Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A11
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: 113101708
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2797742 characters in sequence are not A, C, G, or T
File 5 of 352
Found at i:1517481 original size:35 final size:35
Alignment explanation
Indices: 1517442--1517513 Score: 117
Period size: 35 Copynumber: 2.1 Consensus size: 35
1517432 CATCTCCGGA
*
1517442 GCTTGGCAAATATGGAAAGTAATCTTCAAAGATAT
1 GCTTGGCAAATATGGAAAGGAATCTTCAAAGATAT
* *
1517477 GCTTGGCAAATATGGAAGGGAATCTTCAAGGATAT
1 GCTTGGCAAATATGGAAAGGAATCTTCAAAGATAT
1517512 GC
1 GC
1517514 GATCCTAGAC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.36, C:0.12, G:0.25, T:0.26
Consensus pattern (35 bp):
GCTTGGCAAATATGGAAAGGAATCTTCAAAGATAT
Found at i:1518292 original size:13 final size:14
Alignment explanation
Indices: 1518274--1518306 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
1518264 TTTCCACATG
1518274 AAAATTTAAT-TTT
1 AAAATTTAATGTTT
1518287 AAAATTTAATGTTT
1 AAAATTTAATGTTT
*
1518301 ACAATT
1 AAAATT
1518307 CCATTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (14 bp):
AAAATTTAATGTTT
Found at i:1518757 original size:106 final size:106
Alignment explanation
Indices: 1518646--1518917 Score: 395
Period size: 106 Copynumber: 2.6 Consensus size: 106
1518636 TAAGTTGTAA
* * *
1518646 AAAAAGGCTTATATAATTTCTCAAGTTTTATGATATAAGTATGTGAGGTGTATAAAGGTCGCATG
1 AAAAAGGCTTATATAATTTCTCAAGTTTCATGAGATAAATATGTGAGGTGTATAAAGGTCGCATG
* *
1518711 TAGATCATGCATAACCCATATCATTCTCAATTAAGTCATTG
66 TAGATCATGCATAACCCATATCATTCTCAATTAAATCATAG
* *
1518752 AAAAAGGCTTGTATAATTTTTCAAGTTTCATGAGATAAATATGTGAGGTGTATAAAGGTCGCATG
1 AAAAAGGCTTATATAATTTCTCAAGTTTCATGAGATAAATATGTGAGGTGTATAAAGGTCGCATG
* **
1518817 TAGATCATGTATAGTCCATATCATTCTCAATTAAATCATAG
66 TAGATCATGCATAACCCATATCATTCTCAATTAAATCATAG
* **
1518858 AAAAAGGCTTATATAATTTCTCAA-ATTCAAT-AGGATAAATATGTGAGGAATATAAAGGTC
1 AAAAAGGCTTATATAATTTCTCAAGTTTC-ATGA-GATAAATATGTGAGGTGTATAAAGGTC
1518918 ACGAATAGAT
Statistics
Matches: 149, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
105 4 0.03
106 145 0.97
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (106 bp):
AAAAAGGCTTATATAATTTCTCAAGTTTCATGAGATAAATATGTGAGGTGTATAAAGGTCGCATG
TAGATCATGCATAACCCATATCATTCTCAATTAAATCATAG
Found at i:1518958 original size:15 final size:15
Alignment explanation
Indices: 1518934--1518969 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
1518924 AGATCATGAC
*
1518934 TAGTCCACATGTTTG
1 TAGTCAACATGTTTG
1518949 TAGTCAACATGTTTG
1 TAGTCAACATGTTTG
1518964 TAGTCA
1 TAGTCA
1518970 TGGGTTGCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.39
Consensus pattern (15 bp):
TAGTCAACATGTTTG
Found at i:1524708 original size:4 final size:4
Alignment explanation
Indices: 1524699--1524749 Score: 102
Period size: 4 Copynumber: 12.8 Consensus size: 4
1524689 ATCAATTTTA
1524699 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1524747 ACA
1 ACA
1524750 CGGACACGCA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 47 1.00
ACGTcount: A:0.51, C:0.25, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:1532217 original size:31 final size:31
Alignment explanation
Indices: 1532154--1532236 Score: 80
Period size: 31 Copynumber: 2.7 Consensus size: 31
1532144 AATTTCAAAT
* * *
1532154 TTCAAAAAGTACAA-AGATTATAATTGACCAA
1 TTCAAAAAGTACAATA-ACTAAAATCGACCAA
*
1532185 TTCAAAAAGTACAATAACTAAAATCGATCAA
1 TTCAAAAAGTACAATAACTAAAATCGACCAA
***
1532216 TT-TTGAAGTACAATAACTAAA
1 TTCAAAAAGTACAATAACTAAA
1532237 TCCATAACTT
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
30 16 0.36
31 27 0.61
32 1 0.02
ACGTcount: A:0.52, C:0.13, G:0.08, T:0.27
Consensus pattern (31 bp):
TTCAAAAAGTACAATAACTAAAATCGACCAA
Found at i:1533297 original size:44 final size:44
Alignment explanation
Indices: 1533238--1533322 Score: 116
Period size: 44 Copynumber: 1.9 Consensus size: 44
1533228 ATAATATATC
* * *
1533238 AAATATACTACAAACATCAAAATAAATATTTTCTAATAAATTAA
1 AAATATACTAAAAACATCAAAATAAATATTTACTAACAAATTAA
* **
1533282 AAATATATTAAAAACATTGAAATAAATATTTACTAACAAAT
1 AAATATACTAAAAACATCAAAATAAATATTTACTAACAAAT
1533323 ATTAAAAAGA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 35 1.00
ACGTcount: A:0.58, C:0.09, G:0.01, T:0.32
Consensus pattern (44 bp):
AAATATACTAAAAACATCAAAATAAATATTTACTAACAAATTAA
Found at i:1535686 original size:31 final size:31
Alignment explanation
Indices: 1535632--1535697 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
1535622 AGGTTGAATA
* *
1535632 ACTAAAATGAAAAAAAATTAATAGTTGAGTG
1 ACTAAAATGAAAAAAAATGAATAGATGAGTG
*
1535663 ACTAAAAT-AAAAAGAACTGAATAGATGAGTG
1 ACTAAAATGAAAAA-AAATGAATAGATGAGTG
1535694 ACTA
1 ACTA
1535698 TTCATGTACT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 5 0.16
31 26 0.84
ACGTcount: A:0.55, C:0.06, G:0.17, T:0.23
Consensus pattern (31 bp):
ACTAAAATGAAAAAAAATGAATAGATGAGTG
Found at i:1541559 original size:21 final size:19
Alignment explanation
Indices: 1541533--1541602 Score: 70
Period size: 21 Copynumber: 3.5 Consensus size: 19
1541523 TATAAAAATT
*
1541533 AAAAATAATAATAATTATTTA
1 AAAAATAATAA-AA-AATTTA
1541554 AAAAATAA-AAAAAATTTA
1 AAAAATAATAAAAAATTTA
*
1541572 AAAAAGTTAATAAAAACCTTTA
1 AAAAA--TAATAAAAA-ATTTA
1541594 AAAAATAAT
1 AAAAATAAT
1541603 TTCATATTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
18 10 0.23
19 2 0.05
20 9 0.21
21 13 0.30
22 9 0.21
ACGTcount: A:0.67, C:0.03, G:0.01, T:0.29
Consensus pattern (19 bp):
AAAAATAATAAAAAATTTA
Found at i:1542272 original size:9 final size:9
Alignment explanation
Indices: 1542250--1542280 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
1542240 TAATTTATTT
1542250 ATTTTTAAA
1 ATTTTTAAA
1542259 GATTTTTAAA
1 -ATTTTTAAA
1542269 ATTTTTAAA
1 ATTTTTAAA
1542278 ATT
1 ATT
1542281 ATGTTTGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (9 bp):
ATTTTTAAA
Found at i:1547790 original size:15 final size:17
Alignment explanation
Indices: 1547770--1547810 Score: 68
Period size: 15 Copynumber: 2.5 Consensus size: 17
1547760 TTTAATTTTT
1547770 TAAAATTATTAAAAT-A
1 TAAAATTATTAAAATAA
1547786 T-AAATTATTAAAATAA
1 TAAAATTATTAAAATAA
1547802 TAAAATTAT
1 TAAAATTAT
1547811 ATTTATATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 13 0.57
16 3 0.13
17 7 0.30
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TAAAATTATTAAAATAA
Found at i:1556128 original size:33 final size:33
Alignment explanation
Indices: 1556091--1556160 Score: 97
Period size: 33 Copynumber: 2.1 Consensus size: 33
1556081 TAATAACAAA
* * *
1556091 AAAATAATA-GCAACATAATAATAAAATAGTAGT
1 AAAATAATACG-AAAATAACAAGAAAATAGTAGT
1556124 AAAATAATACGAAAATAACAAGAAAATAGTAGT
1 AAAATAATACGAAAATAACAAGAAAATAGTAGT
1556157 AAAA
1 AAAA
1556161 CAGAAAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
33 32 0.97
34 1 0.03
ACGTcount: A:0.64, C:0.06, G:0.10, T:0.20
Consensus pattern (33 bp):
AAAATAATACGAAAATAACAAGAAAATAGTAGT
Found at i:1556130 original size:22 final size:22
Alignment explanation
Indices: 1556082--1556141 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 22
1556072 ATATCTAAAT
*
1556082 AATAACAAAAAAATAATAGCAA
1 AATAATAAAAAAATAATAGCAA
* * * *
1556104 CATAATAATAAAATAGTAGTAA
1 AATAATAAAAAAATAATAGCAA
**
1556126 AATAATACGAAAATAA
1 AATAATAAAAAAATAA
1556142 CAAGAAAATA
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.67, C:0.07, G:0.07, T:0.20
Consensus pattern (22 bp):
AATAATAAAAAAATAATAGCAA
Found at i:1564324 original size:18 final size:18
Alignment explanation
Indices: 1564301--1564343 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
1564291 GGAGGAAGAA
1564301 GAAGAAGAAGAACCAGAG
1 GAAGAAGAAGAACCAGAG
*
1564319 GAAGAAGAGGAACCAGAG
1 GAAGAAGAAGAACCAGAG
1564337 GAAGAAG
1 GAAGAAG
1564344 GAGTTCAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.53, C:0.09, G:0.37, T:0.00
Consensus pattern (18 bp):
GAAGAAGAAGAACCAGAG
Found at i:1568837 original size:30 final size:31
Alignment explanation
Indices: 1568797--1568854 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
1568787 AATAAAAAAG
* *
1568797 ATTTAAGTCTTAATGTGAGAATAATTACTTA
1 ATTTAAGTCTTAATATAAGAATAATTACTTA
1568828 ATTT-AGTCTTAATATAAGAATAATTAC
1 ATTTAAGTCTTAATATAAGAATAATTAC
1568855 AAAGTTATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.41
Consensus pattern (31 bp):
ATTTAAGTCTTAATATAAGAATAATTACTTA
Found at i:1571459 original size:89 final size:89
Alignment explanation
Indices: 1571308--1571485 Score: 347
Period size: 89 Copynumber: 2.0 Consensus size: 89
1571298 TCTACTTATC
*
