Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold193
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: 3104049
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.32
Warning! 172765 characters in sequence are not A, C, G, or T
File 9 of 18
Found at i:1545662 original size:24 final size:25
Alignment explanation
Indices: 1545607--1545672 Score: 64
Period size: 24 Copynumber: 2.7 Consensus size: 25
1545597 TAAAATTTTA
* *
1545607 AATAATTTTATTTTA-TTTTATAAT
1 AATATTTTTATTTAATTTTTATAAT
*
1545631 TATAATTTTTATTTAATTTTTAT-AT
1 AAT-ATTTTTATTTAATTTTTATAAT
* *
1545656 AATATTTTAATTAAATT
1 AATATTTTTATTTAATT
1545673 AATATTCCGA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
24 14 0.41
25 14 0.41
26 6 0.18
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (25 bp):
AATATTTTTATTTAATTTTTATAAT
Found at i:1546220 original size:3 final size:3
Alignment explanation
Indices: 1546207--1546237 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
1546197 GCTGGGTTTC
*
1546207 TCT TTT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1546238 ATTTTTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (3 bp):
TCT
Found at i:1547203 original size:29 final size:28
Alignment explanation
Indices: 1547170--1547241 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 28
1547160 ATATTATTAT
1547170 AATTAATTATAATAAATATT-AATTATAA
1 AATTAATTATAATAAA-ATTAAATTATAA
*
1547198 ATATTAATAATAA-AAAATTAAAATTATAA
1 A-ATTAATTATAATAAAATT-AAATTATAA
*
1547227 AATAATATTATAATA
1 AATTA-ATTATAATA
1547242 TTATATTACC
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
27 3 0.08
28 7 0.19
29 25 0.69
30 1 0.03
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (28 bp):
AATTAATTATAATAAAATTAAATTATAA
Found at i:1547247 original size:13 final size:13
Alignment explanation
Indices: 1547164--1547249 Score: 50
Period size: 13 Copynumber: 6.4 Consensus size: 13
1547154 ATATACATAT
1547164 TATTATAATTAATTA
1 TATTATAA-T-ATTA
*
1547179 TAATA-AATATTA
1 TATTATAATATTA
1547191 -ATTATAAATATTAA
1 TATTAT-AATATT-A
* * *
1547205 TAATAAAAAATTAA
1 TATTATAATATT-A
* * *
1547219 AATTATAAAATAA
1 TATTATAATATTA
1547232 TATTATAATATTA
1 TATTATAATATTA
1547245 TATTA
1 TATTA
1547250 CCATCATTAT
Statistics
Matches: 55, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
11 3 0.05
12 4 0.07
13 23 0.42
14 18 0.33
15 7 0.13
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
TATTATAATATTA
Found at i:1547441 original size:33 final size:33
Alignment explanation
Indices: 1547404--1547486 Score: 112
Period size: 34 Copynumber: 2.5 Consensus size: 33
1547394 ACTACTCCAA
* *
1547404 TGTTGATTAAATGGTGATTTGGTAATTTATCAT
1 TGTTGATTAAATGGTGATTTAGTAAGTTATCAT
* *
1547437 TGTTGATTAAATGGGTGATTTAGTAGGTTGTCAT
1 TGTTGATTAAAT-GGTGATTTAGTAAGTTATCAT
*
1547471 TATTGATTAAATGGTG
1 TGTTGATTAAATGGTG
1547487 GTTTTTACCA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
33 16 0.36
34 28 0.64
ACGTcount: A:0.27, C:0.02, G:0.25, T:0.46
Consensus pattern (33 bp):
TGTTGATTAAATGGTGATTTAGTAAGTTATCAT
Found at i:1551950 original size:34 final size:33
Alignment explanation
Indices: 1551893--1552113 Score: 280
Period size: 34 Copynumber: 6.5 Consensus size: 33
1551883 ATGTGGGAGA
*
1551893 ATTGTTGATTAAATGGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGTGATTTGGTAGCTTACC
* * *
1551926 ATTGTTGATTAAATCGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAAT-GGTGATTTGGTAGCTTACC
* *
1551960 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAAT-GGTGATTTGGTAGCTTACC
**
1551994 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATG-GTGATTTGGTAGCTTACC
* *
1552028 ATTATTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAAT-GGTGATTTGGTAGCTTACC
* * *
1552062 ATTGTTGACTAAATGGTAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGT-GATTTGGTAGCTTACC
1552096 ATTGTTGATTAAATGGTG
1 ATTGTTGATTAAATGGTG
1552114 GTTTTTACCA
Statistics
Matches: 164, Mismatches: 20, Indels: 8
0.85 0.10 0.04
Matches are distributed among these distances:
33 19 0.12
34 144 0.88
35 1 0.01
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.41
Consensus pattern (33 bp):
ATTGTTGATTAAATGGTGATTTGGTAGCTTACC
Found at i:1552036 original size:102 final size:101
Alignment explanation
Indices: 1551893--1552111 Score: 339
Period size: 102 Copynumber: 2.2 Consensus size: 101
1551883 ATGTGGGAGA
** * * * *
1551893 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGATTAAATCGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATCGGTGATTTGGTGGCTTA
1551958 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
66 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
*
1551994 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTT
1 ATTGTTGATTAAATG-GAAATTTGGTAGCTTACCATTATTGATTAAATCGGTGATTTGGTGGCTT
* * *
1552059 ACCATTGTTGACTAAATGGTAGATTTGGTAGGTTGCC
65 ACCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1552096 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
1552112 TGGTTTTTAC
Statistics
Matches: 107, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
101 16 0.15
102 91 0.85
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.41
Consensus pattern (101 bp):
ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATCGGTGATTTGGTGGCTTA
CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
Found at i:1554579 original size:3 final size:3
Alignment explanation
Indices: 1554571--1554614 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
1554561 AGATCAAGCT
1554571 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1554615 GGTAATAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1557010 original size:20 final size:20
Alignment explanation
Indices: 1556982--1557056 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
1556972 TTTTACCTTG
1556982 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
1557002 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
1557022 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
1557042 ATGTATCGATACATT
1 ATGTATCGATACATT
1557057 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1557049 original size:40 final size:39
Alignment explanation
Indices: 1556982--1557059 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
1556972 TTTTACCTTG
* *
1556982 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
1557022 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
1557060 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:1571072 original size:12 final size:12
Alignment explanation
Indices: 1571051--1571086 Score: 54
Period size: 14 Copynumber: 2.8 Consensus size: 12
1571041 CCTTTACACC
1571051 CAAAAAAAAAAA
1 CAAAAAAAAAAA
1571063 CAAAACAAAAAAAA
1 C-AAA-AAAAAAAA
1571077 CAAAAAAAAA
1 CAAAAAAAAA
1571087 GAAAAAATAG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 7 0.32
13 6 0.27
14 9 0.41
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (12 bp):
CAAAAAAAAAAA
Found at i:1571074 original size:14 final size:14
Alignment explanation
Indices: 1571055--1571104 Score: 59
Period size: 14 Copynumber: 3.5 Consensus size: 14
1571045 TACACCCAAA
1571055 AAAAAAAACAAAAC
1 AAAAAAAACAAAAC
1571069 AAAAAAAACAAAA-
1 AAAAAAAACAAAAC
1571082 AAAAAGAAA-AAATAGC
1 AAAAA-AAACAAA-A-C
1571098 AAAAAAA
1 AAAAAAA
1571105 TAGAAGGGTC
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
13 8 0.25
14 17 0.53
15 2 0.06
16 5 0.16
ACGTcount: A:0.86, C:0.08, G:0.04, T:0.02
Consensus pattern (14 bp):
AAAAAAAACAAAAC
Found at i:1571076 original size:9 final size:9
Alignment explanation
Indices: 1571051--1571104 Score: 58
Period size: 9 Copynumber: 5.9 Consensus size: 9
1571041 CCTTTACACC
1571051 CAAAAAAAA
1 CAAAAAAAA
*
1571060 -AAACAAAA
1 CAAAAAAAA
1571068 CAAAAAAAA
1 CAAAAAAAA
1571077 CAAAAAAAA
1 CAAAAAAAA
1571086 -AGAAAAAATA
1 CA-AAAAAA-A
1571096 GCAAAAAAA
1 -CAAAAAAA
1571105 TAGAAGGGTC
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
8 8 0.21
9 22 0.58
10 1 0.03
11 6 0.16
12 1 0.03
ACGTcount: A:0.85, C:0.09, G:0.04, T:0.02
Consensus pattern (9 bp):
CAAAAAAAA
Found at i:1571100 original size:20 final size:19
Alignment explanation
Indices: 1571052--1571109 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
1571042 CTTTACACCC
* *
1571052 AAAAAAA-AAAACAAAACA
1 AAAAAAACAAAAAAAAAGA
1571070 AAAAAAACAAAAAAAAAGA
1 AAAAAAACAAAAAAAAAGA
* *
1571089 AAAAATAGCAAAAAAATAGA
1 AAAAA-AACAAAAAAAAAGA
1571109 A
1 A
1571110 GGGTCTAGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
18 7 0.21
19 14 0.41
20 13 0.38
ACGTcount: A:0.84, C:0.07, G:0.05, T:0.03
Consensus pattern (19 bp):
AAAAAAACAAAAAAAAAGA
Found at i:1572454 original size:28 final size:28
Alignment explanation
Indices: 1572319--1573482 Score: 1468
Period size: 28 Copynumber: 40.8 Consensus size: 28
1572309 AGGTTCATCT
*
1572319 CTTTCAAAGCCCACAAGTCAGTGGCAATC
1 CTTTCAAAGCCCACAAGTCAGTGGC-ACC
1572348 CTTTCAAAGCCCACAAGTCAGTGGCACTC
1 CTTTCAAAGCCCACAAGTCAGTGGCAC-C
* *
1572377 TTTTCAAAGCCCACAAATCAGTGGCACTC
1 CTTTCAAAGCCCACAAGTCAGTGGCAC-C
* *
1572406 TTTTTAAAGCCCACAAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* *
1572434 CTTTCAAAGCCCACAAATCAGTAGCACTC
1 CTTTCAAAGCCCACAAGTCAGTGGCAC-C
*
1572463 TTTTCAAAGCCCACAAGTCAGTGGCACTC
1 CTTTCAAAGCCCACAAGTCAGTGGCAC-C
*
1572492 TTTTCAAAGCCCACAAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
*
1572520 CTTTCAAAGCCCATAAGTCAGTGGCACTC
1 CTTTCAAAGCCCACAAGTCAGTGGCAC-C
* *
1572549 TTTTCAAAGCCCACAAGTCAGTAGCACTC
1 CTTTCAAAGCCCACAAGTCAGTGGCAC-C
* * *
1572578 TTTTCAAAGCCCACAAATCAGTGGCACTT
1 CTTTCAAAGCCCACAAGTCAGTGGCAC-C
* *
1572607 TTTTTAAAGCCCACAAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
*
1572635 CTTTCAAAGCCCACAAGTTAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
*
1572663 CTTTCAGAGCCCACAAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* *
1572691 CTTTCAAAGCCCACAAATTAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* * *
