Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A10
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: 111961792
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4980000 characters in sequence are not A, C, G, or T
File 330 of 344
Found at i:107366375 original size:73 final size:71
Alignment explanation
Indices: 107366224--107366425 Score: 262
Period size: 73 Copynumber: 2.8 Consensus size: 71
107366214 CAGAAATTAA
* * *
107366224 AAGGCTCAACTCACCTCTCGCAATATGAATTGATTTTTGACAAACAGAAATTGAAATTACCTCAG
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG--AAACAGTAATTGAAAATACCTCAG
* *
107366289 CGTGTCCT
64 CGTGACCC
* *
107366297 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAACA-TAATTGAAAATACCTCGGCA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAACAGTAATTGAAAATACCTCAGC-
107366361 TGTGAACCC
65 -GTG-ACCC
* *
107366370 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATTAAATTGAAAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAACAGT-AATTGAAAA
107366426 AAACAAAAAT
Statistics
Matches: 115, Mismatches: 9, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
70 16 0.14
71 5 0.04
72 3 0.03
73 81 0.70
74 1 0.01
75 9 0.08
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (71 bp):
AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAACAGTAATTGAAAATACCTCAGCG
TGACCC
Found at i:107366490 original size:90 final size:90
Alignment explanation
Indices: 107366342--107366608 Score: 342
Period size: 91 Copynumber: 2.9 Consensus size: 90
107366332 TTTGAAACAT
* *
107366342 AATTGAAAATACCTCGGCATGTGAACCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTT
1 AATTGAAAATACCTCAGCATGTG-A-CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGACTTT
107366406 TTGAAAAATTAAATTGAAAAAAACAAA
64 TTGAAAAATTAAATTGAAAAAAACAAA
* * *
107366433 AATTAAAAATACCTCAGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGACTTTT
1 AATTGAAAATACCTCAGCATGTGACC-GAGGCTCAACTCACCTCTCGCAATATGAGTTGACTTTT
** ** *
107366498 AAAAAAAACAGGAATTG--AAAAACAGA
65 TGAAAAATTA--AATTGAAAAAAACAAA
* *
107366524 AATTGAAAATACGTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
1 AATTGAAAATACCTCAGCATGTGA-CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGACTTTT
107366589 TGAAAAATATAAATTGAAAA
65 TGAAAAAT-TAAATTGAAAA
107366609 GCAGAAATTA
Statistics
Matches: 149, Mismatches: 19, Indels: 15
0.81 0.10 0.08
Matches are distributed among these distances:
89 2 0.01
90 37 0.25
91 100 0.67
92 5 0.03
93 5 0.03
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.25
Consensus pattern (90 bp):
AATTGAAAATACCTCAGCATGTGACCGAGGCTCAACTCACCTCTCGCAATATGAGTTGACTTTTT
GAAAAATTAAATTGAAAAAAACAAA
Found at i:107366532 original size:13 final size:14
Alignment explanation
Indices: 107366501--107366532 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
107366491 GACTTTTAAA
*
107366501 AAAAACAGGAATTG
1 AAAAACAGAAATTG
107366515 AAAAACAGAAATTG
1 AAAAACAGAAATTG
107366529 AAAA
1 AAAA
107366533 TACGTCAGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.66, C:0.06, G:0.16, T:0.12
Consensus pattern (14 bp):
AAAAACAGAAATTG
Found at i:107366616 original size:14 final size:14
Alignment explanation
Indices: 107366599--107366636 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
107366589 TGAAAAATAT
*
107366599 AAATTGAAAAGCAG
1 AAATTGAAAAGCAA
*
107366613 AAATTAAAAAGCAA
1 AAATTGAAAAGCAA
107366627 AAATTGAAAA
1 AAATTGAAAA
107366637 TACCTCAGCG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.66, C:0.05, G:0.13, T:0.16
Consensus pattern (14 bp):
AAATTGAAAAGCAA
Found at i:107366708 original size:14 final size:14
Alignment explanation
Indices: 107366685--107366735 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
107366675 ATATGAGTTG
107366685 ATTTGAAAAGCAGA
1 ATTTGAAAAGCAGA
*
107366699 ATTTGTAAAGCAGA
1 ATTTGAAAAGCAGA
* *
107366713 AATTGAAAAACAGA
1 ATTTGAAAAGCAGA
*
107366727 AATTGAAAA
1 ATTTGAAAA
107366736 TACCTCAGCG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.55, C:0.06, G:0.18, T:0.22
Consensus pattern (14 bp):
ATTTGAAAAGCAGA
Found at i:107366806 original size:14 final size:14
Alignment explanation
Indices: 107366787--107366821 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
107366777 GAGTTAATTT
* *
107366787 TTGAAAAGCATAAA
1 TTGAAAAACAGAAA
107366801 TTGAAAAACAGAAA
1 TTGAAAAACAGAAA
107366815 TTGAAAA
1 TTGAAAA
107366822 TACGTCAGCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.60, C:0.06, G:0.14, T:0.20
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:107375362 original size:22 final size:21
Alignment explanation
Indices: 107375337--107375378 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
107375327 ATATTAAGAT
107375337 AAAACAATAAGTGATAATAATG
1 AAAACAATAAGT-ATAATAATG
* *
107375359 AAAAGAATAGGTATAATAAT
1 AAAACAATAAGTATAATAAT
107375379 AAATAAAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.60, C:0.02, G:0.14, T:0.24
Consensus pattern (21 bp):
AAAACAATAAGTATAATAATG
Found at i:107375483 original size:23 final size:26
Alignment explanation
Indices: 107375431--107375484 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 26
107375421 TGTATACAAG
* *
107375431 AATAATAAAATATATGTACTAATATT
1 AATAATAAAATATATGTACGAATATA
107375457 AATAAT-AAATATA-GTACGAATA-A
1 AATAATAAAATATATGTACGAATATA
107375480 AATAA
1 AATAA
107375485 ATGTAATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 5 0.19
24 8 0.31
25 7 0.27
26 6 0.23
ACGTcount: A:0.59, C:0.04, G:0.06, T:0.31
Consensus pattern (26 bp):
AATAATAAAATATATGTACGAATATA
Found at i:107375602 original size:26 final size:25
Alignment explanation
Indices: 107375527--107375653 Score: 81
Period size: 24 Copynumber: 5.2 Consensus size: 25
107375517 AAAAATATAC
* *
107375527 ATATACATATAATAGTATTTAAGAAT
1 ATATACATA-AATAGTATATAAAAAT
**
107375553 ATATACATAAGAT-G-ATATGGAAAT
1 ATATACATAA-ATAGTATATAAAAAT
*
107375577 ATGTACATAGAATAGTATATAAAAAT
1 ATATACATA-AATAGTATATAAAAAT
*
107375603 ATA-AC-T-AATAATAT-TGAAAATAT
1 ATATACATAAATAGTATAT-AAAA-AT
*
107375626 AGATACAT-AATA-TATATAAAACAT
1 ATATACATAAATAGTATATAAAA-AT
107375650 ATAT
1 ATAT
107375654 GATATATACA
Statistics
Matches: 80, Mismatches: 12, Indels: 20
0.71 0.11 0.18
Matches are distributed among these distances:
21 1 0.01
22 11 0.14
23 4 0.05
24 31 0.39
25 12 0.15
26 21 0.26
ACGTcount: A:0.54, C:0.05, G:0.09, T:0.33
Consensus pattern (25 bp):
ATATACATAAATAGTATATAAAAAT
Found at i:107375673 original size:21 final size:20
Alignment explanation
Indices: 107375635--107375682 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 20
107375625 TAGATACATA
* *
107375635 ATATATATAAAACATATATG
1 ATATATACAAAACATATACG
*
107375655 ATATATACATAAACGTATACG
1 ATATATACA-AAACATATACG
*
107375676 ACATATA
1 ATATATA
107375683 TATTAGAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.52, C:0.10, G:0.06, T:0.31
Consensus pattern (20 bp):
ATATATACAAAACATATACG
Found at i:107375980 original size:12 final size:13
Alignment explanation
Indices: 107375948--107375980 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
107375938 TGAAAAAAAG
107375948 TAATAATA-ATAA
1 TAATAATATATAA
107375960 TAATAATATA-AA
1 TAATAATATATAA
107375972 TAATAATAT
1 TAATAATAT
107375981 TGAGATACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 19 0.95
13 1 0.05
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
TAATAATATATAA
Found at i:107376085 original size:3 final size:3
Alignment explanation
Indices: 107376071--107376104 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
107376061 AAGTAAACAC
107376071 TAA TACA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
107376105 ATTAAAGTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:107376688 original size:18 final size:19
Alignment explanation
Indices: 107376661--107376699 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
107376651 AAAGGTAAAA
107376661 TTTTTCCTTTTTTAT-TAT
1 TTTTTCCTTTTTTATATAT
*
107376679 TTTTTTCTTTTTTATATAT
1 TTTTTCCTTTTTTATATAT
107376698 TT
1 TT
107376700 ATTAAATATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.13, C:0.08, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTTTCCTTTTTTATATAT
Found at i:107380760 original size:17 final size:17
Alignment explanation
Indices: 107380734--107380772 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
107380724 CTCATAAAAG
*
107380734 TGGTTGTTTTTAATAAA
1 TGGTTATTTTTAATAAA
107380751 TGGTTATTTTTAATAAA
1 TGGTTATTTTTAATAAA
107380768 TGGTT
1 TGGTT
107380773 TGATTTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.18, T:0.54
Consensus pattern (17 bp):
TGGTTATTTTTAATAAA
Found at i:107382182 original size:57 final size:54
Alignment explanation
Indices: 107382113--107382227 Score: 185
Period size: 57 Copynumber: 2.1 Consensus size: 54
107382103 AGGAATAAAC
*
107382113 TTTTCTCCATATGTCTAAATAGGTATAACTTGTTGAAAACTATAATAATATGATTCT
1 TTTTCTCCATATGTCTAAATAGGTATAACTTGTCGAAAAC--T-ATAATATGATTCT
*
107382170 TTTTCTCTATATGTCTAAATAGGTATAACTTGTCGAAAACTATAATATGATTCT
1 TTTTCTCCATATGTCTAAATAGGTATAACTTGTCGAAAACTATAATATGATTCT
107382224 TTTT
1 TTTT
107382228 ACGCCTATTT
Statistics
Matches: 56, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