1571308 TAAAGTGTAGGATTTAGTCTATATTAATTATTTTAATAAATATATATTACAATTTTTATAAACAT
1 TAAAGTGTAGGATTTAGTCTATATTAATTATTTTAATAAATATATATTACAATTTTAATAAACAT
1571373 TGAATAAATAATTATAATATAATG
66 TGAATAAATAATTATAATATAATG
1571397 TAAAGTGTAGGATTTAGTCTATATTAATTATTTTAATAAATATATATTACAATTTTAATAAACAT
1 TAAAGTGTAGGATTTAGTCTATATTAATTATTTTAATAAATATATATTACAATTTTAATAAACAT
1571462 TGAATAAATAATTATAATATAATG
66 TGAATAAATAATTATAATATAATG
1571486 GGATAAATCT
Statistics
Matches: 88, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
89 88 1.00
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.43
Consensus pattern (89 bp):
TAAAGTGTAGGATTTAGTCTATATTAATTATTTTAATAAATATATATTACAATTTTAATAAACAT
TGAATAAATAATTATAATATAATG
Found at i:1576184 original size:3 final size:3
Alignment explanation
Indices: 1576145--1576169 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1576135 CTTATTACAA
1576145 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
1576170 CGTCGTTGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1578232 original size:23 final size:23
Alignment explanation
Indices: 1578201--1578267 Score: 66
Period size: 22 Copynumber: 2.9 Consensus size: 23
1578191 TATTATTTTA
1578201 AAATAAAAAAAT-TTAAAAATGTT
1 AAATAAAAAAATATT-AAAATGTT
* *
1578224 AAAT-TAAAAATATTAAAATTTT
1 AAATAAAAAAATATTAAAATGTT
*
1578246 ATAATAAAAAAATCAATAAAAT
1 A-AATAAAAAAAT-ATTAAAAT
1578268 AGATTCTAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
22 14 0.39
23 9 0.25
24 6 0.17
25 7 0.19
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (23 bp):
AAATAAAAAAATATTAAAATGTT
Found at i:1578368 original size:15 final size:14
Alignment explanation
Indices: 1578330--1578372 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
1578320 AATCCTTGAA
1578330 ATTATTTTTAAAAT
1 ATTATTTTTAAAAT
*
1578344 TTTAGTTTTTTAATAAT
1 ATTA--TTTTTAA-AAT
1578361 ATTATTTTTAAA
1 ATTATTTTTAAA
1578373 GTATAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
14 4 0.17
15 7 0.29
16 7 0.29
17 6 0.25
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (14 bp):
ATTATTTTTAAAAT
Found at i:1579713 original size:59 final size:56
Alignment explanation
Indices: 1579624--1579773 Score: 156
Period size: 59 Copynumber: 2.6 Consensus size: 56
1579614 ATTGAACCTA
* *
1579624 AAAAAAAAGCTTAGGTACCAAATTAGGAAAAAAAATCAAGTTCAGGTACCAAATTGGGC
1 AAAAAAAA-TTTA-GTACCAAA-TAAGAAAAAAAATCAAGTTCAGGTACCAAATTGGGC
* *** * *
1579683 TCAAAAAAATTTATGTACCAAACTAAGAAAAAGTGTCAAGTTCAGGTATCAAATTTGGC
1 -AAAAAAAATTTA-GTACCAAA-TAAGAAAAAAAATCAAGTTCAGGTACCAAATTGGGC
*
1579742 AAAAAAAATTTAGATACCAAATTAGAAAAAAA
1 AAAAAAAATTTAG-TACCAAATAAGAAAAAAA
1579774 TGTTAAATTC
Statistics
Matches: 75, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
57 9 0.12
58 18 0.24
59 41 0.55
60 7 0.09
ACGTcount: A:0.51, C:0.12, G:0.15, T:0.22
Consensus pattern (56 bp):
AAAAAAAATTTAGTACCAAATAAGAAAAAAAATCAAGTTCAGGTACCAAATTGGGC
Found at i:1579760 original size:58 final size:58
Alignment explanation
Indices: 1579659--1579771 Score: 158
Period size: 59 Copynumber: 1.9 Consensus size: 58
1579649 GGAAAAAAAA
*
1579659 TCAAGTTCAGGTACCAAATTGGGCTCAAAAAAATTTATGTACCAAACTAAGAAAAAGTG
1 TCAAGTTCAGGTACCAAATTGGGCTAAAAAAAATTTATGTACCAAA-TAAGAAAAAGTG
* * *
1579718 TCAAGTTCAGGTATCAAATTTGGC-AAAAAAAATTTA-GATACCAAATTAGAAAAA
1 TCAAGTTCAGGTACCAAATTGGGCTAAAAAAAATTTATG-TACCAAATAAGAAAAA
1579772 AATGTTAAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
57 9 0.18
58 18 0.37
59 22 0.45
ACGTcount: A:0.47, C:0.13, G:0.15, T:0.25
Consensus pattern (58 bp):
TCAAGTTCAGGTACCAAATTGGGCTAAAAAAAATTTATGTACCAAATAAGAAAAAGTG
Found at i:1580635 original size:29 final size:29
Alignment explanation
Indices: 1580601--1580656 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
1580591 TAATAATTAG
*
1580601 GTGACTATTAATGCAATTTAT-CCTTAAAT
1 GTGACTATTAATACAATTT-TCCCTTAAAT
1580630 GTGACTATTAATACAATTTTCCCTTAA
1 GTGACTATTAATACAATTTTCCCTTAA
1580657 TATATTAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 1 0.04
29 24 0.96
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.41
Consensus pattern (29 bp):
GTGACTATTAATACAATTTTCCCTTAAAT
Found at i:1584704 original size:46 final size:46
Alignment explanation
Indices: 1584632--1584723 Score: 166
Period size: 46 Copynumber: 2.0 Consensus size: 46
1584622 TAAAGTTATG
1584632 TCTAATCACTTAGATTTGGTAATTGATTCATATTAAATGTATAATA
1 TCTAATCACTTAGATTTGGTAATTGATTCATATTAAATGTATAATA
* *
1584678 TCTAATCAGTTAGATTTGGTAGTTGATTCATATTAAATGTATAATA
1 TCTAATCACTTAGATTTGGTAATTGATTCATATTAAATGTATAATA
1584724 AAAAACAAAG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.36, C:0.08, G:0.13, T:0.43
Consensus pattern (46 bp):
TCTAATCACTTAGATTTGGTAATTGATTCATATTAAATGTATAATA
Found at i:1587357 original size:46 final size:46
Alignment explanation
Indices: 1587293--1587387 Score: 156
Period size: 46 Copynumber: 2.1 Consensus size: 46
1587283 TTTAAAATAA
*
1587293 TTTAACCCTCAATCTTTACACGTTGAGT-ATTTTTTTTTTGTGCAAT
1 TTTAACCCTCAATCTTTACACGTTGAGTAAATTTTTTTTT-TGCAAT
*
1587339 TTTAACCCTCAATCTTTACACGTTGTGTAAATTTTTTTTTTGCAAT
1 TTTAACCCTCAATCTTTACACGTTGAGTAAATTTTTTTTTTGCAAT
1587385 TTT
1 TTT
1587388 GATTTCTTTC
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
46 36 0.78
47 10 0.22
ACGTcount: A:0.22, C:0.17, G:0.09, T:0.52
Consensus pattern (46 bp):
TTTAACCCTCAATCTTTACACGTTGAGTAAATTTTTTTTTTGCAAT
Found at i:1593089 original size:18 final size:17
Alignment explanation
Indices: 1593060--1593095 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
1593050 TAATCATACT
*
1593060 CTGAACCGAACCTGAAC
1 CTGAACCGAACCCGAAC
1593077 CTGAACTCGAACCCGAAC
1 CTGAAC-CGAACCCGAAC
1593095 C
1 C
1593096 GAATCAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.33, C:0.39, G:0.17, T:0.11
Consensus pattern (17 bp):
CTGAACCGAACCCGAAC
Found at i:1598402 original size:31 final size:31
Alignment explanation
Indices: 1598361--1598419 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
1598351 AAATAGTTAC
*
1598361 TAAATTATTTGAAAATTTTTATTTAAGTAAT
1 TAAACTATTTGAAAATTTTTATTTAAGTAAT
*
1598392 TAAACTATTTGATAATTTTTATTTAAGT
1 TAAACTATTTGAAAATTTTTATTTAAGT
1598420 TATTGAGTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.53
Consensus pattern (31 bp):
TAAACTATTTGAAAATTTTTATTTAAGTAAT
Found at i:1599972 original size:16 final size:16
Alignment explanation
Indices: 1599951--1599989 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
1599941 GTAAATTTAG
1599951 TTTTTAAT-ATTTATAT
1 TTTTTAATAATTTAT-T
*
1599967 TTTTTATTAATTTATT
1 TTTTTAATAATTTATT
1599983 TTTTTAA
1 TTTTTAA
1599990 ATTAAATTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTTAATAATTTATT
Found at i:1599982 original size:15 final size:15
Alignment explanation
Indices: 1599944--1599986 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
1599934 TATAATGGTA
*
1599944 AATTTAGTTTTTAAT
1 AATTTATTTTTTAAT
* *
1599959 ATTTATATTTTTTATT
1 AATT-TATTTTTTAAT
1599975 AATTTATTTTTT
1 AATTTATTTTTT
1599987 TAAATTAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (15 bp):
AATTTATTTTTTAAT
Found at i:1604957 original size:30 final size:30
Alignment explanation
Indices: 1604909--1604982 Score: 109
Period size: 30 Copynumber: 2.6 Consensus size: 30
1604899 TTGGACATAG
1604909 AGTCAAATATTA--TTTTTTTCCAAGAAAA
1 AGTCAAATATTATTTTTTTTTCCAAGAAAA
* *
1604937 AGTCAAATATTATTTTTTTTTCCTATAAAA
1 AGTCAAATATTATTTTTTTTTCCAAGAAAA
1604967 AGTCAAATATT-TTTTT
1 AGTCAAATATTATTTTT
1604983 CTATAAACGT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
28 12 0.29
29 5 0.12
30 25 0.60
ACGTcount: A:0.38, C:0.09, G:0.05, T:0.47
Consensus pattern (30 bp):
AGTCAAATATTATTTTTTTTTCCAAGAAAA
Found at i:1605482 original size:22 final size:21
Alignment explanation
Indices: 1605456--1605515 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 21
1605446 AATATTAAAA
1605456 TAATATTAAAAAATAAAATTAT
1 TAATATTAAAAAATAAAA-TAT
*
1605478 TAATATTAAAATAATATAATAT
1 TAATATTAAAA-AATAAAATAT
* **
1605500 AAATATTTTAAAATAA
1 TAATATTAAAAAATAA
1605516 TATTTAAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
21 4 0.12
22 22 0.69
23 6 0.19
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TAATATTAAAAAATAAAATAT
Found at i:1610785 original size:21 final size:21
Alignment explanation
Indices: 1610723--1610787 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
1610713 CCTAATCAGT
* *
1610723 ATACGACACATAAAGTTCCTA
1 ATACGACACATAAAGTGCCTG
* ** *
1610744 AAACGACACACGAGGTGCCTG
1 ATACGACACATAAAGTGCCTG
1610765 ATACGACACATAAAGTGCCTG
1 ATACGACACATAAAGTGCCTG
1610786 AT
1 AT
1610788 CGATAAAGCC