1572719 CTTTTAGAGCCCACAAGTTAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* *
1572747 TTTTCAAAGCCCACAAGCCAGTGGCACTC
1 CTTTCAAAGCCCACAAGTCAGTGGCAC-C
1572776 CTTTCAAAGCCCACAAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
*
1572804 CTTTCAAAGCCCATAAGTCAGTGGCACTC
1 CTTTCAAAGCCCACAAGTCAGTGGCAC-C
* *
1572833 TTTTCAAAGCCCACACAAGTCGGTGGCGACTC
1 CTTTCAAAG-CC-CACAAGTCAGTGGC-AC-C
*
1572865 TTTTCAAAGCCCACAAGTCAGTGGCACTC
1 CTTTCAAAGCCCACAAGTCAGTGGCAC-C
* *
1572894 TTTTCAAAGCCCACAAGCCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
*
1572922 CTTTCAAAGCCCACAAGTCAGTGGCATC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* *
1572950 CTTTCAAAGCCCACGAGTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* * * *
1572978 TTTTCAAAGCCCACGAGTTAGTGGCACA
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* * *
1573006 TTTTC-AAGCCCACTAGTCAGTGGCACA
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
1573033 CTTTCAAAGCCCACAAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
*
1573061 CTTTCAAAGCCCACAAGTTAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* * * *
1573089 CTTTTAGAGCACACAAGTCAGTGGCATC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
*
1573117 CTTTCGAAGCCCACAAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* * * *
1573145 CTTGCGAAGCCCACAATTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
1573173 CTTTCAAAGCCCACAAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
*
1573201 CTTTCAAAGCCCACACAAGTCACTGGCACTC
1 CTTTCAAAG-CC-CACAAGTCAGTGGCAC-C
*
1573232 CTTTTAAAGCCCACGCAAGTCAGTGGCACC
1 CTTTCAAAGCCCA--CAAGTCAGTGGCACC
* * * *
1573262 TTTTCAAAGCCCACGAGTCAGTGGTACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
*
1573290 CTTTCAAAGCCCACAAGTCAGAGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* *
1573318 CTTTC-AAGCCCACGAGTCAGTGGTACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* * *
1573345 TTTTCAAAGCCCACGAGTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* *
1573373 CTTTCAAAGCCCATAAGTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
* **
1573401 CTTTCAAAGCCCACGAGTCAGTGGCATT
1 CTTTCAAAGCCCACAAGTCAGTGGCACC
1573429 CTTTCAAAGCCCATGCAAGTCAGTGGCACC
1 CTTTCAAAGCCCA--CAAGTCAGTGGCACC
*
1573459 CTTTTAAAGCCCACGCAAGTCAGT
1 CTTTCAAAGCCCA--CAAGTCAGT
1573483 AACACTTTTT
Statistics
Matches: 1009, Mismatches: 109, Indels: 33
0.88 0.09 0.03
Matches are distributed among these distances:
27 47 0.05
28 556 0.55
29 279 0.28
30 78 0.08
31 36 0.04
32 13 0.01
ACGTcount: A:0.28, C:0.32, G:0.18, T:0.22
Consensus pattern (28 bp):
CTTTCAAAGCCCACAAGTCAGTGGCACC
Found at i:1574159 original size:20 final size:19
Alignment explanation
Indices: 1574109--1574185 Score: 73
Period size: 20 Copynumber: 3.9 Consensus size: 19
1574099 TTTTACCCTG
*
1574109 ATGTATCGATACATTTTTCA
1 ATGTATCGATACA-TTATCA
* * *
1574129 ATATATTGATACATGTATGA
1 ATGTATCGATACAT-TATCA
* *
1574149 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTAT-CA
1574169 ATGTATCGATACATTAT
1 ATGTATCGATACATTAT
1574186 GTCTTTTTAC
Statistics
Matches: 44, Mismatches: 11, Indels: 4
0.75 0.19 0.07
Matches are distributed among these distances:
19 3 0.07
20 41 0.93
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.42
Consensus pattern (19 bp):
ATGTATCGATACATTATCA
Found at i:1574180 original size:40 final size:39
Alignment explanation
Indices: 1574109--1574186 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
1574099 TTTTACCCTG
* * *
1574109 ATGTATCGATACATTTTTCAATATATTGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
1574149 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
1574187 TCTTTTTACC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.41
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:1580560 original size:15 final size:15
Alignment explanation
Indices: 1580542--1580570 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1580532 TAATTAATTA
1580542 AAAAATAA-AAAAAT
1 AAAAATAATAAAAAT
1580556 AAAAATAATAAAAAT
1 AAAAATAATAAAAAT
1580571 GAGACAAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (15 bp):
AAAAATAATAAAAAT
Found at i:1581183 original size:11 final size:10
Alignment explanation
Indices: 1581167--1581228 Score: 51
Period size: 8 Copynumber: 6.3 Consensus size: 10
1581157 GAAAAAAATC
1581167 AAAGAAGGAAG
1 AAAGAA-GAAG
1581178 AAAG-A-AAG
1 AAAGAAGAAG
1581186 AAAGAAGAAG
1 AAAGAAGAAG
*
1581196 -AA-AAGAAA
1 AAAGAAGAAG
1581204 AAAGAAGTAAGG
1 AAAGAAG-AA-G
*
1581216 AGAGAAGAAG
1 AAAGAAGAAG
1581226 AAA
1 AAA
1581229 AAGGGAAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 13
0.71 0.07 0.22
Matches are distributed among these distances:
8 12 0.29
9 5 0.12
10 10 0.24
11 8 0.20
12 6 0.15
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (10 bp):
AAAGAAGAAG
Found at i:1581187 original size:15 final size:14
Alignment explanation
Indices: 1581167--1581228 Score: 61
Period size: 15 Copynumber: 4.2 Consensus size: 14
1581157 GAAAAAAATC
*
1581167 AAAGAAGGAAGAAAG
1 AAAGAAAGAAG-AAG
1581182 AAAGAAAGAAGAAG
1 AAAGAAAGAAGAAG
*
1581196 AAAAGAAAAAAGAAG
1 -AAAGAAAGAAGAAG
* *
1581211 TAAGGAGAGAAGAAG
1 -AAAGAAAGAAGAAG
1581226 AAA
1 AAA
1581229 AAGGGAAAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
14 5 0.13
15 34 0.87
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (14 bp):
AAAGAAAGAAGAAG
Found at i:1581221 original size:19 final size:19
Alignment explanation
Indices: 1581167--1581221 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
1581157 GAAAAAAATC
1581167 AAAGAAGGAA-GAAAGAAAG
1 AAAGAA-GAAGGAAAGAAAG
*
1581186 AAAGAAGAAGAAAAGAAA-
1 AAAGAAGAAGGAAAGAAAG
*
1581204 AAAGAAGTAAGGAGAGAA
1 AAAGAAG-AAGGAAAGAA
1581222 GAAGAAAAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
18 10 0.32
19 21 0.68
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (19 bp):
AAAGAAGAAGGAAAGAAAG
Found at i:1585424 original size:190 final size:189
Alignment explanation
Indices: 1585102--1585454 Score: 523
Period size: 190 Copynumber: 1.9 Consensus size: 189
1585092 CATGAATACT
* **
1585102 AGAGCCAAGCCTTTACAACAAAAAACTACACCAATTCCATTTATATTGGTGAACCCATTAAAAAT
1 AGAGCCAAGCCTTTACAACAAAAAACTACACCAATTCCACTTATATTAATGAACCCATTAAAAAT
** * *
1585167 GCCATATTCAATGGCATTTTAACACTTTATTTATAAGTTATAGGTTCATTAAAAGTATTAACTCA
66 GCCATATGAAATGGCATTTTAACACTTTATTTACAAGCTATAGGTTCATTAAAAGTATTAACTCA
* *
1585232 ACCTCTTTCCTTAACAAATGGTTCCAAGCACTTTATTTATCTTTTCCATGAGTATTATA
131 ACCTCTCTCCTTAACAAACGGTTCCAAGCACTTTATTTATCTTTTCCATGAGTATTATA
* * * *
1585291 AGAGCCAAGCCTTTACAATAGAAAACTACACCAATTCCACTTATATTAATGAACTCTATTGAAAA
1 AGAGCCAAGCCTTTACAACAAAAAACTACACCAATTCCACTTATATTAATGAAC-CCATTAAAAA
*
1585356 TGCCAT-TGAATATGAG-ATTTTAACACTTTATTTACAAGCTAT-GAGTTCATTTAAAGTATTAA
65 TGCCATATGAA-ATG-GCATTTTAACACTTTATTTACAAGCTATAG-GTTCATTAAAAGTATTAA
1585418 CTCAACCTCTCTCCTTAACAAACGGTTCCAAGCACTT
127 CTCAACCTCTCTCCTTAACAAACGGTTCCAAGCACTT
1585455 AACTAACTAA
Statistics
Matches: 146, Mismatches: 14, Indels: 7
0.87 0.08 0.04
Matches are distributed among these distances:
189 52 0.36
190 93 0.64
191 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.10, T:0.34
Consensus pattern (189 bp):
AGAGCCAAGCCTTTACAACAAAAAACTACACCAATTCCACTTATATTAATGAACCCATTAAAAAT
GCCATATGAAATGGCATTTTAACACTTTATTTACAAGCTATAGGTTCATTAAAAGTATTAACTCA
ACCTCTCTCCTTAACAAACGGTTCCAAGCACTTTATTTATCTTTTCCATGAGTATTATA
Found at i:1588897 original size:58 final size:57
Alignment explanation
Indices: 1588747--1588897 Score: 137
Period size: 58 Copynumber: 2.6 Consensus size: 57
1588737 TAAACGGTCT
* * *****
1588747 TAAATCAT-AACAAATTACTAAAATGATCCTAAAGTACATGAAAATACATAAGTGGTTT
1 TAAATCATGAAC-AATTACTAAAATAAT-CTAAAATACATGAAAATACATAAGTACAGC
* * *
1588805 TAAATCATTGAA-ATTTACTAAAATAATGCAAAAATACATGAAATTACATAA-TAACAGC
1 TAAATCA-TGAACAATTACTAAAATAAT-CTAAAATACATGAAAATACATAAGT-ACAGC
1588863 TAAATCATGAACAATTACTAAAATAATCTTAAAAT
1 TAAATCATGAACAATTACTAAAATAATC-TAAAAT
1588898 GCTTAAAATT
Statistics
Matches: 75, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
57 6 0.08
58 66 0.88
59 1 0.01
60 2 0.03
ACGTcount: A:0.52, C:0.12, G:0.07, T:0.29
Consensus pattern (57 bp):
TAAATCATGAACAATTACTAAAATAATCTAAAATACATGAAAATACATAAGTACAGC
Found at i:1588981 original size:58 final size:58
Alignment explanation
Indices: 1588919--1589031 Score: 140
Period size: 58 Copynumber: 1.9 Consensus size: 58
1588909 TATAAATGAT
* * * *
1588919 CTTAAAACAAAGCAAAATA-CTAGAGTAA-TCCTAAAATGCATGAAGTTGCATAATAACC
1 CTTAAAAC-AAGAAAAATAGCTAAAGTAACTCC-AAAATGCATGAAATTACATAATAACC
* *
1588977 CTTAAATCATGAAAAATAGCTAAAGTAACTCCAAAATGCATGAAATTACATAATA
1 CTTAAAACAAGAAAAATAGCTAAAGTAACTCCAAAATGCATGAAATTACATAATA
1589032 GTAACTAAGA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
57 8 0.17
58 36 0.77
59 3 0.06
ACGTcount: A:0.50, C:0.16, G:0.11, T:0.24
Consensus pattern (58 bp):
CTTAAAACAAGAAAAATAGCTAAAGTAACTCCAAAATGCATGAAATTACATAATAACC
Found at i:1589170 original size:29 final size:28
Alignment explanation
Indices: 1589136--1589228 Score: 70
Period size: 29 Copynumber: 3.2 Consensus size: 28
1589126 GGATTATGAA
1589136 AAATGACTTTAATATCTTTAAAGTGCATG
1 AAATGACTTTAATATCTTTAAA-TGCATG
*
1589165 AAATGA-TATAATA-CTTTTAAAAT-CATAG
1 AAATGACTTTAATATC-TTT-AAATGCAT-G
*
1589193 ATAATGAC-TTAA-ATCTACCTAAATGCATG
1 A-AATGACTTTAATATCT--TTAAATGCATG
1589222 AAATGAC
1 AAATGAC
1589229 ATAGTAATCT
Statistics
Matches: 52, Mismatches: 3, Indels: 19
0.70 0.04 0.26
Matches are distributed among these distances:
27 4 0.08
28 20 0.38
29 24 0.46
30 4 0.08
ACGTcount: A:0.44, C:0.12, G:0.11, T:0.33
Consensus pattern (28 bp):
AAATGACTTTAATATCTTTAAATGCATG
Found at i:1592955 original size:14 final size:14
Alignment explanation
Indices: 1592936--1592964 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1592926 GTAATAAATA
1592936 ATTAATTTTTTTAT
1 ATTAATTTTTTTAT
1592950 ATTAATTTTTTTAT