54 17 0.30
55 1 0.02
57 38 0.68
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.44
Consensus pattern (54 bp):
TTTTCTCCATATGTCTAAATAGGTATAACTTGTCGAAAACTATAATATGATTCT
Found at i:107383261 original size:80 final size:82
Alignment explanation
Indices: 107383150--107383308 Score: 191
Period size: 80 Copynumber: 2.0 Consensus size: 82
107383140 TTTAAAATTT
* * * * * *
107383150 TAATAATTTTTCTATAAGTTTCCTATATTTTTTTATAATTCTTAACAAAAATTGTAA-TATTTTA
1 TAATAATTTATCTAGAAGTTTCCTATATTTTTTAATAATTCTTAAAAAAAATTATAACT-TTTAA
107383214 ATAA-TTTTTATTAACAG
65 ATAACTTTTTATTAACAG
* *
107383231 TAATAATTTATCTAGAA-TTT-TTATAATTTTTTAATAATTTTTAAAAAAAATTATAACTTTTAA
1 TAATAATTTATCTAGAAGTTTCCTAT-ATTTTTTAATAATTCTTAAAAAAAATTATAACTTTTAA
*
107383294 ATAACTTTTTTTTAA
65 ATAACTTTTTATTAA
107383309 ATCCACATCA
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
79 3 0.05
80 38 0.58
81 25 0.38
ACGTcount: A:0.40, C:0.06, G:0.03, T:0.52
Consensus pattern (82 bp):
TAATAATTTATCTAGAAGTTTCCTATATTTTTTAATAATTCTTAAAAAAAATTATAACTTTTAAA
TAACTTTTTATTAACAG
Found at i:107387525 original size:21 final size:21
Alignment explanation
Indices: 107387499--107387539 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
107387489 ATCTGCTCAA
* *
107387499 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
107387520 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
107387540 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:107392344 original size:16 final size:17
Alignment explanation
Indices: 107392312--107392345 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
107392302 AATAAAATTT
107392312 TAAAATATTAATTTAATA
1 TAAAATATT-ATTTAATA
107392330 TAAAATATT-TTTAATA
1 TAAAATATTATTTAATA
107392346 CTATAATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
18 9 0.56
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TAAAATATTATTTAATA
Found at i:107392804 original size:16 final size:17
Alignment explanation
Indices: 107392775--107392817 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
107392765 TAAACAATAA
107392775 TATATAATATACTACTAT
1 TATAT-ATATACTACTAT
*
107392793 TATATATA-ACTATTAT
1 TATATATATACTACTAT
107392809 TATA-ATATA
1 TATATATATA
107392818 GATTATAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 3 0.13
16 12 0.52
17 3 0.13
18 5 0.22
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (17 bp):
TATATATATACTACTAT
Found at i:107393443 original size:13 final size:13
Alignment explanation
Indices: 107393425--107393452 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
107393415 TTCATGTGTT
107393425 TATACATTATTGG
1 TATACATTATTGG
107393438 TATACATTATTGG
1 TATACATTATTGG
107393451 TA
1 TA
107393453 AAAGAAGACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.07, G:0.14, T:0.46
Consensus pattern (13 bp):
TATACATTATTGG
Found at i:107393773 original size:48 final size:48
Alignment explanation
Indices: 107393717--107393812 Score: 183
Period size: 48 Copynumber: 2.0 Consensus size: 48
107393707 AAGGTGTAAG
107393717 GTGCAGATTCAAACAAGAAAGCCTACTATCTACCACATTGCGAGTTTA
1 GTGCAGATTCAAACAAGAAAGCCTACTATCTACCACATTGCGAGTTTA
*
107393765 GTGCAGATTCAAACAAGAAAGCCTACTATCTACCACATTGCGATTTTA
1 GTGCAGATTCAAACAAGAAAGCCTACTATCTACCACATTGCGAGTTTA
107393813 CATGTTAGCA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.26
Consensus pattern (48 bp):
GTGCAGATTCAAACAAGAAAGCCTACTATCTACCACATTGCGAGTTTA
Found at i:107398122 original size:18 final size:18
Alignment explanation
Indices: 107398090--107398127 Score: 69
Period size: 17 Copynumber: 2.2 Consensus size: 18
107398080 AATTTAAATA
107398090 AATGATAATTCTTTTTTT
1 AATGATAATTCTTTTTTT
107398108 AATG-TAATTCTTTTTTT
1 AATGATAATTCTTTTTTT
107398125 AAT
1 AAT
107398128 ATATTCATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.61
Consensus pattern (18 bp):
AATGATAATTCTTTTTTT
Found at i:107398704 original size:16 final size:17
Alignment explanation
Indices: 107398675--107398717 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
107398665 TAAACAATAA
107398675 TATATAATATACTACTAT
1 TATAT-ATATACTACTAT
*
107398693 TATATATA-ACTATTAT
1 TATATATATACTACTAT
107398709 TATA-ATATA
1 TATATATATA
107398718 GATTTTAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 3 0.13
16 12 0.52
17 3 0.13
18 5 0.22
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (17 bp):
TATATATATACTACTAT
Found at i:107398985 original size:18 final size:17
Alignment explanation
Indices: 107398940--107398985 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
107398930 AAATAATACA
107398940 TTTTATCTTTTTATTAT
1 TTTTATCTTTTTATTAT
* * *
107398957 TTCTATTTTTTTTTCTAT
1 TTTTATCTTTTTAT-TAT
107398975 TTTTATCTTTT
1 TTTTATCTTTT
107398986 AGTAAGAGTA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.13, C:0.09, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTATCTTTTTATTAT
Found at i:107402760 original size:30 final size:30
Alignment explanation
Indices: 107402726--107402786 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
107402716 TCCTTAACTC
107402726 AAACTTTAGAAAAATTACAATTTTGCCCCT
1 AAACTTTAGAAAAATTACAATTTTGCCCCT
* * * * *
107402756 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTAGAAAAATTACAATTTTGCCCCT
107402786 A
1 A
107402787 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.38
Consensus pattern (30 bp):
AAACTTTAGAAAAATTACAATTTTGCCCCT
Found at i:107406509 original size:26 final size:26
Alignment explanation
Indices: 107406480--107406553 Score: 130
Period size: 26 Copynumber: 2.8 Consensus size: 26
107406470 TTATTATGAC
*
107406480 ACATTTACCTAACCCATTATCATGGA
1 ACATTTACCTAACCTATTATCATGGA
*
107406506 ACATTTACCTAACCTTTTATCATGGA
1 ACATTTACCTAACCTATTATCATGGA
107406532 ACATTTACCTAACCTATTATCA
1 ACATTTACCTAACCTATTATCA
107406554 ATTTGTATCA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 45 1.00
ACGTcount: A:0.34, C:0.26, G:0.05, T:0.35
Consensus pattern (26 bp):
ACATTTACCTAACCTATTATCATGGA
Found at i:107407256 original size:46 final size:47
Alignment explanation
Indices: 107407196--107407292 Score: 178
Period size: 46 Copynumber: 2.1 Consensus size: 47
107407186 TATAAGTGCC
*
107407196 TAAACTTTTTATTTTCAGTAGTGATTTTTATTGTTATACAATTATAG
1 TAAACTTTTTATTTTCAGTAGTGATTCTTATTGTTATACAATTATAG
107407243 TAAAC-TTTTATTTTCAGTAGTGATTCTTATTGTTATACAATTATAG
1 TAAACTTTTTATTTTCAGTAGTGATTCTTATTGTTATACAATTATAG
107407289 TAAA
1 TAAA
107407293 AACAATCCAA
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
46 44 0.90
47 5 0.10
ACGTcount: A:0.32, C:0.07, G:0.10, T:0.51
Consensus pattern (47 bp):
TAAACTTTTTATTTTCAGTAGTGATTCTTATTGTTATACAATTATAG
Found at i:107408138 original size:16 final size:17
Alignment explanation
Indices: 107408109--107408146 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
107408099 AATAATATAC
107408109 AATAT-ACTACTATTAT
1 AATATAACTACTATTAT
*
107408125 -ATATAACTATTATTAT
1 AATATAACTACTATTAT
107408141 AATATA
1 AATATA
107408147 GATTATAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 4 0.21
16 10 0.53
17 5 0.26
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (17 bp):
AATATAACTACTATTAT
Found at i:107408311 original size:33 final size:33
Alignment explanation
Indices: 107408272--107408337 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
107408262 AGGGATAATT
107408272 TTTTGAATCCATGGATTTGCTAGAGACCTGTAA
1 TTTTGAATCCATGGATTTGCTAGAGACCTGTAA
107408305 TTTTGAATCCATGGATTTGCTAGAGACCTGTAA
1 TTTTGAATCCATGGATTTGCTAGAGACCTGTAA
107408338 CGCCCCAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.36
Consensus pattern (33 bp):
TTTTGAATCCATGGATTTGCTAGAGACCTGTAA
Found at i:107408668 original size:32 final size:32
Alignment explanation
Indices: 107408632--107408696 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
107408622 TGTATGCATT
107408632 TTAGCATTTTAATAGTTAATGGATGATGGGCA
1 TTAGCATTTTAATAGTTAATGGATGATGGGCA
107408664 TTAGCATTTTAATAGTTAATGGATGATGGGCA
1 TTAGCATTTTAATAGTTAATGGATGATGGGCA
107408696 T
1 T
107408697 GGTAAGCATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.31, C:0.06, G:0.25, T:0.38
Consensus pattern (32 bp):
TTAGCATTTTAATAGTTAATGGATGATGGGCA
Found at i:107410247 original size:26 final size:26
Alignment explanation
Indices: 107410218--107410270 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
107410208 TTTACAGTTT
107410218 TACCCCTAGGTGATAAATT-ACCGAAA
1 TACCCCTAGG-GATAAATTGACCGAAA
* *
107410244 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGGGATAAATTGACCGAAA
107410270 T
1 T
107410271 GCATGTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (26 bp):
TACCCCTAGGGATAAATTGACCGAAA
Found at i:107411892 original size:12 final size:12
Alignment explanation
Indices: 107411875--107411905 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
107411865 ACTCGAGGAA
107411875 GAGGCCGTGATC
1 GAGGCCGTGATC
*
107411887 GAGGCCGTGGTC
1 GAGGCCGTGATC
107411899 GAGGCCG
1 GAGGCCG
107411906 AGGTAGTACT
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:0.13, C:0.26, G:0.48, T:0.13
Consensus pattern (12 bp):
GAGGCCGTGATC
Found at i:107416758 original size:32 final size:32
Alignment explanation
Indices: 107416722--107416786 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