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.18
Consensus pattern (21 bp):
ATACGACACATAAAGTGCCTG
Found at i:1611183 original size:15 final size:15
Alignment explanation
Indices: 1611158--1611215 Score: 80
Period size: 15 Copynumber: 3.8 Consensus size: 15
1611148 TCATATATAT
*
1611158 TATATAATTCATTCAA
1 TATA-AATTCAATCAA
1611174 TATAAATTCAATCAA
1 TATAAATTCAATCAA
* *
1611189 AATAATTTCAATCAA
1 TATAAATTCAATCAA
1611204 TATAAATTCAAT
1 TATAAATTCAAT
1611216 AAATTCATCG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
15 33 0.89
16 4 0.11
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (15 bp):
TATAAATTCAATCAA
Found at i:1612493 original size:5 final size:5
Alignment explanation
Indices: 1612485--1612511 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
1612475 TCTTTAGTTT
1612485 ATATA ATATA ATATA ATATA ATATA AT
1 ATATA ATATA ATATA ATATA ATATA AT
1612512 TAAAACATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:1612547 original size:8 final size:8
Alignment explanation
Indices: 1612534--1612562 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
1612524 TATCTTTATT
1612534 ATATAATA
1 ATATAATA
1612542 ATATAATA
1 ATATAATA
1612550 ATATAATA
1 ATATAATA
1612558 ATATA
1 ATATA
1612563 TTAAACATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
ATATAATA
Found at i:1614657 original size:46 final size:46
Alignment explanation
Indices: 1614600--1614749 Score: 147
Period size: 46 Copynumber: 3.1 Consensus size: 46
1614590 ACACACCGTA
*
1614600 GCCATAGCCCAGCCATGGTCTTACACGAATCACATATCACACTGAT
1 GCCATAGCCCAGCTATGGTCTTACACGAATCACATATCACACTGAT
* * * * * *
1614646 GTCATATCCCAGATATGGTCTTATACGGAAGCACGTAATCACATATCTCTGAT
1 GCCATAGCCCAGCTATGGTCTTACAC-GAATCACAT-ATCAC--A---CTGAT
* * *
1614699 ACCATAGCCCAGCTATGGTCTTACACAAATCACATATCACATTGAT
1 GCCATAGCCCAGCTATGGTCTTACACGAATCACATATCACACTGAT
1614745 GCCAT
1 GCCAT
1614750 GGTCCAACCA
Statistics
Matches: 80, Mismatches: 17, Indels: 14
0.72 0.15 0.13
Matches are distributed among these distances:
46 29 0.36
47 7 0.09
48 5 0.06
49 1 0.01
50 1 0.01
51 5 0.06
52 6 0.08
53 26 0.32
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (46 bp):
GCCATAGCCCAGCTATGGTCTTACACGAATCACATATCACACTGAT
Found at i:1615933 original size:23 final size:23
Alignment explanation
Indices: 1615831--1615937 Score: 111
Period size: 21 Copynumber: 5.0 Consensus size: 23
1615821 CCTGATCAGT
*
1615831 ATACGACACATAA-GTGCCT-AA
1 ATACGACACACAAGGTGCCTGAA
* *
1615852 A-ACGACACACGAGGTACCTG-A
1 ATACGACACACAAGGTGCCTGAA
*
1615873 A-ACGACACACGAGGTGCCTG--
1 ATACGACACACAAGGTGCCTGAA
1615893 ATACGACACACAAGGTGCCTGAA
1 ATACGACACACAAGGTGCCTGAA
* *
1615916 ATACGACACATAAAGTGCCTGA
1 ATACGACACACAAGGTGCCTGA
1615938 TCAGTATAGC
Statistics
Matches: 74, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
20 10 0.14
21 44 0.59
23 20 0.27
ACGTcount: A:0.38, C:0.26, G:0.21, T:0.14
Consensus pattern (23 bp):
ATACGACACACAAGGTGCCTGAA
Found at i:1616154 original size:23 final size:24
Alignment explanation
Indices: 1616128--1616222 Score: 93
Period size: 28 Copynumber: 3.6 Consensus size: 24
1616118 AGATGTCCAA
1616128 CCAAAACACACCAG-TATAATCCT
1 CCAAAACACACCAGATATAATCCT
1616151 CCAAAACACACCAGTATCATATAATCCT
1 CCAAAACACACCAG----ATATAATCCT
*
1616179 CCCAAACACACCAGAATAATATAATCCAT
1 CCAAAACACACCAG----ATATAATCC-T
1616208 CCAAAACACACCAGA
1 CCAAAACACACCAGA
1616223 ATAGCACAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
23 14 0.23
25 1 0.02
28 33 0.53
29 14 0.23
ACGTcount: A:0.46, C:0.34, G:0.04, T:0.16
Consensus pattern (24 bp):
CCAAAACACACCAGATATAATCCT
Found at i:1616224 original size:29 final size:28
Alignment explanation
Indices: 1616142--1616225 Score: 132
Period size: 28 Copynumber: 3.0 Consensus size: 28
1616132 AACACACCAG
* *
1616142 TATAATCCTCCAAAACACACCAGTATCA
1 TATAATCCTCCAAAACACACCAGAATAA
*
1616170 TATAATCCTCCCAAACACACCAGAATAA
1 TATAATCCTCCAAAACACACCAGAATAA
1616198 TATAATCCATCCAAAACACACCAGAATA
1 TATAATCC-TCCAAAACACACCAGAATA
1616226 GCACAAAGTG
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 33 0.65
29 18 0.35
ACGTcount: A:0.46, C:0.31, G:0.04, T:0.19
Consensus pattern (28 bp):
TATAATCCTCCAAAACACACCAGAATAA
Found at i:1620218 original size:16 final size:17
Alignment explanation
Indices: 1620188--1620220 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1620178 TTAGATTTTT
*
1620188 TTTTATAATTTATAATA
1 TTTTATAATTAATAATA
1620205 TTTTA-AATTAATAATA
1 TTTTATAATTAATAATA
1620221 ATAAAATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTTATAATTAATAATA
Found at i:1629367 original size:19 final size:19
Alignment explanation
Indices: 1629317--1629368 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
1629307 TCTTATATTA
1629317 TTAAATTTAATTATTAACC
1 TTAAATTTAATTATTAACC
** *
1629336 TT-AATACATATTATTAATC
1 TTAAATTTA-ATTATTAACC
1629355 TTAAATTTAATTAT
1 TTAAATTTAATTAT
1629369 ATTTCGAGTC
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
18 4 0.15
19 18 0.69
20 4 0.15
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (19 bp):
TTAAATTTAATTATTAACC
Found at i:1633437 original size:31 final size:31
Alignment explanation
Indices: 1633400--1633459 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 31
1633390 TTTAATTTGC
1633400 TCAATTTTAGTCCCTAT-GTTTTTTGAATTGG
1 TCAATTTTAGTCCCTATAG-TTTTTGAATTGG
*
1633431 TCAATTTTAGTCCTTATAGTTTTTGAATT
1 TCAATTTTAGTCCCTATAGTTTTTGAATT
1633460 ATGAAATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 26 0.96
32 1 0.04
ACGTcount: A:0.22, C:0.12, G:0.13, T:0.53
Consensus pattern (31 bp):
TCAATTTTAGTCCCTATAGTTTTTGAATTGG
Found at i:1633468 original size:31 final size:31
Alignment explanation
Indices: 1633402--1633475 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
1633392 TAATTTGCTC
* *
1633402 AATTTTAGTCCCTATGTTTTTTGAATTGGTC
1 AATTTTAGTCCTTATGTTTTTTGAATTGGTA
*
1633433 AATTTTAGTCCTTATAG-TTTTTGAATT-ATGA
1 AATTTTAGTCCTTAT-GTTTTTTGAATTGGT-A
1633464 AATTTTAGTCCT
1 AATTTTAGTCCT
1633476 GACTTGGTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
30 1 0.03
31 36 0.95
32 1 0.03
ACGTcount: A:0.24, C:0.11, G:0.14, T:0.51
Consensus pattern (31 bp):
AATTTTAGTCCTTATGTTTTTTGAATTGGTA
Found at i:1639844 original size:40 final size:40
Alignment explanation
Indices: 1639799--1639879 Score: 135
Period size: 40 Copynumber: 2.0 Consensus size: 40
1639789 ATAATTATAT
* *
1639799 TTCATACTTATATTTCAACTTTACTGGTACAAGTGTGTAC
1 TTCATACTTATATTTCAACTTTACAGATACAAGTGTGTAC
*
1639839 TTCATACTTATATTTTAACTTTACAGATACAAGTGTGTAC
1 TTCATACTTATATTTCAACTTTACAGATACAAGTGTGTAC
1639879 T
1 T
1639880 GGTAAAAGTA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.43
Consensus pattern (40 bp):
TTCATACTTATATTTCAACTTTACAGATACAAGTGTGTAC
Found at i:1651010 original size:253 final size:252
Alignment explanation
Indices: 1650555--1651014 Score: 674
Period size: 253 Copynumber: 1.8 Consensus size: 252
1650545 AATCATTTGA
* * * * *
1650555 GGGGGGCCAAAGTGTAATTTTACCTTTTGCTAAATTAAAATCTTGTAAAAATTAAAAGGCTAAAG
1 GGGGGGCCAAAGTATAATTTTACCTTTTACTAAATTAAAATCTTGTAAAAATTAAAAGACCAAAA
* * *
1650620 TGAAATTTTCCATTTTTGGAGGTCGGCTCCTTGTCAGCCACCTAGCTTCACCCTTGGCATAAAGT
66 TGAAATTTTCCATTTTTGGAGGTCGGCCCCTTGTCAGCCACCTAACTTCACCCTTGGCATAAAGC
* * *
1650685 ACATGTAAGCTGTCACAAATTATCATGCCAACCTCATTAAAGACTTAATATTTTAGCCAGTATTT
131 ACATATAAGCTGCCACAAATTATCATGCCAACCTCATTAAAAACTTAATA-TTTAGCCAGTATTT
1650750 CCGTTAAAAAAACAAATGATGTCGTGTTAGCATGAAGTAGGGGTGAAACCAAATTTTT
195 CCGTTAAAAAAACAAATGATGTCGTGTTAGCATGAAGTAGGGGTGAAACCAAATTTTT
1650808 GGGGGGCCAAAGTATAATTTTACCTTTTACTAAATTAAAATCTTGTAAAAATTAAAAGACCAAAA
1 GGGGGGCCAAAGTATAATTTTACCTTTTACTAAATTAAAATCTTGTAAAAATTAAAAGACCAAAA
* * * *
1650873 TGAAATTTTCCATTTTTAGGTGGTCGGCCCCTTGTCAGCCACCCTAACTTCGCCCTTGGCATGAT
66 TGAAATTTTCCATTTTT-GGAGGTCGGCCCCTTGTCAGCCA-CCTAACTTCACCCTTGGCATAAA
* * * *
1650938 GCACATATAAGCTGCCACGCAAGTTATCATGCCAACTTCGTTAAAAACTT-A-A-TTAGCTAGTA
129 GCACATATAAGCTGCCA--CAAATTATCATGCCAACCTCATTAAAAACTTAATATTTAGCCAGTA
*
1651000 TTTTCGTTAAAAAAA
192 TTTCCGTTAAAAAAA
1651015 AGGACAAGAT
Statistics
Matches: 183, Mismatches: 20, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
253 100 0.55
254 21 0.11
255 34 0.19
256 1 0.01
257 27 0.15
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (252 bp):
GGGGGGCCAAAGTATAATTTTACCTTTTACTAAATTAAAATCTTGTAAAAATTAAAAGACCAAAA
TGAAATTTTCCATTTTTGGAGGTCGGCCCCTTGTCAGCCACCTAACTTCACCCTTGGCATAAAGC
ACATATAAGCTGCCACAAATTATCATGCCAACCTCATTAAAAACTTAATATTTAGCCAGTATTTC
CGTTAAAAAAACAAATGATGTCGTGTTAGCATGAAGTAGGGGTGAAACCAAATTTTT
Found at i:1656707 original size:31 final size:31
