Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 10 of 182
Found at i:3830639 original size:3 final size:3
Alignment explanation
Indices: 3830631--3830660 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
3830621 ACTGTTTAGT
3830631 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3830661 GTGAAATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:3831081 original size:2 final size:2
Alignment explanation
Indices: 3831074--3831098 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3831064 ATCAATAAAG
3831074 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 T
3831099 GATAATTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3831377 original size:19 final size:19
Alignment explanation
Indices: 3831337--3831378 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
3831327 ATTACAAAAT
**
3831337 AATTCAAAATAATTTTTTA
1 AATTCAAAATAATTTTAAA
3831356 AATTCAAAAT-ATTTATAAA
1 AATTCAAAATAATTT-TAAA
3831375 AATT
1 AATT
3831379 TTAAAATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (19 bp):
AATTCAAAATAATTTTAAA
Found at i:3850464 original size:97 final size:97
Alignment explanation
Indices: 3850298--3850495 Score: 387
Period size: 97 Copynumber: 2.0 Consensus size: 97
3850288 ATAAGAAATT
3850298 AAGTAAAGTTGGTAAAATTTAGAGCGCACATGACCTCTGCAAACCATTTTTACCTTTTCCTTTGG
1 AAGTAAAGTTGGTAAAATTTAGAGCGCACATGACCTCTGCAAACCATTTTTACCTTTTCCTTTGG
3850363 TTGAAAATGAATGGAAAGTAGAATCCCTAGGA
66 TTGAAAATGAATGGAAAGTAGAATCCCTAGGA
3850395 AAGTAAAGTTGGTAAAATTTAGAGCGCACATGACCTCTGCAAACCATTTTTACCTTTTCCTTTGG
1 AAGTAAAGTTGGTAAAATTTAGAGCGCACATGACCTCTGCAAACCATTTTTACCTTTTCCTTTGG
*
3850460 TTGAAAATGAATGGAAAGTAGAATCCCTAGTA
66 TTGAAAATGAATGGAAAGTAGAATCCCTAGGA
3850492 AAGT
1 AAGT
3850496 TGAAAATTTT
Statistics
Matches: 100, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
97 100 1.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.30
Consensus pattern (97 bp):
AAGTAAAGTTGGTAAAATTTAGAGCGCACATGACCTCTGCAAACCATTTTTACCTTTTCCTTTGG
TTGAAAATGAATGGAAAGTAGAATCCCTAGGA
Found at i:3862283 original size:2 final size:2
Alignment explanation
Indices: 3862278--3862303 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3862268 GGTAAAAAAA
3862278 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
3862304 TTTTTTTTTT
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:3871852 original size:20 final size:20
Alignment explanation
Indices: 3871816--3871853 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3871806 ATAAAAATGA
*
3871816 TTATTTTTATTTGATTTAGG
1 TTATTTTTAGTTGATTTAGG
3871836 TTATATTTTAGTT-ATTTA
1 TTAT-TTTTAGTTGATTTA
3871854 TGTTTAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.24, C:0.00, G:0.11, T:0.66
Consensus pattern (20 bp):
TTATTTTTAGTTGATTTAGG
Found at i:3874168 original size:18 final size:20
Alignment explanation
Indices: 3874136--3874172 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
3874126 AATGTAAAAG
3874136 TAATTATTTTCTTAATAATA
1 TAATTATTTTCTTAATAATA
3874156 TAATT-TTTT-TTAATAAT
1 TAATTATTTTCTTAATAAT
3874173 CTCATTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 4 0.24
20 5 0.29
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (20 bp):
TAATTATTTTCTTAATAATA
Found at i:3890779 original size:24 final size:25
Alignment explanation
Indices: 3890751--3890803 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
3890741 TTAATGTTTA
3890751 TATTTTT-GTGAATTTGATTATT-AT
1 TATTTTTAGTGAATTT-ATTATTAAT
* *
3890775 TATTTTTAGTTAATTTTTTATTAAT
1 TATTTTTAGTGAATTTATTATTAAT
3890800 TATT
1 TATT
3890804 AAATTGCTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 12 0.48
25 13 0.52
ACGTcount: A:0.26, C:0.00, G:0.08, T:0.66
Consensus pattern (25 bp):
TATTTTTAGTGAATTTATTATTAAT
Found at i:3894323 original size:24 final size:23
Alignment explanation
Indices: 3894272--3894330 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 23
3894262 TTAATGTTCA
*
3894272 CGAACATGTTCATTTAACTTAAT
1 CGAACATGTTCATTGAACTTAAT
3894295 CGAACATGTTCA-TGAACATATAAT
1 CGAACATGTTCATTGAAC-T-TAAT
* *
3894319 TGAACATATTCA
1 CGAACATGTTCA
3894331 CGAAGAATGT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
22 4 0.13
23 13 0.42
24 14 0.45
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.34
Consensus pattern (23 bp):
CGAACATGTTCATTGAACTTAAT
Found at i:3895285 original size:2 final size:2
Alignment explanation
Indices: 3895280--3895323 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
3895270 ACACACATAT
3895280 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3895322 AG
1 AG
3895324 CAAAGCAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3897218 original size:29 final size:29
Alignment explanation
Indices: 3897186--3897241 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
3897176 GTTTTTAAAT
*
3897186 AATTTTAATGATTTCT-AATTTTTAAAAAA
1 AATTTGAA-GATTTCTGAATTTTTAAAAAA
* *
3897215 AATTTGAAGTTTTTTGAATTTTTAAAA
1 AATTTGAAGATTTCTGAATTTTTAAAA
3897242 TTTGTAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 5 0.22
29 18 0.78
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (29 bp):
AATTTGAAGATTTCTGAATTTTTAAAAAA
Found at i:3897775 original size:15 final size:18
Alignment explanation
Indices: 3897743--3897786 Score: 58
Period size: 16 Copynumber: 2.6 Consensus size: 18
3897733 GATAGTAAAA
3897743 ATATAATTTTATTA-TTTT
1 ATAT-ATTTTATTATTTTT
3897761 A-ATATTTTA-TATTTTT
1 ATATATTTTATTATTTTT
3897777 ATATATTTTA
1 ATATATTTTA
3897787 AAGGGTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 2 0.08
16 11 0.46
17 10 0.42
18 1 0.04
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
ATATATTTTATTATTTTT
Found at i:3898578 original size:16 final size:17
Alignment explanation
Indices: 3898547--3898579 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3898537 TAATTTACTA
*
3898547 AAATCCAAATGATTTAC
1 AAATACAAATGATTTAC
3898564 AAATACAAA-GATTTAC
1 AAATACAAATGATTTAC
3898580 CGGTTGCACC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.52, C:0.15, G:0.06, T:0.27
Consensus pattern (17 bp):
AAATACAAATGATTTAC
Found at i:3901057 original size:18 final size:18
Alignment explanation
Indices: 3901000--3901057 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
3900990 GCACTAGTAC
* *
3901000 CAACACAATCATCATCTA
1 CAACACAATCACCAGCTA
*
3901018 CAACAGCAA-CACCAGCTC
1 CAACA-CAATCACCAGCTA
* *
3901036 CAACACAATCAGCGGCTA
1 CAACACAATCACCAGCTA
3901054 CAAC
1 CAAC
3901058 GACACCATCA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
17 3 0.09
18 26 0.81
19 3 0.09
ACGTcount: A:0.41, C:0.38, G:0.09, T:0.12
Consensus pattern (18 bp):
CAACACAATCACCAGCTA
Found at i:3901069 original size:27 final size:27
Alignment explanation
Indices: 3901039--3901095 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
3901029 CCAGCTCCAA
3901039 CACAATCAGCGGCTACAACGACACCAT
1 CACAATCAGCGGCTACAACGACACCAT
*
3901066 CACAATTAGCGGCTACAACGACACCAT
1 CACAATCAGCGGCTACAACGACACCAT
3901093 CAC
1 CAC
3901096 CATCTGTAGC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.37, C:0.37, G:0.14, T:0.12
Consensus pattern (27 bp):
CACAATCAGCGGCTACAACGACACCAT
Found at i:3901296 original size:15 final size:15
Alignment explanation
Indices: 3901276--3901307 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
3901266 TCACCGTCGC
3901276 CATCACCAGCACCAG
1 CATCACCAGCACCAG
3901291 CATCACCAGCACCAG
1 CATCACCAGCACCAG
3901306 CA
1 CA
3901308 ACGACAACGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.34, C:0.47, G:0.12, T:0.06
Consensus pattern (15 bp):
CATCACCAGCACCAG
Found at i:3904426 original size:58 final size:56
Alignment explanation
Indices: 3904349--3904491 Score: 164
Period size: 58 Copynumber: 2.5 Consensus size: 56
3904339 AGACAAAAAG
* * *
3904349 AAAACTTAGGTATTAAATTAAAAAAAAATG-TAAAGCTTAAG-TACCAAATTAAACTAA
1 AAAACTTAAGTATCAAATTAAGAAAAAATGTTAAA--TTAAGATACCAAATTAAA-TAA
* * *
3904406 AAAAGTTTAAGTATCAAATTAAGAAAAAATGTTAAATTTAGATACCAAATTGAATAA
1 AAAA-CTTAAGTATCAAATTAAGAAAAAATGTTAAATTAAGATACCAAATTAAATAA
* *
3904463 AAAACTTAAGTACCAAACTAAGAAAAAAT
1 AAAACTTAAGTATCAAATTAAGAAAAAAT
3904492 ATCATGTTAG
Statistics
Matches: 74, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
56 22 0.30
57 15 0.20
58 33 0.45
59 4 0.05
ACGTcount: A:0.57, C:0.08, G:0.09, T:0.26
Consensus pattern (56 bp):
AAAACTTAAGTATCAAATTAAGAAAAAATGTTAAATTAAGATACCAAATTAAATAA
Found at i:3906132 original size:2 final size:2
Alignment explanation
Indices: 3906119--3906150 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3906109 TTCAAAGAGG
