Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr6
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: 26303135
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.30
Warning! 1968672 characters in sequence are not A, C, G, or T
File 11 of 66
Found at i:3591116 original size:13 final size:13
Alignment explanation
Indices: 3591098--3591122 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3591088 TTTTAAATGT
3591098 ACTTGGGATTAAA
1 ACTTGGGATTAAA
3591111 ACTTGGGATTAA
1 ACTTGGGATTAA
3591123 TCCAATCATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.08, G:0.24, T:0.32
Consensus pattern (13 bp):
ACTTGGGATTAAA
Found at i:3609509 original size:2 final size:2
Alignment explanation
Indices: 3609502--3609550 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
3609492 AAATATTATT
3609502 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3609544 TC TC TC T
1 TC TC TC T
3609551 TGATTCCAAC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:3609618 original size:25 final size:25
Alignment explanation
Indices: 3609584--3609658 Score: 82
Period size: 25 Copynumber: 3.0 Consensus size: 25
3609574 TTAATATTTT
*
3609584 TAAAATATTAATATTAAATTATAAA
1 TAAATTATTAATATTAAATTATAAA
*
3609609 TAAATTATTAATATTTAAATTATCAA
1 TAAATTATTAATA-TTAAATTATAAA
* * *
3609635 T-TATTAATAA-AATAAATTATAAA
1 TAAATTATTAATATTAAATTATAAA
3609658 T
1 T
3609659 TATTCCTATT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
23 11 0.26
24 1 0.02
25 19 0.44
26 12 0.28
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (25 bp):
TAAATTATTAATATTAAATTATAAA
Found at i:3609619 original size:19 final size:19
Alignment explanation
Indices: 3609595--3609661 Score: 63
Period size: 19 Copynumber: 3.6 Consensus size: 19
3609585 AAAATATTAA
3609595 TATTAAATTATAAATAAAT
1 TATTAAATTATAAATAAAT
3609614 TATTAATATT-TAAATTATCAAT
1 TATTAA-ATTATAAA-TA--AAT
3609636 TATT-AA-TA-AAATAAAT
1 TATTAAATTATAAATAAAT
3609652 TA-TAAATTAT
1 TATTAAATTAT
3609662 TCCTATTTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 17
0.70 0.00 0.30
Matches are distributed among these distances:
15 1 0.03
16 7 0.17
17 2 0.05
18 2 0.05
19 14 0.35
20 6 0.15
21 1 0.03
22 7 0.17
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (19 bp):
TATTAAATTATAAATAAAT
Found at i:3609650 original size:42 final size:41
Alignment explanation
Indices: 3609565--3609651 Score: 95
Period size: 42 Copynumber: 2.1 Consensus size: 41
3609555 TCCAACTTTT
* **
3609565 AATAAAATATTAATATTTTTAAAATATTAATATTAAATTATA
1 AATAAAATATTAATA-TTTTAAAATATCAATATTAAAAAATA
* *
3609607 AATAAATTATTAATA-TTTAAATTATCAATTATTAATAAAATA
1 AATAAAATATTAATATTTTAAAATATCAA-TATTAA-AAAATA
3609649 AAT
1 AAT
3609652 TATAAATTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
40 11 0.29
41 6 0.16
42 21 0.55
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (41 bp):
AATAAAATATTAATATTTTAAAATATCAATATTAAAAAATA
Found at i:3609654 original size:23 final size:22
Alignment explanation
Indices: 3609608--3609662 Score: 74
Period size: 23 Copynumber: 2.5 Consensus size: 22
3609598 TAAATTATAA
**
3609608 ATAAATTATTAATATTTAAATT
1 ATAAATTATTAATAAATAAATT
*
3609630 ATCAATTATTAATAAAATAAATT
1 ATAAATTATTAAT-AAATAAATT
3609653 ATAAATTATT
1 ATAAATTATT
3609663 CCTATTTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 12 0.43
23 16 0.57
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
ATAAATTATTAATAAATAAATT
Found at i:3610174 original size:22 final size:23
Alignment explanation
Indices: 3610128--3610211 Score: 80
Period size: 22 Copynumber: 3.5 Consensus size: 23
3610118 TTAATCATAA
3610128 TAATATTTAAATTAAATAAATTAT
1 TAATATTTAAATT-AATAAATTAT
* *
3610152 TAATATTTACATT-ATTAATTAT
1 TAATATTTAAATTAATAAATTAT
* *
3610174 TAATATTTTAATTAAATTCTATATTAT
1 TAATATTTAAATT-AA---TAAATTAT
3610201 TAATATTTAAA
1 TAATATTTAAA
3610212 AAATCTAATA
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
22 19 0.40
24 13 0.27
27 16 0.33
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (23 bp):
TAATATTTAAATTAATAAATTAT
Found at i:3611234 original size:48 final size:48
Alignment explanation
Indices: 3611144--3611247 Score: 131
Period size: 48 Copynumber: 2.2 Consensus size: 48
3611134 CTCAAACTCA
* * * *
3611144 ACCTATATGTCTAAGTTTTCTTAACTTCCCTGATTCGATGCAACGTCT
1 ACCTACATGACTAAGTTTTCTTAACTTCCCTAATTAGATGCAACGTCT
3611192 ACCTACATGACTAAGTTTTCTTAAC-TCTCCTAATTTAG-TGCAACGTCT
1 ACCTACATGACTAAGTTTTCTTAACTTC-CCTAA-TTAGATGCAACGTCT
*
3611240 ACTTACAT
1 ACCTACAT
3611248 ACTGATTGGG
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
47 2 0.04
48 44 0.90
49 3 0.06
ACGTcount: A:0.26, C:0.25, G:0.11, T:0.38
Consensus pattern (48 bp):
ACCTACATGACTAAGTTTTCTTAACTTCCCTAATTAGATGCAACGTCT
Found at i:3611307 original size:30 final size:30
Alignment explanation
Indices: 3611273--3611336 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 30
3611263 TTTTCATAAC
*
3611273 TCTCCTTATTTGGTGTAAC-GTTCACTTCAT
1 TCTCCTGATTTGGTG-AACTGTTCACTTCAT
*
3611303 TCTCCTGATTTGGTGCACTGTTCACTTCAT
1 TCTCCTGATTTGGTGAACTGTTCACTTCAT
3611333 TCTC
1 TCTC
3611337 TGCCTATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 2 0.06
30 29 0.94
ACGTcount: A:0.14, C:0.27, G:0.14, T:0.45
Consensus pattern (30 bp):
TCTCCTGATTTGGTGAACTGTTCACTTCAT
Found at i:3625534 original size:15 final size:15
Alignment explanation
Indices: 3625500--3625534 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
3625490 TAATAATAAC
*
3625500 AATATTAAAATTATT
1 AATATTAAAATTATA
*
3625515 TATATTAAAATTATA
1 AATATTAAAATTATA
3625530 AATAT
1 AATAT
3625535 AAGGTTTTTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
AATATTAAAATTATA
Found at i:3633855 original size:3 final size:3
Alignment explanation
Indices: 3633837--3633909 Score: 53
Period size: 3 Copynumber: 24.0 Consensus size: 3
3633827 GAGCTGGAGG
* *
3633837 AGA AAA AGA AGCA AGA AGA AGA AGCA A-A A-A AGA AGCA GGA AGA AGA
1 AGA AGA AGA AG-A AGA AGA AGA AG-A AGA AGA AGA AG-A AGA AGA AGA
* *
3633883 AGA AG- AGA AAA AGA AGCA AAA AGA AGA
1 AGA AGA AGA AGA AGA AG-A AGA AGA AGA
3633910 GGAGAAAGCT
Statistics
