTTAATATAACTTTAACTATTCTTTAATATAACTTT
1 AACTAATAAACTATTATTTAATATAACTTAAACTAAAAACTAATATAACTTT
1566503 AACTAATAAACTATTATTTAATATAACTTAAACTAAAAAACTAAT-TAACT
1 AACTAATAAACTATTATTTAATATAACTTAAACT-AAAAACTAATATAACT
1566553 AATTTTTTAT
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
52 36 0.88
53 5 0.12
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (52 bp):
AACTAATAAACTATTATTTAATATAACTTAAACTAAAAACTAATATAACTTT
Found at i:1566569 original size:73 final size:73
Alignment explanation
Indices: 1566491--1566947 Score: 173
Period size: 73 Copynumber: 6.1 Consensus size: 73
1566481 AACTATTCTT
1566491 TAATATAACTTTAACTAATAAACTATTATTTAATATAACTTAAACTAAAAAACTAATTAACTAAT
1 TAATATAACTTTAACTAATAAACTATTATTTAATATAACTTAAACTAAAAAACTAATTAACTAAT
1566556 TTTTTATA
66 TTTTTATA
* * * * *
1566564 TAATATAAATTTAACAAACAAA-TATAACTTAACTAT---TT-AACTAACACAAACTAATT-AC-
1 TAATATAACTTTAACTAATAAACTATTATTTAA-TATAACTTAAACTAA-A-AAACTAATTAACT
1566622 ATATTTTTTATA
63 A-ATTTTTTATA
* ** * ** *
1566634 TATAAATAACGACTAACAAACT-AACTAATTATTTTTTATTAA-TATGTAACTATCAAACATACT
1 TA-ATATAAC-TTTAACTAA-TAAACT-ATTATTTAATA-TAACT-T-AAACTA--AAA-A-ACT
* *
1566697 AATTAAATAATTTTTTATT
55 AATTAACTAATTTTTTATA
* * * ** * *
1566716 TCTATATGA-TATAACT--TAAACTAACA-ATAATATAACTTAAACTAACAAACTAATTAACTAA
1 T-AATATAACTTTAACTAATAAACTATTATTTAATATAACTTAAACTAAAAAACTAATTAACTAA
* *
1566777 TTTTTTGTTT
65 TTTTTT-ATA
*** * * * *
1566787 TACCCTAA-TTTATAGTAATAAACTA--A-TAAACTAATAATTTATAAC-AATAAACTAATTTAA
1 TAATATAACTTTA-ACTAATAAACTATTATTTAA-T-ATAACTTA-AACTAAAAAACTAA-TTAA
*
1566847 ATAATTATTCTT-T-
61 CTAATT-TT-TTATA
* *
1566860 T-ATATAACTTAAACTAATAAACTATTTTTTATTATAATAAAACTTAAACTACTAATAAACTAAT
1 TAATATAACTTTAACTAATAAACTA----TTATT-TAATATAACTTAAACTA--AA-AAACTAAT
*
1566924 TAACTAATTTTGTATA
58 TAACTAATTTTTTATA
1566940 TAATATAA
1 TAATATAA
1566948 ATTCAACAAC
Statistics
Matches: 280, Mismatches: 54, Indels: 92
0.66 0.13 0.22
Matches are distributed among these distances:
69 7 0.03
70 40 0.14
71 23 0.08
72 34 0.12
73 52 0.19
74 24 0.09
75 6 0.02
76 7 0.03
77 7 0.03
78 13 0.05
79 11 0.04
80 19 0.07
81 21 0.08
82 15 0.05
83 1 0.00
ACGTcount: A:0.48, C:0.11, G:0.01, T:0.40
Consensus pattern (73 bp):
TAATATAACTTTAACTAATAAACTATTATTTAATATAACTTAAACTAAAAAACTAATTAACTAAT
TTTTTATA
Found at i:1566748 original size:21 final size:21
Alignment explanation
Indices: 1566724--1566763 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1566714 TTTCTATATG
1566724 ATATAACTTAAACTAACAATA
1 ATATAACTTAAACTAACAATA
1566745 ATATAACTTAAACTAACAA
1 ATATAACTTAAACTAACAA
1566764 ACTAATTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (21 bp):
ATATAACTTAAACTAACAATA
Found at i:1567092 original size:364 final size:363
Alignment explanation
Indices: 1566484--1567159 Score: 949
Period size: 369 Copynumber: 1.8 Consensus size: 363
1566474 TAACTTTAAC
* *
1566484 TATTCTTTAATATAACTTTAACTAATAAACTATTATTTAATATAACTTAAACTAAAAAACTAATT
1 TATTCTTTAATATAACTTAAACTAATAAACTATTATTTAATAAAACTTAAACTAAAAAACTAATT
* *
1566549 AACTAATTTTTTATATAATATAAATTTAACAAACAAATATAACTTAACTATTTAACTAACACAAA