1 ATTAATTTTTTTAT
1592964 A
1 A
1592965 AATCTGATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
ATTAATTTTTTTAT
Found at i:1609080 original size:28 final size:28
Alignment explanation
Indices: 1609049--1609207 Score: 146
Period size: 28 Copynumber: 5.8 Consensus size: 28
1609039 AAACTTAGTA
*
1609049 TAAAAAGTTTCATTAAAAATTTTATTTG
1 TAAAAAGTTTAATTAAAAATTTTATTTG
* * * * *
1609077 TAAAAAATTGAATTAAAAAAATTTATATA
1 TAAAAAGTTTAATT-AAAAATTTTATTTG
*
1609106 TAAAAGGTTTAATTAAAAATTTTATTTG
1 TAAAAAGTTTAATTAAAAATTTTATTTG
* * * *
1609134 TTAAAA-TTTAATTGAAAATTCTA--TA
1 TAAAAAGTTTAATTAAAAATTTTATTTG
* *
1609159 CAACAAGTTTAATTAAAAATTTTATTTTG
1 TAAAAAGTTTAATTAAAAATTTTA-TTTG
*
1609188 TAAAAA-TTTAGTTAAAAATT
1 TAAAAAGTTTAATTAAAAATT
1609208 AATTATGGTA
Statistics
Matches: 100, Mismatches: 26, Indels: 10
0.74 0.19 0.07
Matches are distributed among these distances:
25 4 0.04
26 15 0.15
27 15 0.15
28 39 0.39
29 27 0.27
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.43
Consensus pattern (28 bp):
TAAAAAGTTTAATTAAAAATTTTATTTG
Found at i:1609108 original size:57 final size:54
Alignment explanation
Indices: 1609047--1609208 Score: 184
Period size: 57 Copynumber: 3.0 Consensus size: 54
1609037 AAAAACTTAG
*
1609047 TATAAAAAGTTTCATTAAAAATTTTATTTGTAAAAAATTGAATTAAAAAAATTTATA
1 TATAAAAAGTTTAATTAAAAATTTTATTTGTAAAAAATTGAATT--AAAAA-TTATA
* * * * *
1609104 TATAAAAGGTTTAATTAAAAATTTTATTTGT-TAAAATTTAATTGAAAATTCTA
1 TATAAAAAGTTTAATTAAAAATTTTATTTGTAAAAAATTGAATTAAAAATTATA
* * * *
1609157 TACAACAAGTTTAATTAAAAATTTTATTTTGT-AAAAATTTAGTTAAAAATTA
1 TATAAAAAGTTTAATTAAAAATTTTA-TTTGTAAAAAATTGAATTAAAAATTA
1609209 ATTATGGTAT
Statistics
Matches: 91, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
53 27 0.30
54 25 0.27
56 10 0.11
57 29 0.32
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (54 bp):
TATAAAAAGTTTAATTAAAAATTTTATTTGTAAAAAATTGAATTAAAAATTATA
Found at i:1609182 original size:53 final size:53
Alignment explanation
Indices: 1609051--1609207 Score: 190
Period size: 54 Copynumber: 2.9 Consensus size: 53
1609041 ACTTAGTATA
* * *
1609051 AAAAGTTTCATTAAAAATTTTATTTGTAAAAAATTGAATTAAAAAAATTTATATAT
1 AAAAGTTTAATTAAAAATTTTATTTGT-AAAAATTTAATT--AAAAATTTATACAT
* *
1609107 AAAAGGTTTAATTAAAAATTTTATTTGTTAAAATTTAATTGAAAATTCTATACA-
1 AAAA-GTTTAATTAAAAATTTTATTTGTAAAAATTTAATTAAAAATT-TATACAT
* *
1609161 ACAAGTTTAATTAAAAATTTTATTTTGTAAAAATTTAGTTAAAAATT
1 AAAAGTTTAATTAAAAATTTTA-TTTGTAAAAATTTAATTAAAAATT
1609208 AATTATGGTA
Statistics
Matches: 89, Mismatches: 9, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
53 18 0.20
54 30 0.34
55 5 0.06
56 14 0.16
57 22 0.25
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.43
Consensus pattern (53 bp):
AAAAGTTTAATTAAAAATTTTATTTGTAAAAATTTAATTAAAAATTTATACAT
Found at i:1610903 original size:27 final size:27
Alignment explanation
Indices: 1610833--1610903 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
1610823 AAAAATCACC
* *
1610833 TTTTATTTGTCAAAAACAGTGGTTATT
1 TTTTATTTGTCAAAAATAGTAGTTATT
*
1610860 TTGTATTTGTCAAAAATAGTAGTT-TCT
1 TTTTATTTGTCAAAAATAGTAGTTAT-T
1610887 TTTTATTTGTCAAAAAT
1 TTTTATTTGTCAAAAAT
1610904 GATGACATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
26 1 0.03
27 38 0.97
ACGTcount: A:0.31, C:0.07, G:0.13, T:0.49
Consensus pattern (27 bp):
TTTTATTTGTCAAAAATAGTAGTTATT
Found at i:1615424 original size:27 final size:27
Alignment explanation
Indices: 1615393--1615459 Score: 100
Period size: 27 Copynumber: 2.5 Consensus size: 27
1615383 CATTTGTTTC
1615393 TCAAAAATGGTGGTTAT-TTTGTATTTG
1 TCAAAAATGGTGGTT-TCTTTGTATTTG
* *
1615420 TCAAAAATAGTGGTTTCTTTTTATTTG
1 TCAAAAATGGTGGTTTCTTTGTATTTG
1615447 TCAAAAATGGTGG
1 TCAAAAATGGTGG
1615460 CATGTTATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
26 1 0.03
27 35 0.97
ACGTcount: A:0.28, C:0.06, G:0.21, T:0.45
Consensus pattern (27 bp):
TCAAAAATGGTGGTTTCTTTGTATTTG
Found at i:1620332 original size:161 final size:160
Alignment explanation
Indices: 1619990--1620443 Score: 698
Period size: 161 Copynumber: 2.8 Consensus size: 160
1619980 GAAAATATTC
* * *
1619990 AATTTTATTTTATTTTTGAAAATACCA-TTCATACCCTAATGAAAGCTTGAAAGGATACGAAAGA
1 AATTTTA-TTTATTTTTGAAAATATCATTTCATACCCTAATGGAAGCTTGAAAGAATACGAAAG-
* *
1620054 TTTTTTGAAATCTTTTATACTCCTACGGATGCCCATAGGAATATAAAAGATTAGAAAAAATAAAT
64 GTTTTTGAAATCTTTTATACTCCTATGGATG-CCATAGGAATATAAAAGATTA-AAAAAATAAAT
1620119 ATTAGAATCTATCCCAATAATACCAATTTAATTT
127 ATTAGAATCTATCCCAATAATACCAATTTAATTT
* * *
1620153 AATTTTATTTATTTTTGAAAATATCATTTTATATCCTAATGGAAGCCTGAAAGAATACGAAAGGT
1 AATTTTATTTATTTTTGAAAATATCATTTCATACCCTAATGGAAGCTTGAAAGAATACGAAAGGT
1620218 TTTTGAAATCTTTTATA-TCCCTATGGATGTCCATAGGAATATAAAAGATTAAAAAAATAAATAT
66 TTTTGAAATCTTTTATACT-CCTATGGATG-CCATAGGAATATAAAAGATTAAAAAAATAAATAT
*
1620282 TAGAATTTATCCTC-ATAATACCAATTTAATTT
129 TAGAATCTATCC-CAATAATACCAATTTAATTT
* *
1620314 TATTTTATTTATTTTTGAAAATATCATTTCGTACCCTAATGGAAGCTTGAAAGAATACGAAAGGT
1 AATTTTATTTATTTTTGAAAATATCATTTCATACCCTAATGGAAGCTTGAAAGAATACGAAAGGT
* *
1620379 TTTTGAAATCTTTTATACTCCTATAGATGCTCACAGGAATATAAAAGATTAAAAAAATAAATATT
66 TTTTGAAATCTTTTATACTCCTATGGATGC-CATAGGAATATAAAAGATTAAAAAAATAAATATT
1620444 GTTTAATTTT
Statistics
Matches: 269, Mismatches: 17, Indels: 12
0.90 0.06 0.04
Matches are distributed among these distances:
160 1 0.00
161 162 0.60
162 68 0.25
163 38 0.14
ACGTcount: A:0.41, C:0.12, G:0.11, T:0.37
Consensus pattern (160 bp):
AATTTTATTTATTTTTGAAAATATCATTTCATACCCTAATGGAAGCTTGAAAGAATACGAAAGGT
TTTTGAAATCTTTTATACTCCTATGGATGCCATAGGAATATAAAAGATTAAAAAAATAAATATTA
GAATCTATCCCAATAATACCAATTTAATTT
Found at i:1621246 original size:2 final size:2
Alignment explanation
Indices: 1621239--1621277 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1621229 AACTTGAAAA
1621239 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1621278 CATGCTGATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1622266 original size:163 final size:161
Alignment explanation
Indices: 1622065--1623053 Score: 906
Period size: 162 Copynumber: 6.1 Consensus size: 161
1622055 AAATTCAAGG
* * *
1622065 AAAAAATTCAAAATACATGGAAATAAATGAATTTTTGAAAAGTAAATTACTATGAAATAAATAAT
1 AAAAAATTCAAAAT-TATGGAAATAAATGAATTTTTGAAAAGTAAATTAATATAAAATAAATAAT
* * *
1622130 AACATTTAATGAATTTTAAAAATTAAAAACCAAGAAAATTCCCTCAAAAAAATTTACGGAGTAGA
65 AATATTTAATGAATTTTAAAAATTAAAAA-CAAGAAAATTCCCTCGAAAAAATTTACGGAGTAAA
* *
1622195 AAACTCCATATTTCGAAAAAGAGGAATTTCATGA
129 AAACTCCGTATTTCGAAAAAAAGGAATTTCA-GA
* * * * * * *
1622229 AAAAAATT-AAGATGTATGGAAATGAATGAAATTTTGAAAACTGATTTAATATGAAATAAATAAT
1 AAAAAATTCAAAAT-TATGGAAATAAATGAATTTTTGAAAAGTAAATTAATATAAAATAAATAAT
* * *
1622293 AATATTT-ATGAATTTTAAACATTAAAAACCAAGAAAAATAT-TC-CGAAAAAATTTACAGAGTA
65 AATATTTAATGAATTTTAAAAATTAAAAA-CAAG-AAAAT-TCCCTCGAAAAAATTTACGGAGTA
* * * *
1622355 TAAAACTCTGTATTTCG-AAAAAAGAGAATTTTAAGG
127 AAAAACTCCGTATTTCGAAAAAAAG-GAA-TTTCAGA
* * *
1622391 AAAAAATTCAAAATTTATGGAAATCAATGAATTTTTGAAACGTAAATTAATATAAAATAGATAAT
1 AAAAAATTCAAAA-TTATGGAAATAAATGAATTTTTGAAAAGTAAATTAATATAAAATAAATAAT
* * * * * *
1622456 AATATTTGATAAATTTTAAAAAATTTTTAAAAA-AAGAAAAATCTCTCCAAAAAATTTACGAAGT
65 AATATTTAATGAATTTT-AAAAA---TTAAAAACAAGAAAATTCCCTCGAAAAAATTTACGGAGT
* * * *
1622520 AAAAAATTCTGCATTTC-AAAAAAAAGAATTT-A-A
126 AAAAAACTCCGTATTTCGAAAAAAAGGAATTTCAGA
* * * * * *
1622553 AAAAAATTCAAAACTTATGAAAATAAATGAATTTTTAAAAATTGAATTAACATGAAATAAATAAT
1 AAAAAATTCAAAA-TTATGGAAATAAATGAATTTTTGAAAAGTAAATTAATATAAAATAAATAAT
*
1622618 AATATTTAATGAATTTTAAAAA-T---AA-AA-AAAA-TCCCCCTGAAAAAATTTACGGAGTAAA
65 AATATTTAATGAATTTTAAAAATTAAAAACAAGAAAATTCCCTC-GAAAAAATTTACGGAGTAAA
*
1622676 AAACTTCGTATTTC-AAAAAAAGGGAAATTTCAAGA
129 AAACTCCGTATTTCGAAAAAAA-GG-AATTTC-AGA
* * * ** *
1622711 AAACAAGTCAAAATTTTTGGAAACGAATGAATTTTTG-AAAGCTGAATTAATATAAAATAAATAA
1 AAAAAATTCAAAA-TTATGGAAATAAATGAATTTTTGAAAAG-TAAATTAATATAAAATAAATAA
* * * * *
1622775 TAATATTTAATGAATTTTAAAAATCAAAAAACAGGAAAAATCCGCCCAAAAAAATTTACGGAGTA
64 TAATATTTAATGAATTTTAAAAAT-TAAAAACAAGAAAATTCC-CTCGAAAAAATTTACGGAGTA
* * * * *
1622840 GAAAACTTCGTATTTTGGAAAAGCAA--ATTTTCA-A
127 AAAAACTCCGTA-TTTCGAAAA-AAAGGAATTTCAGA
* * *
1622874 AGAAAAATTGAAAATTCATGGAAATAAATGAATTTTTGAAAACTAAATTACTATAAAATAAATAA
1 A-AAAAATTCAAAATT-ATGGAAATAAATGAATTTTTGAAAAGTAAATTAATATAAAATAAATAA
** * *
1622939 TAATATTTTGGTGAATTTTAAAAATCAAAAAATAAGAAAAATTCCCTCGAAAAAATTTACGGAGT
64 TAATA-TTTAATGAATTTTAAAAAT-TAAAAACAAG-AAAATTCCCTCGAAAAAATTTACGGAGT
* ** *
1623004 AAAAAACTTCG-ATTTAAAAAAAAAGAAAATTTCAAGA
126 AAAAAACTCCGTATTTCGAAAAAAAG-GAATTTC-AGA
1623041 AAAAAATTCAAAA
1 AAAAAATTCAAAA
1623054 ATTTATAAAA
Statistics
Matches: 681, Mismatches: 101, Indels: 84
0.79 0.12 0.10
Matches are distributed among these distances:
152 4 0.01
153 39 0.06
154 5 0.01
155 5 0.01
157 5 0.01
158 73 0.11
161 11 0.02
162 140 0.21
163 129 0.19
164 77 0.11
165 84 0.12
166 88 0.13
167 8 0.01
168 11 0.02
169 2 0.00
ACGTcount: A:0.53, C:0.08, G:0.10, T:0.29
Consensus pattern (161 bp):
AAAAAATTCAAAATTATGGAAATAAATGAATTTTTGAAAAGTAAATTAATATAAAATAAATAATA
ATATTTAATGAATTTTAAAAATTAAAAACAAGAAAATTCCCTCGAAAAAATTTACGGAGTAAAAA
ACTCCGTATTTCGAAAAAAAGGAATTTCAGA
Found at i:1622933 original size:484 final size:486
Alignment explanation
Indices: 1622053--1623123 Score: 1208
Period size: 484 Copynumber: 2.2 Consensus size: 486
1622043 CGGAGAAAGG
* * * * * * *
1622053 AGAAATTCAAGGAAAAAATTCAAAATACATGGAAATAAATGAATTTTTGAAAAGTAAATT-ACTA
1 AGAAATTTAAGAAAAAAATTCAAAAT-TATGAAAATAAATGAATTTTTAAAAACTGAATTAAC-A
* *
1622117 TGAAATAAATAATAACATTTAATGAATTTTAAAAATTAAAAACCAAGAAAATTCCCTCAAAAAAA
64 TGAAATAAATAATAATATTTAATGAATTTTAAAAATT--AAA-CAAGAAAATCCCCTCAAAAAAA
* * * * *
1622182 TTTACGGAGTAGAAAACTCCATATTTCGAAAAAGAGGAATTTCATGAAAAAAATTAAGATGTATG
126 TTTACGGAGTAAAAAACTCCATATTTCAAAAAAGAGGAATTTCAAGAAAAAAATCAAAATGTATG
* * *
1622247 GAAATGAATGAAATTTTGAAAACTGATTTAATATGAAATAAATAATAATATTTATGAATTTTAAA