*
3906119 TA TA TA TC TA TA 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
3906151 CTGCTTTCAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3909235 original size:24 final size:22
Alignment explanation
Indices: 3909182--3909236 Score: 58
Period size: 24 Copynumber: 2.4 Consensus size: 22
3909172 AATTTCGAGA
3909182 AATTATTTTATGAATCTTTTTC
1 AATTATTTTATGAATCTTTTTC
*
3909204 ATTGTATTATTCATG-ATCTTTTTC
1 AAT-TATT-TT-ATGAATCTTTTTC
3909228 TAATTATTT
1 -AATTATTT
3909237 AATAATATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
22 2 0.07
23 5 0.19
24 15 0.56
25 5 0.19
ACGTcount: A:0.25, C:0.09, G:0.05, T:0.60
Consensus pattern (22 bp):
AATTATTTTATGAATCTTTTTC
Found at i:3910048 original size:24 final size:21
Alignment explanation
Indices: 3909978--3910028 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
3909968 AGTGAGTTAA
*
3909978 ACAAAAAGAGAAGCAACTTGG
1 ACAAAAAGAGAAGTAACTTGG
3909999 ACAAAAAGAGAAGTAACTTGG
1 ACAAAAAGAGAAGTAACTTGG
3910020 ACAAAAAGA
1 ACAAAAAGA
3910029 AACGAAGTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.57, C:0.12, G:0.22, T:0.10
Consensus pattern (21 bp):
ACAAAAAGAGAAGTAACTTGG
Found at i:3916603 original size:2 final size:2
Alignment explanation
Indices: 3916596--3916626 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3916586 GAATGAATGA
3916596 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
3916627 TATATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:3920089 original size:23 final size:25
Alignment explanation
Indices: 3920046--3920103 Score: 84
Period size: 24 Copynumber: 2.4 Consensus size: 25
3920036 ATTAAATCAT
3920046 AAAAATTAGATATTTTTTG-AATAA
1 AAAAATTAGATATTTTTTGAAATAA
*
3920070 ACAAATTAGATA-TTTTTGAAATAA
1 AAAAATTAGATATTTTTTGAAATAA
3920094 AAAAACTTAG
1 AAAAA-TTAG
3920104 CATGAATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
23 6 0.20
24 20 0.67
25 4 0.13
ACGTcount: A:0.52, C:0.03, G:0.09, T:0.36
Consensus pattern (25 bp):
AAAAATTAGATATTTTTTGAAATAA
Found at i:3929448 original size:30 final size:31
Alignment explanation
Indices: 3929412--3929472 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
3929402 CATTTTAATT
3929412 CCTCAAC-TTTAAAAATATGACAAAACAGTC
1 CCTCAACTTTTAAAAATATGACAAAACAGTC
* * *
3929442 CCTCAACTTTTGAAAATGTGATAAAACAGTC
1 CCTCAACTTTTAAAAATATGACAAAACAGTC
3929473 TTTTTCCATC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 7 0.26
31 20 0.74
ACGTcount: A:0.43, C:0.21, G:0.10, T:0.26
Consensus pattern (31 bp):
CCTCAACTTTTAAAAATATGACAAAACAGTC
Found at i:3929599 original size:30 final size:31
Alignment explanation
Indices: 3929563--3929634 Score: 103
Period size: 30 Copynumber: 2.4 Consensus size: 31
3929553 ATCACGTTTA
*
3929563 ACAAAATAGTCACTCAACTT-T-GAAAATGTG
1 ACAAAATAGTCACTAAACTTATCGAAAA-GTG
*
3929593 ACAAAATAGTCACTAAAGTTATCGAAAAGTG
1 ACAAAATAGTCACTAAACTTATCGAAAAGTG
3929624 ACAAAATAGTC
1 ACAAAATAGTC
3929635 CTCTTGTTGT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
30 18 0.47
31 15 0.39
32 5 0.13
ACGTcount: A:0.47, C:0.15, G:0.14, T:0.24
Consensus pattern (31 bp):
ACAAAATAGTCACTAAACTTATCGAAAAGTG
Found at i:3930939 original size:30 final size:31
Alignment explanation
Indices: 3930871--3930942 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 31
3930861 ATAACAAGAG
* *
3930871 GACTATTTTGTCACTTTTCGATAACTTTAGT
1 GACTGTTTTGTCACTTTTCGATAACTTGAGT
* *
3930902 GATTGTTTTGTCACATTTTC-A-AAGTTGAGT
1 GACTGTTTTGTCAC-TTTTCGATAACTTGAGT
3930932 GACTGTTTTGT
1 GACTGTTTTGT
3930943 TACACGTAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
30 17 0.49
31 13 0.37
32 5 0.14
ACGTcount: A:0.21, C:0.12, G:0.18, T:0.49
Consensus pattern (31 bp):
GACTGTTTTGTCACTTTTCGATAACTTGAGT
Found at i:3951487 original size:19 final size:20
Alignment explanation
Indices: 3951450--3951488 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
3951440 AAACATGGAT
3951450 ACAAATTGAAATAGATCAAA
1 ACAAATTGAAATAGATCAAA
3951470 ACAAATT--AATATGATCAAA
1 ACAAATTGAAATA-GATCAAA
3951489 TCACATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.22
19 7 0.39
20 7 0.39
ACGTcount: A:0.59, C:0.10, G:0.08, T:0.23
Consensus pattern (20 bp):
ACAAATTGAAATAGATCAAA
Found at i:3953113 original size:15 final size:17
Alignment explanation
Indices: 3953093--3953126 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
3953083 CAAATGATAA
3953093 AAATTA-TAAAAA-TAT
1 AAATTACTAAAAATTAT
3953108 AAATTACTAAAAATTAT
1 AAATTACTAAAAATTAT
3953125 AA
1 AA
3953127 TTTAATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 6 0.35
17 5 0.29
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (17 bp):
AAATTACTAAAAATTAT
Found at i:3954141 original size:50 final size:52
Alignment explanation
Indices: 3954048--3954149 Score: 154
Period size: 50 Copynumber: 2.0 Consensus size: 52
3954038 TTTAATTGGA
*
3954048 TATATTGAATAAAAAATAACAAAGTAAAAAAAGATAACTTTGACCCTATTTAT
1 TATATTGAATAAAAAATAACAAAGT-AAAAAAGACAACTTTGACCCTATTTAT
* *
3954101 TATATTGAAT-AAAAATCATAAAGT-AAAAAGACAACTTTGACCCTATTTA
1 TATATTGAATAAAAAATAACAAAGTAAAAAAGACAACTTTGACCCTATTTA
3954150 CTCCTATACG
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
50 24 0.52
52 12 0.26
53 10 0.22
ACGTcount: A:0.51, C:0.11, G:0.08, T:0.30
Consensus pattern (52 bp):
TATATTGAATAAAAAATAACAAAGTAAAAAAGACAACTTTGACCCTATTTAT
Found at i:3954474 original size:19 final size:19
Alignment explanation
Indices: 3954450--3954488 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
3954440 CATTGCTTTA
3954450 ATGTGGGAGACCACGGCAG
1 ATGTGGGAGACCACGGCAG
3954469 ATGTGGGAGACCACGGCAG
1 ATGTGGGAGACCACGGCAG
3954488 A
1 A
3954489 CTTCCACTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.28, C:0.21, G:0.41, T:0.10
Consensus pattern (19 bp):
ATGTGGGAGACCACGGCAG
Found at i:3960796 original size:65 final size:65
Alignment explanation
Indices: 3960718--3960848 Score: 253
Period size: 65 Copynumber: 2.0 Consensus size: 65
3960708 GCCTGTGAAT
*
3960718 ATAGTACTGTTGATTTTGAATAAGGTGTAAAACCAGAGAGATGCATCCTCTGTGATTCTTCTTGA
1 ATAGTACTGTTGATTCTGAATAAGGTGTAAAACCAGAGAGATGCATCCTCTGTGATTCTTCTTGA
3960783 ATAGTACTGTTGATTCTGAATAAGGTGTAAAACCAGAGAGATGCATCCTCTGTGATTCTTCTTGA
1 ATAGTACTGTTGATTCTGAATAAGGTGTAAAACCAGAGAGATGCATCCTCTGTGATTCTTCTTGA
3960848 A
1 A
3960849 GAATCATGGA
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 65 1.00
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (65 bp):
ATAGTACTGTTGATTCTGAATAAGGTGTAAAACCAGAGAGATGCATCCTCTGTGATTCTTCTTGA
Found at i:3962590 original size:22 final size:21
Alignment explanation
Indices: 3962543--3962596 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
3962533 TCACAAGATT
3962543 AAAAAATTAATAAATATCTTA
1 AAAAAATTAATAAATATCTTA
* *
3962564 TAAAAATATAATAAA-ATGTTA
1 AAAAAAT-TAATAAATATCTTA
*
3962585 AAAAAAGTAATA
1 AAAAAATTAATA
3962597 TTTTGAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 5 0.18
21 16 0.57
22 7 0.25
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.30
Consensus pattern (21 bp):
AAAAAATTAATAAATATCTTA
Found at i:3963027 original size:10 final size:10
Alignment explanation
Indices: 3962973--3963032 Score: 50
Period size: 10 Copynumber: 5.8 Consensus size: 10
3962963 ATTAATATTT
*
3962973 AAAAATTTAA
1 AAAAATATAA
3962983 AAAAATATATA
1 AAAAATATA-A
*
3962994 AAAATTATTATA
1 AAAAATA-TA-A
*
3963006 AAAAGTAT-A
1 AAAAATATAA
3963015 AAAAATATAA
1 AAAAATATAA
*
3963025 AAATATAT
1 AAAAATAT
3963033 TTTACTAATG
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
9 8 0.19
10 16 0.38
11 8 0.19
12 10 0.24
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (10 bp):
AAAAATATAA
Found at i:3974353 original size:17 final size:17
Alignment explanation
Indices: 3974331--3974381 Score: 75
Period size: 17 Copynumber: 3.0 Consensus size: 17
3974321 ACCACATATA
3974331 AAAAATAATATTTTAAT
1 AAAAATAATATTTTAAT
* *
3974348 AAAAATAATAATATAAT
1 AAAAATAATATTTTAAT
*
3974365 AAAAATTATATTTTAAT
1 AAAAATAATATTTTAAT
3974382 TCAAAAAGGG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AAAAATAATATTTTAAT
Found at i:3974548 original size:25 final size:24
Alignment explanation
Indices: 3974520--3974566 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
3974510 AAATTTATTT
* *
3974520 TTTTTAATATTTTATAATTATAAAC
1 TTTTGAATA-TTTATAATAATAAAC
3974545 TTTTGAATATTTATAATAATAA
1 TTTTGAATATTTATAATAATAA
3974567 TCGAGTTGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (24 bp):
TTTTGAATATTTATAATAATAAAC