66 AACTAATTTTGTATATAATATAAATTCAACAAACAAATATAACTTAACTATTTAACTAACACAAA
1566614 CTAATTACATATTTTTTATATATAAATAACGACTAACAAACTAACTAATTATTTTTTATTAATAT
131 CTAATTACATA-----TATATATAAATAAC-ACTAACAAACTAACTAATTA-TTTTTATTAATAT
* * * * *
1566679 GTAACTATCAAACATACTAATTAAATAATTTTTTATTTCTATATGATATAAC-T-TAAACTAACA
189 ATAACCATCAAACAAACTAATTAAATAATTTTATATTTATATATGATATAACTTATAAACTAACA
*
1566742 ATAATATAACTTAAACTAACAAACTAATTAACTAATTTTTTGTTTTACCCTAATTTATAGTAATA
254 ATAATATAACTTAAACTAACAAACTAATTAACTAAATTTTTGTTTTACCCTAATTTATAGTAATA
1566807 AACTAATAAACTAATAATTTATAACAATAAACTAATTTAAATAAT
319 AACTAATAAACTAATAATTTATAACAATAAACTAATTTAAATAAT
*
1566852 TATTCTTTTATATAACTTAAACTAATAAACTATTTTTTATTATAATAAAACTTAAACTACTAATA
1 TATTCTTTAATATAACTTAAACTAATAAACTA----TTATT-TAATAAAACTTAAACTA--AA-A
*
1566917 AACTAATTAACTAATTTTGTATATAATATAAATTCAACAACCAAAATATAACTTAACTATTTAAC
58 AACTAATTAACTAATTTTGTATATAATATAAATTCAACAAAC-AAATATAACTTAACTATTTAAC
* * *
1566982 TAACTACAAACTAATTA-A-A-ATAT-TAGACT-A-ACTAACACACTAATTAATTA-TTTT-TTA
122 TAAC-ACAAACTAATTACATATATATATA-AATAACACTAACAAACTAACTAATTATTTTTATTA
*
1567039 ATATATAACCATCAAACAAACTAATTAAATAATTTTATATTTATGTATGATATAACTTAAACTAA
185 ATATATAACCATCAAACAAACTAATTAAATAATTTTATATTTATATATGATATAACTT--A-TAA
1567104 ACTAACAATAATATAACTTAAACTAACAAACTAATTAACTAAATTTTTGTTTTACC
247 ACTAACAATAATATAACTTAAACTAACAAACTAATTAACTAAATTTTTGTTTTACC
1567160 TTAAACTAAC
Statistics
Matches: 276, Mismatches: 16, Indels: 31
0.85 0.05 0.10
Matches are distributed among these distances:
364 53 0.19
365 5 0.02
367 18 0.07
368 30 0.11
369 61 0.22
370 6 0.02
372 5 0.02
373 16 0.06
375 2 0.01
376 41 0.15
377 27 0.10
378 12 0.04
ACGTcount: A:0.47, C:0.12, G:0.01, T:0.39
Consensus pattern (363 bp):
TATTCTTTAATATAACTTAAACTAATAAACTATTATTTAATAAAACTTAAACTAAAAAACTAATT
AACTAATTTTGTATATAATATAAATTCAACAAACAAATATAACTTAACTATTTAACTAACACAAA
CTAATTACATATATATATAAATAACACTAACAAACTAACTAATTATTTTTATTAATATATAACCA
TCAAACAAACTAATTAAATAATTTTATATTTATATATGATATAACTTATAAACTAACAATAATAT
AACTTAAACTAACAAACTAATTAACTAAATTTTTGTTTTACCCTAATTTATAGTAATAAACTAAT
AAACTAATAATTTATAACAATAAACTAATTTAAATAAT
Found at i:1567146 original size:21 final size:20
Alignment explanation
Indices: 1567098--1567146 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 20
1567088 ATATAACTTA
1567098 AACTAAACTAACAATAATAT
1 AACTAAACTAACAATAATAT
1567118 AACTTAAACTAACAAACTAAT-T
1 AAC-TAAACTAAC-AA-TAATAT
1567140 AACTAAA
1 AACTAAA
1567147 TTTTTGTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
20 3 0.12
21 13 0.50
22 6 0.23
23 4 0.15
ACGTcount: A:0.59, C:0.16, G:0.00, T:0.24
Consensus pattern (20 bp):
AACTAAACTAACAATAATAT
Found at i:1567178 original size:35 final size:35
Alignment explanation
Indices: 1567132--1567200 Score: 120
Period size: 35 Copynumber: 2.0 Consensus size: 35
1567122 TAAACTAACA
*
1567132 AACTAATTAACTAAATTTTTGTTTTACCTTAAACT
1 AACTAATTAACTAAAATTTTGTTTTACCTTAAACT
*
1567167 AACTATTTAACTAAAATTTTGTTTTACCTTAAAC
1 AACTAATTAACTAAAATTTTGTTTTACCTTAAAC
1567201 CATAAACTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.38, C:0.14, G:0.03, T:0.45
Consensus pattern (35 bp):