107416712 TGTATGCATT
107416722 TTAGCATTTTAATAGTTAATGGATAATGGGCA
1 TTAGCATTTTAATAGTTAATGGATAATGGGCA
*
107416754 TTAGCATTTTAATAGTTAATGGATGATGGGCA
1 TTAGCATTTTAATAGTTAATGGATAATGGGCA
107416786 T
1 T
107416787 GGTAAGCATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.32, C:0.06, G:0.23, T:0.38
Consensus pattern (32 bp):
TTAGCATTTTAATAGTTAATGGATAATGGGCA
Found at i:107420147 original size:26 final size:26
Alignment explanation
Indices: 107420118--107420173 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
107420108 TGATACAAAT
*
107420118 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
107420144 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
107420170 TGAT
1 TGAT
107420174 GGGAATTTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.30, C:0.05, G:0.27, T:0.38
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:107423081 original size:25 final size:25
Alignment explanation
Indices: 107423032--107423080 Score: 91
Period size: 24 Copynumber: 2.0 Consensus size: 25
107423022 AATGTAAAAA
107423032 AAAAAGAATTTTACTTTTATCTTTT
1 AAAAAGAATTTTACTTTTATCTTTT
107423057 AAAAA-AATTTTACTTTTATCTTTT
1 AAAAAGAATTTTACTTTTATCTTTT
107423081 TTGGAATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 19 0.79
25 5 0.21
ACGTcount: A:0.37, C:0.08, G:0.02, T:0.53
Consensus pattern (25 bp):
AAAAAGAATTTTACTTTTATCTTTT
Found at i:107424221 original size:16 final size:17
Alignment explanation
Indices: 107424192--107424234 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
107424182 TAAACAATAA
107424192 TATATAATATACTACTAT
1 TATAT-ATATACTACTAT
*
107424210 TATATATA-ACTATTAT
1 TATATATATACTACTAT
107424226 TATA-ATATA
1 TATATATATA
107424235 GATTATAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 3 0.13
16 12 0.52
17 3 0.13
18 5 0.22
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (17 bp):
TATATATATACTACTAT
Found at i:107424407 original size:227 final size:231
Alignment explanation
Indices: 107423982--107424408 Score: 569
Period size: 227 Copynumber: 1.9 Consensus size: 231
107423972 TAATACATAA
*
107423982 ATAACTATTATTATAATATAGATTATAATAAAAGATATAATATTACATGATATTATAATGTTTAA
1 ATAACTATTATTATAATATAGATTATAATAAAAGATATAATATTACATGATATTATAACGTTTAA
* * * * *
107424047 TCATCGATGCATATATATAAATTATTATCAGATTATATATGTTATGATATAGCATTATATAATAT
66 TCATCGATGCATATATAT-AATTA-TAGCAGATTATATATGTTAGGACATAACATTATATAACAT
* * * ** * * *
107424112 AGTAAGAGGGTTAACTTTTAAATGTATGAAAAGTATAGAGACTTGGAGCATATTTCAACTAGTAT
129 AGGAAGAGGGATAACTTTTAAATATAAAAAAAATATAGAGACTTAGAGCATATTTCAACTAATAT
107424177 AATAATAAACAATAATATATAATATACTACTATTATAT
194 AATAATAAACAATAATATATAATATACTACTATTATAT
* *
107424215 ATAACTATTATTATAATATAGATTATAATAAAA-ATATAGTATTACATTATATTATAACGTTTAA
1 ATAACTATTATTATAATATAGATTATAATAAAAGATATAATATTACATGATATTATAACGTTTAA
* ** *
107424279 TTATTTATGCATATATAT-A-TA-AGC-TATTA-ATATGTGATAGGACATAACATTATATAACAT
66 TCATCGATGCATATATATAATTATAGCAGATTATATATGT--TAGGACATAACATTATATAACAT
* * *
107424339 AGGAGGAGGGATAATTTTTAAATATAAAAAAAATATAGGGACTTAGAGCATATTTCAACTAATAT
129 AGGAAGAGGGATAACTTTTAAATATAAAAAAAATATAGAGACTTAGAGCATATTTCAACTAATAT
107424404 AATAA
194 AATAA
107424409 ATAATAATAT
Statistics
Matches: 169, Mismatches: 23, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
225 6 0.04
226 4 0.02
227 80 0.47
229 2 0.01
230 1 0.01
232 43 0.25
233 33 0.20
ACGTcount: A:0.45, C:0.06, G:0.11, T:0.38
Consensus pattern (231 bp):
ATAACTATTATTATAATATAGATTATAATAAAAGATATAATATTACATGATATTATAACGTTTAA
TCATCGATGCATATATATAATTATAGCAGATTATATATGTTAGGACATAACATTATATAACATAG
GAAGAGGGATAACTTTTAAATATAAAAAAAATATAGAGACTTAGAGCATATTTCAACTAATATAA
TAATAAACAATAATATATAATATACTACTATTATAT
Found at i:107424459 original size:227 final size:231
Alignment explanation
Indices: 107423982--107424459 Score: 544
Period size: 227 Copynumber: 2.1 Consensus size: 231
107423972 TAATACATAA
* * *
107423982 ATAACTATTATTATAATATAGATTATAATAAAAGATATAATATTACATGATATTATAATGTTTAA
1 ATAACTACTACTATAATATAGATTATAATAAAAGATATAATATTACATGATATTATAACGTTTAA
* * * * *
107424047 TCATCGATGCATATATATAAATTATTATCAGATTATATATGTTATGATATAGCATTATATAATAT
66 TCATCGATGCATATATAT-AATTA-TAGCAGATTATATATGTTAGGACATAACATTATATAACAT
* * * ** * * *
107424112 AGTAAGAGGGTTAACTTTTAAATGTATGAAAAGTATAGAGACTTGGAGCATATTTCAACTAGTAT
129 AGGAAGAGGGATAACTTTTAAATATAAAAAAAATATAGAGACTTAGAGCATATTTCAACTAATAT
*
107424177 AATAATAAACAATAATATATAATATACTACTATTATAT
194 AATAATAAACAATAATATATAATATAATACTATTATAT
* * * *
107424215 ATAACTATTATTATAATATAGATTATAATAAAA-ATATAGTATTACATTATATTATAACGTTTAA
1 ATAACTACTACTATAATATAGATTATAATAAAAGATATAATATTACATGATATTATAACGTTTAA
* ** *
107424279 TTATTTATGCATATATAT-A-TA-AGC-TATTA-ATATGTGATAGGACATAACATTATATAACAT
66 TCATCGATGCATATATATAATTATAGCAGATTATATATGT--TAGGACATAACATTATATAACAT
* * *
107424339 AGGAGGAGGGATAATTTTTAAATATAAAAAAAATATAGGGACTTAGAGCATATTTCAACTAATAT
129 AGGAAGAGGGATAACTTTTAAATATAAAAAAAATATAGAGACTTAGAGCATATTTCAACTAATAT
*
107424404 AATAA-ATAATAATATATGATAGTAAT-TAATA-TATTATAT
194 AATAATA-AACAATA-AT-ATA-TAATATAATACTATTATAT
*
107424443 ATTACT-CTACTATAATA
1 ATAACTACTACTATAATA
107424460 ATATGTAATA
Statistics
Matches: 211, Mismatches: 28, Indels: 18
0.82 0.11 0.07
Matches are distributed among these distances:
225 6 0.03
226 5 0.02
227 95 0.45
228 15 0.07
229 9 0.04
230 5 0.02
232 43 0.20
233 33 0.16
ACGTcount: A:0.46, C:0.06, G:0.10, T:0.38
Consensus pattern (231 bp):
ATAACTACTACTATAATATAGATTATAATAAAAGATATAATATTACATGATATTATAACGTTTAA
TCATCGATGCATATATATAATTATAGCAGATTATATATGTTAGGACATAACATTATATAACATAG
GAAGAGGGATAACTTTTAAATATAAAAAAAATATAGAGACTTAGAGCATATTTCAACTAATATAA
TAATAAACAATAATATATAATATAATACTATTATAT
Found at i:107424532 original size:16 final size:16
Alignment explanation
Indices: 107424498--107424546 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
107424488 ACAATTTATC
* *
107424498 TTTT-TATTATTTCTA
1 TTTTCTATTTTTTCTT
*
107424513 TTTTCTTTTTTTTCTT
1 TTTTCTATTTTTTCTT
107424529 TTTTCTATTTTTTCTT
1 TTTTCTATTTTTTCTT
107424545 TT
1 TT
107424547 AGTAAGAGTA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
15 4 0.14
16 25 0.86
ACGTcount: A:0.08, C:0.10, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTCTATTTTTTCTT
Found at i:107427824 original size:18 final size:20
Alignment explanation
Indices: 107427787--107427824 Score: 53
Period size: 18 Copynumber: 1.9 Consensus size: 20
107427777 AATTTTAATA
107427787 ATTTTTGTATAAGTTTCCTAT
1 ATTTTTGTATAAG-TTCCTAT
107427808 ATTTTT-TATAA-TTCCTA
1 ATTTTTGTATAAGTTCCTA
107427825 ACTAAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.35
20 5 0.29
21 6 0.35
ACGTcount: A:0.26, C:0.11, G:0.05, T:0.58
Consensus pattern (20 bp):
ATTTTTGTATAAGTTCCTAT
Found at i:107427872 original size:11 final size:11
Alignment explanation
Indices: 107427858--107427891 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
107427848 TTATCTAGAA
*
107427858 TTTTCATAATT
1 TTTTAATAATT
107427869 TTTTAATAATT
1 TTTTAATAATT
*
107427880 TTTTAAAAATT
1 TTTTAATAATT
107427891 T
1 T
107427892 ATAACTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (11 bp):
TTTTAATAATT
Found at i:107429872 original size:66 final size:66
Alignment explanation
Indices: 107429796--107429929 Score: 241
Period size: 66 Copynumber: 2.0 Consensus size: 66
107429786 ATAGAATAAT
* *
107429796 AAAAATAATCATGCTAAGCAAATGGGAATATACCCAAAAGAAAACATAATAAACGCACTAATTAT
1 AAAAACAATCATGCTAAGCAAATGGGAATATACCCAAAAGAAAACATAATAAACGCACTAATCAT
107429861 A
66 A
*
107429862 AAAAACAATCATGCTAAGCAAATGGGAATATACCCAAAAGAAAACATAATAAATGCACTAATCAT
1 AAAAACAATCATGCTAAGCAAATGGGAATATACCCAAAAGAAAACATAATAAACGCACTAATCAT
107429927 A
66 A
107429928 AA
1 AA
107429930 TAAAACATTA
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.55, C:0.16, G:0.10, T:0.19
Consensus pattern (66 bp):
AAAAACAATCATGCTAAGCAAATGGGAATATACCCAAAAGAAAACATAATAAACGCACTAATCAT
A
Found at i:107430532 original size:21 final size:21
Alignment explanation
Indices: 107430489--107430532 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
107430479 AATGAACAAT
*
107430489 AAAAAATTTAATAAATATTCA
1 AAAAAATTTAATAAATATGCA
*
107430510 AAAAAATTT-ATACAATGTGCA
1 AAAAAATTTAATA-AATATGCA
107430531 AA
1 AA
107430533 TTTTAAAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.59, C:0.07, G:0.05, T:0.30
Consensus pattern (21 bp):
AAAAAATTTAATAAATATGCA
Found at i:107435740 original size:18 final size:19
Alignment explanation
Indices: 107435713--107435751 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
107435703 TTCGTTTTTG
107435713 TTTCAAATTT-AGTCCATT
1 TTTCAAATTTAAGTCCATT
* *
107435731 TTTCAGATTTAAGTTCATT
1 TTTCAAATTTAAGTCCATT
107435750 TT
1 TT
107435752 CATATTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.26, C:0.13, G:0.08, T:0.54
Consensus pattern (19 bp):
TTTCAAATTTAAGTCCATT
Found at i:107435904 original size:21 final size:22
Alignment explanation
Indices: 107435871--107435937 Score: 68
Period size: 24 Copynumber: 3.1 Consensus size: 22
107435861 TATGACGTAC
107435871 ATATTT-T-TAATATTA-TAAT
1 ATATTTATATAATATTATTAAT
107435890 ATATTTATATAATATTATTAAT
1 ATATTTATATAATATTATTAAT
* * *
107435912 AAATTTTATATTAATAATATTCAT
1 ATA-TTTATA-TAATATTATTAAT