Found at i:3975468 original size:32 final size:32
Alignment explanation
Indices: 3975414--3975478 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
3975404 ATTTTAAAAA
**
3975414 TTGTTAACGATTTTACCCATTTACT-TCGATTT
1 TTGTTAACGATTTTACAAATTTACTCT-GATTT
* *
3975446 TTGTTAATGATTTTATAAATTTACTCTGATTT
1 TTGTTAACGATTTTACAAATTTACTCTGATTT
3975478 T
1 T
3975479 AAAAATACAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 27 0.96
33 1 0.04
ACGTcount: A:0.25, C:0.12, G:0.09, T:0.54
Consensus pattern (32 bp):
TTGTTAACGATTTTACAAATTTACTCTGATTT
Found at i:3981280 original size:3 final size:3
Alignment explanation
Indices: 3981272--3981301 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
3981262 AAGAAAAAAT
*
3981272 ATA ATA ATA ATA ATA ATA GTA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3981302 CGTAACAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3990643 original size:16 final size:17
Alignment explanation
Indices: 3990604--3990644 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
3990594 ATAATAAAAA
3990604 TATAATTTTATTATTTT
1 TATAATTTTATTATTTT
*
3990621 AAT-ATTTTA-TATTTT
1 TATAATTTTATTATTTT
3990636 TATAATTTT
1 TATAATTTT
3990645 TAAAATTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 8 0.38
16 11 0.52
17 2 0.10
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TATAATTTTATTATTTT
Found at i:3990653 original size:24 final size:24
Alignment explanation
Indices: 3990604--3990653 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
3990594 ATAATAAAAA
* *
3990604 TATAATTTTATTATTTTAATATTT
1 TATAATTTTATAATTTTAATAATT
*
3990628 TATATTTTTATAATTTTTAA-AATT
1 TATAATTTTATAA-TTTTAATAATT
3990652 TA
1 TA
3990654 AAAAAAATCA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 16 0.73
25 6 0.27
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (24 bp):
TATAATTTTATAATTTTAATAATT
Found at i:4001588 original size:23 final size:20
Alignment explanation
Indices: 4001546--4001588 Score: 50
Period size: 23 Copynumber: 2.0 Consensus size: 20
4001536 AAATTCATTG
*
4001546 TTATATTTTGAGCTTGAGTA
1 TTATATTTTGAGCTTAAGTA
4001566 TTATGATTTTGAATGCTTAAGTA
1 TTAT-ATTTTG-A-GCTTAAGTA
4001589 AGAAAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 4 0.21
21 6 0.32
22 1 0.05
23 8 0.42
ACGTcount: A:0.28, C:0.05, G:0.19, T:0.49
Consensus pattern (20 bp):
TTATATTTTGAGCTTAAGTA
Found at i:4005097 original size:23 final size:24
Alignment explanation
Indices: 4005051--4005103 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 24
4005041 AAATTATATT
*
4005051 TTTATTAAGTTATTATATAATAAA
1 TTTATTAAGTTATTATAAAATAAA
4005075 TTTATT-AGTTA-TATAAAATTAAA
1 TTTATTAAGTTATTATAAAA-TAAA
*
4005098 ATTATT
1 TTTATT
4005104 GACATCACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 6 0.23
23 14 0.54
24 6 0.23
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (24 bp):
TTTATTAAGTTATTATAAAATAAA
Found at i:4009450 original size:13 final size:12
Alignment explanation
Indices: 4009380--4009461 Score: 60
Period size: 13 Copynumber: 6.6 Consensus size: 12
4009370 TATACATATA
*
4009380 TATATATATTAGT
1 TATA-ATATTAAT
*
4009393 TAATAATAATAA-
1 T-ATAATATTAAT
*
4009405 TATAATACTAAT
1 TATAATATTAAT
*
4009417 TA-AATAATAATT
1 TATAATATTAA-T
*
4009429 TATATTATTATAT
1 TATAATATTA-AT
4009442 TATAATATTAAT
1 TATAATATTAAT
4009454 TAATAATA
1 T-ATAATA
4009462 AATTAAAAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
11 16 0.29
12 9 0.16
13 27 0.48
14 4 0.07
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (12 bp):
TATAATATTAAT
Found at i:4012650 original size:13 final size:12
Alignment explanation
Indices: 4012580--4012661 Score: 60
Period size: 13 Copynumber: 6.6 Consensus size: 12
4012570 TATATATATA
*
4012580 TATATATATTAGT
1 TATA-ATATTAAT
*
4012593 TAATAATAATAA-
1 T-ATAATATTAAT
*
4012605 TATAATACTAAT
1 TATAATATTAAT
*
4012617 TA-AATAATAATT
1 TATAATATTAA-T
*
4012629 TATATTATTATAT
1 TATAATATTA-AT
4012642 TATAATATTAAT
1 TATAATATTAAT
4012654 TAATAATA
1 T-ATAATA
4012662 AATTAAAAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
11 16 0.29
12 9 0.16
13 27 0.48
14 4 0.07
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (12 bp):
TATAATATTAAT
Found at i:4014608 original size:10 final size:10
Alignment explanation
Indices: 4014576--4014609 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
4014566 CAAATCAATT
4014576 AAATAAA-ATA
1 AAATAAATA-A
4014586 AAATAAATAA
1 AAATAAATAA
4014596 AAATAAATAA
1 AAATAAATAA
4014606 AAAT
1 AAAT
4014610 GTAAAAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 22 0.96
11 1 0.04
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (10 bp):
AAATAAATAA
Found at i:4014921 original size:21 final size:23
Alignment explanation
Indices: 4014896--4014950 Score: 60
Period size: 25 Copynumber: 2.4 Consensus size: 23
4014886 TGTACTATCA
4014896 ATTAATAATAA-CAT-AACATAT
1 ATTAATAATAATCATAAACATAT
* *
4014917 ATTAAATAAAAAATCATAAATATAT
1 ATT-AAT-AATAATCATAAACATAT
4014942 ATTAATAAT
1 ATTAATAAT
4014951 TTTATTTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
21 3 0.11
22 3 0.11
23 6 0.22
24 6 0.22
25 9 0.33
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (23 bp):
ATTAATAATAATCATAAACATAT
Found at i:4016152 original size:51 final size:51
Alignment explanation
Indices: 4016071--4016173 Score: 129
Period size: 51 Copynumber: 2.0 Consensus size: 51
4016061 GAAACTCTTT
** * * *
4016071 CGGATCCGATTTCTCGTCAAACGTATGATTATGAATTGG-GCTTGGTTAATC
1 CGGATCCGATTTCTCCCCAAACGTACGATTACGAAATGGAG-TTGGTTAATC
4016122 CGGATCCGATTTCTCACCCAAA-GTACGATTACGAAATGGAGTTGGTTAATC
1 CGGATCCGATTTCTC-CCCAAACGTACGATTACGAAATGGAGTTGGTTAATC
4016173 C
1 C
4016174 AATGGGGTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
51 40 0.89
52 5 0.11
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.31
Consensus pattern (51 bp):
CGGATCCGATTTCTCCCCAAACGTACGATTACGAAATGGAGTTGGTTAATC
Found at i:4021259 original size:18 final size:17
Alignment explanation
Indices: 4021242--4021282 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
4021232 AATATTTATT
4021242 TTTATATA-TTTTAATA
1 TTTATATATTTTTAATA
*
4021258 TTTATATATTTTTAAAA
1 TTTATATATTTTTAATA
*
4021275 ATTATATA
1 TTTATATA
4021283 AAAAAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTATATATTTTTAATA
Found at i:4023134 original size:23 final size:23
Alignment explanation
Indices: 4023104--4023149 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
4023094 AGTCGATGAA
4023104 GGTCTGGTTCTCTATCACAGCAG
1 GGTCTGGTTCTCTATCACAGCAG
4023127 GGTCTGGTTCTCTATCACAGCAG
1 GGTCTGGTTCTCTATCACAGCAG
4023150 AATGATGATG
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:0.17, C:0.26, G:0.26, T:0.30
Consensus pattern (23 bp):
GGTCTGGTTCTCTATCACAGCAG
Found at i:4026112 original size:2 final size:2
Alignment explanation
Indices: 4026099--4026129 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
4026089 AATTAAAACA
*
4026099 AC AC AT AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
4026130 AAAAAAACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.45, G:0.00, T:0.03
Consensus pattern (2 bp):
AC
Found at i:4047546 original size:17 final size:17
Alignment explanation
Indices: 4047520--4047552 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4047510 AGGTGAACAC
*
4047520 AATTAGTTTTGATTTAA
1 AATTACTTTTGATTTAA
4047537 AATTACTTTTGATTTA
1 AATTACTTTTGATTTA
4047553 CAACTTAGAA
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:0.33, C:0.03, G:0.09, T:0.55
Consensus pattern (17 bp):
AATTACTTTTGATTTAA
Found at i:4066015 original size:88 final size:88
Alignment explanation
Indices: 4065863--4066174 Score: 597
Period size: 88 Copynumber: 3.5 Consensus size: 88
4065853 AACTTGTGTT
* * *
4065863 CTGATTGTAAGATCTGCTTCTGACTATTTCCATATTATCTTTTTTTGAACTTTGAAGTATTATCT
1 CTGATTGTATGATCTGCTTCTGACTATTTCCATATGATCTTTTTTTGAACTTTGAAGTACTATCT
4065928 TCAATGACTAGTTTTCAATGGTC
66 TCAATGACTAGTTTTCAATGGTC
4065951 CTGATTGTATGATCTGCTTCTGACTATTTCCATATGATCTTTTTTTGAACTTTGAAGTACTATCT
1 CTGATTGTATGATCTGCTTCTGACTATTTCCATATGATCTTTTTTTGAACTTTGAAGTACTATCT
4066016 TCAATGACTAGTTTTCAATGGTC
66 TCAATGACTAGTTTTCAATGGTC
4066039 CTGATTGTATGATCTGCTTCTGACTATTTCCATATGATCTTTTTTTGAACTTTGAAGTACTATCT
1 CTGATTGTATGATCTGCTTCTGACTATTTCCATATGATCTTTTTTTGAACTTTGAAGTACTATCT
4066104 TCAATGACTAGTTTTCAATGGTC
66 TCAATGACTAGTTTTCAATGGTC
4066127 CTGATTGTATGATCTGCTTCTGACTATTTCCATATGATCTTTTTTTGA
1 CTGATTGTATGATCTGCTTCTGACTATTTCCATATGATCTTTTTTTGA
4066175 TTAGTCTTTT
Statistics