191 GAAACGAATGAAATTTTGAAAACTGAATTAATATAAAATAAATAATAATATTTATGAATTTTAAA
* * * ** * *
1622312 CATTAAAAACCAAGAAAAATATTCCGAAAAAATTTACAGAGTATAAAACTCTGTATTTCGAAAAA
256 AATCAAAAAACAAGAAAAATAGCCCAAAAAAATTTACAGAGTAGAAAACTCTGTATTTCGAAAAA
* * *
1622377 AGAGAATTTTAAGGAAAAAATTCAAAATTTATGGAAATCAATGAATTTTTGAAACGTAAATTAAT
321 AGAGAATTTTAAAGAAAAAATTCAAAATTCATGGAAATAAATGAATTTTTGAAACGTAAATTAAT
* ** *
1622442 ATAAAATAGATAATAATA-TTTGATAAATTTTAAAAAATTTTTAAAAA-AAGAAAAA-TCTCTCC
386 ATAAAATAAATAATAATATTTTGATAAATTTT-AAAAA--TCAAAAAATAAGAAAAATTCCCTCC
*
1622504 AAAAAATTTACGAAGTAAAAAA-TTCTGCATTTCAAAAAAA
448 AAAAAATTTACGAAGTAAAAAACTTC-G-ATTTAAAAAAAA
*
1622544 AG-AATTT-A-AAAAAAATTCAAAACTTATGAAAATAAATGAATTTTTAAAAATTGAATTAACAT
1 AGAAATTTAAGAAAAAAATTCAAAA-TTATGAAAATAAATGAATTTTTAAAAACTGAATTAACAT
*
1622606 GAAATAAATAATAATATTTAATGAATTTTAAAAA-T-AA-AA-AAAATCCCC-CTGAAAAAATTT
65 GAAATAAATAATAATATTTAATGAATTTTAAAAATTAAACAAGAAAATCCCCTC-AAAAAAATTT
* * * * *
1622666 ACGGAGTAAAAAACTTCGTATTTCAAAAAA-AGGGAAATTTCAAGAAAACAAGTCAAAATTTTTG
129 ACGGAGTAAAAAACTCCATATTTCAAAAAAGA-GG-AATTTCAAGAAAA-AAATCAAAATGTATG
* *
1622730 GAAACGAATGAATTTTTGAAAGCTGAATTAATATAAAATAAATAATAATATTTAATGAATTTTAA
191 GAAACGAATGAAATTTTGAAAACTGAATTAATATAAAATAAATAATAATATTT-ATGAATTTTAA
* * * * *
1622795 AAATCAAAAAACAGGAAAAATCCGCCCAAAAAAATTTACGGAGTAGAAAACT-TCGTATTTTG-G
255 AAATCAAAAAACAAGAAAAAT-AGCCCAAAAAAATTTACAGAGTAGAAAACTCT-GTATTTCGAA
*
1622858 AAAAGCA-AATTTTCAAAG-AAAAATTGAAAATTCATGGAAATAAATGAATTTTTGAAAAC-TAA
318 AAAAG-AGAATTTT-AAAGAAAAAATTCAAAATTCATGGAAATAAATGAATTTTTG-AAACGTAA
* * *
1622920 ATTACTATAAAATAAATAATAATATTTTGGTGAATTTTAAAAATCAAAAAATAAGAAAAATTCCC
380 ATTAATATAAAATAAATAATAATATTTTGATAAATTTTAAAAATCAAAAAATAAGAAAAATTCCC
* *
1622985 TCGAAAAAATTTACGGAGTAAAAAACTTCGATTTAAAAAAAA
445 TCCAAAAAATTTACGAAGTAAAAAACTTCGATTTAAAAAAAA
* * * * * *
1623027 AGAAAATTTCAAGAAAAAAATTCAAAAATTTATAAAAATGAGTGAATTTTTTAGAACTGATTTAA
1 AG-AAATTT-AAGAAAAAAATTC-AAAA-TTATGAAAATAAATGAATTTTTAAAAACTGAATTAA
* * * * * *
1623092 TAAGAATTAAATTATAATATTTGAGGAATTTT
62 CATGAAATAAATAATAATATTTAATGAATTTT
1623124 GAGGTTTAAA
Statistics
Matches: 493, Mismatches: 65, Indels: 46
0.82 0.11 0.08
Matches are distributed among these distances:
480 2 0.00
481 45 0.09
482 20 0.04
483 79 0.16
484 132 0.27
485 58 0.12
487 2 0.00
488 86 0.17
489 63 0.13
490 4 0.01
491 2 0.00
ACGTcount: A:0.52, C:0.08, G:0.10, T:0.30
Consensus pattern (486 bp):
AGAAATTTAAGAAAAAAATTCAAAATTATGAAAATAAATGAATTTTTAAAAACTGAATTAACATG
AAATAAATAATAATATTTAATGAATTTTAAAAATTAAACAAGAAAATCCCCTCAAAAAAATTTAC
GGAGTAAAAAACTCCATATTTCAAAAAAGAGGAATTTCAAGAAAAAAATCAAAATGTATGGAAAC
GAATGAAATTTTGAAAACTGAATTAATATAAAATAAATAATAATATTTATGAATTTTAAAAATCA
AAAAACAAGAAAAATAGCCCAAAAAAATTTACAGAGTAGAAAACTCTGTATTTCGAAAAAAGAGA
ATTTTAAAGAAAAAATTCAAAATTCATGGAAATAAATGAATTTTTGAAACGTAAATTAATATAAA
ATAAATAATAATATTTTGATAAATTTTAAAAATCAAAAAATAAGAAAAATTCCCTCCAAAAAATT
TACGAAGTAAAAAACTTCGATTTAAAAAAAA
Found at i:1623159 original size:165 final size:160
Alignment explanation
Indices: 1622058--1623160 Score: 814
Period size: 162 Copynumber: 6.8 Consensus size: 160
1622048 AAAGGAGAAA
* ** * * * *
1622058 TTCAAGGAAAAAATTCAAAATACATGGAAATAAATGAATTTTTGAAAAGTAAATTACTATGAAAT
1 TTCAAGAAAAAAATTCAAAATTTATGGAAATGAATGAATTTTTG-AAACTGAATTA--ATAAAAT
* * * * *
1622123 AAATAATAACATTTAATGAATTTTAAAAATTAAAAACCAAGAAAATTCCCTCAAAAAAATTTACG
63 AAATAATAATATTTGAGGAATTTTAAAAATCAAAAAACAAGAAAATTCCC-CAAAAAAATTTACG
* * * ** *
1622188 GAGTAGAAAACTCCATATTT-CGAAAAAGAGGAAT
127 GAGTAAAAAACTTCGTATTTAAAAAAAAGA-AAAT
* * * * *
1622222 TTCATGAAAAAAATT-AAGATGTATGGAAATGAATGAAATTTTGAAAACTGATTTAATATGAAAT
1 TTCAAGAAAAAAATTCAAAATTTATGGAAATGAATGAATTTTTG-AAACTGAATTAATA--AAAT
* * * * * *
1622286 AAATAATAATATTT-ATGAATTTTAAACATTAAAAACCAAGAAAAATAT-TCCGAAAAAATTTAC
63 AAATAATAATATTTGAGGAATTTTAAAAATCAAAAAACAAG-AAAAT-TCCCCAAAAAAATTTAC
* * ** *
1622349 AGAGTATAAAAC-TCTGTATTTCGAAAAAAGAGAAT
126 GGAGTAAAAAACTTC-GTATTTAAAAAAAAGAAAAT
* * * *
1622384 TTTAAGGAAAAAATTCAAAATTTATGGAAATCAATGAATTTTTGAAACGTAAATTAATATAAAAT
1 TTCAAGAAAAAAATTCAAAATTTATGGAAATGAATGAATTTTTGAAAC-TGAATT-A-ATAAAAT
* ** ** *
1622449 AGATAATAATATTTGATAAATTTTAAAAAATTTTTAAAAA-AAGAAAAATCTCTCC-AAAAAATT
63 AAATAATAATATTTGAGGAATTTT-AAAAA--TCAAAAAACAAG-AAAAT-TCCCCAAAAAAATT
* *
1622512 TACGAAGTAAAAAA-TTCTGCATTTCAAAAAAAAG--AAT
123 TACGGAGTAAAAAACTTC-GTATTT-AAAAAAAAGAAAAT
* * * * * *
1622549 TT--A-AAAAAAATTCAAAACTTATGAAAATAAATGAATTTTTAAAAATTGAATTAACATGAAAT
1 TTCAAGAAAAAAATTCAAAATTTATGGAAATGAATGAATTTTT-GAAACTGAATT-A-ATAAAAT
* * * *
1622611 AAATAATAATATTTAATGAATTTTAAAAAT-----AA-AA-AAAATCCCCCTGAAAAAATTTACG
63 AAATAATAATATTTGAGGAATTTTAAAAATCAAAAAACAAGAAAATTCCCC-AAAAAAATTTACG
* *
1622669 GAGTAAAAAACTTCGTATTTCAAAAAAAGGGAAAT
127 GAGTAAAAAACTTCGTATTT-AAAAAAAAGAAAAT
* * * *
1622704 TTCAAGAAAACAAGTCAAAATTTTTGGAAACGAATGAATTTTTGAAAGCTGAATTAATATAAAAT
1 TTCAAGAAAAAAATTCAAAATTTATGGAAATGAATGAATTTTTGAAA-CTGAATT-A-ATAAAAT
* * * *
1622769 AAATAATAATATTTAATGAATTTTAAAAATCAAAAAACAGGAAAAATCCGCCCAAAAAAATTTAC
63 AAATAATAATATTTGAGGAATTTTAAAAATCAAAAAACAAG-AAAATTC-CCCAAAAAAATTTAC
* *** *
1622834 GGAGTAGAAAACTTCGTATTT-TGGAAAAGCAAATT
126 GGAGTAAAAAACTTCGTATTTAAAAAAAAG-AAAAT
* * * * *
1622869 TTCAA-AGAAAAATTGAAAATTCATGGAAATAAATGAATTTTTGAAAACTAAATTACTATAAAAT
1 TTCAAGAAAAAAATTCAAAATTTATGGAAATGAATGAATTTTTG-AAACTGAATTA--ATAAAAT
* *
1622933 AAATAATAATATTTTG-GTGAATTTTAAAAATCAAAAAATAAGAAAAATTCCCTCGAAAAAATTT
63 AAATAATAATA-TTTGAG-GAATTTTAAAAATCAAAAAACAAG-AAAATTCCC-CAAAAAAATTT
1622997 ACGGAGTAAAAAACTTCG-ATTTAAAAAAAAAGAAAAT
124 ACGGAGTAAAAAACTTCGTATTT-AAAAAAAAGAAAAT
** * * *
1623034 TTCAAGAAAAAAATTCAAAAATTTATAAAAATGAGTGAATTTTTTAGAACTGATTTAATAAGAAT
1 TTCAAGAAAAAAATTC-AAAATTTATGGAAATGAATGAATTTTTGA-AACTGAATTAATAA-AA-
* * *** * **
1623099 TAAATTATAATATTTGAGGAATTTTGAGGTTTAAAACCCAAGAAAATTCCACCAAAAAAATT
62 TAAATAATAATATTTGAGGAATTTTAAAAATCAAAAAACAAGAAAATTCC-CCAAAAAAATT
1623161 ATGAAAAAAA
Statistics
Matches: 769, Mismatches: 119, Indels: 101
0.78 0.12 0.10
Matches are distributed among these distances:
151 3 0.00
152 5 0.01
153 35 0.05
154 7 0.01
155 5 0.01
157 4 0.01
158 74 0.10
159 1 0.00
161 8 0.01
162 139 0.18
163 114 0.15
164 89 0.12
165 112 0.15
166 112 0.15
167 61 0.08
ACGTcount: A:0.52, C:0.08, G:0.10, T:0.29
Consensus pattern (160 bp):
TTCAAGAAAAAAATTCAAAATTTATGGAAATGAATGAATTTTTGAAACTGAATTAATAAAATAAA
TAATAATATTTGAGGAATTTTAAAAATCAAAAAACAAGAAAATTCCCCAAAAAAATTTACGGAGT
AAAAAACTTCGTATTTAAAAAAAAGAAAAT
Found at i:1624933 original size:20 final size:20
Alignment explanation
Indices: 1624905--1624979 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
1624895 TTTTACCTTG
1624905 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
1624925 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
1624945 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
1624965 ATGTATCGATACATT
1 ATGTATCGATACATT
1624980 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1624972 original size:40 final size:39
Alignment explanation
Indices: 1624905--1624982 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
1624895 TTTTACCTTG
* *
1624905 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
1624945 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
1624983 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:1625913 original size:23 final size:23
Alignment explanation
Indices: 1625877--1625934 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
1625867 AGCCTTTGAC
1625877 CATGCA-TTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
1625899 CATGCATTTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
1625922 CATG--TTTTTTTTA
1 CATGCATTTTTTTTA
1625935 ACATGTCCAG
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
21 9 0.26
22 6 0.17
23 20 0.57
ACGTcount: A:0.17, C:0.09, G:0.09, T:0.66
Consensus pattern (23 bp):
CATGCATTTTTTTTATTATGTTT
Found at i:1633886 original size:13 final size:13
Alignment explanation
Indices: 1633870--1633894 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1633860 AGCTTTAATC
1633870 TGTTTCTTTGAAT
1 TGTTTCTTTGAAT
1633883 TGTTTCTTTGAA
1 TGTTTCTTTGAA
1633895 CCCTGATTAT
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:0.16, C:0.08, G:0.16, T:0.60
Consensus pattern (13 bp):
TGTTTCTTTGAAT
Found at i:1636291 original size:17 final size:17
Alignment explanation
Indices: 1636265--1636297 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1636255 CAATTTCACA
1636265 TATATATATATATATTT
1 TATATATATATATATTT
*
1636282 TATATTTATATATATT
1 TATATATATATATATT
1636298 AATATGTCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TATATATATATATATTT
Found at i:1636699 original size:45 final size:45
Alignment explanation
Indices: 1636649--1636738 Score: 153
Period size: 45 Copynumber: 2.0 Consensus size: 45
1636639 AACTAGTAGG
*
1636649 GAAAACGATACTTCTTCATTGTAGTAGATGTAATGTTACAGTTTA
1 GAAAACGATACTTCTTCATTGTAGTAGATGAAATGTTACAGTTTA
* *
1636694 GAAAACTATATTTCTTCATTGTAGTAGATGAAATGTTACAGTTTA
1 GAAAACGATACTTCTTCATTGTAGTAGATGAAATGTTACAGTTTA
1636739 TCTACTCATT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.39
Consensus pattern (45 bp):
GAAAACGATACTTCTTCATTGTAGTAGATGAAATGTTACAGTTTA
Found at i:1637079 original size:17 final size:18
Alignment explanation
Indices: 1637042--1637079 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
1637032 TATATATATA
* *
1637042 TATATGCTTATAATTATT
1 TATATACTTATAATTAGT
1637060 TATATACTTA-AATTAGT
1 TATATACTTATAATTAGT
1637077 TAT
1 TAT
1637080 CTCAAAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.53
Consensus pattern (18 bp):
TATATACTTATAATTAGT
Found at i:1637828 original size:24 final size:26
Alignment explanation
Indices: 1637782--1637829 Score: 64
Period size: 24 Copynumber: 1.9 Consensus size: 26
1637772 GTAATAAATA
* *
1637782 AATTATTATAAATTGACTGAATATAT
1 AATTATTATAAATTGAATCAATATAT
1637808 AATT-TTAT-AATTGAATCAATAT