107435936 AT
1 AT
107435938 TAGGTATATA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
19 6 0.15
20 1 0.03
21 8 0.21
22 6 0.15
23 6 0.15
24 12 0.31
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (22 bp):
ATATTTATATAATATTATTAAT
Found at i:107435926 original size:24 final size:23
Alignment explanation
Indices: 107435877--107435932 Score: 71
Period size: 24 Copynumber: 2.5 Consensus size: 23
107435867 GTACATATTT
*
107435877 TTAATATTA-TAATATATTTATA
1 TTAATATTATTAATAAATTTATA
107435899 -TAATATTATTAATAAATTTTATA
1 TTAATATTATTAATAAA-TTTATA
*
107435922 TTAATAATATT
1 TTAATATTATT
107435933 CATATTAGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 8 0.28
22 6 0.21
23 6 0.21
24 9 0.31
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
TTAATATTATTAATAAATTTATA
Found at i:107435959 original size:15 final size:14
Alignment explanation
Indices: 107435884--107435955 Score: 50
Period size: 13 Copynumber: 5.4 Consensus size: 14
107435874 TTTTTAATAT
107435884 TATAATATAT-TTA
1 TATAATATATATTA
107435897 TATAATAT-TATTA
1 TATAATATATATTA
107435910 -ATAA-AT-T-TTA
1 TATAATATATATTA
107435920 TATTAATA-ATATTCA
1 TA-TAATATATATT-A
*
107435935 TATTAGGTATATATTA
1 TA-TA-ATATATATTA
107435951 TATAA
1 TATAA
107435956 GTATTCTAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 17
0.72 0.03 0.25
Matches are distributed among these distances:
10 3 0.06
11 4 0.08
12 8 0.17
13 13 0.27
14 2 0.04
15 8 0.17
16 5 0.10
17 5 0.10
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (14 bp):
TATAATATATATTA
Found at i:107436054 original size:19 final size:21
Alignment explanation
Indices: 107436019--107436061 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
107436009 TCTTAATATC
107436019 ATACTTTTATTGTTATG-TAT
1 ATACTTTTATTGTTATGTTAT
107436039 ATAC-TTTATATG-TATGTTAT
1 ATACTTTTAT-TGTTATGTTAT
107436059 ATA
1 ATA
107436062 TGTTATGTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.30, C:0.05, G:0.09, T:0.56
Consensus pattern (21 bp):
ATACTTTTATTGTTATGTTAT
Found at i:107436076 original size:15 final size:15
Alignment explanation
Indices: 107436045--107436091 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
107436035 GTATATACTT
107436045 TATATG-TATGT-TA
1 TATATGTTATGTATA
107436058 TATATGTTATGTATA
1 TATATGTTATGTATA
107436073 TATATGGTTA-GTAT-
1 TATAT-GTTATGTATA
107436087 TATAT
1 TATAT
107436092 TTCTATATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
13 6 0.19
14 10 0.32
15 11 0.35
16 4 0.13
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53
Consensus pattern (15 bp):
TATATGTTATGTATA
Found at i:107436352 original size:29 final size:28
Alignment explanation
Indices: 107436318--107436408 Score: 75
Period size: 28 Copynumber: 3.3 Consensus size: 28
107436308 ATATAAGCTA
107436318 TGTATATA-CCTTTAATACCATATTATT
1 TGTATATATCCTTTAATACCATATTATT
* * *
107436345 TGTATATATTCTTAAATACCAT-TACATT
1 TGTATATATCCTTTAATACCATAT-TATT
* *
107436373 TATATA-ATTCCTTTTAATACCACATTA--
1 TGTATATA-TCC-TTTAATACCATATTATT
107436400 TGTATATAT
1 TGTATATAT
107436409 TATGCTTTTT
Statistics
Matches: 49, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
27 16 0.33
28 22 0.45
29 10 0.20
30 1 0.02
ACGTcount: A:0.35, C:0.14, G:0.03, T:0.47
Consensus pattern (28 bp):
TGTATATATCCTTTAATACCATATTATT
Found at i:107438033 original size:18 final size:20
Alignment explanation
Indices: 107438010--107438049 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
107438000 AATATACTAC
*
107438010 TATAATTAAA-ATATAG-AT
1 TATAATAAAAGATATAGTAT
107438028 TATAATAAAAGATATAGTAT
1 TATAATAAAAGATATAGTAT
107438048 TA
1 TA
107438050 CATGATATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 9 0.47
19 6 0.32
20 4 0.21
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (20 bp):
TATAATAAAAGATATAGTAT
Found at i:107440990 original size:118 final size:118
Alignment explanation
Indices: 107440766--107440996 Score: 345
Period size: 118 Copynumber: 2.0 Consensus size: 118
107440756 TATTTCCGGT
*
107440766 TAGCGGAGTTTTACCCAACACGTCACACAACTTTTTGACGCGAAGTAGAATGACAACCCAAGCAC
1 TAGCGGAGTTTTACCCAACACGTCACACAACCTTTTGACGCGAAGTAGAATGACAACCCAAGCAC
* * *
107440831 CCTACCCCGGTTACTCAGTCAGTCACGATTTGAGCCATACTCATAACCTCGGC
66 CCTACCCCGATTACTCAGTCAGTCACGATCTAAGCCATACTCATAACCTCGGC
**** *
107440884 TAGCGGAGTTTTACTTGTCACGTCACACAACCTTTTGACGCGAAGTAGAATGACAACCTAAGCAC
1 TAGCGGAGTTTTACCCAACACGTCACACAACCTTTTGACGCGAAGTAGAATGACAACCCAAGCAC
* ***
107440949 CCTACCCTGATTACTCAGTCAGTCACGATCTAAGTTGTACTCATAACC
66 CCTACCCCGATTACTCAGTCAGTCACGATCTAAGCCATACTCATAACC
107440997 ATGGAAAACA
Statistics
Matches: 100, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
118 100 1.00
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.24
Consensus pattern (118 bp):
TAGCGGAGTTTTACCCAACACGTCACACAACCTTTTGACGCGAAGTAGAATGACAACCCAAGCAC
CCTACCCCGATTACTCAGTCAGTCACGATCTAAGCCATACTCATAACCTCGGC
Found at i:107441916 original size:5 final size:5
Alignment explanation
Indices: 107441906--107441978 Score: 60
Period size: 5 Copynumber: 13.8 Consensus size: 5
107441896 AATATTTAAC
* *
107441906 TAAAA TAAAA TAAAA TAAAA TAATAA -ATAA TAAAA TAAAA GAAAGA -AAAA
1 TAAAA TAAAA TAAAA TAAAA TAA-AA TAAAA TAAAA TAAAA TAAA-A TAAAA
107441956 TAATAAA TAAAAA TAAAAA TAAA
1 T-A-AAA T-AAAA T-AAAA TAAA
107441979 GATTGGGTTG
Statistics
Matches: 59, Mismatches: 3, Indels: 12
0.80 0.04 0.16
Matches are distributed among these distances:
4 3 0.05
5 36 0.61
6 14 0.24
7 6 0.10
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (5 bp):
TAAAA
Found at i:107441940 original size:30 final size:29
Alignment explanation
Indices: 107441906--107441980 Score: 72
Period size: 25 Copynumber: 2.8 Consensus size: 29
107441896 AATATTTAAC
*
107441906 TAAA-ATAAAATAAAAT-AA-AATAATAA
1 TAAATATAAAATAAAATAAAGAAAAATAA
* *
107441932 -ATA-ATAAAATAAAAGAAAGAAAAATAA
1 TAAATATAAAATAAAATAAAGAAAAATAA
107441959 TAAATA-AAAATAAAAATAAAGA
1 TAAATATAAAAT-AAAATAAAGA
107441981 TTGGGTTGCC
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
25 13 0.33
26 2 0.05
27 7 0.18
28 7 0.18
29 10 0.26
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (29 bp):
TAAATATAAAATAAAATAAAGAAAAATAA
Found at i:107447239 original size:26 final size:26
Alignment explanation
Indices: 107447202--107447259 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
107447192 TGATACAAAT
107447202 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
107447228 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
107447254 TGATAA
1 TGATAA
107447260 GAATTTCATG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:107452249 original size:26 final size:24
Alignment explanation
Indices: 107452196--107452272 Score: 81
Period size: 23 Copynumber: 3.2 Consensus size: 24
107452186 ATAGCAATAG
*
107452196 TAATAATA-TAATAATAAAGTAAAA
1 TAATAATAGTAATAATTAA-TAAAA
107452220 -AATAATAGTAATACATTAATAAGAA
1 TAATAATAGTAATA-ATTAATAA-AA
107452245 TAATAATAGT-AT-ATTAATAACAA
1 TAATAATAGTAATAATTAATAA-AA
107452268 TAATA
1 TAATA
107452273 GAAAATAATG
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
23 22 0.47
24 8 0.17
25 8 0.17
26 9 0.19
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.31
Consensus pattern (24 bp):
TAATAATAGTAATAATTAATAAAA
Found at i:107452458 original size:3 final size:3
Alignment explanation
Indices: 107452191--107452428 Score: 59
Period size: 3 Copynumber: 79.7 Consensus size: 3
107452181 TGATGATAGC
* * *
107452191 AAT AGT AAT AAT -AT AAT AAT AA- AGT AA- AA- AAT AAT AGT AAT ACATT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-A-T
* * * * *
107452237 AAT AAG AAT AAT AAT AGT -AT ATT AAT AAC AAT AAT AGAA AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT
** * * * * *
107452282 GACG AGAT AGT AAT AAT AAT AAT AA- ACT AA- AGAGT ACT AAT AGT ACT
1 -AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT A-A-T AAT AAT AAT AAT
* * * * *
107452329 AAC AAT AAT -AT AAAT AAT AAT GAA- AAC AAC AAG AGA- AAT AAT AAC
1 AAT AAT AAT AAT -AAT AAT AAT -AAT AAT AAT AAT A-AT AAT AAT AAT
* * * * **
107452374 AAT AA- CAG AAT AAA AAT AAT GAT AAT AAT AAT AGC AAT AAT AAT AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
107452420 AATT AAT AA
1 AA-T AAT AA
107452429 ATAAATATAA
Statistics
Matches: 168, Mismatches: 45, Indels: 44
0.65 0.18 0.17
Matches are distributed among these distances:
2 18 0.11
3 134 0.80
4 13 0.08
5 3 0.02
ACGTcount: A:0.61, C:0.05, G:0.08, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:107453109 original size:22 final size:22
Alignment explanation
Indices: 107453084--107453142 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 22
107453074 TTACAAACGG
*
107453084 TTCTCCCTTAAAATACGATCGA
1 TTCTCCCTTAAAATACCATCGA
*
107453106 TTCTTCCC-CAAAATACCATCGA
1 TTC-TCCCTTAAAATACCATCGA
* *
107453128 TCCCCCCTTACAAAT
1 TTCTCCCTTA-AAAT
107453143 GATAGATTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
21 3 0.10
22 18 0.62
23 8 0.28
ACGTcount: A:0.31, C:0.36, G:0.05, T:0.29
Consensus pattern (22 bp):
TTCTCCCTTAAAATACCATCGA
Found at i:107454618 original size:68 final size:69
Alignment explanation
Indices: 107454509--107454651 Score: 279
Period size: 68 Copynumber: 2.1 Consensus size: 69