Matches: 56, Mismatches: 8, Indels: 12
0.74 0.11 0.16
Matches are distributed among these distances:
2 6 0.11
3 41 0.73
4 9 0.16
ACGTcount: A:0.67, C:0.05, G:0.27, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:3633870 original size:24 final size:24
Alignment explanation
Indices: 3633836--3633916 Score: 101
Period size: 24 Copynumber: 3.2 Consensus size: 24
3633826 GGAGCTGGAG
3633836 GAGAAAAAGAAGCAAGAAGAAGAA
1 GAGAAAAAGAAGCAAGAAGAAGAA
3633860 GCA-AAAAAGAAGCAGGAAGAAGAAGAA
1 G-AGAAAAAGAAGC---AAGAAGAAGAA
* *
3633887 GAGAAAAAGAAGCAAAAAGAAGAG
1 GAGAAAAAGAAGCAAGAAGAAGAA
3633911 GAGAAA
1 GAGAAA
3633917 GCTAAAGAGA
Statistics
Matches: 50, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
24 26 0.52
25 1 0.02
26 1 0.02
27 22 0.44
ACGTcount: A:0.65, C:0.05, G:0.30, T:0.00
Consensus pattern (24 bp):
GAGAAAAAGAAGCAAGAAGAAGAA
Found at i:3633887 original size:27 final size:27
Alignment explanation
Indices: 3633836--3633909 Score: 93
Period size: 27 Copynumber: 2.9 Consensus size: 27
3633826 GGAGCTGGAG
3633836 GAGAAAAAGAAGC---AAGAAGAAGAA
1 GAGAAAAAGAAGCAAAAAGAAGAAGAA
**
3633860 GCA-AAAAAGAAGCAGGAAGAAGAAGAA
1 G-AGAAAAAGAAGCAAAAAGAAGAAGAA
3633887 GAGAAAAAGAAGCAAAAAGAAGA
1 GAGAAAAAGAAGCAAAAAGAAGA
3633910 GGAGAAAGCT
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
24 11 0.26
25 1 0.02
26 1 0.02
27 30 0.70
ACGTcount: A:0.66, C:0.05, G:0.28, T:0.00
Consensus pattern (27 bp):
GAGAAAAAGAAGCAAAAAGAAGAAGAA
Found at i:3641968 original size:30 final size:33
Alignment explanation
Indices: 3641919--3641979 Score: 92
Period size: 30 Copynumber: 1.9 Consensus size: 33
3641909 TGCGGTGTGG
*
3641919 AATAAAATATAATAAAATAATTATT-TTATAAA
1 AATAAAATATAATAAAATAATAATTATTATAAA
3641951 AATAAAATA-AA-AAAATAATAATTATTATA
1 AATAAAATATAATAAAATAATAATTATTATA
3641980 TTATTTTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 11 0.41
31 7 0.26
32 9 0.33
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (33 bp):
AATAAAATATAATAAAATAATAATTATTATAAA
Found at i:3642274 original size:120 final size:120
Alignment explanation
Indices: 3642139--3642369 Score: 333
Period size: 120 Copynumber: 1.9 Consensus size: 120
3642129 TACTATAAAC
* * *
3642139 TTTTTCAATCTTTTAA-TTTTATTTTTATTAAAAATTTAAAATATTAATAATTTATTATTAAATT
1 TTTTTCAATCTTTTAATTTTTATTTTCATTAAAAATGT-AAACATTAATAATTTATTATTAAATT
3642203 ATTAATATGA-TTTTTTATTTCAATTTCTTCTTA-TTTTGTCTCTATTTGCATTTTCA
65 ATTAAT-TGATTTTTTTATTTCAATTTCTTCTTACTTTT-TCTCTATTTGCATTTTCA
* *
3642259 TTTTTTAATCTTTTAATTTTTATTTTCATTCAAAATGTAAACATTAATAATTTATTATTAAATTA
1 TTTTTCAATCTTTTAATTTTTATTTTCATTAAAAATGTAAACATTAATAATTTATTATTAAATTA
* * * *
3642324 TTAATTTATTTTTTTATTTTAATTTCTTTTTACTTTTTCTTTATTT
66 TTAATTGATTTTTTTATTTCAATTTCTTCTTACTTTTTCTCTATTT
3642370 TTTATTTTTT
Statistics
Matches: 99, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
119 2 0.02
120 75 0.76
121 22 0.22
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.61
Consensus pattern (120 bp):
TTTTTCAATCTTTTAATTTTTATTTTCATTAAAAATGTAAACATTAATAATTTATTATTAAATTA
TTAATTGATTTTTTTATTTCAATTTCTTCTTACTTTTTCTCTATTTGCATTTTCA
Found at i:3646388 original size:16 final size:17
Alignment explanation
Indices: 3646345--3646385 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
3646335 TTTTATTAAT
*
3646345 TATTTTTTACTTTTATA
1 TATTTTTTAATTTTATA
3646362 TATTTTTTAATTTTATA
1 TATTTTTTAATTTTATA
3646379 TATTTTT
1 TATTTTT
3646386 AATATAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (17 bp):
TATTTTTTAATTTTATA
Found at i:3649403 original size:2 final size:2
Alignment explanation
Indices: 3649396--3649474 Score: 121
Period size: 2 Copynumber: 41.5 Consensus size: 2
3649386 AACGAAGTAG
*
3649396 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT CT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3649437 A- AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3649475 GATCCAATAG
Statistics
Matches: 71, Mismatches: 2, Indels: 8
0.88 0.02 0.10
Matches are distributed among these distances:
1 4 0.06
2 67 0.94
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3649471 original size:19 final size:19
Alignment explanation
Indices: 3649396--3649474 Score: 126
Period size: 19 Copynumber: 4.2 Consensus size: 19
3649386 AACGAAGTAG
3649396 ATATATATATATATATA-T
1 ATATATATATATATATATT
3649414 ATATATAATATATATATATCT
1 ATATAT-ATATATATATAT-T
3649435 ATA-ATATATATATATATT
1 ATATATATATATATATATT
3649453 ATATATATATATATATATT
1 ATATATATATATATATATT
3649472 ATA
1 ATA
3649475 GATCCAATAG
Statistics
Matches: 57, Mismatches: 0, Indels: 7
0.89 0.00 0.11
Matches are distributed among these distances:
18 10 0.18
19 41 0.72
20 2 0.04
21 4 0.07
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (19 bp):
ATATATATATATATATATT
Found at i:3652391 original size:22 final size:22
Alignment explanation
Indices: 3652348--3652391 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
3652338 CAATTAGCGA
* * *
3652348 TTAAGCATTACGTTATTAGTTT
1 TTAAGCATTAAGTCACTAGTTT
*
3652370 TTAAGCATTAAGTCACTGGTTT
1 TTAAGCATTAAGTCACTAGTTT
3652392 CTAGGCATAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.27, C:0.11, G:0.16, T:0.45
Consensus pattern (22 bp):
TTAAGCATTAAGTCACTAGTTT
Found at i:3652618 original size:22 final size:22
Alignment explanation
Indices: 3652593--3652635 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
3652583 ATTTTTAAGC
3652593 ATTACATGACTAGGTTGTAGGA
1 ATTACATGACTAGGTTGTAGGA
** *
3652615 ATTATGTGACTGGGTTGTAGG
1 ATTACATGACTAGGTTGTAGG
3652636 GATTGTGGGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.07, G:0.33, T:0.35
Consensus pattern (22 bp):
ATTACATGACTAGGTTGTAGGA
Found at i:3652678 original size:22 final size:21
Alignment explanation
Indices: 3652632--3652674 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
3652622 GACTGGGTTG
*
3652632 TAGGGATTGTGGGATTGATTT
1 TAGGGATTGTGGGACTGATTT
*
3652653 TAGGTATTGTGGGACTGATTT
1 TAGGGATTGTGGGACTGATTT
3652674 T
1 T
3652675 TAGGCATTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.19, C:0.02, G:0.35, T:0.44
Consensus pattern (21 bp):
TAGGGATTGTGGGACTGATTT
Found at i:3661489 original size:22 final size:22