Alignment explanation
Indices: 1656671--1656737 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
1656661 TTAACAGTTT
*
1656671 AATGATTTAAATAAAAAATTTTAAATAATTA
1 AATGATTTAAATAAAAAAGTTTAAATAATTA
* * *
1656702 AATGATTTAAATGAAAACGTTTAAATAATTT
1 AATGATTTAAATAAAAAAGTTTAAATAATTA
1656733 AATGA
1 AATGA
1656738 CCATTTTATA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.54, C:0.01, G:0.07, T:0.37
Consensus pattern (31 bp):
AATGATTTAAATAAAAAAGTTTAAATAATTA
Found at i:1658426 original size:18 final size:18
Alignment explanation
Indices: 1658405--1658441 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1658395 TAAAAGATTT
*
1658405 AAAGTAAAAAAAATTAAA
1 AAAGTAAAAAAAAATAAA
1658423 AAAGTAAAAAAAAATAAA
1 AAAGTAAAAAAAAATAAA
1658441 A
1 A
1658442 GTTCAATGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.81, C:0.00, G:0.05, T:0.14
Consensus pattern (18 bp):
AAAGTAAAAAAAAATAAA
Found at i:1658858 original size:29 final size:27
Alignment explanation
Indices: 1658826--1658887 Score: 70
Period size: 29 Copynumber: 2.2 Consensus size: 27
1658816 TTGAAACTCG
1658826 AAAAATAAAGAACTAAATTTCTAAAAATA
1 AAAAATAAAG-ACTAAATTT-TAAAAATA
* **
1658855 AAAATATAATGACTAAATTTTAAATTTA
1 AAAA-ATAAAGACTAAATTTTAAAAATA
1658883 AAAAA
1 AAAAA
1658888 ATATATACAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 1 0.03
28 10 0.34
29 13 0.45
30 5 0.17
ACGTcount: A:0.63, C:0.05, G:0.03, T:0.29
Consensus pattern (27 bp):
AAAAATAAAGACTAAATTTTAAAAATA
Found at i:1672396 original size:19 final size:20
Alignment explanation
Indices: 1672357--1672399 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
1672347 GAACTTGATA
1672357 TTTTAAGCGGTCCTAATTTT
1 TTTTAAGCGGTCCTAATTTT
1672377 TTTTAAGCGGTCCTAATTTT
1 TTTTAAGCGGTCCTAATTTT
1672397 TTT
1 TTT
1672400 GTCTAAATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.19, C:0.14, G:0.14, T:0.53
Consensus pattern (20 bp):
TTTTAAGCGGTCCTAATTTT
Found at i:1678148 original size:21 final size:21
Alignment explanation
Indices: 1678123--1678165 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1678113 ATTAAAGAAA
*
1678123 ATAAAAATATTAAGTTCCTTC
1 ATAAAAATATTAAGTTACTTC
1678144 ATAAAAATATTAAGTTACTTC
1 ATAAAAATATTAAGTTACTTC
1678165 A
1 A
1678166 CGTAGCATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.47, C:0.12, G:0.05, T:0.37
Consensus pattern (21 bp):
ATAAAAATATTAAGTTACTTC
Found at i:1678735 original size:21 final size:21
Alignment explanation
Indices: 1678693--1678735 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1678683 AATAATTATT
*
1678693 AGATATTGTTAAAATTTGTAA
1 AGATATTGTTAAAATTTATAA
*
1678714 AGATGTTGTTGAAAA-TTATAA
1 AGATATTGTT-AAAATTTATAA
1678735 A
1 A
1678736 ATAATATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (21 bp):
AGATATTGTTAAAATTTATAA
Found at i:1679073 original size:10 final size:10
Alignment explanation
Indices: 1679058--1679082 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1679048 TTATTTTCGA
1679058 TTTTTAATAT
1 TTTTTAATAT
1679068 TTTTTAATAT
1 TTTTTAATAT
1679078 TTTTT
1 TTTTT
1679083 GGGTCCGGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTTTAATAT
Found at i:1679353 original size:29 final size:30
Alignment explanation
Indices: 1679317--1679381 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
1679307 ACATCTTTTC
*
1679317 AAAATTTTAT-TTTTCTAAAT-TTTTTATAT
1 AAAATTTTATATTTT-TAAATAATTTTATAT
* *
1679346 AGAATTTTCTATTTTTAAATAATTTTATAT
1 AAAATTTTATATTTTTAAATAATTTTATAT
1679376 AAAATT
1 AAAATT
1679382 AAGGTAAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 13 0.43
30 17 0.57
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (30 bp):
AAAATTTTATATTTTTAAATAATTTTATAT
Found at i:1679797 original size:41 final size:43
Alignment explanation
Indices: 1679750--1679835 Score: 140
Period size: 43 Copynumber: 2.0 Consensus size: 43
1679740 TCAATTGCCA
*
1679750 TTCAACGTTCATCTTA-AATTTGAA-TTTGAAAAATCAGACCG
1 TTCAACGTTCATCTTATAATTTGAATTTTGAAAAACCAGACCG
*
1679791 TTCAACGTTCATCTTATATTTTGAATTTTGAAAAACCAGACCG
1 TTCAACGTTCATCTTATAATTTGAATTTTGAAAAACCAGACCG
1679834 TT
1 TT
1679836 GCTCACCTCG
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
41 16 0.39
42 7 0.17
43 18 0.44
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.37
Consensus pattern (43 bp):
TTCAACGTTCATCTTATAATTTGAATTTTGAAAAACCAGACCG
Found at i:1680440 original size:6 final size:6
Alignment explanation
Indices: 1680425--1680465 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
1680415 TAAAATGTCT
1680425 TTTTTG -TTTTG TTTTTG TTTTTG ATTTTTTG TTTTT- TTTTT
1 TTTTTG TTTTTG TTTTTG TTTTTG --TTTTTG TTTTTG TTTTT
1680466 ACATTGGGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
5 10 0.31
6 16 0.50
8 6 0.19
ACGTcount: A:0.02, C:0.00, G:0.12, T:0.85
Consensus pattern (6 bp):
TTTTTG
Found at i:1680455 original size:14 final size:13
Alignment explanation
Indices: 1680424--1680465 Score: 54
Period size: 14 Copynumber: 3.4 Consensus size: 13
1680414 GTAAAATGTC
1680424 TTTTTTG-TTTTG
1 TTTTTTGTTTTTG
1680436 -TTTTTGTTTTTG
1 TTTTTTGTTTTTG
1680448 ATTTTTTGTTTTT-
1 -TTTTTTGTTTTTG
1680461 TTTTT
1 TTTTT
1680466 ACATTGGGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
11 6 0.22
12 10 0.37
14 11 0.41
ACGTcount: A:0.02, C:0.00, G:0.12, T:0.86
Consensus pattern (13 bp):
TTTTTTGTTTTTG
Found at i:1680882 original size:12 final size:12
Alignment explanation
Indices: 1680867--1680899 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
1680857 GAAGAAGCTG
1680867 AGAAAGAAACCA
1 AGAAAGAAACCA
*
1680879 AGAAAAAAACCA
1 AGAAAGAAACCA
1680891 AGAAAGAAA
1 AGAAAGAAA
1680900 GGGATCCCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.73, C:0.12, G:0.15, T:0.00
Consensus pattern (12 bp):
AGAAAGAAACCA
Found at i:1689199 original size:9 final size:9
Alignment explanation
Indices: 1689185--1689263 Score: 56
Period size: 9 Copynumber: 8.8 Consensus size: 9
1689175 CTTGCCATGG
1689185 AAAGAAGGA
1 AAAGAAGGA
1689194 AAAGAA-G-
1 AAAGAAGGA
* *
1689201 -ATGAAAGA
1 AAAGAAGGA
*
1689209 CAAGAAGGA
1 AAAGAAGGA
1689218 GAAAGACAAGGA
1 -AAAG--AAGGA
* *
1689230 CAGGAAGGA
1 AAAGAAGGA
*
1689239 AAAGAAAGA
1 AAAGAAGGA
1689248 AAAGAAGGA
1 AAAGAAGGA
1689257 AAAGAAG
1 AAAGAAG
1689264 ACCGAGAGCA
Statistics
Matches: 54, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
6 4 0.07
7 1 0.02
8 1 0.02
9 38 0.70
10 3 0.06
11 2 0.04
12 5 0.09
ACGTcount: A:0.63, C:0.04, G:0.32, T:0.01
Consensus pattern (9 bp):
AAAGAAGGA
Found at i:1691462 original size:20 final size:20
Alignment explanation
Indices: 1691437--1691492 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
1691427 TTTAATATCA
*
1691437 CTATTATGATTTTTTTATTG
1 CTATTATGATTATTTTATTG
*
1691457 CTATTATTATTATTTTATT-
1 CTATTATGATTATTTTATTG
*
1691476 -TATTAT-AATATTTTATT
1 CTATTATGATTATTTTATT
1691493 TTTACTATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
17 10 0.30
18 6 0.18
20 17 0.52
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.66
Consensus pattern (20 bp):
CTATTATGATTATTTTATTG
Found at i:1691487 original size:23 final size:23
Alignment explanation
Indices: 1691417--1691494 Score: 70
Period size: 23 Copynumber: 3.4 Consensus size: 23
1691407 TTTCTGTTAC
* * *
1691417 TATTACTTTATTTAATATCACTAT
1 TATTATTTTATTTATTAT-AATAT
* * *
1691441 TATGATTTT-TTTATTGCTATTAT
1 TATTATTTTATTTATT-ATAATAT
1691464 TATTATTTTATTTATTATAATAT
1 TATTATTTTATTTATTATAATAT
1691487 T-TTATTTT
1 TATTATTTT
1691495 TACTATTATT
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
22 7 0.16
23 23 0.52
24 14 0.32
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (23 bp):
TATTATTTTATTTATTATAATAT
Found at i:1691504 original size:17 final size:17
Alignment explanation
Indices: 1691438--1691510 Score: 67
Period size: 17 Copynumber: 4.0 Consensus size: 17
1691428 TTAATATCAC
*
1691438 TATTATGATTTTTTTATT
1 TATTAT-ATTATTTTATT
1691456 GCTATTATTATTATTTTATT
1 --TATTA-TATTATTTTATT
*
1691476 TATTATAATATTTTATT
1 TATTATATTATTTTATT
1691493 T-TTACTATTATTGTTATT
1 TATTA-TATTATT-TTATT
1691511 ATCACTACTA
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
16 3 0.06
17 18 0.38
18 10 0.21
20 15 0.32
21 1 0.02
ACGTcount: A:0.26, C:0.03, G:0.04, T:0.67
Consensus pattern (17 bp):
TATTATATTATTTTATT
Found at i:1696716 original size:35 final size:35
Alignment explanation
Indices: 1696670--1696741 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
1696660 CAAAAACATG
*
1696670 ATCTCAATCTAATTAAAACCAAATCATGACATTAC
1 ATCTCAATCTAATCAAAACCAAATCATGACATTAC
*
1696705 ATCTCAATCTAATCAAAATCAAATCATGACATTAC