AACTAATTAACTAAAATTTTGTTTTACCTTAAACT
Found at i:1567656 original size:29 final size:29
Alignment explanation
Indices: 1567623--1567681 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
1567613 ATGCACACTC
1567623 CTTGGTCGCCCGGAGTGCATGACGACCTA
1 CTTGGTCGCCCGGAGTGCATGACGACCTA
* *
1567652 CTTGGTCGCCCGGAGTGTATGGCGACCTA
1 CTTGGTCGCCCGGAGTGCATGACGACCTA
1567681 C
1 C
1567682 GGCTTCACTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.15, C:0.31, G:0.32, T:0.22
Consensus pattern (29 bp):
CTTGGTCGCCCGGAGTGCATGACGACCTA
Found at i:1572816 original size:16 final size:16
Alignment explanation
Indices: 1572795--1572839 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
1572785 TTCGTTTAAA
1572795 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
1572811 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
1572827 ACGAACATAAACG
1 ACGAACATAAACG
1572840 TTGGAGACCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.56, C:0.22, G:0.13, T:0.09
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1575499 original size:16 final size:16
Alignment explanation
Indices: 1575478--1575508 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1575468 TATGTTCACG
1575478 AACAAACTCTTTTATT
1 AACAAACTCTTTTATT
1575494 AACAAACTCTTTTAT
1 AACAAACTCTTTTAT
1575509 AAGTTTGTTT
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:0.39, C:0.19, G:0.00, T:0.42
Consensus pattern (16 bp):
AACAAACTCTTTTATT
Found at i:1612522 original size:18 final size:18
Alignment explanation
Indices: 1612486--1612522 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1612476 TTCTACTTAC
*
1612486 ACCATACTAATTCAAAAA
1 ACCATACTAATTAAAAAA
*
1612504 ACCATATTAATTAAAAAA
1 ACCATACTAATTAAAAAA
1612522 A
1 A
1612523 GGTAAACTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.59, C:0.16, G:0.00, T:0.24
Consensus pattern (18 bp):
ACCATACTAATTAAAAAA
Found at i:1612662 original size:11 final size:12
Alignment explanation
Indices: 1612636--1612674 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
1612626 CTGACGTGAC
1612636 ATTTTTAAATTA
1 ATTTTTAAATTA
*
1612648 ATTTTTATATT-
1 ATTTTTAAATTA
*
1612659 ATTTTTTAATTA
1 ATTTTTAAATTA
1612671 ATTT
1 ATTT
1612675 ATTCACTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
11 9 0.39
12 14 0.61
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATTTTTAAATTA
Found at i:1616213 original size:14 final size:14
Alignment explanation
Indices: 1616190--1616223 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
1616180 TATTAGAAAA
*
1616190 TTTTAATTCTATTT
1 TTTTACTTCTATTT
1616204 TTTTACTTCTATTT
1 TTTTACTTCTATTT
1616218 TTTTAC
1 TTTTAC
1616224 CGTTATCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.18, C:0.12, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTACTTCTATTT
Found at i:1617856 original size:16 final size:17
Alignment explanation
Indices: 1617826--1617861 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
1617816 AATTCAGGAG
1617826 CTCGATTGAAGCTCGAA
1 CTCGATTGAAGCTCGAA
1617843 CTCGATTG-AGCTCGAA
1 CTCGATTGAAGCTCGAA
1617859 CTC
1 CTC