Alignment explanation
Indices: 3661460--3661525 Score: 69
Period size: 23 Copynumber: 3.0 Consensus size: 22
3661450 TGCTTCAACA
*
3661460 AACAAGTCACGCAATGCCTACC
1 AACAAGTCATGCAATGCCTACC
* * * * *
3661482 AACTAGTCGTACAATACCCTATC
1 AACAAGTCATGCAAT-GCCTACC
3661505 AACAAGTCATGCAATGCCTAC
1 AACAAGTCATGCAATGCCTAC
3661526 ACCCCATTCA
Statistics
Matches: 32, Mismatches: 11, Indels: 2
0.71 0.24 0.04
Matches are distributed among these distances:
22 15 0.47
23 17 0.53
ACGTcount: A:0.36, C:0.32, G:0.12, T:0.20
Consensus pattern (22 bp):
AACAAGTCATGCAATGCCTACC
Found at i:3661939 original size:295 final size:295
Alignment explanation
Indices: 3661342--3662115 Score: 1039
Period size: 295 Copynumber: 2.6 Consensus size: 295
3661332 TAAATTGTGG
* * * *
3661342 TATCTATCGATAGTTTCCAAGCCTCTTTGATTTGCAAAGTTCTCAAGTGGTCATCCATCGATAGA
1 TATCTATCGATAGTTTTCGAGCCTCTTTGATTTGCAAAGTTCTCGAGTGGTCATCTATCGATAGA
* * * * *
3661407 TAGTTTAATCTATCTATAAATGTTCATCTAAATTGCTTTCACATGCTTCAACAAACAAGTCACGC
66 TAGTGTAATTTATCAATAAATGTTCATCCAAATTGCCTTCACATGCTTCAACAAACAAGTCACGC
** *
3661472 AATGCCTACCAACTAGT--CGTACAATACCCTATCAACAAGTCATGCAATGCCTACACCCCATTC
131 AATG-CTACCAACTAGTCACGT--AATACCCTATCAACAAGTCACACAATGACTACACCCCATTC
*
3661535 ACACAATGCCTAAGTTACGCAATGACTAAAAACCAGTCACACAATGCCTTAATTACACAATGACT
193 ACACAATGCCTAAGTTACGCAATGACTAAAAACCAGCCACACAATGCCTTAATTACACAATGACT
* *** * * *
3661600 ATCAACTAGCCATGCAATACCTTATCGATAGATAGTGC
258 ATCAACCAGCCAAAAAATACCCTATCAATAGATAGTGA
* * * *
3661638 TATCTATCGATAGTTTTTGAGTCTCTTTGGTTTGCAAAGTTCTCGTGTGGTCATCTATCGATAGA
1 TATCTATCGATAGTTTTCGAGCCTCTTTGATTTGCAAAGTTCTCGAGTGGTCATCTATCGATAGA
* *
3661703 TAGTGGAATTTATCAATAAATGTTCATCCAAATTGCCTTCACATGCTTCAACAAGCAAGTCACGC
66 TAGTGTAATTTATCAATAAATGTTCATCCAAATTGCCTTCACATGCTTCAACAAACAAGTCACGC
* *
3661768 AATGCTGCCAACTAGTCACGTGATACCCTATCAACAAGTCACACAATGACTACACCCCATTCACA
131 AATGCTACCAACTAGTCACGTAATACCCTATCAACAAGTCACACAATGACTACACCCCATTCACA
* * * * * *
3661833 CAATGCCTAAGTTATGCAATGACTAAAAACTAGCCATACAATGCCTTAGTTGCACAATGACTATT
196 CAATGCCTAAGTTACGCAATGACTAAAAACCAGCCACACAATGCCTTAATTACACAATGACTATC
** *
3661898 AACCAGGTAAAAAATGCCCTATCAATAGATAGTGA
261 AACCAGCCAAAAAATACCCTATCAATAGATAGTGA
* * * * * * *
3661933 TATCTATTGATAATTTTCGGGCCTTTTTGATTTGTAAAGTTCTCGAATGGTCATCTATCGATAGT
1 TATCTATCGATAGTTTTCGAGCCTCTTTGATTTGCAAAGTTCTCGAGTGGTCATCTATCGATAGA
* *
3661998 TATTGTAATTTATCGATAAATGTTCATCCAAATTGCCTTCACATGCTTCAACAAACAAGTCACGC
66 TAGTGTAATTTATCAATAAATGTTCATCCAAATTGCCTTCACATGCTTCAACAAACAAGTCACGC
* * * * *
3662063 AATACCTACCAACTAGTCAAGTAATGCCCTATCAACTAGTCACACAATTACTA
131 AAT-GCTACCAACTAGTCACGTAATACCCTATCAACAAGTCACACAATGACTA
3662116 AAAATCAGTC
Statistics
Matches: 416, Mismatches: 59, Indels: 6
0.86 0.12 0.01
Matches are distributed among these distances:
295 252 0.61
296 161 0.39
297 3 0.01
ACGTcount: A:0.33, C:0.24, G:0.13, T:0.30
Consensus pattern (295 bp):
TATCTATCGATAGTTTTCGAGCCTCTTTGATTTGCAAAGTTCTCGAGTGGTCATCTATCGATAGA
TAGTGTAATTTATCAATAAATGTTCATCCAAATTGCCTTCACATGCTTCAACAAACAAGTCACGC
AATGCTACCAACTAGTCACGTAATACCCTATCAACAAGTCACACAATGACTACACCCCATTCACA
CAATGCCTAAGTTACGCAATGACTAAAAACCAGCCACACAATGCCTTAATTACACAATGACTATC
AACCAGCCAAAAAATACCCTATCAATAGATAGTGA
Found at i:3663531 original size:27 final size:27
Alignment explanation
Indices: 3663471--3663602 Score: 138
Period size: 27 Copynumber: 4.9 Consensus size: 27
3663461 TTTGAGGCAC
* *
3663471 GTAACAACTACATTTTTCAACATGATAT
1 GTAACAACTA-AATTTTCAACATGGTAT
* *
3663499 GAAACAACTAAATTTTCAACATGGTGT
1 GTAACAACTAAATTTTCAACATGGTAT
* * * * *
3663526 GTAACAATTATATTTTCAATATAGTGT
1 GTAACAACTAAATTTTCAACATGGTAT
* *
3663553 GCAACAACTAAATTTTCAGCATGGTAT
1 GTAACAACTAAATTTTCAACATGGTAT
* *
3663580 GTAAAAACTACATTTTCAACATG
1 GTAACAACTAAATTTTCAACATG
3663603 ATTTTTTTTT
Statistics
Matches: 84, Mismatches: 20, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
27 75 0.89
28 9 0.11
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.34
Consensus pattern (27 bp):
GTAACAACTAAATTTTCAACATGGTAT
Found at i:3664878 original size:20 final size:21
Alignment explanation
Indices: 3664837--3664885 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
3664827 GGTCCAAATT
*
3664837 TATCGATACATGTTCTTCATG
1 TATCGATACATGTTCGTCATG
*
3664858 TATCGATACAT-TTGGTCATG
1 TATCGATACATGTTCGTCATG
*
3664878 TATTGATA
1 TATCGATA
3664886 GAAATTGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.27, C:0.14, G:0.16, T:0.43
Consensus pattern (21 bp):
TATCGATACATGTTCGTCATG
Found at i:3666159 original size:20 final size:20
Alignment explanation
Indices: 3666110--3666162 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
3666100 CTAAATAATG
*
3666110 TCTATTGATAGATGAGCCAA
1 TCTATTGATAGATGAGCAAA
*
3666130 TCTATCGATAGATG-GTCAAA
1 TCTATTGATAGATGAG-CAAA
*
3666150 TTTATTGATAGAT
1 TCTATTGATAGAT
3666163 AGGCCTGATC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 1 0.04
20 27 0.96
ACGTcount: A:0.34, C:0.11, G:0.19, T:0.36
Consensus pattern (20 bp):
TCTATTGATAGATGAGCAAA
Found at i:3669092 original size:17 final size:17
Alignment explanation
Indices: 3669070--3669104 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
3669060 TGAAAAAATG
3669070 AGAAAAAATAAG-AATAA
1 AGAAAAAA-AAGAAATAA
3669087 AGAAAAAAAAGAAATAA
1 AGAAAAAAAAGAAATAA
3669104 A
1 A
3669105 AATTATATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.18
17 14 0.82
ACGTcount: A:0.80, C:0.00, G:0.11, T:0.09
Consensus pattern (17 bp):
AGAAAAAAAAGAAATAA
Found at i:3669266 original size:121 final size:120
Alignment explanation
Indices: 3669098--3669374 Score: 328
Period size: 121 Copynumber: 2.3 Consensus size: 120
3669088 GAAAAAAAAG
** * * *
3669098 AAAT-AAAAATTATATTAATAATAAAATTATTAAATTATTAAAGTTTCAAAATTTTATAA-AAAA
1 AAATAAAAAATTATATTAATAATTTAA-TAATAAATAATTAAAATTTCAAAATTTTA-AAGAAAA
*
3669161 AAGAAATTAAAAGATTAAAAAATG-AAAATGCAAATAAAGAAAAAA-TAAAAGAAAACTA
64 AAGAAATT-AAAGATT-AAAAATGAAAAATGAAAATAAAGAAAAAATTAAAA-AAAACTA
* *
3669219 AAATAAAAAATTATATTATTAATTTAATAATAAATAATTAAAATTTCAAAATTTTAAAGAAAATA
1 AAATAAAAAATTATATTAATAATTTAATAATAAATAATTAAAATTTCAAAATTTTAAAGAAAAAA