Matches: 221, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
88 221 1.00
ACGTcount: A:0.22, C:0.17, G:0.14, T:0.46
Consensus pattern (88 bp):
CTGATTGTATGATCTGCTTCTGACTATTTCCATATGATCTTTTTTTGAACTTTGAAGTACTATCT
TCAATGACTAGTTTTCAATGGTC
Found at i:4068331 original size:31 final size:31
Alignment explanation
Indices: 4068296--4068357 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 31
4068286 AAAAAGTTGC
4068296 CAAGTCCCAATATGGGAA-AAGTAGTCAAGTT
1 CAAGTCCCAATATGGGAATAA-TAGTCAAGTT
** * *
4068327 CAAGTTTCAATGTGGGAATAATTGTCAAGTT
1 CAAGTCCCAATATGGGAATAATAGTCAAGTT
4068358 TAAGATTTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
31 24 0.92
32 2 0.08
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.29
Consensus pattern (31 bp):
CAAGTCCCAATATGGGAATAATAGTCAAGTT
Found at i:4071555 original size:17 final size:17
Alignment explanation
Indices: 4071535--4071568 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
4071525 TCAATTCTTT
4071535 TATTAGTTAAAAGTAAA
1 TATTAGTTAAAAGTAAA
4071552 TATTAGTTAAAAGTAAA
1 TATTAGTTAAAAGTAAA
4071569 AATTGTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.12, T:0.35
Consensus pattern (17 bp):
TATTAGTTAAAAGTAAA
Found at i:4083667 original size:15 final size:15
Alignment explanation
Indices: 4083643--4083706 Score: 56
Period size: 15 Copynumber: 4.2 Consensus size: 15
4083633 TAAAAATTAA
* *
4083643 AAAAAATTAAGTATT
1 AAAAATTTAAATATT
4083658 AAAAATTTAAATATT
1 AAAAATTTAAATATT
* *
4083673 AGAAATTTAAAATTTT
1 AAAAATTT-AAATATT
* * *
4083689 AAATATTAAAAAATT
1 AAAAATTTAAATATT
4083704 AAA
1 AAA
4083707 TAGTAAATTT
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
15 28 0.72
16 11 0.28
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (15 bp):
AAAAATTTAAATATT
Found at i:4083682 original size:23 final size:23
Alignment explanation
Indices: 4083655--4083706 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
4083645 AAAATTAAGT
*
4083655 ATTAAAAATTTAAATATTAGAAA
1 ATTAAAAATTTAAATATTAAAAA
* *
4083678 TTTAAAATTTTAAATATTAAAAA
1 ATTAAAAATTTAAATATTAAAAA
4083701 ATTAAA
1 ATTAAA
4083707 TAGTAAATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (23 bp):
ATTAAAAATTTAAATATTAAAAA
Found at i:4102231 original size:20 final size:20
Alignment explanation
Indices: 4102191--4102241 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
4102181 ATAAGTAAAT
**
4102191 AATTTTAAAAAATATTTTAA
1 AATTTTAAAAAATATAATAA
*
4102211 AATTTTATAAAATATAATAA
1 AATTTTAAAAAATATAATAA
*
4102231 ATTCTTTAAAA
1 AAT-TTTAAAA
4102242 GAAATTAACT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 19 0.76
21 6 0.24
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (20 bp):
AATTTTAAAAAATATAATAA
Found at i:4102289 original size:23 final size:24
Alignment explanation
Indices: 4102262--4102306 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
4102252 TCATGAATGA
*
4102262 TAATAAAATTCCCTTA-ATTTTTT
1 TAATAAAATCCCCTTATATTTTTT
4102285 TAATAAAATCCCCTTATATTTT
1 TAATAAAATCCCCTTATATTTT
4102307 GAAATATTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.36, C:0.16, G:0.00, T:0.49
Consensus pattern (24 bp):
TAATAAAATCCCCTTATATTTTTT
Found at i:4102312 original size:23 final size:23
Alignment explanation
Indices: 4102263--4102312 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
4102253 CATGAATGAT
* **
4102263 AATAAAATTCCCTTAATTTTTTT
1 AATAAAATCCCCTTAATTTTTGA
4102286 AATAAAATCCCCTT-ATATTTTGA
1 AATAAAATCCCCTTAAT-TTTTGA
4102309 AATA
1 AATA
4102313 TTCGTTCAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 2 0.09
23 21 0.91
ACGTcount: A:0.40, C:0.14, G:0.02, T:0.44
Consensus pattern (23 bp):
AATAAAATCCCCTTAATTTTTGA
Found at i:4103576 original size:18 final size:18
Alignment explanation
Indices: 4103543--4103584 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
4103533 GTGAAAATTG
4103543 GAAAAA-GAAAAGAAAAA
1 GAAAAAGGAAAAGAAAAA
4103560 GAAAAAGGACAAA-AAAAA
1 GAAAAAGGA-AAAGAAAAA
*
4103578 GGAAAAG
1 GAAAAAG
4103585 ACGTGAGCGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 6 0.27
18 13 0.59
19 3 0.14
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.00
Consensus pattern (18 bp):
GAAAAAGGAAAAGAAAAA
Found at i:4110911 original size:2 final size:2
Alignment explanation
Indices: 4110906--4110941 Score: 56
Period size: 2 Copynumber: 18.0 Consensus size: 2
4110896 TCTCTCTCTC
4110906 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TGA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA
4110942 AAGAATGAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 29 0.91
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4118717 original size:94 final size:94
Alignment explanation
Indices: 4118556--4118744 Score: 342
Period size: 94 Copynumber: 2.0 Consensus size: 94
4118546 GGGTTTTTTG
* *
4118556 AAGATGTAAAAATATAGGTCGATTTTGAAGAGAGTGTAAAAACGCGTTCAGCTAGATGAGCTTTT
1 AAGATGTAAAAATATAGGTCGATTTTGAAGAGAGTGTAAAAACGCGTCCAGCTAGACGAGCTTTT
4118621 ACTGACATGTCAAGAAAGTGCGTCCAGTT
66 ACTGACATGTCAAGAAAGTGCGTCCAGTT
* *
4118650 AAGATTTAAAAATATAGGTCGATTTTGAAGAGAGTGTAAAAGCGCGTCCAGCTAGACGAGCTTTT
1 AAGATGTAAAAATATAGGTCGATTTTGAAGAGAGTGTAAAAACGCGTCCAGCTAGACGAGCTTTT
4118715 ACTGACATGTCAAGAAAGTGCGTCCAGTT
66 ACTGACATGTCAAGAAAGTGCGTCCAGTT
4118744 A
1 A
4118745 GAAGTATTTT
Statistics
Matches: 91, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
94 91 1.00
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (94 bp):
AAGATGTAAAAATATAGGTCGATTTTGAAGAGAGTGTAAAAACGCGTCCAGCTAGACGAGCTTTT
ACTGACATGTCAAGAAAGTGCGTCCAGTT
Found at i:4118963 original size:2 final size:2
Alignment explanation
Indices: 4118952--4118983 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
4118942 GTTAAAGAAA
4118952 AT AT -T 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 A
4118984 ATTTAGCCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4122391 original size:22 final size:21
Alignment explanation
Indices: 4122361--4122401 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
4122351 TTAATTGGTT
*
4122361 TTTTTAAAATTTAAAAAAATA
1 TTTTTAAAAATTAAAAAAATA
4122382 TTTTTAAAAATTAAAAAAAT
1 TTTTTAAAAATTAAAAAAAT
4122402 TAAATATTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TTTTTAAAAATTAAAAAAATA
Found at i:4123912 original size:14 final size:15
Alignment explanation
Indices: 4123884--4123928 Score: 65
Period size: 15 Copynumber: 3.1 Consensus size: 15
4123874 TAAAATATAC
4123884 AAAAAGTATAAAATT
1 AAAAAGTATAAAATT
*
4123899 AAAAAGT-TATAATT
1 AAAAAGTATAAAATT
*
4123913 AAAAAATATAAAATT
1 AAAAAGTATAAAATT
4123928 A
1 A
4123929 GTTATAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
14 12 0.46
15 14 0.54
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (15 bp):
AAAAAGTATAAAATT
Found at i:4125042 original size:42 final size:42
Alignment explanation
Indices: 4124995--4125078 Score: 134
Period size: 42 Copynumber: 2.0 Consensus size: 42
4124985 AAAAGGAGTT
*
4124995 GTTTATGAGTGTTATTT-AGGAATAAAATTATATTTGGGTTTA
1 GTTTATGAGTGTT-TTTGAAGAATAAAATTATATTTGGGTTTA
*
4125037 GTTTATGAGTGTTTTTGAAGAATGAAATTATATTTGGGTTTA
1 GTTTATGAGTGTTTTTGAAGAATAAAATTATATTTGGGTTTA
4125079 AAAGTATTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
41 3 0.08
42 36 0.92
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.48
Consensus pattern (42 bp):
GTTTATGAGTGTTTTTGAAGAATAAAATTATATTTGGGTTTA
Found at i:4125250 original size:9 final size:9
Alignment explanation
Indices: 4125236--4125264 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
4125226 TAATATAGTT
4125236 TTATTCGAA
1 TTATTCGAA
4125245 TTATTCGAA
1 TTATTCGAA
4125254 TTATTCGAA
1 TTATTCGAA
4125263 TT
1 TT
4125265 CAAAAATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.48
Consensus pattern (9 bp):
TTATTCGAA
Found at i:4125380 original size:13 final size:14
Alignment explanation
Indices: 4125363--4125398 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
4125353 ATAATTCGAA
4125363 ATTCGAATTTTTT-
1 ATTCGAATTTTTTG
*
4125376 TTTCGAATTTTTTG
1 ATTCGAATTTTTTG
4125390 ATTCGAATT
1 ATTCGAATT
4125399 GAGTTTCGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.22, C:0.08, G:0.11, T:0.58
Consensus pattern (14 bp):
ATTCGAATTTTTTG
Found at i:4134178 original size:21 final size:21
Alignment explanation
Indices: 4134146--4134200 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 21
4134136 AAAAAATTAT
*
4134146 AAATTTATAAAATA-TA-ATTA
1 AAATTTAAAAAATATTACA-TA
4134166 AAATTTATAAAAATATTACATA
1 AAATTTA-AAAAATATTACATA
4134188 AAATTTAAAAAAT