1 ATCTCAATCTAATCAAAACCAAATCATGACATTAC
1696740 AT
1 AT
1696742 ACATTCAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.46, C:0.22, G:0.03, T:0.29
Consensus pattern (35 bp):
ATCTCAATCTAATCAAAACCAAATCATGACATTAC
Found at i:1700374 original size:23 final size:23
Alignment explanation
Indices: 1700344--1700416 Score: 82
Period size: 21 Copynumber: 3.3 Consensus size: 23
1700334 GCTTTACTGA
* *
1700344 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACCTCATGTGTCGTATT
*
1700367 TCAGGCACCTCGTGTGTCGTA--
1 TCAGGCACCTCATGTGTCGTATT
*
1700388 TCAGGCACCTCGTGTGTCGT-TT
1 TCAGGCACCTCATGTGTCGTATT
1700410 T-AGGCAC
1 TCAGGCAC
1700417 TTTATGTAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
21 26 0.58
22 1 0.02
23 18 0.40
ACGTcount: A:0.15, C:0.25, G:0.26, T:0.34
Consensus pattern (23 bp):
TCAGGCACCTCATGTGTCGTATT
Found at i:1700391 original size:21 final size:21
Alignment explanation
Indices: 1700356--1700416 Score: 86
Period size: 21 Copynumber: 2.8 Consensus size: 21
1700346 AGGCACTTTA
1700356 TGTGTCGTATTTCAGGCACCTCG
1 TGTGTCGTA--TCAGGCACCTCG
1700379 TGTGTCGTATCAGGCACCTCG
1 TGTGTCGTATCAGGCACCTCG
* *
1700400 TGTGTCGTTTTAGGCAC
1 TGTGTCGTATCAGGCAC
1700417 TTTATGTAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 27 0.75
23 9 0.25
ACGTcount: A:0.13, C:0.25, G:0.28, T:0.34
Consensus pattern (21 bp):
TGTGTCGTATCAGGCACCTCG
Found at i:1703149 original size:46 final size:46
Alignment explanation
Indices: 1703085--1703234 Score: 167
Period size: 46 Copynumber: 3.1 Consensus size: 46
1703075 ACACACTGTA
*
1703085 GCCATAGCCCAGCCATGGTCTTACACGAATCACATATCACATTGAT
1 GCCATAGCCCAGCTATGGTCTTACACGAATCACATATCACATTGAT
* * * * *
1703131 GCCATATCCCAGATATGGTCTTATACGGAAGCACGTAATCACATATCTCTGAT
1 GCCATAGCCCAGCTATGGTCTTACAC-GAATCACAT-ATCAC--A--T-TGAT
1703184 GCCATAGCCCAGCTATGGTCTTACAC-AGATCACATATCACATTGAT
1 GCCATAGCCCAGCTATGGTCTTACACGA-ATCACATATCACATTGAT
1703230 GCCAT
1 GCCAT
1703235 GGTCCAACCA
Statistics
Matches: 85, Mismatches: 11, Indels: 16
0.76 0.10 0.14
Matches are distributed among these distances:
46 31 0.36
47 8 0.09
48 5 0.06
49 1 0.01
50 1 0.01
51 6 0.07
52 6 0.07
53 27 0.32
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (46 bp):
GCCATAGCCCAGCTATGGTCTTACACGAATCACATATCACATTGAT
Found at i:1704367 original size:21 final size:21
Alignment explanation
Indices: 1704319--1704381 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
1704309 TGATCAGTAT
* *
1704319 ACGACACATAAG-TGGCTGAA
1 ACGACACACAAGATGCCTGAA
* * *
1704339 ACGACACACGAGGTGCCTGAT
1 ACGACACACAAGATGCCTGAA
*
1704360 ACGGCACACAAGATGCCTGAA
1 ACGACACACAAGATGCCTGAA
1704381 A
1 A
1704382 TATGACACAT
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
20 10 0.29
21 24 0.71
ACGTcount: A:0.37, C:0.25, G:0.25, T:0.13
Consensus pattern (21 bp):
ACGACACACAAGATGCCTGAA
Found at i:1704643 original size:26 final size:25
Alignment explanation
Indices: 1704593--1704688 Score: 124
Period size: 26 Copynumber: 3.7 Consensus size: 25
1704583 AAATGTCCAA
1704593 CCAAAACACACCAG--TATAATCCT
1 CCAAAACACACCAGAATATAATCCT
1704616 CCAAAACACACCAGTAATATAATCCT
1 CCAAAACACACCAG-AATATAATCCT
*
1704642 CCCAAACACACCAGAATAATATAATCCAT
1 CCAAAACACACCAG---AATATAATCC-T
1704671 CCAAAACACACCAGAATA
1 CCAAAACACACCAGAATA
1704689 GCACAAAGTG
Statistics
Matches: 65, Mismatches: 2, Indels: 9
0.86 0.03 0.12
Matches are distributed among these distances:
23 14 0.22
26 26 0.40
28 11 0.17
29 14 0.22
ACGTcount: A:0.48, C:0.32, G:0.04, T:0.16
Consensus pattern (25 bp):
CCAAAACACACCAGAATATAATCCT
Found at i:1704687 original size:29 final size:28
Alignment explanation
Indices: 1704607--1704688 Score: 132
Period size: 26 Copynumber: 3.0 Consensus size: 28
1704597 AACACACCAG
1704607 TATAATCCTCCAAAACACACCAG--TAA
1 TATAATCCTCCAAAACACACCAGAATAA
*
1704633 TATAATCCTCCCAAACACACCAGAATAA
1 TATAATCCTCCAAAACACACCAGAATAA
1704661 TATAATCCATCCAAAACACACCAGAATA
1 TATAATCC-TCCAAAACACACCAGAATA
1704689 GCACAAAGTG
Statistics
Matches: 51, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
26 22 0.43
28 11 0.22
29 18 0.35
ACGTcount: A:0.48, C:0.30, G:0.04, T:0.18
Consensus pattern (28 bp):
TATAATCCTCCAAAACACACCAGAATAA
Found at i:1720110 original size:19 final size:21
Alignment explanation
Indices: 1720086--1720133 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
1720076 CATTTAAATA
1720086 CCAGAAAAT-TAAATCA-TTT
1 CCAGAAAATGTAAATCATTTT
*
1720105 CCAG-AAATGTAAATTATTTT
1 CCAGAAAATGTAAATCATTTT
*
1720125 CTAGAAAAT
1 CCAGAAAAT
1720134 ATTTTCCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 4 0.17
19 10 0.42
20 6 0.25
21 4 0.17
ACGTcount: A:0.46, C:0.12, G:0.08, T:0.33
Consensus pattern (21 bp):
CCAGAAAATGTAAATCATTTT
Found at i:1723032 original size:27 final size:27
Alignment explanation
Indices: 1722991--1723042 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
1722981 GACGATCAGC
* *
1722991 ATCAGCATCAGCACCACCACCACCACT
1 ATCACCATCAACACCACCACCACCACT
* *
1723018 ATCACCATCAACACCGCCGCCACCA
1 ATCACCATCAACACCACCACCACCA
1723043 TCACCACCGC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.33, C:0.50, G:0.08, T:0.10
Consensus pattern (27 bp):
ATCACCATCAACACCACCACCACCACT
Found at i:1723041 original size:18 final size:18
Alignment explanation
Indices: 1723020--1723057 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
1723010 CCACCACTAT
1723020 CACCATCAACACCGCCGC
1 CACCATCAACACCGCCGC
*
1723038 CACCATCACCACCGCCGC
1 CACCATCAACACCGCCGC
1723056 CA
1 CA
1723058 TAACGGAGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.26, C:0.58, G:0.11, T:0.05
Consensus pattern (18 bp):
CACCATCAACACCGCCGC
Found at i:1728197 original size:13 final size:14
Alignment explanation
Indices: 1728177--1728209 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
1728167 ACTTGAATTC
*
1728177 AGTTTTAATATTTA
1 AGTTTTAATACTTA
1728191 A-TTTTAATACTTA
1 AGTTTTAATACTTA
1728204 AGTTTT
1 AGTTTT
1728210 TCAAATTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.33, C:0.03, G:0.06, T:0.58
Consensus pattern (14 bp):
AGTTTTAATACTTA
Found at i:1741703 original size:18 final size:18
Alignment explanation
Indices: 1741624--1741717 Score: 131
Period size: 18 Copynumber: 5.4 Consensus size: 18
1741614 CAAGGTCACG
*
1741624 ATCAATAGCGTCACTATC
1 ATCAATATCGTCACTATC
* *
1741642 ATCAATAGCGTCACTAGC
1 ATCAATATCGTCACTATC
*
1741660 ATCAATATCGTCACTAGC
1 ATCAATATCGTCACTATC
1741678 ATCAATATCGTCACTATC
1 ATCAATATCGTCACTATC
1741696 ATCAATATCG--A-TATC
1 ATCAATATCGTCACTATC
1741711 ATCAATA
1 ATCAATA
1741718 AGAAAACCTT
Statistics
Matches: 73, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
15 11 0.15
16 1 0.01
18 61 0.84
ACGTcount: A:0.36, C:0.26, G:0.10, T:0.29
Consensus pattern (18 bp):
ATCAATATCGTCACTATC
Found at i:1741704 original size:9 final size:9
Alignment explanation
Indices: 1741624--1741704 Score: 54
Period size: 9 Copynumber: 9.0 Consensus size: 9
1741614 CAAGGTCACG
*
1741624 ATCAATAGC
1 ATCAATATC
* *
1741633 GTCACTATC
1 ATCAATATC
*
1741642 ATCAATAGC
1 ATCAATATC
* * *
1741651 GTCACTAGC
1 ATCAATATC
1741660 ATCAATATC
1 ATCAATATC
* * *
1741669 GTCACTAGC
1 ATCAATATC
1741678 ATCAATATC
1 ATCAATATC
* *
1741687 GTCACTATC
1 ATCAATATC
1741696 ATCAATATC
1 ATCAATATC
1741705 GATATCATCA
Statistics
Matches: 51, Mismatches: 21, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
9 51 1.00
ACGTcount: A:0.35, C:0.27, G:0.10, T:0.28
Consensus pattern (9 bp):
ATCAATATC
Found at i:1756475 original size:18 final size:19
Alignment explanation
Indices: 1756452--1756500 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
1756442 GGTTTCTTGA
1756452 TTTTTTTAGGGGTTAGGTT
1 TTTTTTTAGGGGTTAGGTT
* *
1756471 TTTTTTTTGGGATTAGG-T
1 TTTTTTTAGGGGTTAGGTT
1756489 TTTTTTTAGGGG
1 TTTTTTTAGGGG
1756501 CTTAATGGGC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
18 11 0.42
19 15 0.58
ACGTcount: A:0.10, C:0.00, G:0.31, T:0.59
Consensus pattern (19 bp):
TTTTTTTAGGGGTTAGGTT
Found at i:1760953 original size:30 final size:30
Alignment explanation
Indices: 1760919--1761002 Score: 91
Period size: 29 Copynumber: 2.8 Consensus size: 30
1760909 TAGCTTGACA
* *
1760919 TAATTTTTTAAATCTAAAAAATAGAGAAAC
1 TAATTTTTTAAATATAAAAAATACAGAAAC
* *
1760949 TAATTTTTTAAAAAT-AAAAATACATAAAC
1 TAATTTTTTAAATATAAAAAATACAGAAAC
* *
1760978 TAA-ATTTTAAATTTAAAAATATACA
1 TAATTTTTTAAATATAAAAA-ATACA
1761003 ATAACATAGG
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
28 8 0.18
29 19 0.42
30 18 0.40
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.36
Consensus pattern (30 bp):
TAATTTTTTAAATATAAAAAATACAGAAAC