1617862 AAACTCGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (17 bp):
CTCGATTGAAGCTCGAA
Found at i:1630154 original size:15 final size:15
Alignment explanation
Indices: 1630136--1630164 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1630126 GTACGAGAGT
1630136 TTTGGATTGGATTGG
1 TTTGGATTGGATTGG
1630151 TTTGGATTGGATTG
1 TTTGGATTGGATTG
1630165 AAGGTTGGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.00, G:0.38, T:0.48
Consensus pattern (15 bp):
TTTGGATTGGATTGG
Found at i:1643778 original size:39 final size:41
Alignment explanation
Indices: 1643679--1643795 Score: 148
Period size: 39 Copynumber: 2.9 Consensus size: 41
1643669 GGTTCTATTT
* *
1643679 GGTTAATAATGTGAACTTTAGTATTGAGCTGAATCCATTGTTA
1 GGTTAATAGTGTGAACTTTAGAATTGAGCTGAAT-CA-TGTTA
1643722 GGTTAATAGTGTGAACTTTAGAATTGAGCTGAATC-T-TTA
1 GGTTAATAGTGTGAACTTTAGAATTGAGCTGAATCATGTTA
** * *
1643761 TTTTAATAGTGTGAACTTTATAACTGAGCTGAATC
1 GGTTAATAGTGTGAACTTTAGAATTGAGCTGAATC
1643796 CTTTGAGTCT
Statistics
Matches: 68, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
39 34 0.50
40 1 0.01
42 1 0.01
43 32 0.47
ACGTcount: A:0.31, C:0.09, G:0.21, T:0.39
Consensus pattern (41 bp):
GGTTAATAGTGTGAACTTTAGAATTGAGCTGAATCATGTTA
Found at i:1643914 original size:25 final size:25
Alignment explanation
Indices: 1643880--1643939 Score: 95
Period size: 25 Copynumber: 2.4 Consensus size: 25
1643870 CGTGTTGAGG
*
1643880 TAAGT-TTATACTAGTGAGGTCTCT
1 TAAGTCTTATACTAGTGAAGTCTCT
1643904 TAAGTCTTATACTAGTGAAGTCTCT
1 TAAGTCTTATACTAGTGAAGTCTCT
*
1643929 CAAGTCTTATA
1 TAAGTCTTATA
1643940 TAATTAACAC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
24 5 0.15
25 28 0.85
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (25 bp):
TAAGTCTTATACTAGTGAAGTCTCT
Found at i:1650587 original size:21 final size:22
Alignment explanation
Indices: 1650549--1650603 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
1650539 ATGTTAGGGG
* * *
1650549 CGAACTTAAACTTAAGGGG-GA
1 CGAACTAAAATTTCAGGGGAGA
* *
1650570 TGAACTAAAATTTCAGGGGAGG
1 CGAACTAAAATTTCAGGGGAGA
1650592 CGAACTAAAATT
1 CGAACTAAAATT
1650604 CTAAGAGGTG
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 15 0.56
22 12 0.44
ACGTcount: A:0.40, C:0.13, G:0.25, T:0.22
Consensus pattern (22 bp):
CGAACTAAAATTTCAGGGGAGA
Found at i:1658971 original size:21 final size:21
Alignment explanation
Indices: 1658945--1658989 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
1658935 AGAATTGTTA
*
1658945 AAAAATATTAATATTTTAAAT
1 AAAAATAATAATATTTTAAAT
1658966 AAAAATAATAATATTTTAAAT
1 AAAAATAATAATATTTTAAAT
1658987 AAA
1 AAA
1658990 TTTTTATCGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
AAAAATAATAATATTTTAAAT
Found at i:1673254 original size:15 final size:16
Alignment explanation
Indices: 1673216--1673256 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
1673206 ATAGAGCCTC
* *
1673216 TGAATCATTCAGCATT
1 TGAATCATTCAACACT
1673232 TGAATCATTCAACACT
1 TGAATCATTCAACACT
1673248 T-AATCATTC
1 TGAATCATTC
1673257 TGAAATAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.34, C:0.22, G:0.07, T:0.37