1 AATTATTATAAATTGAATCAATAT
1637830 CAATATTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 12 0.60
25 4 0.20
26 4 0.20
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (26 bp):
AATTATTATAAATTGAATCAATATAT
Found at i:1638693 original size:13 final size:12
Alignment explanation
Indices: 1638644--1638694 Score: 57
Period size: 12 Copynumber: 3.9 Consensus size: 12
1638634 ACCTTCACTG
1638644 TTTCAAATTGAA
1 TTTCAAATTGAA
*
1638656 TTTCAACATTTACTA
1 TTTCAA-ATTGA--A
1638671 TTTCAAATTGAA
1 TTTCAAATTGAA
1638683 TTTCAAAATTGA
1 TTTC-AAATTGA
1638695 CGGCACAGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
12 11 0.33
13 11 0.33
14 4 0.12
15 7 0.21
ACGTcount: A:0.39, C:0.12, G:0.06, T:0.43
Consensus pattern (12 bp):
TTTCAAATTGAA
Found at i:1638716 original size:12 final size:12
Alignment explanation
Indices: 1638697--1638734 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
1638687 AAAATTGACG
1638697 GCACAGTTGGCA
1 GCACAGTTGGCA
*
1638709 GTACAGTTGGCA
1 GCACAGTTGGCA
1638721 GCACAGTTGGCA
1 GCACAGTTGGCA
1638733 GC
1 GC
1638735 CTTTGTTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.24, C:0.24, G:0.34, T:0.18
Consensus pattern (12 bp):
GCACAGTTGGCA
Found at i:1643458 original size:13 final size:12
Alignment explanation
Indices: 1643409--1643459 Score: 57
Period size: 12 Copynumber: 3.9 Consensus size: 12
1643399 ACCTTCACCG
1643409 TTTCAAATTGAA
1 TTTCAAATTGAA
*
1643421 TTTCAACATTTACTA
1 TTTCAA-ATTGA--A
1643436 TTTCAAATTGAA
1 TTTCAAATTGAA
1643448 TTTCAAAATTGA
1 TTTC-AAATTGA
1643460 CGGCACAGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
12 11 0.33
13 11 0.33
14 4 0.12
15 7 0.21
ACGTcount: A:0.39, C:0.12, G:0.06, T:0.43
Consensus pattern (12 bp):
TTTCAAATTGAA
Found at i:1643479 original size:12 final size:12
Alignment explanation
Indices: 1643456--1643499 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
1643446 AATTTCAAAA
*
1643456 TTGACGGCACAG
1 TTGACAGCACAG
**
1643468 TTGGTAGCACAG
1 TTGACAGCACAG
1643480 TTGACAGCACAG
1 TTGACAGCACAG
1643492 TTGACAGC
1 TTGACAGC
1643500 CTTTGTTTTC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.27, C:0.23, G:0.30, T:0.20
Consensus pattern (12 bp):
TTGACAGCACAG
Found at i:1643565 original size:16 final size:16
Alignment explanation
Indices: 1643544--1643575 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1643534 TTTCTTCTTT
1643544 CACATGGGCTGAACCC
1 CACATGGGCTGAACCC
*
1643560 CACATGGGCTGGACCC
1 CACATGGGCTGAACCC
1643576 TACAGATACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.22, C:0.38, G:0.28, T:0.12
Consensus pattern (16 bp):
CACATGGGCTGAACCC
Found at i:1644549 original size:23 final size:20
Alignment explanation
Indices: 1644519--1644569 Score: 59
Period size: 23 Copynumber: 2.5 Consensus size: 20
1644509 AATAATAAAA
*
1644519 TAAGAAAATTATTTATTTTATT
1 TAAGAAAAATATTT-TTTT-TT
1644541 TAAGTAAAAATATTTTTTTTT
1 TAAG-AAAAATATTTTTTTTT
1644562 TAA-AAAAA
1 TAAGAAAAA
1644570 AAGAAGAAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 5 0.19
21 5 0.19
22 8 0.30
23 9 0.33
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (20 bp):
TAAGAAAAATATTTTTTTTT
Found at i:1646188 original size:2 final size:2
Alignment explanation
Indices: 1646181--1646225 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1646171 TTCATGTTTC
1646181 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1646223 AT A
1 AT A
1646226 GTACAGATTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1651704 original size:2 final size:2
Alignment explanation
Indices: 1651697--1651722 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1651687 AAAGGTTCAC
1651697 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1651723 GTAACGTTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1652187 original size:24 final size:24
Alignment explanation
Indices: 1652153--1652198 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1652143 TGTCTCTCTC
* *
1652153 TAACTTGCAGATCATAAGCCACTT
1 TAACTTACAGATAATAAGCCACTT
1652177 TAACTTACAGATAATAAGCCAC
1 TAACTTACAGATAATAAGCCAC
1652199 CACTTCTCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.39, C:0.24, G:0.11, T:0.26
Consensus pattern (24 bp):
TAACTTACAGATAATAAGCCACTT
Found at i:1657582 original size:24 final size:22
Alignment explanation
Indices: 1657553--1657614 Score: 56
Period size: 24 Copynumber: 2.7 Consensus size: 22
1657543 TTTATTTTAT
1657553 TTTTAAAAAATTAATAAAATTAAA
1 TTTTAAAAAATTAATAAAATT--A
*
1657577 TTTTAATTTAAA-TAA-AAAATTA
1 TTTTAA--AAAATTAATAAAATTA
*
1657599 TTTTAAAAAATAAATA
1 TTTTAAAAAATTAATA
1657615 TTTGATACAT
Statistics
Matches: 31, Mismatches: 3, Indels: 10
0.70 0.07 0.23
Matches are distributed among these distances:
20 3 0.10
21 2 0.06
22 8 0.26
24 12 0.39
25 3 0.10
26 3 0.10
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTTAAAAAATTAATAAAATTA
Found at i:1657980 original size:12 final size:14
Alignment explanation
Indices: 1657970--1658137 Score: 76
Period size: 13 Copynumber: 12.7 Consensus size: 14
1657960 TTGATAATTT
1657970 TAAATATAATTATA
1 TAAATATAATTATA
1657984 TAAATATAA-TATA
1 TAAATATAATTATA
* * *
1657997 TATATAAAATAATA
1 TAAATATAATTATA
1658011 T-AA-AT-ATTATA
1 TAAATATAATTATA
*
1658022 T-AATATAAATATA
1 TAAATATAATTATA
** * *
1658035 TAGTTAAAATT-TT
1 TAAATATAATTATA
1658048 TATAATATAAATTAT-
1 TA-AATAT-AATTATA
* *
1658063 T-AATATATTTAAA
1 TAAATATAATTATA
* *
1658076 TATATAT-ATAATA
1 TAAATATAATTATA
1658089 TAAA-AT-ATT-T-
1 TAAATATAATTATA
1658099 TAAATATAATTATA
1 TAAATATAATTATA
* *
1658113 -ATATTATAAAATATA
1 TA-AATAT-AATTATA
1658128 TAAATATAAT
1 TAAATATAAT
1658138 ATAAATTATT
Statistics
Matches: 111, Mismatches: 27, Indels: 32
0.65 0.16 0.19
Matches are distributed among these distances:
10 4 0.04
11 11 0.10
12 14 0.13
13 35 0.32
14 30 0.27
15 15 0.14
16 2 0.02
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (14 bp):
TAAATATAATTATA
Found at i:1658010 original size:16 final size:16
Alignment explanation
Indices: 1657981--1658034 Score: 72
Period size: 16 Copynumber: 3.3 Consensus size: 16
1657971 AAATATAATT
*
1657981 ATATAAATATAATATAT
1 ATATAAA-ATAATATAA
1657998 ATATAAAATAATATAA
1 ATATAAAATAATATAA
* *
1658014 ATATTATATAATATAA
1 ATATAAAATAATATAA
1658030 ATATA
1 ATATA
1658035 TAGTTAAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
16 26 0.79
17 7 0.21
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
ATATAAAATAATATAA
Found at i:1658016 original size:27 final size:27
Alignment explanation
Indices: 1657981--1658140 Score: 98
Period size: 29 Copynumber: 5.6 Consensus size: 27
1657971 AAATATAATT
1657981 ATATAAATATAATATATATATAAAATA
1 ATATAAATATAATATATATATAAAATA
*
1658008 ATATAAATATTATATA-ATAT-AAATA
1 ATATAAATATAATATATATATAAAATA
* *
1658033 TATAGTTAAA-AT-TTTTATAATATAAATTATTA
1 -ATA--TAAATATAATATAT-ATATAAA--A-TA
1658065 ATATATTTAA-ATATATATATAATATAAAATA
1 ATATA---AATATA-ATATAT-ATATAAAATA
* *
1658096 TTTTAAATATAATTATAATATTATAAAAT-
1 ATATAAATATAA-TAT-ATA-TATAAAATA
1658125 ATATAAATATAATATA
1 ATATAAATATAATATA
1658141 AATTATTAAA
Statistics
Matches: 106, Mismatches: 9, Indels: 36
0.70 0.06 0.24
Matches are distributed among these distances:
25 5 0.05
26 10 0.09
27 18 0.17
28 14 0.13
29 21 0.20
30 10 0.09
31 9 0.08
32 7 0.07
34 12 0.11
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (27 bp):
ATATAAATATAATATATATATAAAATA
Found at i:1658042 original size:28 final size:27
Alignment explanation
Indices: 1657981--1658165 Score: 119
Period size: 27 Copynumber: 7.1 Consensus size: 27
1657971 AAATATAATT
*
1657981 ATATAAATATAATATATATATAAA-ATA
1 ATATAAATATTATATA-ATATAAATATA
1658008 ATATAAATATTATATAATATAAATAT-
1 ATATAAATATTATATAATATAAATATA
*
1658034 ATAGTTAAA-ATTTTTATAATATAAAT-T-
1 ATA--TAAATA-TTATATAATATAAATATA
*
1658061 AT-TAATATATT-TA-AATATATATATA
1 ATATAA-ATATTATATAATATAAATATA
* *
1658086 ATATAAAATATTTTA-AATATAATTATA
1 ATAT-AAATATTATATAATATAAATATA
* *
1658113 ATAT---TATAAAAT-ATATAAATATA
1 ATATAAATATTATATAATATAAATATA
* * *
1658136 ATATAAATTATTAAATTAT-TAAATTTA
1 ATATAAA-TATTATATAATATAAATATA
1658163 ATA
1 ATA
1658166 ATGATCGATA
Statistics
Matches: 130, Mismatches: 11, Indels: 34
0.74 0.06 0.19
Matches are distributed among these distances:
23 26 0.20
24 6 0.05
25 5 0.04
26 17 0.13
27 56 0.43
28 20 0.15
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.44
Consensus pattern (27 bp):
ATATAAATATTATATAATATAAATATA
Found at i:1658158 original size:27 final size:28
Alignment explanation
Indices: 1658048--1658165 Score: 129
Period size: 27 Copynumber: 4.2 Consensus size: 28
1658038 TTAAAATTTT
1658048 TATAATATAAATTATT-AATATATTTAAA
1 TATAATATAAATTATTAAATATA-TTAAA
* *
1658076 TAT-ATATATAA-TATAAAATATTTTAAA
1 TATAATATA-AATTATTAAATATATTAAA
*
1658103 TATAATTATAATATTATAAAATATA-TAAA
1 TATAA-TATAA-ATTATTAAATATATTAAA
1658132 TATAATATAAATTATTAAAT-TATTAAA
1 TATAATATAAATTATTAAATATATTAAA
*
1658159 TTTAATA
1 TATAATA
1658166 ATGATCGATA
Statistics
Matches: 78, Mismatches: 5, Indels: 15
0.80 0.05 0.15
Matches are distributed among these distances:
26 2 0.03
27 35 0.45
28 17 0.22
29 14 0.18
30 10 0.13
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (28 bp):
TATAATATAAATTATTAAATATATTAAA
Found at i:1658551 original size:21 final size:20
Alignment explanation
Indices: 1658527--1658569 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
1658517 TGATTTGTCA
*
1658527 AATTAAAATATAATATAAAAT
1 AATTAAAATAT-ATAAAAAAT
1658548 AATTAAAATATATAAAAAAT
1 AATTAAAATATATAAAAAAT
1658568 AA
1 AA
1658570 AAATATAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (20 bp):
AATTAAAATATATAAAAAAT
Found at i:1658556 original size:9 final size:10
Alignment explanation
Indices: 1658536--1658574 Score: 50
Period size: 9 Copynumber: 4.3 Consensus size: 10
1658526 AAATTAAAAT
1658536 ATAATATAAA
1 ATAATATAAA
1658546 ATAAT-TAAA
1 ATAATATAAA