Found at i:1760967 original size:29 final size:29
Alignment explanation
Indices: 1760919--1760998 Score: 90
Period size: 28 Copynumber: 2.8 Consensus size: 29
1760909 TAGCTTGACA
* *
1760919 TAATTTTTTAAATCTAAAAAATAGAGAAAC
1 TAATTTTTTAAATAT-AAAAATACAGAAAC
* *
1760949 TAATTTTTTAAAAATAAAAATACATAAAC
1 TAATTTTTTAAATATAAAAATACAGAAAC
* *
1760978 TAA-ATTTTAAATTTAAAAATA
1 TAATTTTTTAAATATAAAAATA
1760999 TACAATAACA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
28 15 0.35
29 15 0.35
30 13 0.30
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.36
Consensus pattern (29 bp):
TAATTTTTTAAATATAAAAATACAGAAAC
Found at i:1769495 original size:20 final size:22
Alignment explanation
Indices: 1769470--1769519 Score: 70
Period size: 20 Copynumber: 2.4 Consensus size: 22
1769460 AATTAAGTTT
1769470 ATTTAAAAT-AAAAATATTA-A
1 ATTTAAAATAAAAAATATTATA
1769490 ATTT-AAATAAAAAATATTATA
1 ATTTAAAATAAAAAATATTATA
1769511 ATATTAAAA
1 AT-TTAAAA
1769520 CAATTTTCAC
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
19 4 0.15
20 14 0.54
21 3 0.12
22 2 0.08
23 3 0.12
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
ATTTAAAATAAAAAATATTATA
Found at i:1771225 original size:16 final size:15
Alignment explanation
Indices: 1771204--1771252 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
1771194 CAAAATTTTT
1771204 AATTAAATAATTATTA
1 AATT-AATAATTATTA
1771220 AATTAA-AA-T-TTA
1 AATTAATAATTATTA
*
1771232 ACTTAATAATTATTA
1 AATTAATAATTATTA
1771247 AATTAA
1 AATTAA
1771253 ATTTAAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
12 8 0.29
13 3 0.11
14 3 0.11
15 10 0.36
16 4 0.14
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (15 bp):
AATTAATAATTATTA
Found at i:1771239 original size:27 final size:26
Alignment explanation
Indices: 1771201--1771258 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 26
1771191 AATCAAAATT
1771201 TTTAATTAAATAATTATTAAATTAAAA
1 TTTAATTAAATAATTATTAAATT-AAA
1771228 TTTAACTT-AATAATTATTAAATTAAA
1 TTTAA-TTAAATAATTATTAAATTAAA
1771254 TTTAA
1 TTTAA
1771259 AATTTTTTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
26 8 0.27
27 20 0.67
28 2 0.07
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (26 bp):
TTTAATTAAATAATTATTAAATTAAA
Found at i:1773738 original size:19 final size:18
Alignment explanation
Indices: 1773699--1773738 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1773689 GTGATATGCC
* *
1773699 ATAATTTAATTTTTTATA
1 ATAAATTAATTTTTTAAA
1773717 ATAAATTAATTTTTATAAA
1 ATAAATTAATTTTT-TAAA
1773736 ATA
1 ATA
1773739 TTTAAAAGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATAAATTAATTTTTTAAA
Found at i:1773743 original size:18 final size:19
Alignment explanation
Indices: 1773701--1773743 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 19
1773691 GATATGCCAT
1773701 AATTTAATTTTTTATAATA
1 AATTTAATTTTTTATAATA
1773720 AA-TTAA-TTTTTATAA-A
1 AATTTAATTTTTTATAATA
1773736 ATATTTAA
1 A-ATTTAA
1773744 AAGTGTGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 2 0.09
17 10 0.45
18 8 0.36
19 2 0.09
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
AATTTAATTTTTTATAATA
Found at i:1780377 original size:43 final size:43
Alignment explanation
Indices: 1780325--1780412 Score: 158
Period size: 43 Copynumber: 2.0 Consensus size: 43
1780315 GTTTGTGAAA
*
1780325 AGAAAAACAATTTATGGTGACTACCCGCCAAAAAGTTTGGAGG
1 AGAAAAACAATTTATGGTGACTACCCGCCAAAAAGTATGGAGG
*
1780368 AGAAAAACAATTTATGGTGACTACTCGCCAAAAAGTATGGAGG
1 AGAAAAACAATTTATGGTGACTACCCGCCAAAAAGTATGGAGG
1780411 AG
1 AG
1780413 CCATGTCTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.41, C:0.15, G:0.24, T:0.20
Consensus pattern (43 bp):
AGAAAAACAATTTATGGTGACTACCCGCCAAAAAGTATGGAGG
Found at i:1781539 original size:21 final size:22
Alignment explanation
Indices: 1781513--1781559 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
1781503 CTCTGCTCAA
*
1781513 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
1781534 ACTCCACCTGCTGCGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
1781556 ACTC
1 ACTC
1781560 ACTCCTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.21
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:1784741 original size:29 final size:29
Alignment explanation
Indices: 1784662--1784742 Score: 92
Period size: 29 Copynumber: 2.8 Consensus size: 29
1784652 TTATATATTT
* *
1784662 AGAATTTAGTCTATCAATTTTTATTTTTA
1 AGAATTTAGTCTCTCAACTTTTATTTTTA
* * *
1784691 AAAATTTAGTCCCTCAACTTTTGTTTTTA
1 AGAATTTAGTCTCTCAACTTTTATTTTTA
*
1784720 AGAATTTAGTTTCTCTAA-TTTTA
1 AGAATTTAGTCTCTC-AACTTTTA
1784743 AAATTTTAAA
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
29 40 0.95
30 2 0.05
ACGTcount: A:0.30, C:0.11, G:0.07, T:0.52
Consensus pattern (29 bp):
AGAATTTAGTCTCTCAACTTTTATTTTTA
Found at i:1785937 original size:4 final size:4
Alignment explanation
Indices: 1785928--1786044 Score: 225
Period size: 4 Copynumber: 29.2 Consensus size: 4
1785918 CCTGTGGCCG
*
1785928 TACA TACA TATA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1785976 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1786024 TACA TACA TACA TACA TACA T
1 TACA TACA TACA TACA TACA T
1786045 GTTTCCTTTG
Statistics
Matches: 111, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
4 111 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (4 bp):
TACA
Found at i:1786252 original size:26 final size:26
Alignment explanation
Indices: 1786216--1786267 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
1786206 TTTATGGGAA
1786216 ATGCACCCTTAAACCTTCTTGATGTT
1 ATGCACCCTTAAACCTTCTTGATGTT
1786242 ATGCACCCTTAAACCTTCTTGATGTT
1 ATGCACCCTTAAACCTTCTTGATGTT
1786268 CCTTTTCAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.27, G:0.12, T:0.38
Consensus pattern (26 bp):
ATGCACCCTTAAACCTTCTTGATGTT
Found at i:1789499 original size:18 final size:20
Alignment explanation
Indices: 1789476--1789516 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1789466 AAAATAATTA
1789476 AAATATTT-T-TTTGTATAC
1 AAATATTTATCTTTGTATAC
*
1789494 AAATATTTATCTTTTTATAC
1 AAATATTTATCTTTGTATAC
1789514 AAA
1 AAA
1789517 ATCAATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 8 0.40
19 1 0.05
20 11 0.55
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.51
Consensus pattern (20 bp):
AAATATTTATCTTTGTATAC
Found at i:1795812 original size:6 final size:6
Alignment explanation
Indices: 1795801--1795830 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
1795791 CTTGATAAGT
1795801 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA
1795831 ATTCAACGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
TAAAAA
Found at i:1797056 original size:32 final size:33
Alignment explanation
Indices: 1796985--1797062 Score: 99
Period size: 32 Copynumber: 2.5 Consensus size: 33
1796975 ATAATAAGAT
1796985 AGTTATTAAATTA-TTTAAAAGTTTTTATTTAA
1 AGTTATTAAATTATTTTAAAAGTTTTTATTTAA
* * *
1797017 AG-CATTAAATTATTTTAATATTTTTTATTT-A
1 AGTTATTAAATTATTTTAAAAGTTTTTATTTAA
*
1797048 AGTTATTAAGTTATT
1 AGTTATTAAATTATT
1797063 AAGATTTAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
31 12 0.31
32 27 0.69
ACGTcount: A:0.37, C:0.01, G:0.06, T:0.55
Consensus pattern (33 bp):
AGTTATTAAATTATTTTAAAAGTTTTTATTTAA
Found at i:1799965 original size:6 final size:6
Alignment explanation
Indices: 1799942--1799984 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
1799932 GAAGATGGAG
* * * *
1799942 TGGGGG TGGGGT TGGGGT TGGGGT TTGGGT TTGGGT TTGGGT T
1 TGGGGT TGGGGT TGGGGT TGGGGT TGGGGT TGGGGT TGGGGT T
1799985 TGGCTTTGGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.60, T:0.40
Consensus pattern (6 bp):
TGGGGT
Found at i:1799985 original size:6 final size:6
Alignment explanation
Indices: 1799950--1799993 Score: 61
Period size: 6 Copynumber: 7.3 Consensus size: 6
1799940 AGTGGGGGTG
* * *
1799950 GGGTTG GGGTTG GGGTTT GGGTTT GGGTTT GGGTTT GGCTTT GG
1 GGGTTT GGGTTT GGGTTT GGGTTT GGGTTT GGGTTT GGGTTT GG
1799994 TTTAGGGGTG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.00, C:0.02, G:0.55, T:0.43
Consensus pattern (6 bp):
GGGTTT
Found at i:1801249 original size:14 final size:14
Alignment explanation
Indices: 1801230--1801256 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1801220 CTTCTTCTTC
1801230 TTTTTCTTTTTTTT
1 TTTTTCTTTTTTTT
1801244 TTTTTCTTTTTTT
1 TTTTTCTTTTTTT
1801257 CCTGAATGCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (14 bp):
TTTTTCTTTTTTTT
Found at i:1812263 original size:26 final size:24
Alignment explanation
Indices: 1812234--1812284 Score: 57