107454499 ATTGTTGTGA
107454509 AAGTGGGTGGACAAGGCCCACTCAAGGAGTAGGAGGCCTGAGTTCTTTGCTGAGAGCAAGGGGAG
1 AAGTGGGTGGACAAGGCCCACTCAAGGAGTAGGAGGCCTGAGTTCTTTGCTGAGAGCAAGGGGAG
107454574 GG-T
66 GGTT
107454577 AAGTGGGTGGACAAGGCCCACTCAAGGAGTAGGAGGCCTGAGTTCTTTGCTGAGAGCAAGGGGAG
1 AAGTGGGTGGACAAGGCCCACTCAAGGAGTAGGAGGCCTGAGTTCTTTGCTGAGAGCAAGGGGAG
107454642 GGTT
66 GGTT
107454646 AAGTGG
1 AAGTGG
107454652 AGAGAGAGCG
Statistics
Matches: 74, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
68 67 0.91
69 7 0.09
ACGTcount: A:0.25, C:0.15, G:0.41, T:0.18
Consensus pattern (69 bp):
AAGTGGGTGGACAAGGCCCACTCAAGGAGTAGGAGGCCTGAGTTCTTTGCTGAGAGCAAGGGGAG
GGTT
Found at i:107459328 original size:13 final size:13
Alignment explanation
Indices: 107459310--107459343 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
107459300 TTATTTTCCC
*
107459310 TTTCATTTATTAT
1 TTTCATCTATTAT
107459323 TTTCATCTATTAT
1 TTTCATCTATTAT
*
107459336 TTACATCT
1 TTTCATCT
107459344 TGCTATTATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.24, C:0.15, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTCATCTATTAT
Found at i:107465802 original size:27 final size:26
Alignment explanation
Indices: 107465764--107465814 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
107465754 CTAAATTAAT
* *
107465764 AATGGTAAAATTGTACTTTAATCTTGA
1 AATGATAAAATT-TAATTTAATCTTGA
107465791 AATGATAAAATTTAATTTAATCTT
1 AATGATAAAATTTAATTTAATCTT
107465815 TTAAAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 11 0.50
27 11 0.50
ACGTcount: A:0.41, C:0.06, G:0.10, T:0.43
Consensus pattern (26 bp):
AATGATAAAATTTAATTTAATCTTGA
Found at i:107469182 original size:83 final size:84
Alignment explanation
Indices: 107469018--107469174 Score: 253
Period size: 83 Copynumber: 1.9 Consensus size: 84
107469008 AATCTGATTC
* ** *
107469018 CTCTTCAAAAATGAAAAAGTTTCAATTTAGTCATCTTATAAATAGAGAAATTATAAATTAATATA
1 CTCTTCAAAAATGAAAAAGTTTCAATTCAAACATCTTATAAATAAAGAAATTATAAATTAATATA
*
107469083 TAGTGAAATAGAACTTTGG
66 TAGTAAAATAGAACTTTGG
*
107469102 CTCTTC-AAAATGAAAAATTTTCAATTCAAACATCTTATAAATAAAGAAATTATAAATTAATATA
1 CTCTTCAAAAATGAAAAAGTTTCAATTCAAACATCTTATAAATAAAGAAATTATAAATTAATATA
107469166 TAGTAAAAT
66 TAGTAAAAT
107469175 TACACTTTAA
Statistics
Matches: 67, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
83 61 0.91
84 6 0.09
ACGTcount: A:0.48, C:0.09, G:0.08, T:0.34
Consensus pattern (84 bp):
CTCTTCAAAAATGAAAAAGTTTCAATTCAAACATCTTATAAATAAAGAAATTATAAATTAATATA
TAGTAAAATAGAACTTTGG
Found at i:107470007 original size:47 final size:47
Alignment explanation
Indices: 107469956--107470121 Score: 181
Period size: 47 Copynumber: 3.5 Consensus size: 47
107469946 TCTACCAGAT
* * * *
107469956 AATACTCTAATAACTCACGTCTTATTTTAATCCCACATTCACTAAAG
1 AATACTTTAATAGCTTACATCTTATTTTAATCCCACATTCACTAAAG
* * * * * *
107470003 AATACTTCAATAGCTTACTTCTTTACTATTAATCTCACA-TCTACTAGAT
1 AATACTTTAATAGCTTACATC-TTA-TTTTAATCCCACATTC-ACTAAAG
* *
107470052 CATACTTTAATAGCTTACATTTTATTTTAATCCCACATTCACTAAAG
1 AATACTTTAATAGCTTACATCTTATTTTAATCCCACATTCACTAAAG
*
107470099 AATACTTTAATAGCTTACTTCTT
1 AATACTTTAATAGCTTACATCTT
107470122 TACTATTTTT
Statistics
Matches: 95, Mismatches: 20, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
47 52 0.55
48 10 0.11
49 33 0.35
ACGTcount: A:0.34, C:0.22, G:0.04, T:0.40
Consensus pattern (47 bp):
AATACTTTAATAGCTTACATCTTATTTTAATCCCACATTCACTAAAG
Found at i:107470042 original size:49 final size:49
Alignment explanation
Indices: 107469982--107470128 Score: 201
Period size: 49 Copynumber: 3.0 Consensus size: 49
107469972 ACGTCTTATT
*
107469982 TTAATCCCACATTCACTAAAGAATACTTCAATAGCTTACTTCTTTACTA
1 TTAATCCCACATTCACTAAAGAATACTTTAATAGCTTACTTCTTTACTA
* * ** * *
107470031 TTAATCTCACA-TCTACTAGATCATACTTTAATAGCTTACAT-TTTA-TT
1 TTAATCCCACATTC-ACTAAAGAATACTTTAATAGCTTACTTCTTTACTA
107470078 TTAATCCCACATTCACTAAAGAATACTTTAATAGCTTACTTCTTTACTA
1 TTAATCCCACATTCACTAAAGAATACTTTAATAGCTTACTTCTTTACTA
107470127 TT
1 TT
107470129 TTTATTAAAA
Statistics
Matches: 81, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
47 34 0.42
48 12 0.15
49 35 0.43
ACGTcount: A:0.33, C:0.22, G:0.04, T:0.41
Consensus pattern (49 bp):
TTAATCCCACATTCACTAAAGAATACTTTAATAGCTTACTTCTTTACTA
Found at i:107470099 original size:96 final size:96
Alignment explanation
Indices: 107469942--107470128 Score: 302
Period size: 96 Copynumber: 1.9 Consensus size: 96
107469932 ATTTTAATTC
*
107469942 CACATCTACCAGATAATACTCTAATAACTCACGTCTTATTTTAATCCCACATTCACTAAAGAATA
1 CACATCTACCAGATAATACTCTAATAACTCACATCTTATTTTAATCCCACATTCACTAAAGAATA
107470007 CTTCAATAGCTTACTTCTTTACTATTAATCT
66 CTTCAATAGCTTACTTCTTTACTATTAATCT
* * * * * *
107470038 CACATCTACTAGATCATACTTTAATAGCTTACATTTTATTTTAATCCCACATTCACTAAAGAATA
1 CACATCTACCAGATAATACTCTAATAACTCACATCTTATTTTAATCCCACATTCACTAAAGAATA
*
107470103 CTTTAATAGCTTACTTCTTTACTATT
66 CTTCAATAGCTTACTTCTTTACTATT
107470129 TTTATTAAAA
Statistics
Matches: 83, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
96 83 1.00
ACGTcount: A:0.34, C:0.23, G:0.04, T:0.39
Consensus pattern (96 bp):
CACATCTACCAGATAATACTCTAATAACTCACATCTTATTTTAATCCCACATTCACTAAAGAATA
CTTCAATAGCTTACTTCTTTACTATTAATCT
Found at i:107470727 original size:15 final size:16
Alignment explanation
Indices: 107470701--107470730 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
107470691 AATTATTTTA
107470701 ATTTATTTATTAAATG
1 ATTTATTTATTAAATG
107470717 ATTTA-TTATTAAAT
1 ATTTATTTATTAAAT
107470731 TCAAAATATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (16 bp):
ATTTATTTATTAAATG
Found at i:107476958 original size:22 final size:22
Alignment explanation
Indices: 107476930--107476975 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
107476920 AATTGATTTA
107476930 TTCTTTAAGTGATACGCCATTG
1 TTCTTTAAGTGATACGCCATTG
107476952 TTCTTTAAGTGATACGCCATTG
1 TTCTTTAAGTGATACGCCATTG
107476974 TT
1 TT
107476976 GTTCTGTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.43
Consensus pattern (22 bp):
TTCTTTAAGTGATACGCCATTG
Found at i:107477181 original size:30 final size:30
Alignment explanation
Indices: 107477096--107477181 Score: 84
Period size: 30 Copynumber: 2.8 Consensus size: 30
107477086 TTGAGGGGAT
* *
107477096 TTAATGAGAATTTTCAAAAGTTTTGGTAGGC
1 TTAATGAGAATTTT-AAAAATTTTTGTAGGC
* * * *
107477127 CTAATTAGAACTTTAGCAAA-TTTTGTAGGC
1 TTAATGAGAATTTTA-AAAATTTTTGTAGGC
*
107477157 TTAATGAGAGTTTTAAAAATTTTTG
1 TTAATGAGAATTTTAAAAATTTTTG
107477182 AAAACCTTCA
Statistics
Matches: 42, Mismatches: 11, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
29 3 0.07
30 26 0.62
31 13 0.31
ACGTcount: A:0.34, C:0.07, G:0.19, T:0.41
Consensus pattern (30 bp):
TTAATGAGAATTTTAAAAATTTTTGTAGGC
Found at i:107477593 original size:22 final size:22
Alignment explanation
Indices: 107477568--107477615 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
107477558 CCAGCAAACC
107477568 TACCCCCACTACAACAGCCCCA
1 TACCCCCACTACAACAGCCCCA
* *
107477590 TACCTCCACTACAACAGTCCCA
1 TACCCCCACTACAACAGCCCCA
107477612 TACC
1 TACC
107477616 GTCTGACACC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.31, C:0.50, G:0.04, T:0.15
Consensus pattern (22 bp):
TACCCCCACTACAACAGCCCCA
Found at i:107478729 original size:16 final size:16
Alignment explanation
Indices: 107478710--107478740 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
107478700 TATTGTTATC
*
107478710 TATTTATTTATATTTA
1 TATTTATTTAAATTTA
107478726 TATTTATTTAAATTT
1 TATTTATTTAAATTT
107478741 TCGGTACATA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TATTTATTTAAATTTA
Found at i:107480301 original size:22 final size:22
Alignment explanation
Indices: 107480270--107480315 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
107480260 TTAAAATATA
*
107480270 TAAAAGTATTAAAATGAAGCTT
1 TAAAAATATTAAAATGAAGCTT
*
107480292 TAAAAATATTTAAATGAAGCTT
1 TAAAAATATTAAAATGAAGCTT
107480314 TA
1 TA
107480316 GTTGAGTGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.04, G:0.11, T:0.35
Consensus pattern (22 bp):
TAAAAATATTAAAATGAAGCTT
Found at i:107499216 original size:3 final size:3
Alignment explanation
Indices: 107499205--107499234 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
107499195 AAAAAAAAAA
107499205 AAG AGAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG A-AG AAG AAG AAG AAG AAG AAG AAG AA
107499235 AAGGCTTTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:107500758 original size:119 final size:119
Alignment explanation
Indices: 107500610--107500844 Score: 434
Period size: 119 Copynumber: 2.0 Consensus size: 119
107500600 TTGAAAAATG
*
107500610 AGGAATAGTTAAAGTACCAAGTTGCATATTAACCCATAAAAAAATGGGGTAAATAAGTCAAAACC
1 AGGAATAGTTAAAGTACCAAGTTGCATATTAACCCATAAAAAAATGGGGCAAATAAGTCAAAACC
*
107500675 GAAAACCCTCCATTTAGGTTTGGTTATTGTATAGCCTACACTACAGTGCAAACT
66 AAAAACCCTCCATTTAGGTTTGGTTATTGTATAGCCTACACTACAGTGCAAACT
*
107500729 AGGAATAGTTAAAGTACCAAGTTGCATATTAACCCATAAAAAAATGGGGCAAATAAGTCAAAACT
1 AGGAATAGTTAAAGTACCAAGTTGCATATTAACCCATAAAAAAATGGGGCAAATAAGTCAAAACC
*
107500794 AAAAACCCTTCATTTAGGTTTGGTTATTGTATAGCCTACACTACAGTGCAA
66 AAAAACCCTCCATTTAGGTTTGGTTATTGTATAGCCTACACTACAGTGCAA
107500845 GCTATCTCCT