1658555 AT-ATATAAA
1 ATAATATAAA
1658564 A-AATA-AAA
1 ATAATATAAA
1658572 ATA
1 ATA
1658575 TAACAAACAC
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
8 6 0.23
9 15 0.58
10 5 0.19
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
ATAATATAAA
Found at i:1658574 original size:17 final size:18
Alignment explanation
Indices: 1658539--1658576 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
1658529 TTAAAATATA
*
1658539 ATATAAAATAATTAAAAT
1 ATATAAAATAATAAAAAT
1658557 ATATAAAA-AATAAAAAT
1 ATATAAAATAATAAAAAT
1658574 ATA
1 ATA
1658577 ACAAACACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
ATATAAAATAATAAAAAT
Found at i:1659432 original size:18 final size:17
Alignment explanation
Indices: 1659405--1659438 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1659395 AAAATGACAA
*
1659405 TATTAGTACAATATATTT
1 TATTAATACAA-ATATTT
1659423 TATTAATACAAATATT
1 TATTAATACAAATATT
1659439 AAAAATTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (17 bp):
TATTAATACAAATATTT
Found at i:1659476 original size:28 final size:29
Alignment explanation
Indices: 1659416--1659468 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
1659406 ATTAGTACAA
*
1659416 TATATTTTATTAATACAAATATTAAAAAT
1 TATATTTTATTAATAAAAATATTAAAAAT
1659445 TATA-TTTATTAA-AAAAAT-TTAAAA
1 TATATTTTATTAATAAAAATATTAAAA
1659469 TACTTATACA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 6 0.26
27 5 0.22
28 8 0.35
29 4 0.17
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (29 bp):
TATATTTTATTAATAAAAATATTAAAAAT
Found at i:1663812 original size:12 final size:11
Alignment explanation
Indices: 1663779--1663809 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
1663769 CAACTTATAT
1663779 TTTATTTTTAA
1 TTTATTTTTAA
1663790 TTTATTTTTAA
1 TTTATTTTTAA
1663801 TTTATTTTT
1 TTTATTTTT
1663810 TAAAAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTATTTTTAA
Found at i:1663821 original size:15 final size:15
Alignment explanation
Indices: 1663803--1663831 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1663793 ATTTTTAATT
1663803 TATTTTTTAAAAATA
1 TATTTTTTAAAAATA
1663818 TATTTTTTAAAAAT
1 TATTTTTTAAAAAT
1663832 TTAATCACTT
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:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TATTTTTTAAAAATA
Found at i:1664585 original size:2 final size:2
Alignment explanation
Indices: 1664580--1664608 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1664570 CTTATATAGA
1664580 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1664609 ATAGACATAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1665588 original size:66 final size:65
Alignment explanation
Indices: 1665492--1665695 Score: 248
Period size: 66 Copynumber: 3.1 Consensus size: 65
1665482 TGACATTTGG
* *
1665492 TTAGTTTAAAGCAATTTCTTAACTGAGGTGAATTTCAATCTAAAGCGACATTTGGTCGAGATGAA
1 TTAGGTTAAAGCAA-TTCTTGACTGAGGTGAATTTCAATCTAAAGCGACATTTGG-CGAGATGAA
1665557 CC
64 CC
** * * *
1665559 TTAGGTTAAAGCAATTCTTGACAAAGGTGAATTTCAGTCTAAAGCGACATTTGGCCAAGGTGAA-
1 TTAGGTTAAAGCAATTCTTGACTGAGGTGAATTTCAATCTAAAGCGACATTTGG-CGAGATGAAC
1665623 C
65 C
* * * * *
1665624 TTCAGGTTAAAACAATTCTTGATTGAGGTGAATTTCAATCCAAAGTGACATTTGGCTGAAATGAA
1 TT-AGGTTAAAGCAATTCTTGACTGAGGTGAATTTCAATCTAAAGCGACATTTGGC-GAGATGAA
1665689 CC
64 CC
1665691 TTAGG
1 TTAGG
1665696 CTAAGGTAAG
Statistics
Matches: 116, Mismatches: 18, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
65 4 0.03
66 96 0.83
67 16 0.14
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (65 bp):
TTAGGTTAAAGCAATTCTTGACTGAGGTGAATTTCAATCTAAAGCGACATTTGGCGAGATGAACC
Found at i:1665602 original size:33 final size:33
Alignment explanation
Indices: 1665561--1665660 Score: 89
Period size: 33 Copynumber: 3.0 Consensus size: 33
1665551 GATGAACCTT
1665561 AGGTTAAAGCAATTCTTGACAAAGGTGAATTTC
1 AGGTTAAAGCAATTCTTGACAAAGGTGAATTTC
* * *
1665594 A-GTCTAAAGCGACA-T-TTGGCCAAGGTGAACTTC
1 AGGT-TAAAGC-A-ATTCTTGACAAAGGTGAATTTC
* ***
1665627 AGGTTAAAACAATTCTTGATTGAGGTGAATTTC
1 AGGTTAAAGCAATTCTTGACAAAGGTGAATTTC
1665660 A
1 A
1665661 ATCCAAAGTG
Statistics
Matches: 52, Mismatches: 9, Indels: 12
0.71 0.12 0.16
Matches are distributed among these distances:
31 1 0.02
32 4 0.08
33 42 0.81
34 4 0.08
35 1 0.02
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.30
Consensus pattern (33 bp):
AGGTTAAAGCAATTCTTGACAAAGGTGAATTTC
Found at i:1665960 original size:16 final size:17
Alignment explanation
Indices: 1665939--1665971 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1665929 TTTTCATTCA
*
1665939 TGTCTATTAT-TTGATC
1 TGTCTATCATGTTGATC
1665955 TGTCTATCATGTTGATC
1 TGTCTATCATGTTGATC
1665972 CTTGAGTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.18, C:0.15, G:0.15, T:0.52
Consensus pattern (17 bp):
TGTCTATCATGTTGATC
Found at i:1669840 original size:11 final size:10
Alignment explanation
Indices: 1669813--1669838 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1669803 TAGTGTATTT
1669813 ATTTTTAAAG
1 ATTTTTAAAG
1669823 ATTTTTAAAG
1 ATTTTTAAAG
1669833 ATTTTT
1 ATTTTT
1669839 TATTTGTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.58
Consensus pattern (10 bp):
ATTTTTAAAG
Found at i:1670173 original size:46 final size:46
Alignment explanation
Indices: 1670106--1670198 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
1670096 TACTATGATT
1670106 ACAGCAAACTCTCATCATGCCATTCGGTGTTAAGTGATGGAAAATC
1 ACAGCAAACTCTCATCATGCCATTCGGTGTTAAGTGATGGAAAATC
1670152 ACAGCAAACTCTCATCATGCCATTCGGTGTTAAGTGATGGAAAATC
1 ACAGCAAACTCTCATCATGCCATTCGGTGTTAAGTGATGGAAAATC
1670198 A
1 A
1670199 TATCTGATAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (46 bp):
ACAGCAAACTCTCATCATGCCATTCGGTGTTAAGTGATGGAAAATC
Found at i:1670907 original size:22 final size:22
Alignment explanation
Indices: 1670882--1670923 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
1670872 ACTTTGTTAG
1670882 TAACAAGACTCTGACTAAGTAC
1 TAACAAGACTCTGACTAAGTAC
1670904 TAACAAGACTCTGACTAAGT
1 TAACAAGACTCTGACTAAGT
1670924 CATCCTAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.40, C:0.21, G:0.14, T:0.24
Consensus pattern (22 bp):
TAACAAGACTCTGACTAAGTAC
Found at i:1672628 original size:16 final size:16
Alignment explanation
Indices: 1672603--1672634 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1672593 ATAAAAGTAA
1672603 TAAAAATTATATTAAC
1 TAAAAATTATATTAAC
*
1672619 TAAAATTTATATTAAC
1 TAAAAATTATATTAAC
1672635 ATGTAAAGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (16 bp):
TAAAAATTATATTAAC
Found at i:1672994 original size:104 final size:105
Alignment explanation
Indices: 1672813--1673025 Score: 356
Period size: 104 Copynumber: 2.0 Consensus size: 105
1672803 ACTTTTAAAT
*
1672813 TAAACAATTGTAAATAAATTAGCTTTTAATTTTTTATTTATAATCATATTAATTTATTTAACAAA
1 TAAACAATTGTAAATAAATTAGCTTTTAATTTTTTATTTATAACCATATTAATTTATTTAACAAA
* *
1672878 AATATTTTAATAAAATTAAATTTGGTACTTGTAAATTAGA
66 AATATTTTAATAAAATTAAATTTAGCACTTGTAAATTAGA
* **
1672918 TAAACAATTGTATATAAATTAGCTTTTAA-TTTTTATTTATAACCATATTAATTTATTTAATGAA
1 TAAACAATTGTAAATAAATTAGCTTTTAATTTTTTATTTATAACCATATTAATTTATTTAACAAA
*
1672982 AATGTTTTAATAAAATTAAATTTAGCACTTGTAAATTAGA
66 AATATTTTAATAAAATTAAATTTAGCACTTGTAAATTAGA
1673022 TAAA
1 TAAA
1673026 TAATAATAAT
Statistics
Matches: 101, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
104 73 0.72
105 28 0.28
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.45
Consensus pattern (105 bp):
TAAACAATTGTAAATAAATTAGCTTTTAATTTTTTATTTATAACCATATTAATTTATTTAACAAA
AATATTTTAATAAAATTAAATTTAGCACTTGTAAATTAGA
Found at i:1673444 original size:15 final size:15
Alignment explanation
Indices: 1673421--1673451 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1673411 TGATATATAT
1673421 TATTAATAATTAAAA
1 TATTAATAATTAAAA
*
1673436 TATTTATAATTAAAA
1 TATTAATAATTAAAA
1673451 T
1 T
1673452 TTAGAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTAATAATTAAAA
Found at i:1673836 original size:2 final size:2
Alignment explanation
Indices: 1673829--1673869 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1673819 ATGAAGTTAT
1673829 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1673870 GTGTGTGTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1674370 original size:12 final size:13
Alignment explanation
Indices: 1674351--1674391 Score: 61
Period size: 12 Copynumber: 3.4 Consensus size: 13
1674341 AATAAGGTAC
1674351 AATATAAAATAAT
1 AATATAAAATAAT
1674364 AAT-TAAAAT-AT
1 AATATAAAATAAT
1674375 AATATAAAATAA-
1 AATATAAAATAAT
1674387 AATAT
1 AATAT
1674392 TATATAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 5 0.19
12 17 0.65
13 4 0.15
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AATATAAAATAAT
Found at i:1674378 original size:17 final size:16
Alignment explanation
Indices: 1674362--1674401 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
1674352 ATATAAAATA
1674362 ATAATTAAAATATAAT
1 ATAATTAAAATATAAT
* *
1674378 ATAAAATAAAATATTAT
1 AT-AATTAAAATATAAT
1674395 ATAATTA
1 ATAATTA
1674402 TTGTATTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
ATAATTAAAATATAAT
Found at i:1674857 original size:15 final size:14
Alignment explanation
Indices: 1674826--1674874 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
1674816 AGTTTAAAAA
* *
1674826 TATTAATATAATAT
1 TATTAACATAATTT
1674840 TATTAACGATAATTT
1 TATTAAC-ATAATTT
*
1674855 TATATATCATAATTT
1 TAT-TAACATAATTT
1674870 TATTA
1 TATTA
1674875 TTAAAAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 8 0.27
15 19 0.63
16 3 0.10
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (14 bp):
TATTAACATAATTT
Found at i:1677044 original size:2 final size:2
Alignment explanation
Indices: 1677037--1677077 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1677027 TTACAAATAC
1677037 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1677078 AGGCACTCGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1677392 original size:15 final size:15