1 AAATTTAAAAAAT
4134201 TAAAAATAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
20 7 0.23
21 12 0.39
22 11 0.35
23 1 0.03
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (21 bp):
AAATTTAAAAAATATTACATA
Found at i:4134209 original size:21 final size:20
Alignment explanation
Indices: 4134146--4134221 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 20
4134136 AAAAAATTAT
* * *
4134146 AAATTTATAAAATATAATTA
1 AAATTTAAAAAATAAAAATA
* *
4134166 AAATTTATAAAAATATTACATA
1 AAATTTA-AAAAATA-AAAATA
4134188 AAATTTAAAAAATTAAAAATA
1 AAATTTAAAAAA-TAAAAATA
*
4134209 AAAATTAATAAAA
1 AAATTTAA-AAAA
4134222 CTATTTAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
20 7 0.15
21 22 0.48
22 17 0.37
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (20 bp):
AAATTTAAAAAATAAAAATA
Found at i:4137729 original size:31 final size:31
Alignment explanation
Indices: 4137694--4137753 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
4137684 AAAAAAAATA
4137694 AAAAAGAATATGTGAAATGAAAATAAAAACC
1 AAAAAGAATATGTGAAATGAAAATAAAAACC
* *
4137725 AAAAAGAATATGTTAATTGAAAATAAAAA
1 AAAAAGAATATGTGAAATGAAAATAAAAA
4137754 AAAGCATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.65, C:0.03, G:0.12, T:0.20
Consensus pattern (31 bp):
AAAAAGAATATGTGAAATGAAAATAAAAACC
Found at i:4141083 original size:18 final size:17
Alignment explanation
Indices: 4141038--4141072 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
4141028 AAGTGTATGG
*
4141038 AAATAAATTAAAAATGT
1 AAATATATTAAAAATGT
4141055 AAATATATTAAAAATGT
1 AAATATATTAAAAATGT
4141072 A
1 A
4141073 TTAAATATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (17 bp):
AAATATATTAAAAATGT
Found at i:4145407 original size:233 final size:232
Alignment explanation
Indices: 4144993--4145454 Score: 807
Period size: 233 Copynumber: 2.0 Consensus size: 232
4144983 GGGTATTCTT
* *
4144993 CATGTCAAATTTATGGTCCATGTTTGAGAATTGTAATTACCTCTCCCAACGATGTCATCTCCAAG
1 CATGTCAAATTTATAGTCCATGTTTGAGAATTGTAATTACCTCTCCCAACGATGTCATATCCAAG
4145058 GTTTAAACTTGTGTCTCCAGTTGAGAGTAAATTATAATATTATATATTTAACTATAATATATATA
66 GTTTAAACTTGTGTCTCCAGTTGAGAGTAAATTATAATATTATATATTTAACTATAATATATATA
* *
4145123 GATTATATAACGTAAATGAGATGAGCTGGGTTCAAGCTTTGAATGTAGAAGCCTGCGCTAGGCCC
131 GATTATATAACGTAAATGAGATGAGCTGAGTTCAAGCTTTGAACGTAGAAGCCTGCGCTAGGCCC
*
4145188 ACTTAAACGGATTTATTTATTTATTTTCTAAGCCTTAC
196 ACTTAAACAGATTTATTTATTT-TTTTCTAAGCCTTAC
*
4145226 CATGTCCAATTTATAGTCCATGTTTGAGAATTGTAATTACCTCTCCCAACGATGTCATATCCAAG
1 CATGTCAAATTTATAGTCCATGTTTGAGAATTGTAATTACCTCTCCCAACGATGTCATATCCAAG
* *
4145291 GTTTAAACTTGTGTCTCCCGTTGGGAGTAAATTATAATATTATATATTTAACTATAATATATATA
66 GTTTAAACTTGTGTCTCCAGTTGAGAGTAAATTATAATATTATATATTTAACTATAATATATATA
* * * *
4145356 GATTATATAACGTAAATTAGCTGAGTTGAGTTCAGGCTTTGAACGTAGAAGCCTGCGCTAGGCCC
131 GATTATATAACGTAAATGAGATGAGCTGAGTTCAAGCTTTGAACGTAGAAGCCTGCGCTAGGCCC
4145421 ACTTAAACAGATTTATTTATTTTTTTCTAAGCCT
196 ACTTAAACAGATTTATTTATTTTTTTCTAAGCCT
4145455 AAAGGCTAGG
Statistics
Matches: 217, Mismatches: 12, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
232 12 0.06
233 205 0.94
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (232 bp):
CATGTCAAATTTATAGTCCATGTTTGAGAATTGTAATTACCTCTCCCAACGATGTCATATCCAAG
GTTTAAACTTGTGTCTCCAGTTGAGAGTAAATTATAATATTATATATTTAACTATAATATATATA
GATTATATAACGTAAATGAGATGAGCTGAGTTCAAGCTTTGAACGTAGAAGCCTGCGCTAGGCCC
ACTTAAACAGATTTATTTATTTTTTTCTAAGCCTTAC
Found at i:4152426 original size:79 final size:79
Alignment explanation
Indices: 4152295--4152452 Score: 307
Period size: 79 Copynumber: 2.0 Consensus size: 79
4152285 TGTTTAGAAG
4152295 TTTGAGTTCTAAGCGAAACAGATTGTGATCTCACTCCAATTGAGTTTCATCTTTCATATTCATAC
1 TTTGAGTTCTAAGCGAAACAGATTGTGATCTCACTCCAATTGAGTTTCATCTTTCATATTCATAC
4152360 ACTCGAATATAAAA
66 ACTCGAATATAAAA
*
4152374 TTTGAGTTCTAAGCGAAACAGGTTGTGATCTCACTCCAATTGAGTTTCATCTTTCATATTCATAC
1 TTTGAGTTCTAAGCGAAACAGATTGTGATCTCACTCCAATTGAGTTTCATCTTTCATATTCATAC
4152439 ACTCGAATATAAAA
66 ACTCGAATATAAAA
4152453 GATAGAACTC
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 78 1.00
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.35
Consensus pattern (79 bp):
TTTGAGTTCTAAGCGAAACAGATTGTGATCTCACTCCAATTGAGTTTCATCTTTCATATTCATAC
ACTCGAATATAAAA
Found at i:4155915 original size:22 final size:22
Alignment explanation
Indices: 4155887--4155930 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
4155877 TTAGAAGGAA
*
4155887 CTAATCATCAAAAAATAACAAG
1 CTAATCATAAAAAAATAACAAG
4155909 CTAATCATAAAAAAATAACAAG
1 CTAATCATAAAAAAATAACAAG
4155931 GAAATTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.61, C:0.16, G:0.05, T:0.18
Consensus pattern (22 bp):
CTAATCATAAAAAAATAACAAG
Found at i:4155944 original size:22 final size:22
Alignment explanation
Indices: 4155889--4155946 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
4155879 AGAAGGAACT
* *
4155889 AATCATCAAAAAATAACAAGCT
1 AATCATAAAAAAATAACAAGCA
*
4155911 AATCATAAAAAAATAACAAGGA
1 AATCATAAAAAAATAACAAGCA
*
4155933 AATTATATAAAAAA
1 AATCATA-AAAAAA
4155947 ATGAAAACCC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
22 25 0.81
23 6 0.19
ACGTcount: A:0.66, C:0.10, G:0.05, T:0.19
Consensus pattern (22 bp):
AATCATAAAAAAATAACAAGCA
Found at i:4158845 original size:6 final size:7
Alignment explanation
Indices: 4158820--4158844 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
4158810 TACATAATTT
4158820 TTTTTAA
1 TTTTTAA
4158827 TTTTTAA
1 TTTTTAA
4158834 TTTTTAA
1 TTTTTAA
4158841 TTTT
1 TTTT
4158845 ATGAATGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTTAA
Found at i:4160787 original size:17 final size:17
Alignment explanation
Indices: 4160765--4160812 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 17
4160755 CAAGCCTACT
4160765 TATTTTTAAGT-TTATAA
1 TATTTTTAA-TATTATAA
4160782 TA-TTTT-ATATTATAA
1 TATTTTTAATATTATAA
4160797 TATTTTTATATATTAT
1 TATTTTTA-ATATTAT
4160813 GTAATTTACA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
14 1 0.04
15 9 0.33
16 8 0.30
17 2 0.07
18 7 0.26
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (17 bp):
TATTTTTAATATTATAA
Found at i:4162170 original size:4 final size:4
Alignment explanation
Indices: 4162163--4162195 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
4162153 ATGGAATGAA
*
4162163 AAAT AAAT AAAT AAAT AAAT AAAT ATAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
4162196 GTGACCAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
AAAT
Found at i:4163264 original size:41 final size:41
Alignment explanation
Indices: 4163213--4163291 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 41
4163203 AAATTTTTTA
* *
4163213 TTTAATTTTTTATAATTGATAAA-ATTTTAAATTTAATTATAT
1 TTTAATTTTTTAAAAGTGATAAATATTTT--ATTTAATTATAT
4163255 TTTAATTTTTTAAAAGTGATAAATATTTTATTTAATT
1 TTTAATTTTTTAAAAGTGATAAATATTTTATTTAATT
4163292 TTTTAAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
41 8 0.24
42 21 0.62
43 5 0.15
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (41 bp):
TTTAATTTTTTAAAAGTGATAAATATTTTATTTAATTATAT
Found at i:4163318 original size:15 final size:16
Alignment explanation
Indices: 4163298--4163336 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
4163288 AATTTTTTAA
4163298 AAATTATAAAAAT-AT
1 AAATTATAAAAATAAT
*
4163313 AAATTATTAAAATAAT
1 AAATTATAAAAATAAT
4163329 AAAGTTAT
1 AAA-TTAT
4163337 TTTTTTACTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 12 0.57
16 5 0.24
17 4 0.19
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (16 bp):
AAATTATAAAAATAAT
Found at i:4165416 original size:2 final size:2
Alignment explanation
Indices: 4165409--4165452 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
4165399 TACCTTTCAC
4165409 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
4165451 AT
1 AT
4165453 CATTTAACTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4165813 original size:23 final size:23
Alignment explanation
Indices: 4165787--4165931 Score: 101
Period size: 23 Copynumber: 6.5 Consensus size: 23
4165777 AGTGTTGGGT
4165787 AACAGAGAGCACAGAAAGTGCTA
1 AACAGAGAGCACAGAAAGTGCTA
* *
4165810 AACAGAGAGTACACAAA--G-T-
1 AACAGAGAGCACAGAAAGTGCTA
* *
4165829 -AC--TGAGCACATAAAGTGCTA
1 AACAGAGAGCACAGAAAGTGCTA
* *
4165849 ATCAGAGAGCACACG-AAGTGTTAA
1 AACAGAGAGCACA-GAAAGTGCT-A
*
4165873 TAACAGTGAGCAC-GAGAAGTGCTA
1 -AACAGAGAGCACAGA-AAGTGCTA
* *
4165897 AACAGAGAGCACACATAGTGCTA
1 AACAGAGAGCACAGAAAGTGCTA
*
4165920 ATCAGAGAGCAC
1 AACAGAGAGCAC
4165932 GCCAGTGTTC
Statistics