Period size: 26 Copynumber: 2.0 Consensus size: 24
1812224 GATTTAAGTT
1812234 ATAAAACAATAATATTACATATTTAA
1 ATAAAACAATAATATTA-AT-TTTAA
* * *
1812260 ATAAGATAATATTATTAATTTTAA
1 ATAAAACAATAATATTAATTTTAA
1812284 A
1 A
1812285 GAAATTCTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 6 0.27
25 2 0.09
26 14 0.64
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (24 bp):
ATAAAACAATAATATTAATTTTAA
Found at i:1816656 original size:4 final size:4
Alignment explanation
Indices: 1816647--1816701 Score: 62
Period size: 4 Copynumber: 14.5 Consensus size: 4
1816637 CTTTTTACAA
* * *
1816647 ATTT ATTT ATTT ATTT GTTC ATTT ATCT ATTT ATTT ATTT A-TT -TTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1816693 ATTT -TTT AT
1 ATTT ATTT AT
1816702 ATTGTTTATA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
3 7 0.17
4 35 0.83
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.73
Consensus pattern (4 bp):
ATTT
Found at i:1821100 original size:23 final size:23
Alignment explanation
Indices: 1821074--1821141 Score: 64
Period size: 28 Copynumber: 2.7 Consensus size: 23
1821064 GATGGATTAT
1821074 ATTATTCTGGTGTGTTTGGGAGG
1 ATTATTCTGGTGTGTTTGGGAGG
*
1821097 ATTATATGATACTGGTGTGTTTTGGAGG
1 A-T-TAT--T-CTGGTGTGTTTGGGAGG
* *
1821125 ATTATACTGGTATGTTT
1 ATTATTCTGGTGTGTTT
1821142 TGGTTGGACA
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
23 11 0.30
24 1 0.03
25 3 0.08
26 3 0.08
27 2 0.05
28 17 0.46
ACGTcount: A:0.19, C:0.04, G:0.31, T:0.46
Consensus pattern (23 bp):
ATTATTCTGGTGTGTTTGGGAGG
Found at i:1821100 original size:28 final size:28
Alignment explanation
Indices: 1821047--1821130 Score: 132
Period size: 28 Copynumber: 3.0 Consensus size: 28
1821037 CACTTTGTGC
1821047 TATTCTGGTGTGTTTTGGATGGATTATAT
1 TATTCTGGTGTGTTTTGGA-GGATTATAT
*
1821076 TATTCTGGTGTGTTTGGGAGGATTATAT
1 TATTCTGGTGTGTTTTGGAGGATTATAT
* *
1821104 GATACTGGTGTGTTTTGGAGGATTATA
1 TATTCTGGTGTGTTTTGGAGGATTATA
1821131 CTGGTATGTT
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 33 0.65
29 18 0.35
ACGTcount: A:0.19, C:0.04, G:0.31, T:0.46
Consensus pattern (28 bp):
TATTCTGGTGTGTTTTGGAGGATTATAT
Found at i:1822846 original size:14 final size:14
Alignment explanation
Indices: 1822815--1822863 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
1822805 AGGAAAGAAA
1822815 AAAGAA-AAGGGA-
1 AAAGAAGAAGGGAG
1822827 AGAAGAAGAAGGGAG
1 A-AAGAAGAAGGGAG
* *
1822842 AAAGAAAAAGAGAG
1 AAAGAAGAAGGGAG
1822856 AAA-AAGAA
1 AAAGAAGAA
1822864 AGAAAAAGGA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
12 1 0.03
13 9 0.29
14 20 0.65
15 1 0.03
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (14 bp):
AAAGAAGAAGGGAG
Found at i:1822857 original size:10 final size:10
Alignment explanation
Indices: 1822840--1822871 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
1822830 AGAAGAAGGG
1822840 AGAAAGAAAA
1 AGAAAGAAAA
*
1822850 AGAGAGAAAA
1 AGAAAGAAAA
1822860 AGAAAGAAAA
1 AGAAAGAAAA
1822870 AG
1 AG
1822872 GAAAATAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (10 bp):
AGAAAGAAAA
Found at i:1822884 original size:13 final size:15
Alignment explanation
Indices: 1822866--1822898 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1822856 AAAAAGAAAG
1822866 AAAAAGG-AA-AATA
1 AAAAAGGTAATAATA
1822879 AAAAAGGTAATAATA
1 AAAAAGGTAATAATA
1822894 AAAAA
1 AAAAA
1822899 AAGTAGCAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.39
14 2 0.11
15 9 0.50
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (15 bp):
AAAAAGGTAATAATA
Found at i:1823282 original size:3 final size:3
Alignment explanation
Indices: 1823274--1823304 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1823264 TATTTTTTAA
1823274 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1823305 TTTTAATGTA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1823448 original size:20 final size:20
Alignment explanation
Indices: 1823423--1823460 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1823413 AAAAATATTC
1823423 AAAAATCCTCGTATTTTAAT
1 AAAAATCCTCGTATTTTAAT
* *
1823443 AAAAATTCTCGTGTTTTA
1 AAAAATCCTCGTATTTTA
1823461 TTAGAATCTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.13, G:0.08, T:0.42
Consensus pattern (20 bp):
AAAAATCCTCGTATTTTAAT
Found at i:1823610 original size:17 final size:17
Alignment explanation
Indices: 1823581--1823626 Score: 67
Period size: 17 Copynumber: 2.6 Consensus size: 17
1823571 AGAAAAATCG
1823581 TGTTTCAAAAATTT-TCA
1 TGTTTC-AAAATTTCTCA
1823598 TGTCTTCAAAATTTCTCA
1 TGT-TTCAAAATTTCTCA
1823616 TGTTTCAAAAT
1 TGTTTCAAAAT
1823627 AATGATAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 18 0.67
18 9 0.33
ACGTcount: A:0.33, C:0.15, G:0.07, T:0.46
Consensus pattern (17 bp):
TGTTTCAAAATTTCTCA
Found at i:1823705 original size:18 final size:16
Alignment explanation
Indices: 1823684--1823760 Score: 57
Period size: 17 Copynumber: 4.6 Consensus size: 16
1823674 TTCTTTAAAA
1823684 AAAAATTTTTCGTGTTT
1 AAAAA-TTTTCGTGTTT
* **
1823701 CAAAAATTCTCGTGAAT
1 -AAAAATTTTCGTGTTT
*
1823718 AAAAAATTTCGTGTTTT
1 AAAAATTTTCGTG-TTT
*
1823735 CAAAAA-TTCCGGTGTTT
1 -AAAAATTTTC-GTGTTT
1823752 AAAAATTTT
1 AAAAATTTT
1823761 TTCGTGTTTT
Statistics
Matches: 46, Mismatches: 9, Indels: 9
0.72 0.14 0.14
Matches are distributed among these distances:
16 16 0.35
17 17 0.37
18 13 0.28
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.42
Consensus pattern (16 bp):
AAAAATTTTCGTGTTT
Found at i:1823713 original size:17 final size:17
Alignment explanation
Indices: 1823693--1823758 Score: 66
Period size: 17 Copynumber: 3.9 Consensus size: 17
1823683 AAAAAATTTT
1823693 TCGTGTTTCAAAAATTC
1 TCGTGTTTCAAAAATTC
** *
1823710 TCGTGAATAAAAAATT-
1 TCGTGTTTCAAAAATTC
1823726 TCGTGTTTTCAAAAATTC
1 TCGTG-TTTCAAAAATTC
1823744 -CGGTGTTT-AAAAATT
1 TC-GTGTTTCAAAAATT
1823759 TTTTCGTGTT
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
16 12 0.30
17 25 0.62
18 3 0.08
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.39
Consensus pattern (17 bp):
TCGTGTTTCAAAAATTC
Found at i:1823755 original size:34 final size:35
Alignment explanation
Indices: 1823684--1823771 Score: 101
Period size: 34 Copynumber: 2.5 Consensus size: 35
1823674 TTCTTTAAAA
*
1823684 AAAAATTTTTCGTG-TTTCAAAAATTCTCGTGAAT
1 AAAAATATTTCGTGTTTTCAAAAATTCTCGTGAAT
**
1823718 AAAAA-ATTTCGTGTTTTCAAAAATTC-CGGTGTTT
1 AAAAATATTTCGTGTTTTCAAAAATTCTC-GTGAAT
*
1823752 AAAAATTTTTTCGTGTTTTC
1 AAAAA-TATTTCGTGTTTTC
1823772 GTGTTTTCAA
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
33 8 0.17
34 26 0.57
36 12 0.26
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.44
Consensus pattern (35 bp):
AAAAATATTTCGTGTTTTCAAAAATTCTCGTGAAT
Found at i:1823774 original size:44 final size:44
Alignment explanation
Indices: 1823724--1823815 Score: 134
Period size: 44 Copynumber: 2.1 Consensus size: 44
1823714 GAATAAAAAA
1823724 TTTCGTGTTTTC-AAAAATTCCGGTGTTT-AAAAATTTTTTCGTGT
1 TTTCGTGTTTTCAAAAAATTCCGGTGTTTCAAAAA--TTTTCGTGT
**
1823768 TTTCGTGTTTTCAAAAAATTCTTGTGTTTCAAAAATTTTCGTGT
1 TTTCGTGTTTTCAAAAAATTCCGGTGTTTCAAAAATTTTCGTGT
1823812 TTTC
1 TTTC
1823816 AAAATTTTCA
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
44 25 0.57
45 14 0.32
46 5 0.11
ACGTcount: A:0.23, C:0.12, G:0.14, T:0.51
Consensus pattern (44 bp):
TTTCGTGTTTTCAAAAAATTCCGGTGTTTCAAAAATTTTCGTGT
Found at i:1823796 original size:63 final size:63
Alignment explanation
Indices: 1823718--1823866 Score: 182
Period size: 63 Copynumber: 2.4 Consensus size: 63
1823708 TCTCGTGAAT
*
1823718 AAAAAATT-TCGTGTTTTCAAAAA-TTCCG-GTGTTTAAAAATTTTTTCGTGTTTTCGTGTTTTC
1 AAAAAATTCTCGTGTTTTCAAAAATTTCCGTGT-TTTAAAAA--TTTTCATGTTTTCGTGTTTTC
1823780 -
63 A
* * *
1823780 AAAAAATTCTTGTG-TTTCAAAAATTTTCGTGTTTTCAAAATTTTCATGTTTTCGTGTTTTCAA
1 AAAAAATTCTCGTGTTTTCAAAAATTTCCGTGTTTTAAAAATTTTCATGTTTTCGTGTTTTC-A
*
1823843 AAAAAATTCTCGTGTTTTTAAAAA
1 AAAAAATTCTCGTGTTTTCAAAAA
1823867 AAAATTCATG
Statistics
Matches: 75, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
61 20 0.27
62 17 0.23
63 28 0.37
64 10 0.13
ACGTcount: A:0.30, C:0.11, G:0.12, T:0.47
Consensus pattern (63 bp):
AAAAAATTCTCGTGTTTTCAAAAATTTCCGTGTTTTAAAAATTTTCATGTTTTCGTGTTTTCA
Found at i:1823797 original size:18 final size:19
Alignment explanation
Indices: 1823767--1824024 Score: 120
Period size: 17 Copynumber: 13.9 Consensus size: 19
1823757 TTTTTTCGTG
1823767 TTTTCGTGTTTTCAAAAAA
1 TTTTCGTGTTTTCAAAAAA
1823786 TTCTT-GTG-TTTC-AAAAA
1 TT-TTCGTGTTTTCAAAAAA
*
1823803 TTTTCGTGTTTTCAAAATTTTCATG
1 TTTTCGTGTTTTCAAAA-----A-A
1823828 TTTTCGTGTTTTCAAAAAAAA
1 TTTTCGTGTTTTC--AAAAAA