Alignment explanation
Indices: 1677374--1677403 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1677364 CACTTTTAAA
1677374 ATAATATATTTTTTT
1 ATAATATATTTTTTT
*
1677389 ATAATTTATTTTTTT
1 ATAATATATTTTTTT
1677404 TATATTTAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
ATAATATATTTTTTT
Found at i:1677410 original size:15 final size:16
Alignment explanation
Indices: 1677382--1677411 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1677372 AAATAATATA
1677382 TTTTTTTATAATTTAT
1 TTTTTTTATAATTTAT
1677398 TTTTTTTAT-ATTTA
1 TTTTTTTATAATTTA
1677412 AATATGTACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTTTTATAATTTAT
Found at i:1680436 original size:19 final size:18
Alignment explanation
Indices: 1680412--1680467 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
1680402 TAAATAATTT
*
1680412 TTTTCACTTTTTTTCTTTC
1 TTTTCAATTTTTTT-TTTC
1680431 TTTTCAATTTTTTTTTTC
1 TTTTCAATTTTTTTTTTC
1680449 AATTTTC--TTTTTTTTTTC
1 --TTTTCAATTTTTTTTTTC
1680467 T
1 T
1680468 CTTTATTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
16 1 0.03
18 15 0.44
19 13 0.38
20 5 0.15
ACGTcount: A:0.09, C:0.14, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTTCAATTTTTTTTTTC
Found at i:1680449 original size:13 final size:14
Alignment explanation
Indices: 1680431--1680461 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
1680421 TTTTTCTTTC
1680431 TTTTCAATTTT-TT
1 TTTTCAATTTTCTT
1680444 TTTTCAATTTTCTT
1 TTTTCAATTTTCTT
1680458 TTTT
1 TTTT
1680462 TTTTCTCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTCAATTTTCTT
Found at i:1680476 original size:14 final size:14
Alignment explanation
Indices: 1680453--1680520 Score: 79
Period size: 14 Copynumber: 4.9 Consensus size: 14
1680443 TTTTTCAATT
1680453 TTCTTT-TTTTTT-
1 TTCTTTATTTTTTA
1680465 TCTCTTTATTTTTTA
1 T-TCTTTATTTTTTA
*
1680480 TTTTTTATTTTTTA
1 TTCTTTATTTTTTA
*
1680494 TTTTTTATTTTTTA
1 TTCTTTATTTTTTA
1680508 TT-TATTATTTTTT
1 TTCT-TTATTTTTT
1680521 TCAAAGCAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 6
0.88 0.02 0.10
Matches are distributed among these distances:
12 1 0.02
13 6 0.12
14 43 0.84
15 1 0.02
ACGTcount: A:0.12, C:0.04, G:0.00, T:0.84
Consensus pattern (14 bp):
TTCTTTATTTTTTA
Found at i:1680479 original size:7 final size:7
Alignment explanation
Indices: 1680469--1680520 Score: 95
Period size: 7 Copynumber: 7.4 Consensus size: 7
1680459 TTTTTTTCTC
1680469 TTTATTT
1 TTTATTT
1680476 TTTATTT
1 TTTATTT
1680483 TTTATTT
1 TTTATTT
1680490 TTTATTT
1 TTTATTT
1680497 TTTATTT
1 TTTATTT
1680504 TTTATTT
1 TTTATTT
*
1680511 ATTATTT
1 TTTATTT
1680518 TTT
1 TTT
1680521 TCAAAGCAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 43 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTATTT
Found at i:1680483 original size:21 final size:21
Alignment explanation
Indices: 1680450--1680520 Score: 83
Period size: 21 Copynumber: 3.3 Consensus size: 21
1680440 TTTTTTTTCA
*
1680450 ATTTTCTT-TTTTTTTTCTCTTT
1 ATTTT-TTATTTTTTAT-TCTTT
*
1680472 ATTTTTTATTTTTTATTTTTT
1 ATTTTTTATTTTTTATTCTTT
1680493 ATTTTTTATTTTTTATT-TATT
1 ATTTTTTATTTTTTATTCT-TT
1680514 ATTTTTT
1 ATTTTTT
1680521 TCAAAGCAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
20 1 0.02
21 32 0.71
22 12 0.27
ACGTcount: A:0.13, C:0.04, G:0.00, T:0.83
Consensus pattern (21 bp):
ATTTTTTATTTTTTATTCTTT
Found at i:1686218 original size:28 final size:27
Alignment explanation
Indices: 1686187--1686285 Score: 112
Period size: 28 Copynumber: 3.6 Consensus size: 27
1686177 AAAATTGGGA
1686187 TTGGAGTATCCCTTCGAAAATAACGGGG
1 TTGGAGTATCCC-TCGAAAATAACGGGG
* *
1686215 TTGGAGTATCCCCTCGGAAGTAACGGGG
1 TTGGAGTAT-CCCTCGAAAATAACGGGG
* *
1686243 TTGGAGTATCCC-CGATGAGATAACGAGG
1 TTGGAGTATCCCTCGA--AAATAACGGGG
1686271 TTGGAGTAT-CCTCGA
1 TTGGAGTATCCCTCGA
1686286 TTGTGAAAAA
Statistics
Matches: 61, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
26 2 0.03
27 5 0.08
28 51 0.84
29 3 0.05
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.24
Consensus pattern (27 bp):
TTGGAGTATCCCTCGAAAATAACGGGG
Found at i:1686419 original size:105 final size:103
Alignment explanation
Indices: 1686269--1686491 Score: 243
Period size: 105 Copynumber: 2.1 Consensus size: 103
1686259 GAGATAACGA
* * * * *
1686269 GGTTGGAGTATCCTCGATTGTGAAAAATTGATATTTTTGGAAATAAAATCGGAATTAGAGTATCC
1 GGTTGGAGTATCCCCGATTGTGAAAAATTGATAGTTTTAGAAATAAAACCGGAATTAGAATATCC
*** *
1686334 CCGATTAAAGAAAAAATTGGTGTTTTGAAAATAAAACCGG
66 CCGATT-AAG-AAAAATCAATATTTTGAAAATAAAACCGG
* ** *
1686374 GGTTGGAGTATCCCCGATTGTGGAAAAATT-AGT-GTTTTAGCAATAAAACCGGGGTTGGAATAT
1 GGTTGGAGTATCCCCGATTGT-GAAAAATTGA-TAGTTTTAGAAATAAAACCGGAATTAGAATAT
* * **
1686437 CCCCGATTATGAAAAATCAATATTTTGGAAATAAAGTCGG
64 CCCCGATTAAGAAAAATCAATATTTTGAAAATAAAACCGG
1686477 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
1686492 TCGGAAAAGT
Statistics
Matches: 99, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
103 37 0.37
104 2 0.02
105 51 0.52
106 9 0.09
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.30
Consensus pattern (103 bp):
GGTTGGAGTATCCCCGATTGTGAAAAATTGATAGTTTTAGAAATAAAACCGGAATTAGAATATCC
CCGATTAAGAAAAATCAATATTTTGAAAATAAAACCGG
Found at i:1686422 original size:52 final size:51
Alignment explanation
Indices: 1686269--1686491 Score: 223
Period size: 52 Copynumber: 4.3 Consensus size: 51
1686259 GAGATAACGA
* * * *
1686269 GGTTGGAGTATCCTCGATTGTGAAAAATT-GATATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTAG-T-GTTTTGGAAATAAAACCGG
** * * * *
1686321 AATTAGAGTATCCCCGATTAAAGAAAAAATTGGTGTTTTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT-ATG-AAAAATTAGTGTTTTGGAAATAAAACCGG
* * *
1686374 GGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCGG
1 GGTTGGAGTATCCCCGATTAT-GAAAAATTAGTGTTTTGGAAATAAAACCGG
* * * * **
1686426 GGTTGGAATATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGGAAATAAAACCGG
1686477 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
1686492 TCGGAAAAGT
Statistics
Matches: 139, Mismatches: 28, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
51 37 0.27
52 59 0.42
53 34 0.24
54 8 0.06
55 1 0.01
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.30
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGGAAATAAAACCGG
Found at i:1686601 original size:56 final size:50
Alignment explanation
Indices: 1686533--1686660 Score: 148
Period size: 51 Copynumber: 2.4 Consensus size: 50
1686523 GATTAACGGG
* * *
1686533 GTTGGAGTATCCCCGATTGTGAAAATTTTGTGTTTTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAAAA-TTAGTG-----TCTTGAAAATAAAATCGGA
*
1686589 GTTGGAGTATCCCCGATTATAGAAAATTAGTGTCTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGT-GAAAATTAGTGTCTTGAAAATAAAATCGGA
*
1686640 GTTGGAATATCCCCGATTGTG
1 GTTGGAGTATCCCCGATTGTG
1686661 GAGAATTGAG
Statistics
Matches: 65, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
50 1 0.02
51 35 0.54
56 24 0.37
57 5 0.08
ACGTcount: A:0.30, C:0.12, G:0.23, T:0.35
Consensus pattern (50 bp):
GTTGGAGTATCCCCGATTGTGAAAATTAGTGTCTTGAAAATAAAATCGGA
Found at i:1687303 original size:11 final size:10
Alignment explanation
Indices: 1687277--1687301 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1687267 TCTTTAAGCG
1687277 AAAAATATCA
1 AAAAATATCA
1687287 AAAAATATCA
1 AAAAATATCA
1687297 AAAAA
1 AAAAA
1687302 ATCGTTTCAA
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:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (10 bp):
AAAAATATCA
Found at i:1689048 original size:33 final size:33
Alignment explanation
Indices: 1689006--1689068 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
1688996 TTTCCAAATG
***
1689006 TATCGATACAAAGATCCATGTATCGATACAATA
1 TATCGATACAAAGAAAAATGTATCGATACAATA
*
1689039 TATCGATACACAGAAAAATGTATCGATACA
1 TATCGATACAAAGAAAAATGTATCGATACA
1689069 TTTCCTTGGC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.44, C:0.17, G:0.13, T:0.25
Consensus pattern (33 bp):
TATCGATACAAAGAAAAATGTATCGATACAATA
Found at i:1689112 original size:19 final size:19
Alignment explanation
Indices: 1689088--1689154 Score: 83
Period size: 19 Copynumber: 3.8 Consensus size: 19
1689078 CAATAGCTAA
1689088 TTATGTATCGATACAATAC
1 TTATGTATCGATACAATAC
1689107 TTATGTATCGAT---ATA-
1 TTATGTATCGATACAATAC
*
1689122 -T-TGTATCGATACAAAAC
1 TTATGTATCGATACAATAC
1689139 TTATGTATCGATACAA
1 TTATGTATCGATACAA
1689155 ATTGTTGAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
13 9 0.22
14 1 0.02
16 5 0.12
18 1 0.02
19 25 0.61
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.37
Consensus pattern (19 bp):
TTATGTATCGATACAATAC
Found at i:1689132 original size:32 final size:32
Alignment explanation
Indices: 1689091--1689151 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
1689081 TAGCTAATTA
*
1689091 TGTATCGATACAATACTTATGTATCGATATAT
1 TGTATCGATACAAAACTTATGTATCGATATAT
1689123 TGTATCGATACAAAACTTATGTATCGATA
1 TGTATCGATACAAAACTTATGTATCGATA
1689152 CAAATTGTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATATAT
Found at i:1691424 original size:16 final size:16
Alignment explanation
Indices: 1691399--1691431 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1691389 TATTGTCGTT
1691399 TTATTCAAGTTTTATA
1 TTATTCAAGTTTTATA
*
1691415 TTATTTAAGTTTTATA
1 TTATTCAAGTTTTATA
1691431 T
1 T
1691432 ACACTATGCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.03, G:0.06, T:0.61
Consensus pattern (16 bp):
TTATTCAAGTTTTATA
Found at i:1691458 original size:2 final size:2
Alignment explanation
Indices: 1691451--1691483 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1691441 CTGTCTTAAT
1691451 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1691484 TCTCTATTCG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1691736 original size:11 final size:11
Alignment explanation