Matches: 93, Mismatches: 16, Indels: 26
0.69 0.12 0.19
Matches are distributed among these distances:
16 9 0.10
18 3 0.03
19 1 0.01
20 1 0.01
21 2 0.02
23 58 0.62
24 3 0.03
25 16 0.17
ACGTcount: A:0.43, C:0.19, G:0.24, T:0.14
Consensus pattern (23 bp):
AACAGAGAGCACAGAAAGTGCTA
Found at i:4165847 original size:39 final size:39
Alignment explanation
Indices: 4165793--4165867 Score: 114
Period size: 39 Copynumber: 1.9 Consensus size: 39
4165783 GGGTAACAGA
*
4165793 GAGCACAGAAAGTGCTAAACAGAGAGTACACAAAGTACT
1 GAGCACAGAAAGTGCTAAACAGAGAGCACACAAAGTACT
* * *
4165832 GAGCACATAAAGTGCTAATCAGAGAGCACACGAAGT
1 GAGCACAGAAAGTGCTAAACAGAGAGCACACAAAGT
4165868 GTTAATAACA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (39 bp):
GAGCACAGAAAGTGCTAAACAGAGAGCACACAAAGTACT
Found at i:4172757 original size:7 final size:7
Alignment explanation
Indices: 4172745--4172770 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
4172735 AACATATTGG
4172745 CATGTGC
1 CATGTGC
4172752 CATGTGC
1 CATGTGC
4172759 CATGTGC
1 CATGTGC
4172766 CATGT
1 CATGT
4172771 ATTTTACCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.27, G:0.27, T:0.31
Consensus pattern (7 bp):
CATGTGC
Found at i:4189827 original size:25 final size:23
Alignment explanation
Indices: 4189799--4189845 Score: 67
Period size: 25 Copynumber: 2.0 Consensus size: 23
4189789 AGTTGGATCC
4189799 AAATTAAATTCTAAAAAGATAATTA
1 AAATTAAA-TCTAAAAA-ATAATTA
*
4189824 AAATTAAATCTAAATAATAATT
1 AAATTAAATCTAAAAAATAATT
4189846 TCCTAATTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 6 0.29
24 7 0.33
25 8 0.38
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (23 bp):
AAATTAAATCTAAAAAATAATTA
Found at i:4190015 original size:8 final size:8
Alignment explanation
Indices: 4190002--4190026 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
4189992 CTAAGTCTTC
4190002 CACACTTT
1 CACACTTT
4190010 CACACTTT
1 CACACTTT
4190018 CACACTTT
1 CACACTTT
4190026 C
1 C
4190027 GGCACTTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.40, G:0.00, T:0.36
Consensus pattern (8 bp):
CACACTTT
Found at i:4204451 original size:15 final size:17
Alignment explanation
Indices: 4204421--4204456 Score: 58
Period size: 15 Copynumber: 2.2 Consensus size: 17
4204411 TTTAAAATTT
4204421 ATAAAAATATTTAAAAA
1 ATAAAAATATTTAAAAA
4204438 ATAAAAA-A-TTAAAAA
1 ATAAAAATATTTAAAAA
4204453 ATAA
1 ATAA
4204457 GTACATGTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 11 0.58
16 1 0.05
17 7 0.37
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (17 bp):
ATAAAAATATTTAAAAA
Found at i:4210183 original size:87 final size:86
Alignment explanation
Indices: 4209891--4210221 Score: 468
Period size: 91 Copynumber: 3.8 Consensus size: 86
4209881 AATTATGTAT
*
4209891 GATA-AAAATTAATAAATAATGTATTGTCAAATCAACACATTATATGATAAAAATTATAATATAA
1 GATATAAAATTAATAAATAATATATTGTCAAATCAACACATTATATGATAAAAATTATAATATAA
4209955 TAATAATAATTTTTATTTAAA
66 TAATAATAATTTTTATTTAAA
* * *
4209976 GATATAAAATTAATAAATAATATGTTGTCAAATCAATACATTATATGATAAAATTGTAATATAAT
1 GATATAAAATTAATAAATAATATATTGTCAAATCAACACATTATATGATAAAA----ATTATAAT
4210041 AATAATAATAATAATTTTTATTTAAA
62 -ATAATAATAATAATTTTTATTTAAA
**
4210067 GATATAAAATTAATAAATAAGGTATTGTCAAATCAACACATTATATGATAAAAATTATAATATAA
1 GATATAAAATTAATAAATAATATATTGTCAAATCAACACATTATATGATAAAAATTATAATATAA
*
4210132 TAATAATAATTTGTACTTTAAA
66 TAATAATAATTTTTA-TTTAAA
* * * * * *
4210154 TATA-AAAATTTAATAAATAATATATTGTCAAATTAACACAATATTTGATATAAATTGTAATATA
1 GATATAAAA-TTAATAAATAATATATTGTCAAATCAACACATTATATGATAAAAATTATAATATA
4210218 ATAA
65 ATAA
4210222 CTATCTTTTT
Statistics
Matches: 220, Mismatches: 18, Indels: 14
0.87 0.07 0.06
Matches are distributed among these distances:
85 4 0.02
86 67 0.30
87 68 0.31
90 7 0.03
91 74 0.34
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.38
Consensus pattern (86 bp):
GATATAAAATTAATAAATAATATATTGTCAAATCAACACATTATATGATAAAAATTATAATATAA
TAATAATAATTTTTATTTAAA
Found at i:4210369 original size:12 final size:12
Alignment explanation
Indices: 4210352--4210402 Score: 57
Period size: 12 Copynumber: 3.9 Consensus size: 12
4210342 AAACATGTTC
4210352 ATTAATTTTTAA
1 ATTAATTTTTAA
4210364 ATTAATTTCAACTTAA
1 ATTAATTT----TTAA
*
4210380 ATTAATTTTCAA
1 ATTAATTTTTAA
4210392 ATTAATTTTTA
1 ATTAATTTTTA
4210403 CACAAATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
12 21 0.64
16 12 0.36
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (12 bp):
ATTAATTTTTAA
Found at i:4210398 original size:16 final size:16
Alignment explanation
Indices: 4210360--4210396 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
4210350 TCATTAATTT
*
4210360 TTAAATTAATTTCAAC
1 TTAAATTAATTTCAAA
4210376 TTAAATTAATTTTCAAA
1 TTAAATTAA-TTTCAAA
4210393 TTAA
1 TTAA
4210397 TTTTTACACA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (16 bp):
TTAAATTAATTTCAAA
Found at i:4210409 original size:28 final size:28
Alignment explanation
Indices: 4210352--4210409 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 28
4210342 AAACATGTTC
* **
4210352 ATTAATTTTTAAATTAATTTCAACTTAA
1 ATTAATTTTCAAATTAATTTCAACACAA
**
4210380 ATTAATTTTCAAATTAATTTTTACACAA
1 ATTAATTTTCAAATTAATTTCAACACAA
4210408 AT
1 AT
4210410 ATACTTCCTG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.48
Consensus pattern (28 bp):
ATTAATTTTCAAATTAATTTCAACACAA
Found at i:4212652 original size:58 final size:57
Alignment explanation
Indices: 4212500--4212830 Score: 353
Period size: 58 Copynumber: 5.7 Consensus size: 57
4212490 GCCATTATCA
* * * * *
4212500 GCCATTTGATGGCTAATACGAAAAAAATTTAAAATTTTTTCTCGAGAATATGGGGTGTCG
1 GCCATTTGATGGCCAACAC-CAAAAAATTT-AAATTTTTT-TCGAGAAAAGGGGGTGTCG
*
4212560 GCCATTTGATGGCCCACACCAAAAAA--TACAATTTTTTTCGAGAAAAGGGGCGTGTCG
1 GCCATTTGATGGCCAACACCAAAAAATTTA-AATTTTTTTCGAGAAAAGGGG-GTGTCG
* * *
4212617 GCCATTTGATAGCCAACACCAAAAAATTTGAATTTTTTTTCTCGAGAATAGGGGGTGTCG
1 GCCATTTGATGGCCAACACCAAAAAATTT-AA-ATTTTTT-TCGAGAAAAGGGGGTGTCG
* * ** *
4212677 GCCATTTGATGACCAACACCCAAAAATACAAATTTCTTTTCGAGAAAAGAGGGTGTCG
1 GCCATTTGATGGCCAACACCAAAAAATTTAAATTT-TTTTCGAGAAAAGGGGGTGTCG
** * * * *
4212735 GTTATTTGATGGCCAACACCCAAAAATGT-AATTTTTTTCGAGAAAAAGGGGTGTCA
1 GCCATTTGATGGCCAACACCAAAAAATTTAAATTTTTTTCGAGAAAAGGGGGTGTCG
* *
4212791 GCCATTTGATGGACAACACAAAAAAATTTTAAATTTTTTT
1 GCCATTTGATGGCCAACACCAAAAAA-TTTAAATTTTTTT
4212831 TCTGAAACAG
Statistics
Matches: 229, Mismatches: 32, Indels: 22
0.81 0.11 0.08
Matches are distributed among these distances:
56 52 0.23
57 46 0.20
58 53 0.23
59 13 0.06
60 53 0.23
61 12 0.05
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (57 bp):
GCCATTTGATGGCCAACACCAAAAAATTTAAATTTTTTTCGAGAAAAGGGGGTGTCG
Found at i:4212706 original size:117 final size:115
Alignment explanation
Indices: 4212521--4212817 Score: 377
Period size: 117 Copynumber: 2.6 Consensus size: 115
4212511 GCTAATACGA
* * *
4212521 AAAAAATTTAAAATTTTTTCTCGAGAATATGGGGTGTCGGCCATTTGATGGCCCACACCAAAAAA
1 AAAAAATTT--AATTTTTTCTCGAGAATAAGGGGTGTCGGCCATTTGATGACCAACACCAAAAAA
*
4212586 TAC-AATTT-TTTTCGAGAAAAGGGGCGTGTCGGCCATTTGATAGCCAACACC
64 TACAAATTTCTTTTCGAGAAAAGAGG-GTGTCGGCCATTTGATAGCCAACACC
* *
4212637 AAAAAATTTGAATTTTTTTTCTCGAGAATAGGGGGTGTCGGCCATTTGATGACCAACACCCAAAA
1 AAAAAATTT-AA--TTTTTTCTCGAGAATAAGGGGTGTCGGCCATTTGATGACCAACACCAAAAA
** *
4212702 ATACAAATTTCTTTTCGAGAAAAGAGGGTGTCGGTTATTTGATGGCCAACACC
63 ATACAAATTTCTTTTCGAGAAAAGAGGGTGTCGGCCATTTGATAGCCAACACC
* * * * *
4212755 CAAAAATGTAATTTTTT-TCGAGAAAAAGGGGTGTCAGCCATTTGATGGA-CAACACAAAAAAAT
1 AAAAAATTTAATTTTTTCTCGAGAATAAGGGGTGTCGGCCATTTGAT-GACCAACACCAAAAAAT
4212818 TTTAAATTTT
Statistics
Matches: 160, Mismatches: 16, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
114 38 0.24
115 10 0.06
116 9 0.06
117 53 0.33
118 35 0.22
119 15 0.09
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.28
Consensus pattern (115 bp):
AAAAAATTTAATTTTTTCTCGAGAATAAGGGGTGTCGGCCATTTGATGACCAACACCAAAAAATA
CAAATTTCTTTTCGAGAAAAGAGGGTGTCGGCCATTTGATAGCCAACACC
Found at i:4214764 original size:20 final size:20
Alignment explanation
Indices: 4214726--4214774 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
4214716 AGTACTTTAC
*
4214726 AATTTTT-AAATATTAACTT
1 AATTTTTAAAATAGTAACTT
4214745 ATATTTTTAAAATAGT-ACTT
1 A-ATTTTTAAAATAGTAACTT
*
4214765 AGTTTTTAAA
1 AATTTTTAAA
4214775 GGGTTTTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 9 0.35
20 11 0.42
21 6 0.23
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.51
Consensus pattern (20 bp):
AATTTTTAAAATAGTAACTT