Consensus pattern (16 bp):
TGAATCATTCAACACT
Found at i:1673555 original size:21 final size:22
Alignment explanation
Indices: 1673529--1673572 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1673519 AAAGAATATC
1673529 AAATTA-TTAAAATAAATAAAA
1 AAATTACTTAAAATAAATAAAA
* *
1673550 AAATTACTTAAATTATATAAAA
1 AAATTACTTAAAATAAATAAAA
1673572 A
1 A
1673573 TTTAATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (22 bp):
AAATTACTTAAAATAAATAAAA
Found at i:1675666 original size:38 final size:37
Alignment explanation
Indices: 1675616--1675694 Score: 97
Period size: 38 Copynumber: 2.1 Consensus size: 37
1675606 CATTAAACAT
* *
1675616 TTTTATATTTTAAATTTTGTAAAAAATTTATATAAA-A
1 TTTTATAATTTAAATTTTGTAAAAAA-ATATATAAATA
* *
1675653 TTTTATGAATTTAATTTTTTTAAAAAAATATATAAATA
1 TTTTAT-AATTTAAATTTTGTAAAAAAATATATAAATA
1675691 TTTT
1 TTTT
1675695 TCAACTTGTT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
37 14 0.39
38 22 0.61
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (37 bp):
TTTTATAATTTAAATTTTGTAAAAAAATATATAAATA
Found at i:1675895 original size:18 final size:18
Alignment explanation
Indices: 1675835--1675902 Score: 77
Period size: 18 Copynumber: 3.8 Consensus size: 18
1675825 AACATTCCCA
1675835 GTAATCTT--ATTCTCTG
1 GTAATCTTACATTCTCTG
* *
1675851 GTAATCTTACTTTCCCACTG
1 GTAATCTTACATT--CTCTG
*
1675871 ATAATCTTACATTCTCTG
1 GTAATCTTACATTCTCTG
1675889 GTAATCTTACATTC
1 GTAATCTTACATTC
1675903 CGTAAACCAA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
16 8 0.19
18 19 0.45
20 15 0.36
ACGTcount: A:0.24, C:0.24, G:0.09, T:0.44
Consensus pattern (18 bp):
GTAATCTTACATTCTCTG
Found at i:1679215 original size:17 final size:16
Alignment explanation
Indices: 1679193--1679226 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1679183 TAGTTTATAT
1679193 ATAATATAATTATATTG
1 ATAATAT-ATTATATTG
*
1679210 ATAATATCTTATATTG
1 ATAATATATTATATTG
1679226 A
1 A
1679227 GGAATTAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (16 bp):
ATAATATATTATATTG
Found at i:1679269 original size:8 final size:7
Alignment explanation
Indices: 1679243--1679267 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1679233 AGATTGTTTG
1679243 AAAATAA
1 AAAATAA
1679250 AAAATAA
1 AAAATAA
1679257 AAAATAA
1 AAAATAA
1679264 AAAA
1 AAAA
1679268 ATGAAATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAATAA
Found at i:1682076 original size:32 final size:34
Alignment explanation
Indices: 1682005--1682086 Score: 114
Period size: 32 Copynumber: 2.4 Consensus size: 34
1681995 AAAAAAATTA
*
1682005 AAACTCATCATACGAACCGAAGAAAAATTGTATG
1 AAACTCATCATACGAACCGAAGAAAAATTATATG
* *
1682039 GAACTCATCATATGAACCG-A-AAAAATTATATG
1 AAACTCATCATACGAACCGAAGAAAAATTATATG
1682071 AAACTCATCATGACGA
1 AAACTCATCAT-ACGA
1682087 GTTCCACTCA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
32 21 0.50
33 4 0.10
34 17 0.40
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.22
Consensus pattern (34 bp):
AAACTCATCATACGAACCGAAGAAAAATTATATG
Found at i:1685434 original size:35 final size:35
Alignment explanation