* * * * *
3669284 GAAATTAAATATTAAATATGAAAAATTAAAATAAAGAAAAAATTAAAATAAATTA
66 GAAATTAAAGATTAAAAATGAAAAATGAAAATAAAGAAAAAATTAAAAAAAACTA
** *
3669339 AAATAAAAAAACCATATTAATATTTTAATAATAAAT
1 AAAT-AAAAAATTATATTAATAATTTAATAATAAAT
3669375 TAATAAATTA
Statistics
Matches: 134, Mismatches: 17, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
119 6 0.04
120 36 0.27
121 73 0.54
122 19 0.14
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (120 bp):
AAATAAAAAATTATATTAATAATTTAATAATAAATAATTAAAATTTCAAAATTTTAAAGAAAAAA
GAAATTAAAGATTAAAAATGAAAAATGAAAATAAAGAAAAAATTAAAAAAAACTA
Found at i:3669336 original size:10 final size:10
Alignment explanation
Indices: 3669306--3669345 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
3669296 TAAATATGAA
3669306 AAATTAAAAT
1 AAATTAAAAT
*
3669316 AAA--GAAA-
1 AAATTAAAAT
3669323 AAATTAAAAT
1 AAATTAAAAT
3669333 AAATTAAAAT
1 AAATTAAAAT
3669343 AAA
1 AAA
3669346 AAAACCATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
7 3 0.12
8 3 0.12
9 3 0.12
10 16 0.64
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.23
Consensus pattern (10 bp):
AAATTAAAAT
Found at i:3669341 original size:17 final size:17
Alignment explanation
Indices: 3669285--3669341 Score: 60
Period size: 17 Copynumber: 3.1 Consensus size: 17
3669275 AAGAAAATAG
3669285 AAATTAAATATTAAATATGAA
1 AAATTAAA-A-TAAAT-T-AA
**
3669306 AAATTAAAATAAAGAAA
1 AAATTAAAATAAATTAA
3669323 AAATTAAAATAAATTAA
1 AAATTAAAATAAATTAA
3669340 AA
1 AA
3669342 TAAAAAAACC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
17 19 0.59
19 4 0.12
20 1 0.03
21 8 0.25
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (17 bp):
AAATTAAAATAAATTAA
Found at i:3669394 original size:121 final size:120
Alignment explanation
Indices: 3669109--3669438 Score: 315
Period size: 121 Copynumber: 2.6 Consensus size: 120
3669099 AATAAAAATT
** * * *
3669109 ATATTAATAATAAAATTATTAAATTATTAAAGTTTCAAAATTTTATAAAAAAAAGAAATTAAAAG
1 ATATTAATAATTTAA-TAATAAATAATTAAAATTTCAAAATTTTA-AAAAAAAAGAAATTAAAAG
* **
3669174 ATTAAAAAATGAAAATGCAAATAAAGAAAAAATAAAAGAAAACTAAAATAAAAAATT
64 ATTAAAAAATGAAAATGAAAATAAAGAAAAAATAAAAGAAAACTAAAATAAAAAACC
* * *
3669231 ATATTATTAATTTAATAATAAATAATTAAAATTTCAAAATTTTAAAGAAAATAGAAATT-AAATA
1 ATATTAATAATTTAATAATAAATAATTAAAATTTCAAAATTTTAAA-AAAAAAGAAATTAAAAGA
* * * *
3669295 TT-AAATATGAAAAATTAAAATAAAGAAAAAATTAAAA-TAAATTAAAATAAAAAAACC
65 TTAAAAAATG-AAAATGAAAATAAAGAAAAAA-TAAAAGAAAACTAAAAT-AAAAAACC
* * * *
3669352 ATATTAATATTTTAATAATAAATTAATAAATTATTAATATTTTAAAATTTTAATGAAATAAGAAA
1 ATATTAATAATTTAATAAT--A--AAT-AATTA--AA-ATTTCAAAATTTTAA-AAAAAAAGAAA
* *
3669417 TTAAAAAATTAAAAAAGGAAAA
57 TTAAAAGATTAAAAAATGAAAA
3669439 ATATTATTAA
Statistics
Matches: 169, Mismatches: 24, Indels: 22
0.79 0.11 0.10
Matches are distributed among these distances:
119 6 0.04
120 36 0.21
121 65 0.38
122 12 0.07
123 1 0.01
125 3 0.02
126 5 0.03
128 2 0.01
129 24 0.14
130 10 0.06
131 5 0.03
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.31
Consensus pattern (120 bp):
ATATTAATAATTTAATAATAAATAATTAAAATTTCAAAATTTTAAAAAAAAAGAAATTAAAAGAT
TAAAAAATGAAAATGAAAATAAAGAAAAAATAAAAGAAAACTAAAATAAAAAACC
Found at i:3669795 original size:6 final size:6
Alignment explanation
Indices: 3669784--3669810 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
3669774 ATAACCATTT
3669784 TGAAAG TGAAAG TGAAAG TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGA
3669811 TTATAAAGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.33, T:0.19
Consensus pattern (6 bp):
TGAAAG
Found at i:3673143 original size:27 final size:27
Alignment explanation
Indices: 3673113--3673188 Score: 91
Period size: 27 Copynumber: 2.8 Consensus size: 27
3673103 GTAAACAATA
*
3673113 TATTATTTTGACGAAAGTAATA-TAATG
1 TATTATTTTGATGAAAGTAA-AGTAATG
* * *
3673140 TATTATTTTGATGTAATTAAAGTCATG
1 TATTATTTTGATGAAAGTAAAGTAATG
*
3673167 TATTATTTTGATGAAAATAAAG
1 TATTATTTTGATGAAAGTAAAG
3673189 CTTGTAGGGA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
26 1 0.02
27 41 0.98
ACGTcount: A:0.39, C:0.03, G:0.14, T:0.43
Consensus pattern (27 bp):
TATTATTTTGATGAAAGTAAAGTAATG
Found at i:3679529 original size:23 final size:23
Alignment explanation
Indices: 3679499--3679550 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
3679489 ATGGAATGTG
3679499 ATGTTTGGATTACATGCATTAGC
1 ATGTTTGGATTACATGCATTAGC
3679522 ATGTTTGGATTACATGCATTAGC
1 ATGTTTGGATTACATGCATTAGC
3679545 ATGTTT
1 ATGTTT
3679551 TGAGTTATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.25, C:0.12, G:0.21, T:0.42
Consensus pattern (23 bp):
ATGTTTGGATTACATGCATTAGC
Found at i:3680395 original size:27 final size:27
Alignment explanation
Indices: 3680355--3680437 Score: 105
Period size: 27 Copynumber: 3.1 Consensus size: 27
3680345 CAAATAATAT
*
3680355 AAACAATGTATTATTTAGATGAAAGTA
1 AAACAATGTATTATTTTGATGAAAGTA
* *
3680382 ATACAATGTATTATTTTGATGGAAGTA
1 AAACAATGTATTATTTTGATGAAAGTA
* *
3680409 AAATC-ATATATTATTTTGATGAAAATA
1 AAA-CAATGTATTATTTTGATGAAAGTA
3680436 AA
1 AA
3680438 GCTTGCAAGC
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
27 47 0.98
28 1 0.02
ACGTcount: A:0.46, C:0.04, G:0.13, T:0.37
Consensus pattern (27 bp):
AAACAATGTATTATTTTGATGAAAGTA
Found at i:3690699 original size:3 final size:3
Alignment explanation
Indices: 3690691--3690724 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
3690681 GCCCAACAGA
3690691 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
3690725 CTTGTTCCTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:3691294 original size:23 final size:24
Alignment explanation
Indices: 3691245--3691295 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
3691235 ATTTGCTATG
3691245 CTTTC-GATTTCTCTCTCCTACGT
1 CTTTCAGATTTCTCTCTCCTACGT
* *
3691268 -TTTCAGATTTCTCTTTCTTAC-T
1 CTTTCAGATTTCTCTCTCCTACGT
3691290 CTTTCA
1 CTTTCA
3691296 ATACACCAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
22 5 0.21
23 19 0.79
ACGTcount: A:0.12, C:0.29, G:0.06, T:0.53
Consensus pattern (24 bp):
CTTTCAGATTTCTCTCTCCTACGT
Found at i:3691700 original size:27 final size:28
Alignment explanation