Found at i:4217618 original size:18 final size:18
Alignment explanation
Indices: 4217597--4217633 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
4217587 TTTGACTTTC
* *
4217597 AATCAAATTTTCTTTCCT
1 AATCAAATTCTATTTCCT
4217615 AATCAAATTCTATTTCCT
1 AATCAAATTCTATTTCCT
4217633 A
1 A
4217634 CAGTTATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.22, G:0.00, T:0.46
Consensus pattern (18 bp):
AATCAAATTCTATTTCCT
Found at i:4227861 original size:11 final size:11
Alignment explanation
Indices: 4227837--4227886 Score: 52
Period size: 9 Copynumber: 4.6 Consensus size: 11
4227827 AAATTAATTA
*
4227837 ATTTTTTATA-
1 ATTTTTAATAT
4227847 ATTTTTAATAT
1 ATTTTTAATAT
4227858 A--TTTAATAT
1 ATTTTTAATAT
4227867 ATTTTTATAATAT
1 A-TTTT-TAATAT
4227880 ATTTTTA
1 ATTTTTA
4227887 TTTTTAATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
9 9 0.26
10 9 0.26
11 3 0.09
12 6 0.18
13 7 0.21
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
ATTTTTAATAT
Found at i:4227872 original size:20 final size:17
Alignment explanation
Indices: 4227847--4227894 Score: 51
Period size: 22 Copynumber: 2.5 Consensus size: 17
4227837 ATTTTTTATA
4227847 ATTTTTAATATATTTAATAT
1 ATTTTTAATATATTT--T-T
4227867 ATTTTTATAATATATTTTT
1 A-TTTT-TAATATATTTTT
4227886 ATTTTTAAT
1 ATTTTTAAT
4227895 TTTTTAGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
17 4 0.15
18 4 0.15
19 2 0.08
20 2 0.08
21 4 0.15
22 10 0.38
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
ATTTTTAATATATTTTT
Found at i:4227879 original size:13 final size:13
Alignment explanation
Indices: 4227861--4227887 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4227851 TTAATATATT
4227861 TAATATATTTTTA
1 TAATATATTTTTA
4227874 TAATATATTTTTA
1 TAATATATTTTTA
4227887 T
1 T
4227888 TTTTAATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TAATATATTTTTA
Found at i:4227880 original size:22 final size:21
Alignment explanation
Indices: 4227843--4227883 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
4227833 ATTAATTTTT
4227843 TATAATTTTTAATATATTTAA
1 TATAATTTTTAATATATTTAA
*
4227864 TATATTTTTATAATATATTT
1 TATAATTTT-TAATATATTT
4227884 TTATTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TATAATTTTTAATATATTTAA
Found at i:4227916 original size:27 final size:27
Alignment explanation
Indices: 4227868--4227920 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
4227858 ATTTAATATA
* *
4227868 TTTTTATAATATATTTTTATTTTTAAT
1 TTTTTAGAATATATTTTAATTTTTAAT
4227895 TTTTTAGAAT-TATTATTAATTTTTAA
1 TTTTTAGAATATATT-TTAATTTTTAA
4227921 AATGATATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 4 0.17
27 19 0.83
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (27 bp):
TTTTTAGAATATATTTTAATTTTTAAT
Found at i:4231936 original size:45 final size:45
Alignment explanation
Indices: 4231872--4231962 Score: 164
Period size: 45 Copynumber: 2.0 Consensus size: 45
4231862 TGCTCATGAA
4231872 TTGGGTTGGGATCAAATCGGATCTAAACATAATATTAATATGTTT
1 TTGGGTTGGGATCAAATCGGATCTAAACATAATATTAATATGTTT
* *
4231917 TTGGGTTGGGATTAAATCGGGTCTAAACATAATATTAATATGTTT
1 TTGGGTTGGGATCAAATCGGATCTAAACATAATATTAATATGTTT
4231962 T
1 T
4231963 ATACTTGTTC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.32, C:0.08, G:0.21, T:0.40
Consensus pattern (45 bp):
TTGGGTTGGGATCAAATCGGATCTAAACATAATATTAATATGTTT
Found at i:4238376 original size:12 final size:11
Alignment explanation
Indices: 4238354--4238387 Score: 59
Period size: 11 Copynumber: 3.0 Consensus size: 11
4238344 AAACAGCAAG
4238354 TTATTATTTTA
1 TTATTATTTTA
4238365 TTATTAATTTTA
1 TTATT-ATTTTA
4238377 TTATTATTTTA
1 TTATTATTTTA
4238388 AAAACATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTATTATTTTA
Found at i:4240084 original size:44 final size:44
Alignment explanation
Indices: 4240034--4240225 Score: 321
Period size: 44 Copynumber: 4.4 Consensus size: 44
4240024 ATTTAAAATT
** *
4240034 TGAGTTAGTTATTTAAGTACTTGTAATATGCAGAAGGAATTAAA
1 TGAGTTAGTTATTTAAGTGTTTGTAATATGTAGAAGGAATTAAA
*
4240078 TGAGTTAGTTATTTAAGTGTTTGTAATATGTAGAAGGCATTAAA
1 TGAGTTAGTTATTTAAGTGTTTGTAATATGTAGAAGGAATTAAA
*
4240122 TGAGTTAATTATTTAAGTGTTTGTAATATGTAGAAGGAATTAAA
1 TGAGTTAGTTATTTAAGTGTTTGTAATATGTAGAAGGAATTAAA
*
4240166 TGAGTTAGTTATTTAAGTGTTTGTAATATGTAGAAGGCATTAAA
1 TGAGTTAGTTATTTAAGTGTTTGTAATATGTAGAAGGAATTAAA
*
4240210 TGAGTTAATTATTTAA
1 TGAGTTAGTTATTTAA
4240226 ATACTTGTTA
Statistics
Matches: 139, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 139 1.00
ACGTcount: A:0.36, C:0.02, G:0.21, T:0.41
Consensus pattern (44 bp):
TGAGTTAGTTATTTAAGTGTTTGTAATATGTAGAAGGAATTAAA
Found at i:4240183 original size:88 final size:88
Alignment explanation
Indices: 4240034--4240238 Score: 356
Period size: 88 Copynumber: 2.3 Consensus size: 88
4240024 ATTTAAAATT
*
4240034 TGAGTTAGTTATTTAAGTACTTGTAATATGCAGAAGGAATTAAATGAGTTAGTTATTTAAGTGTT
1 TGAGTTAATTATTTAAGTACTTGTAATATGCAGAAGGAATTAAATGAGTTAGTTATTTAAGTGTT
4240099 TGTAATATGTAGAAGGCATTAAA
66 TGTAATATGTAGAAGGCATTAAA
** *
4240122 TGAGTTAATTATTTAAGTGTTTGTAATATGTAGAAGGAATTAAATGAGTTAGTTATTTAAGTGTT
1 TGAGTTAATTATTTAAGTACTTGTAATATGCAGAAGGAATTAAATGAGTTAGTTATTTAAGTGTT
4240187 TGTAATATGTAGAAGGCATTAAA
66 TGTAATATGTAGAAGGCATTAAA
* *
4240210 TGAGTTAATTATTTAAATACTTGTTATAT
1 TGAGTTAATTATTTAAGTACTTGTAATAT
4240239 ATGTGTGTAG
Statistics
Matches: 109, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
88 109 1.00
ACGTcount: A:0.36, C:0.02, G:0.20, T:0.41
Consensus pattern (88 bp):
TGAGTTAATTATTTAAGTACTTGTAATATGCAGAAGGAATTAAATGAGTTAGTTATTTAAGTGTT
TGTAATATGTAGAAGGCATTAAA
Found at i:4244799 original size:52 final size:52
Alignment explanation
Indices: 4244729--4244827 Score: 146
Period size: 52 Copynumber: 1.9 Consensus size: 52
4244719 TATTTTTTCG
* * * *
4244729 AGTGTCGTCCATGTCATGATCGACACCCTTTTTATCTGATAAAAAAAAATTA
1 AGTGTCGTCCATGACATGACCGACACCCCTTTTACCTGATAAAAAAAAATTA
4244781 AGTGTCG-CCAATGACATGACCGACACCCCTTTTACCTGATAAAAAAA
1 AGTGTCGTCC-ATGACATGACCGACACCCCTTTTACCTGATAAAAAAA
4244828 TATATTTTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
51 2 0.05
52 40 0.95
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.27
Consensus pattern (52 bp):
AGTGTCGTCCATGACATGACCGACACCCCTTTTACCTGATAAAAAAAAATTA
Found at i:4245816 original size:29 final size:30
Alignment explanation
Indices: 4245765--4245849 Score: 111
Period size: 29 Copynumber: 2.9 Consensus size: 30
4245755 AAAAAATAAT
4245765 AATTAGAAATTAAATTTAAAATATAAACAA
1 AATTAGAAATTAAATTTAAAATATAAACAA
* * *
4245795 AATTAGAAA-TATATTTAAAATACAAACGA
1 AATTAGAAATTAAATTTAAAATATAAACAA
* *
4245824 AA-TACAAATTAAATTTAAAAAATAAA
1 AATTAGAAATTAAATTTAAAATATAAA
4245850 TGAAAAAAAT
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
28 5 0.11
29 33 0.70
30 9 0.19
ACGTcount: A:0.64, C:0.05, G:0.04, T:0.28
Consensus pattern (30 bp):
AATTAGAAATTAAATTTAAAATATAAACAA
Found at i:4247277 original size:8 final size:8
Alignment explanation
Indices: 4247264--4247290 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
4247254 TCTGTAGTGT
4247264 TTGCCACA
1 TTGCCACA
4247272 TTGCCACA
1 TTGCCACA
4247280 TTGCCACA
1 TTGCCACA
4247288 TTG
1 TTG
4247291 TACTAATTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.22, C:0.33, G:0.15, T:0.30
Consensus pattern (8 bp):
TTGCCACA
Found at i:4247569 original size:20 final size:19
Alignment explanation
Indices: 4247536--4247600 Score: 53
Period size: 20 Copynumber: 3.4 Consensus size: 19
4247526 AAGGTAAGAT
*
4247536 ATATTTTTGAATTTTTTTAA
1 ATATTTTT-TATTTTTTTAA
**
4247556 ATATTTTTCTATTTTCGT-A
1 ATATTTTT-TATTTTTTTAA
* *
4247575 ATATTTTTTATATTTTCAA
1 ATATTTTTTATTTTTTTAA
4247594 AT-TTTTT
1 ATATTTTT
4247601 AAAATTATAT
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
18 10 0.28
19 12 0.33
20 14 0.39
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.66
Consensus pattern (19 bp):
ATATTTTTTATTTTTTTAA
Found at i:4247621 original size:43 final size:43
Alignment explanation
Indices: 4247565--4247656 Score: 114
Period size: 43 Copynumber: 2.1 Consensus size: 43
4247555 AATATTTTTC
** * *
4247565 TATTTTCGTAATATTTTTTATATTTTC-AAATTTTTTAAAATTA
1 TATTTTCAAAATATTTTTTAGATTTTCGAAA-ATTTTAAAATTA
*
4247608 TATTTTCAAAATATTTTTTAGCTTTTCGAAAATTTTAAAATTA
1 TATTTTCAAAATATTTTTTAGATTTTCGAAAATTTTAAAATTA
*
4247651 TTTTTT
1 TATTTT
4247657 ATATCTTCAA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
43 39 0.93
44 3 0.07
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59
Consensus pattern (43 bp):
TATTTTCAAAATATTTTTTAGATTTTCGAAAATTTTAAAATTA