Statistics
Matches: 112, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
119 112 1.00
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (119 bp):
AGGAATAGTTAAAGTACCAAGTTGCATATTAACCCATAAAAAAATGGGGCAAATAAGTCAAAACC
AAAAACCCTCCATTTAGGTTTGGTTATTGTATAGCCTACACTACAGTGCAAACT
Found at i:107506651 original size:29 final size:31
Alignment explanation
Indices: 107506590--107506652 Score: 78
Period size: 29 Copynumber: 2.1 Consensus size: 31
107506580 AAAATTATAT
*
107506590 ATGAATTTTGATTTAATGTTCAATTTGATAC
1 ATGAATTTTGATTTAATGTTCAATTTGACAC
*
107506621 ATGAATTTT-ATTT-TTGTTCAATTAT-ACAC
1 ATGAATTTTGATTTAATGTTCAATT-TGACAC
107506650 ATG
1 ATG
107506653 GTATTTTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 15 0.52
30 5 0.17
31 9 0.31
ACGTcount: A:0.32, C:0.08, G:0.11, T:0.49
Consensus pattern (31 bp):
ATGAATTTTGATTTAATGTTCAATTTGACAC
Found at i:107519709 original size:32 final size:32
Alignment explanation
Indices: 107519670--107519737 Score: 100
Period size: 32 Copynumber: 2.1 Consensus size: 32
107519660 GTTAAATTTC
* * *
107519670 TAATTAATACTAATTTTTTCAAGGCTTTGTAT
1 TAATTAATACTAATATATTCAAGGATTTGTAT
*
107519702 TAATTAATCCTAATATATTCAAGGATTTGTAT
1 TAATTAATACTAATATATTCAAGGATTTGTAT
107519734 TAAT
1 TAAT
107519738 CGACCTCTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.35, C:0.09, G:0.09, T:0.47
Consensus pattern (32 bp):
TAATTAATACTAATATATTCAAGGATTTGTAT
Found at i:107521429 original size:23 final size:23
Alignment explanation
Indices: 107521398--107521441 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
107521388 AAACTATTAG
107521398 GAACAAAATCGTGAAATCCTTTA
1 GAACAAAATCGTGAAATCCTTTA
*
107521421 GAACCAAATCGTGAAATCCTT
1 GAACAAAATCGTGAAATCCTT
107521442 AATCTTTCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.25
Consensus pattern (23 bp):
GAACAAAATCGTGAAATCCTTTA
Found at i:107522431 original size:22 final size:22
Alignment explanation
Indices: 107522401--107522442 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
107522391 TAAGCATATG
*
107522401 ATTTGGATAAATGTACTTTACA
1 ATTTCGATAAATGTACTTTACA
107522423 ATTTCGATAAATGTACTTTA
1 ATTTCGATAAATGTACTTTA
107522443 TAAAAGCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.43
Consensus pattern (22 bp):
ATTTCGATAAATGTACTTTACA
Found at i:107523525 original size:40 final size:40
Alignment explanation
Indices: 107523472--107523552 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
107523462 GGAAAAAAGT
*
107523472 AAGCTTTCTTGTAGGTATCAATGTGATAATATTCATGCAA
1 AAGCTTTCTTGTAGGTATCAATGTAATAATATTCATGCAA
107523512 AAGCTTTCTTGTAGGTATCAATGTAATAATATTCATGCAA
1 AAGCTTTCTTGTAGGTATCAATGTAATAATATTCATGCAA
107523552 A
1 A
107523553 TATTCATCTG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (40 bp):
AAGCTTTCTTGTAGGTATCAATGTAATAATATTCATGCAA
Found at i:107525340 original size:51 final size:51
Alignment explanation
Indices: 107525261--107525413 Score: 225
Period size: 51 Copynumber: 3.0 Consensus size: 51
107525251 CTACGTGTAG
* * * *
107525261 CAGCAACATTATCTAGTCCATCTAATGTTGCAAAGTCACCAGCATATTCAT
1 CAGCAACATTATCCACTCCATCTGATGTTGCAAAATCACCAGCATATTCAT
* * *
107525312 CAGCAACATTATCCACTCTATCTGATGTTACAAAATCACCAACATATTCAT
1 CAGCAACATTATCCACTCCATCTGATGTTGCAAAATCACCAGCATATTCAT
* *
107525363 CAGCAACATTATCCACTCCATCTGATGTTGTAAAATCACTAGCATATTCAT
1 CAGCAACATTATCCACTCCATCTGATGTTGCAAAATCACCAGCATATTCAT
107525414 TACCAGCAAC
Statistics
Matches: 90, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 90 1.00
ACGTcount: A:0.35, C:0.26, G:0.09, T:0.30
Consensus pattern (51 bp):
CAGCAACATTATCCACTCCATCTGATGTTGCAAAATCACCAGCATATTCAT
Found at i:107525578 original size:33 final size:33
Alignment explanation
Indices: 107525541--107525610 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
107525531 CATCAGCTTG
* *
107525541 TACCTTTCCTACATCACCCTCCTCACCAGATTC
1 TACCTTTCCTAAATCACCCTCATCACCAGATTC
* * *
107525574 TACCTTTTCTAAATCACCTTCATCATCAGATTC
1 TACCTTTCCTAAATCACCCTCATCACCAGATTC
107525607 TACC
1 TACC
107525611 ACTTTATCAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.24, C:0.39, G:0.03, T:0.34
Consensus pattern (33 bp):
TACCTTTCCTAAATCACCCTCATCACCAGATTC
Found at i:107526694 original size:18 final size:16
Alignment explanation
Indices: 107526651--107526686 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
107526641 GAATGCTATC
* *
107526651 GATTTAGGTATTTGAA
1 GATTTAGGGACTTGAA
107526667 GATTTAGGGACTTGAA
1 GATTTAGGGACTTGAA
107526683 GATT
1 GATT
107526687 GTTAGGGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.31, C:0.03, G:0.28, T:0.39
Consensus pattern (16 bp):
GATTTAGGGACTTGAA
Found at i:107528019 original size:318 final size:321
Alignment explanation
Indices: 107527439--107528049 Score: 953
Period size: 318 Copynumber: 1.9 Consensus size: 321
107527429 CCTAACATCT
107527439 TGTGGCTGTAGTTTAGTGGTAAGAATTCCACGTTGTGGCCGTGGAGACCTGGGCTCGAATCCCAG
1 TGTGGCTGTAGTTTAGTGGTAAGAATTCCACGTTGTGGCCGTGGAGACCTGGGCTCGAATCCCAG
* * *
107527504 CAGCCACACAAAGAAAAAAAATTTTACCTTCATTTTCGCAACCTCTGTTTTTAGGCTCTGTTCCT
66 CAGCCACAC--AGAAAAAAAATTTTACCTTCATTTCCACAACCTCTGTTTCTAGGCTCTGTTCCT
* * *
107527569 TTGGGCCTACTTATAGTTTAAAAAAGAACCCAAAACGCAAGTCGTTTTGTTTCCTAAATCGTTGC
129 TTGGGCCAACTTATAGTTTAAAAAAGAACCCAAAACGCAAGTCGTTTCGTTTCCTAAACCGTTGC
107527634 TACGAACTACACAAATTCTAAAAAACCATCGACTTGAAAAAAACGTATTCTTGTTTTCCGCTTTT
194 TACGAACTACACAAATTCTAAAAAACCATCGACTT-AAAAAAACGTATTCTTGTTTTCCGCTTTT
107527699 CAG-CTTT-GTCATTTTTCC-CCTTGAGATCTAGTGATTATGGATTTGGCTACGATGAATATCC
258 CAGTCTTTCGTCATTTTTCCTCCTTGAGATCTAGTGATTATGGATTTGGCTACGATGAATATCC
107527760 TGTGGCTGTAGTTTAGTGGTAAGAATTCCACGTTGTGGCCGTGGAGACCTGGGCTCGAATCCCAG
1 TGTGGCTGTAGTTTAGTGGTAAGAATTCCACGTTGTGGCCGTGGAGACCTGGGCTCGAATCCCAG
* * * **
107527825 CAGCCACAC-TAATAAATATTTTTTCTTCATTTCCACAACCTCTGTTTCTAGGCTCTGTTCCTTT
66 CAGCCACACAGAAAAAAAATTTTACCTTCATTTCCACAACCTCTGTTTCTAGGCTCTGTTCCTTT
* * *
107527889 GGGCCAACTTCTTGTTTAAAAAAGAACCCAAAATGCAAGTCGTTTCGTTTCCTAAAACCGTTGCT
131 GGGCCAACTTATAGTTTAAAAAAGAACCCAAAACGCAAGTCGTTTCGTTTCCT-AAACCGTTGCT
* * * * *
107527954 ACGAACTACACAAATTCTGAAAAACCATTGACTT-CAAAAACGTTTTTTTTGTTTTCCGCTTTTC
195 ACGAACTACACAAATTCTAAAAAACCATCGACTTAAAAAAACG-TATTCTTGTTTTCCGCTTTTC
* *
107528018 AGTTTTTCGTCATTTTTCCTCCTTGATATCTA
259 AGTCTTTCGTCATTTTTCCTCCTTGAGATCTA
107528050 CTCATTGTTT
Statistics
Matches: 264, Mismatches: 21, Indels: 10
0.89 0.07 0.03
Matches are distributed among these distances:
317 7 0.03
318 116 0.44
319 45 0.17
320 11 0.04
321 85 0.32
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.35
Consensus pattern (321 bp):
TGTGGCTGTAGTTTAGTGGTAAGAATTCCACGTTGTGGCCGTGGAGACCTGGGCTCGAATCCCAG
CAGCCACACAGAAAAAAAATTTTACCTTCATTTCCACAACCTCTGTTTCTAGGCTCTGTTCCTTT
GGGCCAACTTATAGTTTAAAAAAGAACCCAAAACGCAAGTCGTTTCGTTTCCTAAACCGTTGCTA
CGAACTACACAAATTCTAAAAAACCATCGACTTAAAAAAACGTATTCTTGTTTTCCGCTTTTCAG
TCTTTCGTCATTTTTCCTCCTTGAGATCTAGTGATTATGGATTTGGCTACGATGAATATCC
Found at i:107529598 original size:124 final size:128
Alignment explanation
Indices: 107529375--107529699 Score: 442
Period size: 124 Copynumber: 2.5 Consensus size: 128
107529365 TGTAAAACCG
*
107529375 TGTGTAAATGGTTCTCAAAGCATGAGCTAGTTAATATGAATAGAATTGGATGAAATGAAGTAATT
1 TGTGTAAATAGTTCTCAAAGCATGAGCTAGTTAATATGAATAGAATTGGATGAAATGAAGTAATT
* * *
107529440 TTAGACCTGAATAAACGAATGACGGCCCTCTTAGTTTACTGATAA-ACTGCTA-ATG-GT-AA
66 TTAGACCCGAATAAACGAATGACAGCCCTCTTAGTTTACTGATAATACTGATACATGTGTAAA
* *
107529499 TGTGTAAATAGTTCTCAAAGCATGAGCTAGTTGATATGAATAGAAATGGATGAAATGAAGTAATT
1 TGTGTAAATAGTTCTCAAAGCATGAGCTAGTTAATATGAATAGAATTGGATGAAATGAAGTAATT
* * * *
107529564 TTGGACCCGAATAAACGAATGACATCCCTTTTAGTTTACTGATAATTTCTGATACTATGTGTAAA
66 TTAGACCCGAATAAACGAATGACAGCCCTCTTAGTTTACTGATAA-TACTGATAC-ATGTGT---
107529629 ACAA
126 A-AA
* * * *
107529633 TGTGTAAATAGTTCTCGAACCATGAGCTAATTAATATGAATAGAGTTGGATGAAATGAAGTAATT
1 TGTGTAAATAGTTCTCAAAGCATGAGCTAGTTAATATGAATAGAATTGGATGAAATGAAGTAATT
107529698 TT
66 TT
107529700 TAGTGTTGAA
Statistics
Matches: 175, Mismatches: 16, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
124 102 0.58
126 5 0.03
128 3 0.02
129 2 0.01
134 63 0.36
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.32
Consensus pattern (128 bp):
TGTGTAAATAGTTCTCAAAGCATGAGCTAGTTAATATGAATAGAATTGGATGAAATGAAGTAATT
TTAGACCCGAATAAACGAATGACAGCCCTCTTAGTTTACTGATAATACTGATACATGTGTAAA
Found at i:107532697 original size:2 final size:2
Alignment explanation
Indices: 107532692--107532732 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
107532682 CAAAAATATT
107532692 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
107532733 TTTTAAACCT
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:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:107534440 original size:29 final size:31
Alignment explanation
Indices: 107534378--107534445 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 31
107534368 AGTTTTATAC
* *
107534378 ATACATTTGAACCACAATCAAAGTTTCACGT
1 ATACAATTGCACCACAATCAAAGTTTCACGT
* * *
107534409 ATATAATTGCACCA-AATTAAAG-TTCATGT
1 ATACAATTGCACCACAATCAAAGTTTCACGT
107534438 ATACAATT
1 ATACAATT
107534446 ACACATTAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
29 13 0.42
30 7 0.23