Indices: 3691670--3691741 Score: 92
Period size: 29 Copynumber: 2.6 Consensus size: 28
3691660 CATTAGAGTA
* * *
3691670 TAACAA-AATGTTTTTGAATATATCGTG
1 TAACAACAATATTTTTCAACATATCGTG
*
3691697 TAACAACAATATTTTTTCAACATGTCGTG
1 TAACAACAATA-TTTTTCAACATATCGTG
3691726 TAACAACAATATTTTT
1 TAACAACAATATTTTT
3691742 TTTTCAATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
27 6 0.15
28 8 0.21
29 25 0.64
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (28 bp):
TAACAACAATATTTTTCAACATATCGTG
Found at i:3691744 original size:32 final size:30
Alignment explanation
Indices: 3691693--3691820 Score: 124
Period size: 29 Copynumber: 4.4 Consensus size: 30
3691683 TTGAATATAT
* *
3691693 CGTGTAACAACAATA-TTTTTTCAACATGT
1 CGTGTAACAACAATATTTTTTTTAACATGG
*
3691722 CGTGTAACAACAATATTTTTTTTTCAATATGG
1 CGTGTAACAACAATA-TTTTTTTT-AACATGG
* *
3691754 CGTGT---AA-TA-ATCTTTTTTAACCATGG
1 CGTGTAACAACAATATTTTTTTTAA-CATGG
* *
3691780 CGTGTAACAACAGTATTTTTTTTAACATGA
1 CGTGTAACAACAATATTTTTTTTAACATGG
3691810 CGTGTAACAAC
1 CGTGTAACAAC
3691821 CTAACCATGA
Statistics
Matches: 80, Mismatches: 10, Indels: 17
0.75 0.09 0.16
Matches are distributed among these distances:
25 2 0.03
26 16 0.20
27 1 0.01
28 1 0.01
29 19 0.24
30 15 0.19
31 16 0.20
32 10 0.12
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (30 bp):
CGTGTAACAACAATATTTTTTTTAACATGG
Found at i:3691880 original size:34 final size:34
Alignment explanation
Indices: 3691812--3691880 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
3691802 TAACATGACG
* * *
3691812 TGTAACAACCTAACCATGACTTGTCACAGATTTT
1 TGTAACAAACTAACCATAACTTATCACAGATTTT
* *
3691846 TGTAACAAACTAACCATAACTTATCATAGGTTTT
1 TGTAACAAACTAACCATAACTTATCACAGATTTT
3691880 T
1 T
3691881 ATGCATGGTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.35, C:0.20, G:0.10, T:0.35
Consensus pattern (34 bp):
TGTAACAAACTAACCATAACTTATCACAGATTTT
Found at i:3692497 original size:18 final size:20
Alignment explanation
Indices: 3692469--3692506 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
3692459 TTATTTTCAT
3692469 TTAATATTATTTTAA-AATA
1 TTAATATTATTTTAATAATA
3692488 TTAA-ATTATTTTAATAATA
1 TTAATATTATTTTAATAATA
3692507 AATATAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TTAATATTATTTTAATAATA
Found at i:3692515 original size:21 final size:18
Alignment explanation
Indices: 3692474--3692528 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
3692464 TTCATTTAAT
*
3692474 ATTATTTTAAAATATTAA
1 ATTATTTTAAAATAATAA
3692492 ATTATTTT--AATAATAA
1 ATTATTTTAAAATAATAA
*
3692508 ATATAATTT-AAATAGATAA
1 AT-TATTTTAAAATA-ATAA
3692527 AT
1 AT
3692529 CAAGTCGAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
16 9 0.28
17 5 0.16
18 12 0.38
19 6 0.19
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (18 bp):
ATTATTTTAAAATAATAA
Found at i:3696659 original size:2 final size:2
Alignment explanation
Indices: 3696652--3696683 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3696642 TTTTAAGTGT
*
3696652 GA GA GA GA GA GA GA GA GA GA GA GA AA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3696684 AAGACAATCC
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:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3696684 original size:8 final size:8
Alignment explanation
Indices: 3696653--3696687 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
3696643 TTTAAGTGTG
*
3696653 AGAGAGAG
1 AGAGAGAA
*
3696661 AGAGAGAG
1 AGAGAGAA
3696669 AGAGAGAA
1 AGAGAGAA
3696677 AGAGAGAA
1 AGAGAGAA
3696685 AGA
1 AGA
3696688 CAATCCTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (8 bp):
AGAGAGAA
Found at i:3709707 original size:32 final size:32
Alignment explanation
Indices: 3709669--3709739 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
3709659 ACCTCACATT
* ** *
3709669 GCCTTTTCATGGGATCGGGCATAACCTACACC
1 GCCTTTTCATGAGATCAAGCATAACCAACACC
*
3709701 GCCTTTTCATGAGATCAAGCATAACCAACACT
1 GCCTTTTCATGAGATCAAGCATAACCAACACC
3709733 G-CTTTTC
1 GCCTTTTC
3709740 TAAGGAGCAG
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 6 0.18
32 28 0.82
ACGTcount: A:0.25, C:0.30, G:0.17, T:0.28
Consensus pattern (32 bp):
GCCTTTTCATGAGATCAAGCATAACCAACACC
Found at i:3709794 original size:28 final size:27
Alignment explanation
Indices: 3709763--3709842 Score: 97
Period size: 28 Copynumber: 2.9 Consensus size: 27
3709753 TAAGCTCACT
* *
3709763 TTTTCAAGGATTAGACAAACCCTTAGTC
1 TTTTCAAGGATCAGACAAA-CCTTAGCC
**
3709791 TTTTCAAGGATCAGGTAGAACCTTAGCC
1 TTTTCAAGGATCAGACA-AACCTTAGCC
3709819 TTTTCAAGGATCAGACAAATCCTT
1 TTTTCAAGGATCAGACAAA-CCTT
3709843 TACATTATTG
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
27 2 0.05
28 40 0.91
29 2 0.05
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.31
Consensus pattern (27 bp):
TTTTCAAGGATCAGACAAACCTTAGCC
Found at i:3710356 original size:21 final size:21
Alignment explanation
Indices: 3710328--3710427 Score: 96
Period size: 21 Copynumber: 4.8 Consensus size: 21
3710318 TATACATTGT
3710328 GCTAGGTATCAAGACTTTGAA
1 GCTAGGTATCAAGACTTTGAA
*
3710349 GTTAGGTATCAAGACTTTGAA
1 GCTAGGTATCAAGACTTTGAA
* *
3710370 GCCAAGTATCAAGA-TTTGGAA
1 GCTAGGTATCAAGACTTT-GAA
* *
3710391 ACCAGGTATCAAGA-TTTGGAA
1 GCTAGGTATCAAGACTTT-GAA
* * *
3710412 TCCAAGTATCAAGACT
1 GCTAGGTATCAAGACT
3710428 ATGTGAAAAG
Statistics
Matches: 69, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
20 3 0.04
21 65 0.94
22 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (21 bp):
GCTAGGTATCAAGACTTTGAA
Found at i:3717840 original size:22 final size:21
Alignment explanation
Indices: 3717815--3717864 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
3717805 GTTGATGTAA
3717815 TTCATGAAAAAAAATAGATGCT
1 TTCATGAAAAAAAAT-GATGCT
* * *
3717837 TTCATGACAAAGACTGATGCT
1 TTCATGAAAAAAAATGATGCT
3717858 TTCATGA
1 TTCATGA
3717865 CAAAGACAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 13 0.52
22 12 0.48
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (21 bp):
TTCATGAAAAAAAATGATGCT
Found at i:3717857 original size:21 final size:21
Alignment explanation
Indices: 3717831--3717898 Score: 91