Indices: 1685383--1685452 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
1685373 CAGTCATCAG
1685383 TAAACCCCAAAATCCAAAATACTTCAATTACATTC
1 TAAACCCCAAAATCCAAAATACTTCAATTACATTC
* * *
1685418 TAAACCTCAAATTCCAAAATACTTTAATTACATTC
1 TAAACCCCAAAATCCAAAATACTTCAATTACATTC
1685453 CCAACTCCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.44, C:0.26, G:0.00, T:0.30
Consensus pattern (35 bp):
TAAACCCCAAAATCCAAAATACTTCAATTACATTC
Found at i:1685464 original size:35 final size:34
Alignment explanation
Indices: 1685388--1685466 Score: 104
Period size: 35 Copynumber: 2.3 Consensus size: 34
1685378 ATCAGTAAAC
* *
1685388 CCCAAAATCCAAAATACTTCAATTACATTCTAAA
1 CCCAAATTCCAAAATACTTCAATTACATTCCAAA
* *
1685422 CCTCAAATTCCAAAATACTTTAATTACATTCCCAA
1 CC-CAAATTCCAAAATACTTCAATTACATTCCAAA
1685457 CTCCAAATTC
1 C-CCAAATTC
1685467 ATAATACATT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
34 2 0.05
35 36 0.92
36 1 0.03
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (34 bp):
CCCAAATTCCAAAATACTTCAATTACATTCCAAA
Found at i:1686454 original size:35 final size:35
Alignment explanation
Indices: 1686415--1686491 Score: 93
Period size: 35 Copynumber: 2.2 Consensus size: 35
1686405 GTTGGGCATA
* * *
1686415 TAATTGAAGTATTTTGGAATTTGA-GATTTAGAATG
1 TAATTAAAATATTTTGG-ATTTGAGGATTTAAAATG
* *
1686450 TAATTAAAATATTTTGGATTTTAGGGTTTAAAATG
1 TAATTAAAATATTTTGGATTTGAGGATTTAAAATG
1686485 TAATTAA
1 TAATTAA
1686492 TGACTGTGTT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
34 5 0.14
35 31 0.86
ACGTcount: A:0.38, C:0.00, G:0.18, T:0.44
Consensus pattern (35 bp):
TAATTAAAATATTTTGGATTTGAGGATTTAAAATG
Found at i:1690703 original size:8 final size:8
Alignment explanation
Indices: 1690690--1690715 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
1690680 GGTAAACATA
1690690 TTCTTCTG
1 TTCTTCTG
1690698 TTCTTCTG
1 TTCTTCTG
1690706 TTCTTCTG
1 TTCTTCTG
1690714 TT
1 TT
1690716 GGCTTTAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.00, C:0.23, G:0.12, T:0.65
Consensus pattern (8 bp):
TTCTTCTG
Found at i:1694995 original size:23 final size:22
Alignment explanation
Indices: 1694931--1694999 Score: 61
Period size: 23 Copynumber: 3.1 Consensus size: 22
1694921 TAAATAGACC
* *
1694931 AAAAAATTTAAATA-C-ACTTA
1 AAAAAAATTAAATACCTATTTA
* *
1694951 AAATAAAATTCAATTACTTATTTA
1 AAA-AAAATT-AAATACCTATTTA
1694975 AAAAAAACTTAAATACCTATTTA
1 AAAAAAA-TTAAATACCTATTTA
1694998 AA
1 AA
1695000 TTTAATTATT
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
20 3 0.08
21 5 0.13
22 4 0.11
23 17 0.45
24 9 0.24
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (22 bp):
AAAAAAATTAAATACCTATTTA
Found at i:1708474 original size:20 final size:17
Alignment explanation
Indices: 1708435--1708477 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
1708425 TATACTGCAG
*
1708435 ATCATCGATTCAACCCC
1 ATCATCAATTCAACCCC
1708452 ATCATCAATTCAACCCC
1 ATCATCAATTCAACCCC
1708469 ATCATCAAT
1 ATCATCAAT
1708478 GGCCTGTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.35, C:0.37, G:0.02, T:0.26
Consensus pattern (17 bp):
ATCATCAATTCAACCCC
Done.