* *
1823849 TTCTCGTGTTTTTAAAAAAA
1 TTTTCGTG-TTTTCAAAAAA
** *
1823869 AATTCATG-TTT-AAAAAA
1 TTTTCGTGTTTTCAAAAAA
*
1823886 --TTCATGTTTTC--AAAA
1 TTTTCGTGTTTTCAAAAAA
*
1823901 TTTTCGTGTTTTC-AAAAT
1 TTTTCGTGTTTTCAAAAAA
1823919 TTTTCGTG---TCAAAAAA
1 TTTTCGTGTTTTCAAAAAA
* * * *
1823935 TTCTCATG-TAT-AGAAAA
1 TTTTCGTGTTTTCAAAAAA
* * *
1823952 TTTCCTTGTTTTTAAAACAA
1 TTTTCGTGTTTTCAAAA-AA
*
1823972 -TTCCGTGTTTTCAAAAAA
1 TTTTCGTGTTTTCAAAAAA
* *
1823990 ATTTCGTG-TTTC-GAAAA
1 TTTTCGTGTTTTCAAAAAA
*
1824007 TCTTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
1824025 TTATTATTGT
Statistics
Matches: 186, Mismatches: 26, Indels: 54
0.70 0.10 0.20
Matches are distributed among these distances:
15 12 0.06
16 15 0.08
17 46 0.25
18 35 0.19
19 34 0.18
20 14 0.08
21 7 0.04
22 5 0.03
24 1 0.01
25 13 0.07
27 4 0.02
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (19 bp):
TTTTCGTGTTTTCAAAAAA
Found at i:1823803 original size:17 final size:18
Alignment explanation
Indices: 1823767--1824026 Score: 103
Period size: 18 Copynumber: 14.1 Consensus size: 18
1823757 TTTTTTCGTG
1823767 TTTTCGTGTTTTCAAAAAA
1 TTTTCGTGTTTTC-AAAAA
1823786 TTCTT-GTG-TTTCAAAAA
1 TT-TTCGTGTTTTCAAAAA
1823803 TTTTCGTGTTTTCAAAATTTTCA
1 TTTTCGTGTTTTCAAAA-----A
1823826 TGTTTTCGTGTTTTCAAAAAAAA
1 --TTTTCGTGTTTTC---AAAAA
* *
1823849 TTCTCGTGTTTTTAAAAAAA
1 TTTTCGTG-TTTT-CAAAAA
** *
1823869 AATTCATG-TTT-AAAAA
1 TTTTCGTGTTTTCAAAAA
* *
1823885 -ATTCATGTTTTC-AAAA
1 TTTTCGTGTTTTCAAAAA
*
1823901 TTTTCGTGTTTTCAAAAT
1 TTTTCGTGTTTTCAAAAA
1823919 TTTTCGTG---TCAAAAAA
1 TTTTCGTGTTTTC-AAAAA
* * *
1823935 TTCTCATG-TAT-AGAAAA
1 TTTTCGTGTTTTCA-AAAA
* * *
1823952 TTTCCTTGTTTTTAAAACA
1 TTTTCGTGTTTTCAAAA-A
* *
1823971 ATTCCGTGTTTTCAAAAAA
1 TTTTCGTGTTTTC-AAAAA
* *
1823990 ATTTCGTG-TTTCGAAAA
1 TTTTCGTGTTTTCAAAAA
*
1824007 TCTTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
1824025 TT
1 TT
1824027 ATTATTGTGT
Statistics
Matches: 188, Mismatches: 25, Indels: 57
0.70 0.09 0.21
Matches are distributed among these distances:
15 9 0.05
16 25 0.13
17 39 0.21
18 45 0.24
19 25 0.13
20 15 0.08
21 7 0.04
22 4 0.02
23 2 0.01
25 13 0.07
28 4 0.02
ACGTcount: A:0.32, C:0.12, G:0.10, T:0.45
Consensus pattern (18 bp):
TTTTCGTGTTTTCAAAAA
Found at i:1823824 original size:45 final size:44
Alignment explanation
Indices: 1823731--1823825 Score: 104
Period size: 45 Copynumber: 2.1 Consensus size: 44
1823721 AAATTTCGTG
***
1823731 TTTTC-AAAAATTCCGGTGTTTAAAAATTTTTTCGTGTTTTCGTG
1 TTTTCAAAAAATTCCGGTGTTTAAAAA-TTTTTCGTGTTTTCAAA
**
1823775 TTTTCAAAAAATTCTTGTGTTTCAAAAA-TTTTCGTGTTTTCAAAA
1 TTTTCAAAAAATTCCGGTGTTT-AAAAATTTTTCGTGTTTTC-AAA
1823820 TTTTCA
1 TTTTCA
1823826 TGTTTTCGTG
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
44 18 0.42
45 20 0.47
46 5 0.12
ACGTcount: A:0.27, C:0.12, G:0.12, T:0.49
Consensus pattern (44 bp):
TTTTCAAAAAATTCCGGTGTTTAAAAATTTTTCGTGTTTTCAAA
Found at i:1823866 original size:22 final size:21
Alignment explanation
Indices: 1823831--1823873 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
1823821 TTTCATGTTT
*
1823831 TCGTGTTTTCAAAAAAAATTC
1 TCGTGTTTTAAAAAAAAATTC
1823852 TCGTGTTTTTAAAAAAAAATTC
1 TCGTG-TTTTAAAAAAAAATTC
1823874 ATGTTTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.40
Consensus pattern (21 bp):
TCGTGTTTTAAAAAAAAATTC
Found at i:1823900 original size:15 final size:15
Alignment explanation
Indices: 1823867--1823919 Score: 61
Period size: 15 Copynumber: 3.4 Consensus size: 15
1823857 TTTTTAAAAA
**
1823867 AAAATTCATGTTTAA
1 AAAATTCATGTTTTC
1823882 AAAATTCATGTTTTC
1 AAAATTCATGTTTTC
*
1823897 AAAATTTTCGTGTTTTC
1 AAAA--TTCATGTTTTC
1823914 AAAATT
1 AAAATT
1823920 TTTCGTGTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
15 19 0.58
17 14 0.42
ACGTcount: A:0.38, C:0.09, G:0.08, T:0.45
Consensus pattern (15 bp):
AAAATTCATGTTTTC
Found at i:1824938 original size:29 final size:27
Alignment explanation
Indices: 1824890--1824954 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 27
1824880 ATCCAACCCA
* *
1824890 AACACACCCGGAATATTATAAATCCTCCAT
1 AACACA-CCGGAATA--ATATATCCTCCAC
* *
1824920 AACACACCGGTATAATATATCCTCCCC
1 AACACACCGGAATAATATATCCTCCAC
1824947 AACACACC
1 AACACACC
1824955 AATAATGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
27 18 0.58
29 7 0.23
30 6 0.19
ACGTcount: A:0.38, C:0.35, G:0.06, T:0.20
Consensus pattern (27 bp):
AACACACCGGAATAATATATCCTCCAC
Found at i:1826024 original size:12 final size:12
Alignment explanation
Indices: 1826009--1826039 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1825999 TTCTCTTTTA
1826009 TTTTTCTTTCCC
1 TTTTTCTTTCCC
*
1826021 TTTTTCTTTCTC
1 TTTTTCTTTCCC
1826033 TTTTTCT
1 TTTTTCT
1826040 CCCCTGCTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTTCTTTCCC
Found at i:1826140 original size:16 final size:16
Alignment explanation
Indices: 1826119--1826149 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1826109 TTTATTATTT
1826119 TATTAACATAATATAA
1 TATTAACATAATATAA
*
1826135 TATTAATATAATATA
1 TATTAACATAATATA
1826150 TTAAAATATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
TATTAACATAATATAA
Found at i:1834409 original size:5 final size:5
Alignment explanation
Indices: 1834399--1834430 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
1834389 TTATGTTTTA
1834399 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT AT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT AT
1834431 AAACTAAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATTAT
Found at i:1836047 original size:45 final size:45
Alignment explanation
Indices: 1835983--1836131 Score: 228
Period size: 45 Copynumber: 3.3 Consensus size: 45
1835973 CTGTTACCGC
* *
1835983 TACTGCTACTGTTACCGATTCGGCACTTTGTGTGTCGAATATTGT
1 TACTGTTACCGTTACCGATTCGGCACTTTGTGTGTCGAATATTGT
*
1836028 TACTGTTACCGTTACCGATTCGGCACTTTGTGTGTCGAATATTAT
1 TACTGTTACCGTTACCGATTCGGCACTTTGTGTGTCGAATATTGT
* * *
1836073 TACTATTACCGTTACCGATTCGGCACTTTGTGTGTTGGATATTGT
1 TACTGTTACCGTTACCGATTCGGCACTTTGTGTGTCGAATATTGT
*
1836118 TACTG-TACTGTTAC
1 TACTGTTACCGTTAC
1836132 TGTTACTGTT
Statistics
Matches: 95, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
44 8 0.08
45 87 0.92
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.41
Consensus pattern (45 bp):
TACTGTTACCGTTACCGATTCGGCACTTTGTGTGTCGAATATTGT
Found at i:1836134 original size:6 final size:6
Alignment explanation
Indices: 1836115--1836147 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
1836105 TGTTGGATAT
1836115 TGTTAC TG-TAC TGTTAC TGTTAC TGTTAC TGTT
1 TGTTAC TGTTAC TGTTAC TGTTAC TGTTAC TGTT
1836148 CCGGATTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.15, C:0.15, G:0.18, T:0.52
Consensus pattern (6 bp):
TGTTAC
Found at i:1836329 original size:18 final size:18
Alignment explanation
Indices: 1836308--1836499 Score: 160
Period size: 18 Copynumber: 10.7 Consensus size: 18
1836298 TAACTGATTA
1836308 TTACTGAATAATTGACTG
1 TTACTGAATAATTGACTG
* *
1836326 TTACCGGATAATTGACTG
1 TTACTGAATAATTGACTG
* *
1836344 CTACTGGAT-ATTAGACTG
1 TTACTGAATAATT-GACTG
* *
1836362 TTACTGAATAATTGAATA
1 TTACTGAATAATTGACTG
*
1836380 TTACTGAATAATTGA-TCA
1 TTACTGAATAATTGACT-G
* *
1836398 TTACTGAATAACTGATTG
1 TTACTGAATAATTGACTG
*
1836416 TCACTGAATGAA-TGACTG
1 TTACTGAAT-AATTGACTG
* * * *
1836434 TTACTAAATAACGTAATTG
1 TTACTGAATAA-TTGACTG
*
1836453 TTACTGAAT-ATCTGA-TT
1 TTACTGAATAAT-TGACTG
1836470 TTACTGAATAATTGACTG
1 TTACTGAATAATTGACTG
*
1836488 TTACTGGATAAT
1 TTACTGAATAAT
1836500 CGATCAATTG
Statistics
Matches: 142, Mismatches: 22, Indels: 20
0.77 0.12 0.11
Matches are distributed among these distances:
17 19 0.13
18 105 0.74
19 18 0.13
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (18 bp):
TTACTGAATAATTGACTG
Found at i:1839199 original size:53 final size:53
Alignment explanation
Indices: 1839063--1839208 Score: 213
Period size: 53 Copynumber: 2.7 Consensus size: 53
1839053 TGCGCCCATT
**
1839063 TAAGACCATAGCTGGGCTATGGCATCGGTGCAATGTGATAATGTGACTCCGTA
1 TAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACTCCGTA
*
1839116 TAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGATTCCGTA
1 TAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACTCCGTA
* *
1839169 TAAGACCAT-GTCTGGGATATGGCTTCGGTATGATATGTGA
1 TAAGACCATAG-CTGGGCTATGGCATCGGTAT-A-ATGTGA
1839209 ACCGTGTAAG
Statistics
Matches: 85, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
52 1 0.01
53 77 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (53 bp):
TAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACTCCGTA
Done.