Period size: 21 Copynumber: 3.2 Consensus size: 21
3717821 AAAAAAAATA
3717831 GATGCTTTCATGACAAAGACT
1 GATGCTTTCATGACAAAGACT
*
3717852 GATGCTTTCATGACAAAGACA
1 GATGCTTTCATGACAAAGACT
* * * *
3717873 AATGCCTGCATGACAAGGACT
1 GATGCTTTCATGACAAAGACT
3717894 GATGC
1 GATGC
3717899 CATCATTCAA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.34, C:0.21, G:0.22, T:0.24
Consensus pattern (21 bp):
GATGCTTTCATGACAAAGACT
Found at i:3718408 original size:10 final size:10
Alignment explanation
Indices: 3718389--3718444 Score: 58
Period size: 10 Copynumber: 5.4 Consensus size: 10
3718379 AACTTTTAAC
*
3718389 TTTTAGTTAT
1 TTTTATTTAT
3718399 TTTTATTTAT
1 TTTTATTTAT
3718409 GTATTTATTTAT
1 -T-TTTATTTAT
* *
3718421 TTTCATTAAT
1 TTTTATTTAT
*
3718431 CTTTATTTAT
1 TTTTATTTAT
3718441 TTTT
1 TTTT
3718445 TTCAGTAAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
10 26 0.70
11 2 0.05
12 9 0.24
ACGTcount: A:0.21, C:0.04, G:0.04, T:0.71
Consensus pattern (10 bp):
TTTTATTTAT
Found at i:3719533 original size:15 final size:16
Alignment explanation
Indices: 3719502--3719539 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
3719492 ATGATCATTG
3719502 AAATATTCCTTATTAT
1 AAATATTCCTTATTAT
* *
3719518 AATTATT-CTTANTAT
1 AAATATTCCTTATTAT
3719533 AAATATT
1 AAATATT
3719540 TATCAATCGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.50
Consensus pattern (16 bp):
AAATATTCCTTATTAT
Found at i:3719773 original size:21 final size:21
Alignment explanation
Indices: 3719718--3719774 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 21
3719708 ATTAAATAAT
*
3719718 TTAAATATTAATATTTT-AAG
1 TTAAGTATTAATATTTTAAAG
*
3719738 TT-AG-A--AATTTTTTAAAG
1 TTAAGTATTAATATTTTAAAG
3719755 TTAAGTATTAATATTTTAAA
1 TTAAGTATTAATATTTTAAA
3719775 AAATTTTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 9
0.71 0.07 0.22
Matches are distributed among these distances:
16 7 0.24
17 5 0.17
18 3 0.10
19 2 0.07
20 2 0.07
21 10 0.34
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (21 bp):
TTAAGTATTAATATTTTAAAG
Found at i:3727741 original size:21 final size:21
Alignment explanation
Indices: 3727715--3727757 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
3727705 TACAAAAATA
3727715 TGTTACACGCCATGATTAAGT
1 TGTTACACGCCATGATTAAGT
*
3727736 TGTTACACGTCATGATTAAGT
1 TGTTACACGCCATGATTAAGT
3727757 T
1 T
3727758 ATTATATGCC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.37
Consensus pattern (21 bp):
TGTTACACGCCATGATTAAGT
Found at i:3727770 original size:21 final size:21
Alignment explanation
Indices: 3727717--3727770 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
3727707 CAAAAATATG
*
3727717 TTACACGCCATGATTAAGTTG
1 TTACACGCCATGATTAAGTTA
*
3727738 TTACACGTCATGATTAAGTTA
1 TTACACGCCATGATTAAGTTA
* *
3727759 TTATATGCCATG
1 TTACACGCCATG
3727771 TGCAAAAACA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.37
Consensus pattern (21 bp):
TTACACGCCATGATTAAGTTA
Found at i:3727789 original size:45 final size:45
Alignment explanation
Indices: 3727740--3727839 Score: 103
Period size: 45 Copynumber: 2.2 Consensus size: 45
3727730 TTAAGTTGTT
* ** * *
3727740 ACACGTCATGATTAAGTTATTATATGCCATGTGCAAAAACATGTG
1 ACACGTCATGATTAAGTTATTACACACCATGTACAAAAACATGTC
* * * *
3727785 ACACG-CTATGGTTAGGTTGTTACACACCATGTACAGAAACATGTC
1 ACACGTC-ATGATTAAGTTATTACACACCATGTACAAAAACATGTC
3727830 ACACGTCATG
1 ACACGTCATG
3727840 TACAGAAACA
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
44 1 0.02
45 42 0.95
46 1 0.02
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (45 bp):
ACACGTCATGATTAAGTTATTACACACCATGTACAAAAACATGTC
Found at i:3727879 original size:24 final size:24
Alignment explanation
Indices: 3727812--3727887 Score: 116
Period size: 24 Copynumber: 3.2 Consensus size: 24
3727802 TGTTACACAC
*
3727812 CATGTACAGAAACATGTCACACGT
1 CATGTACAGAAACATGTGACACGT
3727836 CATGTACAGAAACATGTGACACGT
1 CATGTACAGAAACATGTGACACGT
* * *
3727860 CATGTACAAAAACATATGACATGT
1 CATGTACAGAAACATGTGACACGT
3727884 CATG
1 CATG
3727888 GTTAGGTTGT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.39, C:0.21, G:0.17, T:0.22
Consensus pattern (24 bp):
CATGTACAGAAACATGTGACACGT
Found at i:3728006 original size:29 final size:31
Alignment explanation
Indices: 3727947--3728027 Score: 103
Period size: 29 Copynumber: 2.6 Consensus size: 31
3727937 AAAAAGGTTG
*
3727947 TTACATGTCATGTTGAAAAAAATATATTATTA
1 TTACACGTCATGTT-AAAAAAATATATTATTA
*
3727979 TTACACGTCATGTTAAAAAAA-A-ATTATTG
1 TTACACGTCATGTTAAAAAAATATATTATTA
* *
3728008 TTACACGTCATATTCAAAAA
1 TTACACGTCATGTTAAAAAA
3728028 CATTTTGTTA
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
29 24 0.53
30 1 0.02
31 7 0.16
32 13 0.29
ACGTcount: A:0.44, C:0.11, G:0.09, T:0.36
Consensus pattern (31 bp):
TTACACGTCATGTTAAAAAAATATATTATTA
Found at i:3730802 original size:56 final size:56
Alignment explanation
Indices: 3730735--3730846 Score: 188
Period size: 56 Copynumber: 2.0 Consensus size: 56
3730725 ATTCATCAAG
*
3730735 GTATTCTTGCTTTTATGATGACATTTGGTATTATACTAAAAATGTAATTACTGAGA
1 GTATTCTTGCTTTTATGATGACATTTGGTATTATACTAAAAATGAAATTACTGAGA
* * *
3730791 GTATTCTTGCTTTTATGATGACATTTGGTGTTTTATTAAAAATGAAATTACTGAGA
1 GTATTCTTGCTTTTATGATGACATTTGGTATTATACTAAAAATGAAATTACTGAGA
3730847 TGATAATGTT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
56 52 1.00
ACGTcount: A:0.31, C:0.08, G:0.17, T:0.44
Consensus pattern (56 bp):
GTATTCTTGCTTTTATGATGACATTTGGTATTATACTAAAAATGAAATTACTGAGA
Found at i:3742739 original size:30 final size:30
Alignment explanation
Indices: 3742705--3742777 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 30
3742695 ATTTGATTCC
* *
3742705 AAATAAAAGTATAAGAAA-TTAGTTAACTCG
1 AAATAAAAATATAA-AAACTTAGTTAACTCA
* *
3742735 AAATAAAAATATAAAAACTTATTTAATTCA
1 AAATAAAAATATAAAAACTTAGTTAACTCA
3742765 AAATAAAAATATA
1 AAATAAAAATATA
3742778 GAGTTTTATT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
29 3 0.08
30 35 0.92
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.29
Consensus pattern (30 bp):
AAATAAAAATATAAAAACTTAGTTAACTCA
Found at i:3743611 original size:198 final size:196
Alignment explanation