31 11 0.35
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.32
Consensus pattern (31 bp):
ATACAATTGCACCACAATCAAAGTTTCACGT
Found at i:107534848 original size:29 final size:29
Alignment explanation
Indices: 107534806--107534864 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
107534796 AATATAAGAG
107534806 ATAAATAACTAAAGTTTAGGCTTAGGACC
1 ATAAATAACTAAAGTTTAGGCTTAGGACC
107534835 ATAAATAACTAAAGTTTAGGCTTAGGACC
1 ATAAATAACTAAAGTTTAGGCTTAGGACC
107534864 A
1 A
107534865 AAGTTAAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (29 bp):
ATAAATAACTAAAGTTTAGGCTTAGGACC
Found at i:107544296 original size:19 final size:18
Alignment explanation
Indices: 107544243--107544303 Score: 50
Period size: 19 Copynumber: 3.2 Consensus size: 18
107544233 ATCAACAAGT
* *
107544243 AATTTAAAATTTATAAAAA
1 AATTCAAAA-TTAAAAAAA
* *
107544262 TATTCAAAAAATAAAAAAA
1 AATTC-AAAATTAAAAAAA
*
107544281 AATTCAAAATTCAAAAAAT
1 AATTCAAAATT-AAAAAAA
107544300 AATT
1 AATT
107544304 ATAAAAAAGT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
18 5 0.15
19 24 0.73
20 4 0.12
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.30
Consensus pattern (18 bp):
AATTCAAAATTAAAAAAA
Found at i:107544317 original size:30 final size:26
Alignment explanation
Indices: 107544263--107544319 Score: 78
Period size: 26 Copynumber: 2.0 Consensus size: 26
107544253 TTATAAAAAT
107544263 ATTCAAAAAATAAAAAAAAATTCAAA
1 ATTCAAAAAATAAAAAAAAATTCAAA
107544289 ATTCAAAAAATAATTATAAAAAAGTTCAAA
1 ATTCAAAAAATAA--A-AAAAAA-TTCAAA
107544319 A
1 A
107544320 ACTAGCATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
26 13 0.48
28 1 0.04
29 6 0.22
30 7 0.26
ACGTcount: A:0.68, C:0.07, G:0.02, T:0.23
Consensus pattern (26 bp):
ATTCAAAAAATAAAAAAAAATTCAAA
Found at i:107550093 original size:21 final size:20
Alignment explanation
Indices: 107550067--107550106 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
107550057 TTAATTGATA
* *
107550067 AATCAATATAAATTAAAAATT
1 AATCAAAAT-AATGAAAAATT
107550088 AATCAAAATAATGAAAAAT
1 AATCAAAATAATGAAAAAT
107550107 AATATTATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.65, C:0.05, G:0.03, T:0.28
Consensus pattern (20 bp):
AATCAAAATAATGAAAAATT
Found at i:107550118 original size:20 final size:21
Alignment explanation
Indices: 107550095--107550134 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
107550085 ATTAATCAAA
*
107550095 ATAATGAAAAAT-AATATTAT
1 ATAACGAAAAATAAATATTAT
107550115 ATAACGAAAAATAAATATTA
1 ATAACGAAAAATAAATATTA
107550135 GATTTAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (21 bp):
ATAACGAAAAATAAATATTAT
Found at i:107551219 original size:16 final size:16
Alignment explanation
Indices: 107551198--107551229 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
107551188 TCAGTAATAC
107551198 GATAAAAAATTTATAT
1 GATAAAAAATTTATAT
107551214 GATAAAAAATTTATAT
1 GATAAAAAATTTATAT
107551230 TTCTGTTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (16 bp):
GATAAAAAATTTATAT
Found at i:107551798 original size:12 final size:13
Alignment explanation
Indices: 107551770--107551818 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
107551760 TCGAGTCCGT
107551770 AGATATTAAATAG
1 AGATATTAAATAG
*
107551783 AGATATTTAA-AG
1 AGATATTAAATAG
* *
107551795 AGATATTATATTG
1 AGATATTAAATAG
*
107551808 ATATATTAAAT
1 AGATATTAAAT
107551819 TTTGATTAAG
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
12 10 0.34
13 19 0.66
ACGTcount: A:0.49, C:0.00, G:0.12, T:0.39
Consensus pattern (13 bp):
AGATATTAAATAG
Found at i:107556943 original size:19 final size:19
Alignment explanation
Indices: 107556906--107556945 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
107556896 ATATTATAAA
*
107556906 ATTTATTTAAATCTTAATT
1 ATTTATTTAAATCTAAATT
107556925 ATTTATTTTAAAT-TAAATT
1 ATTTA-TTTAAATCTAAATT
107556944 AT
1 AT
107556946 GATTAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (19 bp):
ATTTATTTAAATCTAAATT
Found at i:107557077 original size:7 final size:7
Alignment explanation
Indices: 107557062--107557091 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
107557052 AAATAATTTA
*
107557062 AAATAAT
1 AAATTAT
107557069 AAATTAT
1 AAATTAT
107557076 AAATTAT
1 AAATTAT
107557083 AAATTAT
1 AAATTAT
107557090 AA
1 AA
107557092 TATAATATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (7 bp):
AAATTAT
Found at i:107557079 original size:14 final size:14
Alignment explanation
Indices: 107557053--107557103 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
107557043 ACGAAATTTA
*
107557053 AATAATTTA-AAAT
1 AATAAATTATAAAT
107557066 AATAAATTATAAAT
1 AATAAATTATAAAT
*
107557080 TATAAATTATAATAT
1 AATAAATTATAA-AT
107557095 AATATAATT
1 AATA-AATT
107557104 TTTATATATA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
13 8 0.25
14 15 0.47
15 5 0.16
16 4 0.12
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AATAAATTATAAAT
Found at i:107559823 original size:27 final size:26
Alignment explanation
Indices: 107559728--107559824 Score: 69
Period size: 27 Copynumber: 3.7 Consensus size: 26
107559718 AAAAGGAAGA
* *
107559728 AAATATAATATG-TAAACAAAA-ACT
1 AAATATAATATGATAAAAAAAATAAT
*
107559752 AAGTATAATAATGATATAAAGAAAAT-A-
1 AAATATAAT-ATGATA-AAA-AAAATAAT
*
107559779 AAATAATAATATGTTAAAAATAAATAAT
1 AAAT-ATAATATGATAAAAA-AAATAAT
107559807 AAATATAATAATG-TAAAA
1 AAATATAAT-ATGATAAAA
107559825 TAGTAAAAAG
Statistics
Matches: 58, Mismatches: 5, Indels: 17
0.73 0.06 0.21
Matches are distributed among these distances:
24 8 0.14
25 4 0.07
26 9 0.16
27 21 0.36
28 16 0.28
ACGTcount: A:0.64, C:0.02, G:0.06, T:0.28
Consensus pattern (26 bp):
AAATATAATATGATAAAAAAAATAAT
Found at i:107559864 original size:12 final size:13
Alignment explanation
Indices: 107559847--107559885 Score: 64
Period size: 12 Copynumber: 3.2 Consensus size: 13
107559837 TGTCTATACG
107559847 TATATAATAA-AA
1 TATATAATAATAA
107559859 TATATAATAATAA
1 TATATAATAATAA
107559872 TA-ATAATAATAA
1 TATATAATAATAA
107559884 TA
1 TA
107559886 AGGATAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 22 0.85
13 4 0.15
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
TATATAATAATAA
Found at i:107559868 original size:3 final size:3
Alignment explanation
Indices: 107559850--107559886 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
107559840 CTATACGTAT
107559850 ATA ATA A-A ATA TATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA A
107559887 GGATAATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 27 0.84
4 3 0.09
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:107561612 original size:38 final size:40
Alignment explanation
Indices: 107561563--107561650 Score: 117
Period size: 41 Copynumber: 2.2 Consensus size: 40
107561553 AAAATTATAC
* * *
107561563 TTAATACAATAAAATA-TTTATTATATTTAT-TAGTGTTT
1 TTAATATAATAAAACATTTTATTATATCTATGTAGTGTTT
*
107561601 TTAATATAATAAAACATTTTATTATATCTATGGTAGTTTTT
1 TTAATATAATAAAACATTTTATTATATCTAT-GTAGTGTTT
107561642 TTAATATAA
1 TTAATATAA
107561651 ATATTTTTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
38 14 0.33
39 13 0.30
41 16 0.37
ACGTcount: A:0.40, C:0.03, G:0.06, T:0.51
Consensus pattern (40 bp):
TTAATATAATAAAACATTTTATTATATCTATGTAGTGTTT
Found at i:107563989 original size:3 final size:3
Alignment explanation
Indices: 107563983--107564025 Score: 52
Period size: 3 Copynumber: 14.3 Consensus size: 3
107563973 CTCTATTTTT
* *
107563983 TTA TTA TTA TTA TTA CTA -TA TTTA TCA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA T
107564026 ATTTATACTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
2 2 0.06
3 31 0.89
4 2 0.06
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:107564031 original size:12 final size:12
Alignment explanation
Indices: 107563983--107564048 Score: 59
Period size: 12 Copynumber: 5.6 Consensus size: 12
107563973 CTCTATTTTT
107563983 TTATTAT-TATTA
1 TTATTATAT-TTA
*
107563995 TTACTATATTTA
1 TTATTATATTTA
*
107564007 TCATTAT-TATTA
1 TTATTATAT-TTA
107564019 TTATTATATTTA
1 TTATTATATTTA
107564031 -TACTTATATTTA
1 TTA-TTATATTTA
107564043 TT-TTAT
1 TTATTAT
107564049 TCTAATGCCA
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
11 7 0.16
12 35 0.78
13 3 0.07
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.64
Consensus pattern (12 bp):
TTATTATATTTA
Found at i:107564044 original size:24 final size:24
Alignment explanation
Indices: 107563985--107564031 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
107563975 CTATTTTTTT
*
107563985 ATTATTATTATTACTATATTTATC
1 ATTATTATTATTATTATATTTATC
107564009 ATTATTATTATTATTATATTTAT
1 ATTATTATTATTATTATATTTAT
107564032 ACTTATATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (24 bp):
ATTATTATTATTATTATATTTATC
Found at i:107565500 original size:38 final size:39
Alignment explanation
Indices: 107565450--107565546 Score: 103
Period size: 38 Copynumber: 2.6 Consensus size: 39
107565440 GAATATAAAG
* * *
107565450 AATATATATAAGTATGTATATG-A-TGTAAAATAAGCATA
1 AATATATATAAGTATGTATAAGAATTATAAAATAAG-AAA
* *
107565488 AATATATGTAAGTA--TATAAGAATTATAAAATATGAAA
1 AATATATATAAGTATGTATAAGAATTATAAAATAAGAAA
*
107565525 AATATATTTAAGTATGTATAAG