Indices: 1691720--1691749 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
1691710 TGTTAAATAG
1691720 TATTATTTCAA
1 TATTATTTCAA
1691731 TATTATTTCAA
1 TATTATTTCAA
*
1691742 TACTATTT
1 TATTATTT
1691750 AGAATATTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (11 bp):
TATTATTTCAA
Found at i:1696487 original size:38 final size:38
Alignment explanation
Indices: 1696445--1696519 Score: 141
Period size: 38 Copynumber: 2.0 Consensus size: 38
1696435 TATACGGTAT
1696445 AAGATTATTTTACACAATTGACATCCATAGTAAATGAA
1 AAGATTATTTTACACAATTGACATCCATAGTAAATGAA
*
1696483 AAGATTATTTTACACAATTGACATCCATAGTGAATGA
1 AAGATTATTTTACACAATTGACATCCATAGTAAATGA
1696520 GAAATTGTTC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.32
Consensus pattern (38 bp):
AAGATTATTTTACACAATTGACATCCATAGTAAATGAA
Found at i:1700814 original size:14 final size:14
Alignment explanation
Indices: 1700795--1700823 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1700785 CTCTATGCCG
1700795 AACATCTCAAAGGC
1 AACATCTCAAAGGC
1700809 AACATCTCAAAGGC
1 AACATCTCAAAGGC
1700823 A
1 A
1700824 TGATTAGTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.28, G:0.14, T:0.14
Consensus pattern (14 bp):
AACATCTCAAAGGC
Found at i:1704488 original size:36 final size:36
Alignment explanation
Indices: 1704447--1704517 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
1704437 ACACATTCCC
*
1704447 TTGACATAGCTAATTCGGGCTCAACAGTTTTACTTG
1 TTGACATAGCTAATTCGGGCTCAACAGTGTTACTTG
*
1704483 TTGACATAGCTAATTCGGGCTCAACGGTGTTACTT
1 TTGACATAGCTAATTCGGGCTCAACAGTGTTACTT
1704518 TTTTTTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (36 bp):
TTGACATAGCTAATTCGGGCTCAACAGTGTTACTTG
Found at i:1704659 original size:2 final size:2
Alignment explanation
Indices: 1704652--1704691 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
1704642 TAACTCCAAC
* * *
1704652 TA TA TA TA AA CA TA TA TA CA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1704692 ACATTGAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (2 bp):
TA
Found at i:1704819 original size:23 final size:23
Alignment explanation
Indices: 1704789--1704834 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
1704779 ACCCGGGGTC
1704789 GGCTCTAATATATATATATATAT
1 GGCTCTAATATATATATATATAT
1704812 GGCTCTAATATATATATATATAT
1 GGCTCTAATATATATATATATAT
1704835 ATATGCATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.43
Consensus pattern (23 bp):
GGCTCTAATATATATATATATAT
Found at i:1707482 original size:6 final size:6
Alignment explanation
Indices: 1707471--1707496 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1707461 TTAATTCTTA
1707471 TAATTT TAATTT TAATTT TAATTT TA
1 TAATTT TAATTT TAATTT TAATTT TA
1707497 TTATTAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (6 bp):
TAATTT
Found at i:1707582 original size:16 final size:18
Alignment explanation
Indices: 1707559--1707597 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
1707549 TATTAAGATA
*
1707559 TAAAAAATAAAAATT-TT
1 TAAAAATTAAAAATTATT
1707576 TAAAAATTAAAAATTATT
1 TAAAAATTAAAAATTATT
1707594 TAAA
1 TAAA
1707598 TAAAAAAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
TAAAAATTAAAAATTATT
Found at i:1708190 original size:13 final size:13
Alignment explanation
Indices: 1708172--1708197 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1708162 TAGATTTTAC
1708172 TCTTTTAATTAAA
1 TCTTTTAATTAAA
1708185 TCTTTTAATTAAA
1 TCTTTTAATTAAA
1708198 AATTTACCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (13 bp):
TCTTTTAATTAAA
Found at i:1709668 original size:15 final size:16
Alignment explanation
Indices: 1709648--1709677 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1709638 TAAATTTATA
1709648 AAATTATT-TAAATTT
1 AAATTATTATAAATTT
1709663 AAATTATTATAAATT
1 AAATTATTATAAATT
1709678 ATAATTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
AAATTATTATAAATTT
Found at i:1710634 original size:20 final size:20
Alignment explanation
Indices: 1710611--1710649 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1710601 ATATAATAAA
*
1710611 TTAATTTTTTTATTAATTTT
1 TTAATTTTTTTATCAATTTT
1710631 TTAATTTTTTTATCAATTT
1 TTAATTTTTTTATCAATTT
1710650 AATATAATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.72
Consensus pattern (20 bp):
TTAATTTTTTTATCAATTTT
Found at i:1711774 original size:27 final size:29
Alignment explanation
Indices: 1711744--1711815 Score: 71
Period size: 28 Copynumber: 2.6 Consensus size: 29
1711734 AAAATTATTT
1711744 TTTAAATAAAT-TAAAA-ATATTTAATTA
1 TTTAAATAAATATAAAATATATTTAATTA
* * *
1711771 TTT-ATTTAATATAAAATATTTTTAATTA
1 TTTAAATAAATATAAAATATATTTAATTA
*
1711799 -TTAAATATATATCAAAA
1 TTTAAATAAATAT-AAAA
1711816 AGATTGTCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
26 5 0.14
27 10 0.29
28 16 0.46
29 4 0.11
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (29 bp):
TTTAAATAAATATAAAATATATTTAATTA
Found at i:1711805 original size:24 final size:25
Alignment explanation
Indices: 1711757--1711807 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 25
1711747 AAATAAATTA
* *
1711757 AAAATATTTAATTATTTATTTAATAT
1 AAAATATTT-ATTAATTATTAAATAT
1711783 AAAATATTT-TTAATTATTAAATAT
1 AAAATATTTATTAATTATTAAATAT
1711807 A
1 A
1711808 TATCAAAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 14 0.61
26 9 0.39
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
AAAATATTTATTAATTATTAAATAT
Found at i:1714573 original size:16 final size:17
Alignment explanation
Indices: 1714552--1714621 Score: 66
Period size: 16 Copynumber: 4.5 Consensus size: 17
1714542 AATAAATAAA
1714552 ATATATTTAATAAT-TT
1 ATATATTTAATAATATT
*
1714568 ATATATTTATATCATATT
1 ATATATTTA-ATAATATT
1714586 -TATATTT-AT-A-A-T
1 ATATATTTAATAATATT
1714598 -TATATTTAA-AATATT
1 ATATATTTAATAATATT
1714613 ATATATTTA
1 ATATATTTA
1714622 TAAAAATATA
Statistics
Matches: 46, Mismatches: 1, Indels: 14
0.75 0.02 0.23
Matches are distributed among these distances:
12 8 0.17
13 3 0.07
14 2 0.04
15 3 0.07
16 17 0.37
17 11 0.24
18 2 0.04
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (17 bp):
ATATATTTAATAATATT
Found at i:1714591 original size:17 final size:18
Alignment explanation
Indices: 1714569--1714605 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
1714559 TAATAATTTA
1714569 TATATTTAT-ATCATATT
1 TATATTTATAATCATATT
*
1714586 TATATTTATAATTATATT
1 TATATTTATAATCATATT
1714604 TA
1 TA
1714606 AAATATTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (18 bp):
TATATTTATAATCATATT
Found at i:1720253 original size:7 final size:7
Alignment explanation
Indices: 1720241--1720271 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
1720231 CCAAGGGCTC
1720241 TTTCTTT
1 TTTCTTT
1720248 TTTCTTT
1 TTTCTTT
*
1720255 TTTTTTT
1 TTTCTTT
1720262 TTTCTTT
1 TTTCTTT
1720269 TTT
1 TTT
1720272 AAATTTCAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (7 bp):
TTTCTTT
Found at i:1722125 original size:9 final size:9
Alignment explanation
Indices: 1722111--1722143 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
1722101 TTTCTCTCTT
*
1722111 TCTGCTATC
1 TCTGCTGTC
1722120 TCTGCTGTC
1 TCTGCTGTC
1722129 TCTGCTGTC
1 TCTGCTGTC
1722138 TCTGCT
1 TCTGCT
1722144 TGAGCCTTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.03, C:0.33, G:0.18, T:0.45
Consensus pattern (9 bp):
TCTGCTGTC
Found at i:1722240 original size:27 final size:26
Alignment explanation
Indices: 1722202--1722253 Score: 95
Period size: 27 Copynumber: 2.0 Consensus size: 26
1722192 TGTAACTTTT
1722202 ACTATTTCAAATTGAATTTCAAAATTA
1 ACTATTTCAAATTGAA-TTCAAAATTA
1722229 ACTATTTCAAATTGAATTCAAAATT
1 ACTATTTCAAATTGAATTCAAAATT
1722254 GGCTGCACAG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 9 0.36
27 16 0.64
ACGTcount: A:0.44, C:0.12, G:0.04, T:0.40
Consensus pattern (26 bp):
ACTATTTCAAATTGAATTCAAAATTA
Found at i:1722254 original size:12 final size:13
Alignment explanation
Indices: 1722205--1722254 Score: 52
Period size: 12 Copynumber: 3.9 Consensus size: 13
1722195 AACTTTTACT
1722205 ATTTC-AAATTGA
1 ATTTCAAAATTGA
*
1722217 ATTTCAAAATTAA
1 ATTTCAAAATTGA
1722230 CTATTTC-AAATTGA
1 --ATTTCAAAATTGA
1722244 A-TTCAAAATTG
1 ATTTCAAAATTG
1722255 GCTGCACAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
11 3 0.09
12 12 0.38
13 6 0.19
14 6 0.19
15 5 0.16
ACGTcount: A:0.44, C:0.10, G:0.06, T:0.40
Consensus pattern (13 bp):
ATTTCAAAATTGA
Found at i:1726904 original size:9 final size:9
Alignment explanation
Indices: 1726890--1726922 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
1726880 TTTCTCTCTT
*
1726890 TCTGCTATC
1 TCTGCTGTC
1726899 TCTGCTGTC
1 TCTGCTGTC
1726908 TCTGCTGTC
1 TCTGCTGTC
1726917 TCTGCT
1 TCTGCT
1726923 TGAGCCTTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.03, C:0.33, G:0.18, T:0.45
Consensus pattern (9 bp):
TCTGCTGTC
Found at i:1727019 original size:27 final size:26
Alignment explanation
Indices: 1726981--1727032 Score: 95
Period size: 27 Copynumber: 2.0 Consensus size: 26
1726971 TGTAACTTTT
1726981 ACTATTTCAAATTGAATTTCAAAATTA
1 ACTATTTCAAATTGAA-TTCAAAATTA
1727008 ACTATTTCAAATTGAATTCAAAATT
1 ACTATTTCAAATTGAATTCAAAATT
1727033 GGCTGCACAG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 9 0.36
27 16 0.64
ACGTcount: A:0.44, C:0.12, G:0.04, T:0.40
Consensus pattern (26 bp):
ACTATTTCAAATTGAATTCAAAATTA
Found at i:1727033 original size:12 final size:13
Alignment explanation
Indices: 1726984--1727033 Score: 52
Period size: 12 Copynumber: 3.9 Consensus size: 13
1726974 AACTTTTACT
1726984 ATTTC-AAATTGA
1 ATTTCAAAATTGA
*
1726996 ATTTCAAAATTAA
1 ATTTCAAAATTGA
1727009 CTATTTC-AAATTGA
1 --ATTTCAAAATTGA
1727023 A-TTCAAAATTG
1 ATTTCAAAATTG
1727034 GCTGCACAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
11 3 0.09
12 12 0.38
13 6 0.19
14 6 0.19
15 5 0.16
ACGTcount: A:0.44, C:0.10, G:0.06, T:0.40
Consensus pattern (13 bp):
ATTTCAAAATTGA
Done.