Indices: 3743273--3743866 Score: 1008
Period size: 198 Copynumber: 3.0 Consensus size: 196
3743263 GTATAAGGTC
* * * *
3743273 CAAGTGCTTGCACAAGCTTGAGAGTCTAAAAATTTTTATGCACATCACGCAGACATCTACTAGTA
1 CAAGTGCTTGCACAAGCTTAAGAGTCTAAGAATTTTTATACACATCAAGCAGACATCTACTAGTA
* * *
3743338 TTAAAATCGAATTCCGAAACAATTATTGATACGAAACTGTTAATACATCAAAAGTAATATTAGGA
66 TTAAAACCGAATTTCGAAACAATTATTGATACGAAACTGTCAATACATCAAAAGTAATATTAGGA
*
3743403 AGTATAAGAAACCTATAACTATTGATTTTCCGCCGTATGAGAATATCAAAGTTATCATGGTCAAC
131 AGTATAAGAAACCTATAACTATTGATTTT-CGCCGTATGAGAACATCAAAGTTATCATGGTCAAC
3743468 AG
195 AG
3743470 TCAAGTGCTTGCACAAGCTTAAGAGTCTAAGAATTTTTATACACATCAAGCAGACATCTACTAGT
1 -CAAGTGCTTGCACAAGCTTAAGAGTCTAAGAATTTTTATACACATCAAGCAGACATCTACTAGT
*
3743535 ATTAAAACCGAATTTCGAAACAATTATTGATACGAAACTGTCAATACATCAAAAGTAATATTATG
65 ATTAAAACCGAATTTCGAAACAATTATTGATACGAAACTGTCAATACATCAAAAGTAATATTAGG
* * *
3743600 AAGTATAAGAAACCTATAATTATTGACTTTTCGCTGTATGTGAACATCAAAGTTATCATGGTCAA
130 AAGTATAAGAAACCTATAACTATTGA-TTTTCGCCGTATGAGAACATCAAAGTTATCATGGTCAA
3743665 CAG
194 CAG
*
3743668 CTAAGTGCTTGCACGAGCTTAAGAGTCTAAGAATTTTTATACACATCAAGCAGACATCTACTAGT
1 C-AAGTGCTTGCACAAGCTTAAGAGTCTAAGAATTTTTATACACATCAAGCAGACATCTACTAGT
*
3743733 ATTAAAACCGAATTTCGAAACAATTATTGATACGAAACTGTCAATACATCAAAAGTAATATTGGG
65 ATTAAAACCGAATTTCGAAACAATTATTGATACGAAACTGTCAATACATCAAAAGTAATATTAGG
*
3743798 AAGTATAAGAAACCTATAACTATTGATTTTTCGCCGTATGAGAACATCAAAGTTATCATGATCAA
130 AAGTATAAGAAACCTATAACTATTGA-TTTTCGCCGTATGAGAACATCAAAGTTATCATGGTCAA
3743863 CAG
194 CAG
3743866 C
1 C
3743867 CTCATCCTTA
Statistics
Matches: 374, Mismatches: 20, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
197 1 0.00
198 369 0.99
199 4 0.01
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29
Consensus pattern (196 bp):
CAAGTGCTTGCACAAGCTTAAGAGTCTAAGAATTTTTATACACATCAAGCAGACATCTACTAGTA
TTAAAACCGAATTTCGAAACAATTATTGATACGAAACTGTCAATACATCAAAAGTAATATTAGGA
AGTATAAGAAACCTATAACTATTGATTTTCGCCGTATGAGAACATCAAAGTTATCATGGTCAACA
G
Found at i:3744540 original size:18 final size:18
Alignment explanation
Indices: 3744517--3744559 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
3744507 TATTTATATA
3744517 AATAAATACTATCTTGAT
1 AATAAATACTATCTTGAT
*
3744535 AATAAATACTATCTTTAT
1 AATAAATACTATCTTGAT
*
3744553 AACAAAT
1 AATAAAT
3744560 TTGAAGCTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.49, C:0.12, G:0.02, T:0.37
Consensus pattern (18 bp):
AATAAATACTATCTTGAT
Found at i:3747132 original size:19 final size:19
Alignment explanation
Indices: 3747108--3747146 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
3747098 GTTAAGAAAA
3747108 GGCAGAGAAAGTTGAACTT
1 GGCAGAGAAAGTTGAACTT
3747127 GGCAGAGAAAGTTGAACTT
1 GGCAGAGAAAGTTGAACTT
3747146 G
1 G
3747147 AGGCAAAGGG
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:0.36, C:0.10, G:0.33, T:0.21
Consensus pattern (19 bp):
GGCAGAGAAAGTTGAACTT
Found at i:3750309 original size:2 final size:2
Alignment explanation
Indices: 3750302--3750341 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3750292 TATTTAAAAT
3750302 TA TA TA TA TA TA TA TA 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 TA TA TA TA
3750342 ATGGAAAGAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3752512 original size:14 final size:14
Alignment explanation
Indices: 3752471--3752512 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
3752461 GCTAGATAAT
*
3752471 ATACAGACACAGAG
1 ATACAGATACAGAG
*
3752485 AT-CA-ATACATAG
1 ATACAGATACAGAG
3752497 ATACAGATACAGAG
1 ATACAGATACAGAG
3752511 AT
1 AT
3752513 TGATAAATAC
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
12 8 0.35
13 4 0.17
14 11 0.48
ACGTcount: A:0.50, C:0.17, G:0.17, T:0.17
Consensus pattern (14 bp):
ATACAGATACAGAG
Found at i:3753146 original size:39 final size:39
Alignment explanation
Indices: 3753103--3753184 Score: 164
Period size: 39 Copynumber: 2.1 Consensus size: 39
3753093 TCACATCAGA
3753103 AAAAAAAAATGATCTCTGAAGAAAACTCACCAACCTAGG
1 AAAAAAAAATGATCTCTGAAGAAAACTCACCAACCTAGG
3753142 AAAAAAAAATGATCTCTGAAGAAAACTCACCAACCTAGG
1 AAAAAAAAATGATCTCTGAAGAAAACTCACCAACCTAGG
3753181 AAAA
1 AAAA
3753185 GGCAAATTAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.54, C:0.20, G:0.12, T:0.15
Consensus pattern (39 bp):
AAAAAAAAATGATCTCTGAAGAAAACTCACCAACCTAGG
Found at i:3757160 original size:15 final size:15
Alignment explanation
Indices: 3757140--3757174 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
3757130 TAAATATATT
*
3757140 TATATTTAAAGTATA
1 TATATTAAAAGTATA
*
3757155 TATATTAAAAGTGTA
1 TATATTAAAAGTATA
3757170 TATAT
1 TATAT
3757175 ATATAATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.09, T:0.46
Consensus pattern (15 bp):
TATATTAAAAGTATA
Found at i:3757571 original size:14 final size:15
Alignment explanation
Indices: 3757552--3757584 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
3757542 TTGTCCATTT
3757552 GAAAGGAGA-CCCAA
1 GAAAGGAGAGCCCAA
*
3757566 GAAAGGATAGCCCAA
1 GAAAGGAGAGCCCAA
3757581 GAAA
1 GAAA
3757585 CAGGACAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.52, C:0.18, G:0.27, T:0.03
Consensus pattern (15 bp):
GAAAGGAGAGCCCAA
Found at i:3761984 original size:20 final size:20
Alignment explanation
Indices: 3761946--3761984 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3761936 ATGTGGCTCA
* *
3761946 TTTTCAATTTTTCTTTTCTT
1 TTTTCAATTTTTATGTTCTT
*
3761966 TTTTCATTTTTTATGTTCT
1 TTTTCAATTTTTATGTTCT
3761985 GTCCTTTATG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.10, C:0.13, G:0.03, T:0.74
Consensus pattern (20 bp):
TTTTCAATTTTTATGTTCTT
Found at i:3767357 original size:22 final size:21
Alignment explanation
Indices: 3767332--3767372 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3767322 GTAGTTGCTT
3767332 GCACTTAGGGATTGATGTGCAG
1 GCACTTAGGG-TTGATGTGCAG
**
3767354 GCACTTCTGGTTGATGTGC
1 GCACTTAGGGTTGATGTGC
3767373 TACTTGATGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.17, C:0.17, G:0.34, T:0.32
Consensus pattern (21 bp):
GCACTTAGGGTTGATGTGCAG
Found at i:3778037 original size:31 final size:30
Alignment explanation