1 AATATATATAAGTATGTATAAG
107565547 TACGTATATA
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
36 5 0.10
37 16 0.33
38 22 0.45
39 6 0.12
ACGTcount: A:0.52, C:0.01, G:0.12, T:0.35
Consensus pattern (39 bp):
AATATATATAAGTATGTATAAGAATTATAAAATAAGAAA
Found at i:107566020 original size:64 final size:62
Alignment explanation
Indices: 107565892--107566021 Score: 158
Period size: 64 Copynumber: 2.1 Consensus size: 62
107565882 TAAACAACAG
*
107565892 TATATACAATATAATATTAGAAAAATATATAATAGTGTAAAATATAACTAATAATATTAAAA
1 TATATACAATATAATATTAGAAAAATATATAATAGTATAAAATATAACTAATAATATTAAAA
* * *
107565954 TATATACAATGATAATATATATAAAAGATATATGTATA-TATAATTATATAA-T-ATAATATTAA
1 TATATACAAT-ATAATAT-TAGAAAA-ATATAT-AATAGTATAA-AATATAACTAATAATATTAA
107566016 AA
61 AA
107566018 TATA
1 TATA
107566022 ATAATACGAC
Statistics
Matches: 59, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
62 10 0.17
63 7 0.12
64 22 0.37
65 11 0.19
66 9 0.15
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (62 bp):
TATATACAATATAATATTAGAAAAATATATAATAGTATAAAATATAACTAATAATATTAAAA
Found at i:107566391 original size:3 final size:3
Alignment explanation
Indices: 107566360--107566427 Score: 57
Period size: 3 Copynumber: 22.3 Consensus size: 3
107566350 ATACACGTAC
* * * *
107566360 ATA ATA AAA ATA TATA CTA ATA CATA ATA ATA ATA CTA ATA CTA ATA
1 ATA ATA ATA ATA -ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA
* *
107566407 ATA CTA ATA AT- ATA AAA ATA A
1 ATA ATA ATA ATA ATA ATA ATA A
107566428 CAAGGATATT
Statistics
Matches: 50, Mismatches: 12, Indels: 6
0.74 0.18 0.09
Matches are distributed among these distances:
2 2 0.04
3 42 0.84
4 6 0.12
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:107566908 original size:11 final size:12
Alignment explanation
Indices: 107566892--107566927 Score: 58
Period size: 11 Copynumber: 3.2 Consensus size: 12
107566882 AGAAAAAAAA
107566892 GAAGAGAG-AGG
1 GAAGAGAGAAGG
107566903 GAAGAGAGAAGG
1 GAAGAGAGAAGG
107566915 G-AGAGAGAAGG
1 GAAGAGAGAAGG
107566926 GA
1 GA
107566928 GGGGGAAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 19 0.83
12 4 0.17
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (12 bp):
GAAGAGAGAAGG
Found at i:107567721 original size:18 final size:18
Alignment explanation
Indices: 107567694--107567738 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
107567684 CTGTATTTAC
107567694 TTAT-ATTATGACTAATA
1 TTATCATTATGACTAATA
* *
107567711 TTATCATTATGATTACTA
1 TTATCATTATGACTAATA
*
107567729 TTGTCATTAT
1 TTATCATTAT
107567739 TATTTGTTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 4 0.17
18 20 0.83
ACGTcount: A:0.33, C:0.09, G:0.07, T:0.51
Consensus pattern (18 bp):
TTATCATTATGACTAATA
Found at i:107567742 original size:3 final size:3
Alignment explanation
Indices: 107567709--107567791 Score: 51
Period size: 3 Copynumber: 27.0 Consensus size: 3
107567699 TTATGACTAA
* * * * * *
107567709 TAT TAT CAT TAT GAT TAC TAT TGT CAT TAT TATT TGT TACCT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TA--T TAT TAT
* * *
107567757 TAC TAT TAT TAC TAC TAT TA- TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
107567792 ATTTTACCCA
Statistics
Matches: 60, Mismatches: 16, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
2 2 0.03
3 53 0.88
4 2 0.03
5 3 0.05
ACGTcount: A:0.30, C:0.10, G:0.04, T:0.57
Consensus pattern (3 bp):
TAT
Found at i:107567765 original size:9 final size:9
Alignment explanation
Indices: 107567751--107567791 Score: 57
Period size: 9 Copynumber: 4.7 Consensus size: 9
107567741 TTTGTTACCT
107567751 TATTATTAC
1 TATTATTAC
107567760 TATTATTAC
1 TATTATTAC
*
107567769 TACTATTA-
1 TATTATTAC
*
107567777 TATTATTAT
1 TATTATTAC
107567786 TATTAT
1 TATTAT
107567792 ATTTTACCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
8 7 0.24
9 22 0.76
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (9 bp):
TATTATTAC
Found at i:107573386 original size:20 final size:21
Alignment explanation
Indices: 107573349--107573387 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
107573339 TTTTTGAAAA
*
107573349 TTTTAAAAATATTTATATTAT
1 TTTTAAAAATATTAATATTAT
*
107573370 TTTTAATAAT-TTAATATT
1 TTTTAAAAATATTAATATT
107573388 TTTCATTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTTAAAAATATTAATATTAT
Found at i:107574047 original size:38 final size:38
Alignment explanation
Indices: 107574005--107574081 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
107573995 TTCTATTCAA
107574005 ATCTCTACAACATTTTTCCACTTCTTCCATGGGAGACG
1 ATCTCTACAACATTTTTCCACTTCTTCCATGGGAGACG
107574043 ATCTCTACAACATTTTTCCACTTCTTCCATGGGAGACG
1 ATCTCTACAACATTTTTCCACTTCTTCCATGGGAGACG
107574081 A
1 A
107574082 CGATGCTTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.25, C:0.29, G:0.13, T:0.34
Consensus pattern (38 bp):
ATCTCTACAACATTTTTCCACTTCTTCCATGGGAGACG
Found at i:107578078 original size:18 final size:18
Alignment explanation
Indices: 107578055--107578089 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
107578045 TTCTTATTAT
107578055 TAAT-AATAATATTTAAAA
1 TAATAAATAA-ATTTAAAA
107578073 TAATAAATAAATTTAAA
1 TAATAAATAAATTTAAA
107578090 TATCATGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TAATAAATAAATTTAAAA
Found at i:107581240 original size:3 final size:3
Alignment explanation
Indices: 107581222--107581272 Score: 59
Period size: 3 Copynumber: 17.3 Consensus size: 3
107581212 TCAAGCCCTT
* * * *
107581222 TGA TGA TGG TGT TGA TGA TGA TGA TGA TGA GGA TGG TGA TGA TGA TG-
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
107581269 TGA T
1 TGA T
107581273 AGGTCCAAGA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.25, C:0.00, G:0.39, T:0.35
Consensus pattern (3 bp):
TGA
Found at i:107582358 original size:21 final size:22
Alignment explanation
Indices: 107582326--107582369 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
107582316 TTTAAAAGTA
107582326 AAAATAGATAATTT-TTTTAAT
1 AAAATAGATAATTTATTTTAAT
107582347 AAAA-AGACTAATTTAATTTTAAT
1 AAAATAGA-TAATTT-ATTTTAAT
107582370 TTAATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 3 0.15
21 10 0.50
23 7 0.35
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (22 bp):
AAAATAGATAATTTATTTTAAT
Found at i:107583079 original size:14 final size:15
Alignment explanation
Indices: 107583052--107583084 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
107583042 GTAAAAGAAG
107583052 GAAAAAAAAGAAAAA
1 GAAAAAAAAGAAAAA
*
107583067 GAAAAAGAA-AAAAA
1 GAAAAAAAAGAAAAA
107583081 GAAA
1 GAAA
107583085 TACAAATATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (15 bp):
GAAAAAAAAGAAAAA
Found at i:107583734 original size:29 final size:29
Alignment explanation
Indices: 107583692--107583751 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
107583682 AAAAGGCCTC
107583692 CATGATTCTTTTACCCCAATACATACCAA
1 CATGATTCTTTTACCCCAATACATACCAA
107583721 CATGATTCTTTTACCCCAATACATACCAA
1 CATGATTCTTTTACCCCAATACATACCAA
107583750 CA
1 CA
107583752 GAAATCATGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.35, C:0.32, G:0.03, T:0.30
Consensus pattern (29 bp):
CATGATTCTTTTACCCCAATACATACCAA
Found at i:107589438 original size:15 final size:14
Alignment explanation
Indices: 107589418--107589460 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
107589408 CATGATTATA
107589418 ATTTTTATTATTGTT
1 ATTTTTATTATT-TT
*
107589433 ATTTTTATTCCTTTT
1 ATTTTTATT-ATTTT
107589448 ATTATTTATTATT
1 ATT-TTTATTATT
107589461 AATATATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 16 0.67
16 8 0.33
ACGTcount: A:0.21, C:0.05, G:0.02, T:0.72
Consensus pattern (14 bp):
ATTTTTATTATTTT
Found at i:107592332 original size:11 final size:11
Alignment explanation
Indices: 107592316--107592346 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
107592306 ATACCCATAC
107592316 CCCATACCTTG
1 CCCATACCTTG
*
107592327 CCCATACCTTT
1 CCCATACCTTG
107592338 CCCATACCT
1 CCCATACCT
107592347 ACCCATACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.19, C:0.48, G:0.03, T:0.29
Consensus pattern (11 bp):
CCCATACCTTG
Found at i:107592918 original size:18 final size:18
Alignment explanation
Indices: 107592891--107592983 Score: 150
Period size: 18 Copynumber: 5.2 Consensus size: 18
107592881 TACGACCGTT
107592891 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
107592909 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
*
107592927 TATGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
107592945 TACGGAACTATTCACGTA
1 TACGGTACTATTCACGTA
*
107592963 TACGGTACTGTTCACGTA
1 TACGGTACTATTCACGTA
107592981 TAC
1 TAC
107592984 AGTAGTTGGG
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 68 1.00
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:107597053 original size:11 final size:11
Alignment explanation
Indices: 107597037--107597067 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
107597027 ATACCCATAC
107597037 CCCATACCTTG
1 CCCATACCTTG
*
107597048 CCCATACCTTT
1 CCCATACCTTG
107597059 CCCATACCT
1 CCCATACCT
107597068 ACCCATACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.19, C:0.48, G:0.03, T:0.29
Consensus pattern (11 bp):
CCCATACCTTG
Done.