Found at i:4247668 original size:29 final size:30
Alignment explanation
Indices: 4247609--4247669 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
4247599 TTAAAATTAT
* *
4247609 ATTTTCAAAATATTTTTTAGCTTTTCGAAA
1 ATTTTCAAAATATTTTTTAGATCTTCGAAA
*
4247639 ATTTT-AAAATTATTTTTTATATCTTC-AAA
1 ATTTTCAAAA-TATTTTTTAGATCTTCGAAA
4247668 AT
1 AT
4247670 GAAATTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 9 0.33
30 18 0.67
ACGTcount: A:0.36, C:0.08, G:0.03, T:0.52
Consensus pattern (30 bp):
ATTTTCAAAATATTTTTTAGATCTTCGAAA
Found at i:4248838 original size:30 final size:30
Alignment explanation
Indices: 4248802--4248860 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
4248792 GTTTCGTTTG
4248802 TTTTAAATTTAATTTGTAATTTCGTTTATA
1 TTTTAAATTTAATTTGTAATTTCGTTTATA
4248832 TTTTAAATTTAATTTGTAATTTCGTTTAT
1 TTTTAAATTTAATTTGTAATTTCGTTTAT
4248861 TTCGTTTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.29, C:0.03, G:0.07, T:0.61
Consensus pattern (30 bp):
TTTTAAATTTAATTTGTAATTTCGTTTATA
Found at i:4249384 original size:56 final size:57
Alignment explanation
Indices: 4249305--4249501 Score: 180
Period size: 56 Copynumber: 3.6 Consensus size: 57
4249295 GGGTGCCGGT
* * *
4249305 CATGACATGAGCGACACCTAAAAAAATA-TTTTTTATCAAAT-AAAGGAAGTT-TCGAC
1 CATGGCATGAGCGACACCCAAAAAAATATTTTTTTATCAAATAAAAGG--GTTGTCAAC
*
4249361 CATGGCATGAGCGACACCCAAAAAAATATTTTTTTATCAGATAAAAGGGTTGTCAAC
1 CATGGCATGAGCGACACCCAAAAAAATATTTTTTTATCAAATAAAAGGGTTGTCAAC
* * * * * *
4249418 CATGGCATAAACAACACCC-AAAAAA-A---TTTTATCTAATAAAAGGG-TGTCGAT
1 CATGGCATGAGCGACACCCAAAAAAATATTTTTTTATCAAATAAAAGGGTTGTCAAC
* * * *
4249469 CGTGGCATAAGCAACA-CCGAAAAAATATTTTTT
1 CATGGCATGAGCGACACCCAAAAAAATATTTTTT
4249502 ATTTGTATTT
Statistics
Matches: 120, Mismatches: 13, Indels: 17
0.80 0.09 0.11
Matches are distributed among these distances:
50 2 0.02
51 25 0.21
52 17 0.14
55 4 0.03
56 35 0.29
57 32 0.27
58 5 0.04
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.26
Consensus pattern (57 bp):
CATGGCATGAGCGACACCCAAAAAAATATTTTTTTATCAAATAAAAGGGTTGTCAAC
Found at i:4249420 original size:57 final size:55
Alignment explanation
Indices: 4249305--4249444 Score: 174
Period size: 57 Copynumber: 2.5 Consensus size: 55
4249295 GGGTGCCGGT
* * *
4249305 CATGACATGAGCGACACCTAAAAAAATATTTTTTATCAAATAAAGGAAGTTTCGAC
1 CATGGCATGAGCGACACCCAAAAAAATATTTTTTATCAAATAAAGG-AGTTTCAAC
*
4249361 CATGGCATGAGCGACACCCAAAAAAATATTTTTTTATCAGATAAAAGG-GTTGTCAAC
1 CATGGCATGAGCGACACCCAAAAAAATA-TTTTTTATCAAAT-AAAGGAGTT-TCAAC
* * *
4249418 CATGGCATAAACAACACCCAAAAAAAT
1 CATGGCATGAGCGACACCCAAAAAAAT
4249445 TTTATCTAAT
Statistics
Matches: 74, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
56 29 0.39
57 40 0.54
58 5 0.07
ACGTcount: A:0.44, C:0.19, G:0.14, T:0.24
Consensus pattern (55 bp):
CATGGCATGAGCGACACCCAAAAAAATATTTTTTATCAAATAAAGGAGTTTCAAC
Found at i:4249492 original size:51 final size:53
Alignment explanation
Indices: 4249325--4249499 Score: 144
Period size: 57 Copynumber: 3.2 Consensus size: 53
4249315 GCGACACCTA
* * * * *
4249325 AAAAAATATTTTTTATCAAAT-AAAGGAAGTT-TCGACCATGGCATGAGCGACACCC
1 AAAAAATA--TTTTATCAGATAAAAGG--GTTGTCAACCATGGCATAAACAACACCC
4249380 AAAAAAATATTTTTTTATCAGATAAAAGGGTTGTCAACCATGGCATAAACAACACCC
1 -AAAAAATA---TTTTATCAGATAAAAGGGTTGTCAACCATGGCATAAACAACACCC
* * * * *
4249437 AAAAAA-ATTTTATCTA-ATAAAAGGG-TGTCGATCGTGGCATAAGCAACACCG
1 AAAAAATATTTTATC-AGATAAAAGGGTTGTCAACCATGGCATAAACAACACCC
4249488 AAAAAATATTTT
1 AAAAAATATTTT
4249500 TTATTTGTAT
Statistics
Matches: 104, Mismatches: 10, Indels: 14
0.81 0.08 0.11
Matches are distributed among these distances:
51 27 0.26
52 21 0.20
53 1 0.01
55 1 0.01
56 17 0.16
57 32 0.31
58 5 0.05
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.26
Consensus pattern (53 bp):
AAAAAATATTTTATCAGATAAAAGGGTTGTCAACCATGGCATAAACAACACCC
Found at i:4249493 original size:52 final size:52
Alignment explanation
Indices: 4249392--4249499 Score: 130
Period size: 52 Copynumber: 2.1 Consensus size: 52
4249382 AAAAATATTT
*
4249392 TTTTATCAGATAAAAGGGTTGTCAACCATGGCATAAACAACACCCAAAAAAA
1 TTTTATCAGATAAAAGGGTTGTCAACCATGGCATAAACAACACCAAAAAAAA
* * * * *
4249444 TTTTATCTA-ATAAAAGGG-TGTCGATCGTGGCATAAGCAACACCGAAAAAATA
1 TTTTATC-AGATAAAAGGGTTGTCAACCATGGCATAAACAACACC-AAAAAAAA
4249496 TTTT
1 TTTT
4249500 TTATTTGTAT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
51 21 0.44
52 26 0.54
53 1 0.02
ACGTcount: A:0.42, C:0.17, G:0.16, T:0.26
Consensus pattern (52 bp):
TTTTATCAGATAAAAGGGTTGTCAACCATGGCATAAACAACACCAAAAAAAA
Found at i:4250706 original size:3 final size:3
Alignment explanation
Indices: 4250698--4250794 Score: 57
Period size: 3 Copynumber: 34.7 Consensus size: 3
4250688 TGTTGCTAAT
* * *
4250698 TTA TTA TTA -TA TTA CTA TT- TTG TTA TTA -TA TTA TTA TTA TT- TTG
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * *
4250742 TTA TTA TTA TT- TGA ATA TT- GTA TGA TTT TTA TT- TTA TTA TTAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A
4250785 TT- TTA TTA TT
1 TTA TTA TTA TT
4250795 GTTTTAAAGG
Statistics
Matches: 71, Mismatches: 14, Indels: 18
0.69 0.14 0.17
Matches are distributed among these distances:
2 14 0.20
3 54 0.76
4 3 0.04
ACGTcount: A:0.28, C:0.01, G:0.05, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:4250723 original size:22 final size:22
Alignment explanation
Indices: 4250698--4250751 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
4250688 TGTTGCTAAT
4250698 TTATTATTATATTACTATTTTG
1 TTATTATTATATTACTATTTTG
*
4250720 TTATTA-TATTATTATTATTTTG
1 TTATTATTA-TATTACTATTTTG
4250742 TTATTATTAT
1 TTATTATTAT
4250752 TTGAATATTG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 2 0.07
22 25 0.86
23 2 0.07
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.67
Consensus pattern (22 bp):
TTATTATTATATTACTATTTTG
Found at i:4250760 original size:22 final size:21
Alignment explanation
Indices: 4250698--4250760 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 21
4250688 TGTTGCTAAT
*
4250698 TTATTATTATATTACTATTTTG
1 TTATTATTAT-TTAATATTTTG
*
4250720 TTATTA-TATTATTATTATTTTG
1 TTATTATTA-T-TTAATATTTTG
4250742 TTATTATTATTTGAATATT
1 TTATTATTATTT-AATATT
4250761 GTATGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
21 4 0.11
22 30 0.83
23 2 0.06
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.65
Consensus pattern (21 bp):
TTATTATTATTTAATATTTTG
Found at i:4257338 original size:52 final size:52
Alignment explanation
Indices: 4257261--4257369 Score: 173
Period size: 52 Copynumber: 2.1 Consensus size: 52
4257251 ATCTATATTT
** *
4257261 TTTTATATTGACGGTAATACTTAAATTAATTGAGTTAAGATTTAATCAATAA
1 TTTTATATTGACAATAATACTTAAATTAATTGAATTAAGATTTAATCAATAA
* *
4257313 TTTTATATTGACAATAATATTTAAATTAATTGAATTAAGATTTAATCGATAA
1 TTTTATATTGACAATAATACTTAAATTAATTGAATTAAGATTTAATCAATAA
4257365 TTTTA
1 TTTTA
4257370 ATGTTATTTT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45
Consensus pattern (52 bp):
TTTTATATTGACAATAATACTTAAATTAATTGAATTAAGATTTAATCAATAA
Found at i:4257623 original size:67 final size:67
Alignment explanation
Indices: 4257510--4257643 Score: 214
Period size: 67 Copynumber: 2.0 Consensus size: 67
4257500 AATGTCTAAC
* * * * *
4257510 TGCCAATGCAATTGAATAGTGCAGTGCAATGATGCATAGGAATGCCATTTGGCAAATGATGAAGA
1 TGCCAATGCAATTGAATAGTGCAATGCAATGATGCACACGAATGCCAATTGGCAAATGAAGAAGA
4257575 TG
66 TG
*
4257577 TGCCGATGCAATTGAATAGTGCAATGCAATGATGCACACGAATGCCAATTGGCAAATGAAGAAGA
1 TGCCAATGCAATTGAATAGTGCAATGCAATGATGCACACGAATGCCAATTGGCAAATGAAGAAGA
4257642 TG
66 TG
4257644 CATATGAATA
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
67 61 1.00
ACGTcount: A:0.36, C:0.15, G:0.26, T:0.23
Consensus pattern (67 bp):
TGCCAATGCAATTGAATAGTGCAATGCAATGATGCACACGAATGCCAATTGGCAAATGAAGAAGA
TG
Found at i:4257933 original size:35 final size:30
Alignment explanation
Indices: 4257839--4257936 Score: 117
Period size: 29 Copynumber: 3.1 Consensus size: 30
4257829 TAATGATTTA
* * *
4257839 TTTAACTTTTTAATTTCATAAAAATGTTAT
1 TTTAATTTTTTAATTTTATAAAAATATTAT
4257869 TTTAATTTTTT-ATTTTATAAAAATATTAT
1 TTTAATTTTTTAATTTTATAAAAATATTAT
4257898 TTTAATTCTTTATTAAATTTTATAAAAAATATTAT
1 TTTAA-T-TTT-TT-AATTTTAT-AAAAATATTAT
4257933 TTTA
1 TTTA
4257937 GCTCTTTAAA
Statistics
Matches: 59, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
29 21 0.36
30 11 0.19
31 3 0.05
32 2 0.03
34 7 0.12
35 15 0.25
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (30 bp):
TTTAATTTTTTAATTTTATAAAAATATTAT
Done.