Indices: 3777965--3778036 Score: 108
Period size: 32 Copynumber: 2.3 Consensus size: 30
3777955 ATAGAAAAGG
3777965 AAAAGAAAAATAATTTCAAAATTTGAGAAA
1 AAAAGAAAAATAATTTCAAAATTTGAGAAA
* *
3777995 AACAAGGAAAAATAATTTCAAATTTTGGGAAA
1 AA-AA-GAAAAATAATTTCAAAATTTGAGAAA
3778027 AAAAGAAAAA
1 AAAAGAAAAA
3778037 AAAGGGAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
30 8 0.21
31 4 0.11
32 26 0.68
ACGTcount: A:0.62, C:0.04, G:0.12, T:0.21
Consensus pattern (30 bp):
AAAAGAAAAATAATTTCAAAATTTGAGAAA
Found at i:3788973 original size:31 final size:31
Alignment explanation
Indices: 3788935--3788993 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
3788925 CTTTTCAAGA
3788935 CTAAGATAGATTCTCGAATCACTACCTTAAG
1 CTAAGATAGATTCTCGAATCACTACCTTAAG
* *
3788966 CTAAGATAGATTCTCTAATTACTACCTT
1 CTAAGATAGATTCTCGAATCACTACCTT
3788994 TTGAAAGCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.34, C:0.22, G:0.10, T:0.34
Consensus pattern (31 bp):
CTAAGATAGATTCTCGAATCACTACCTTAAG
Found at i:3806996 original size:56 final size:55
Alignment explanation
Indices: 3806935--3807043 Score: 157
Period size: 56 Copynumber: 2.0 Consensus size: 55
3806925 ACACAATATT
3806935 TTTCTTTTAATAAAGTATATTTTCATAAAAAAAATAAAGTAT-TTTTATTATAATAA
1 TTTCTTTTAATAAAGTATATTTTCATAAAAAAAA-AAA-TATATTTTATTATAATAA
** * *
3806991 TTTCTTTTAATTTAGTATATTTTCATCAAAATAAAAATATATTTTATTATAAT
1 TTTCTTTTAATAAAGTATATTTTCATAAAAAAAAAAATATATTTTATTATAAT
3807044 TTAGTAAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
54 3 0.06
55 15 0.31
56 30 0.62
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.50
Consensus pattern (55 bp):
TTTCTTTTAATAAAGTATATTTTCATAAAAAAAAAAATATATTTTATTATAATAA
Found at i:3807051 original size:26 final size:26
Alignment explanation
Indices: 3807022--3807072 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
3807012 TTCATCAAAA
3807022 TAAAAATA-TATTTTATTATAATTTAG
1 TAAAAATACTA-TTTATTATAATTTAG
3807048 TAAAAATACTATTTATTATAATTTA
1 TAAAAATACTATTTATTATAATTTA
3807073 ATATATTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 22 0.92
27 2 0.08
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (26 bp):
TAAAAATACTATTTATTATAATTTAG
Found at i:3807265 original size:13 final size:13
Alignment explanation
Indices: 3807247--3807271 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3807237 TTATTAATAT
3807247 AATTTTTTATTTC
1 AATTTTTTATTTC
3807260 AATTTTTTATTT
1 AATTTTTTATTT
3807272 TTCTTTATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (13 bp):
AATTTTTTATTTC
Found at i:3808347 original size:18 final size:18
Alignment explanation
Indices: 3808317--3808369 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 18
3808307 AAGAAACGGC
3808317 AATAT-TTATATATTACTT
1 AATATATTA-ATATTACTT
*
3808335 AATATATTAATATTATTT
1 AATATATTAATATTACTT
*
3808353 AATTATAATAAATATTA
1 AA-TAT-ATTAATATTA
3808370 TAAAAAATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 15 0.50
19 6 0.20
20 9 0.30
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
AATATATTAATATTACTT
Found at i:3808395 original size:45 final size:45
Alignment explanation
Indices: 3808345--3808438 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 45
3808335 AATATATTAA
*
3808345 TATTATTTA-ATTATAATAAATATTATAAAAAATATTATTTAATAT
1 TATTATTTATA-TATAATAAATATAATAAAAAATATTATTTAATAT
* * *
3808390 TATTATTTGTATATAATAAATGTAATAAAAAATATTATTTAGTAT
1 TATTATTTATATATAATAAATATAATAAAAAATATTATTTAATAT
3808435 TATT
1 TATT
3808439 TAAATTTAGT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
45 43 0.98
46 1 0.02
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (45 bp):
TATTATTTATATATAATAAATATAATAAAAAATATTATTTAATAT
Found at i:3809629 original size:26 final size:27
Alignment explanation
Indices: 3809591--3809654 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
3809581 TTAAAAATTT
* * *
3809591 ATTTGATTTAAAAT-AAAAATATAAAA
1 ATTTAATTAAAAATAAAAAAAATAAAA
3809617 ATTTAATTAAAAATAAAAAAAATAAAA
1 ATTTAATTAAAAATAAAAAAAATAAAA
*
3809644 ATTTATTTAAA
1 ATTTAATTAAA
3809655 TAATTAAGAG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
26 12 0.36
27 21 0.64
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (27 bp):
ATTTAATTAAAAATAAAAAAAATAAAA
Found at i:3809701 original size:32 final size:32
Alignment explanation
Indices: 3809639--3809701 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 32
3809629 ATAAAAAAAA
* * *
3809639 TAAAAATTTATTTAAATAATTAAGAGATTTTT
1 TAAAAATTTATGTAAAAAATTAAGACATTTTT
*
3809671 TAAAAATATTATGTAAAAAATTTA-ACATTTT
1 TAAAAAT-TTATGTAAAAAATTAAGACATTTT
3809702 CCTAAAGAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
32 13 0.50
33 13 0.50
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (32 bp):
TAAAAATTTATGTAAAAAATTAAGACATTTTT
Found at i:3810945 original size:9 final size:9
Alignment explanation
Indices: 3810931--3810984 Score: 99
Period size: 9 Copynumber: 6.0 Consensus size: 9
3810921 AGTTCCATCA
3810931 TCCTTCTTT
1 TCCTTCTTT
3810940 TCCTTCTTT
1 TCCTTCTTT
*
3810949 TCCCTCTTT
1 TCCTTCTTT
3810958 TCCTTCTTT
1 TCCTTCTTT
3810967 TCCTTCTTT
1 TCCTTCTTT
3810976 TCCTTCTTT
1 TCCTTCTTT
3810985 GTTTCTTCCC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 43 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (9 bp):
TCCTTCTTT
Found at i:3811222 original size:12 final size:12
Alignment explanation
Indices: 3811189--3811232 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
3811179 GCGATAACGG
*
3811189 TCCCTATCCCTG
1 TCCCTATCCCTC
* *
3811201 TCTCTGTCCCTC
1 TCCCTATCCCTC
3811213 TCCCTATCCCTC
1 TCCCTATCCCTC
*
3811225 TCTCTATC
1 TCCCTATC
3811233 TCGGCCACGT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.07, C:0.50, G:0.05, T:0.39
Consensus pattern (12 bp):
TCCCTATCCCTC
Found at i:3814521 original size:40 final size:40
Alignment explanation
Indices: 3814445--3814522 Score: 93
Period size: 40 Copynumber: 1.9 Consensus size: 40
3814435 AGACAACCTT
* *
3814445 ATATTAGAATATTTTGCTATTAAAGGTTGTAGAACCTTTA
1 ATATTAGAATATTTTGCTATTAAAGATTCTAGAACCTTTA
* * * * *
3814485 ATATTGGAATGTTTTTCTGTTAAAGATTCTATAACCTT
1 ATATTAGAATATTTTGCTATTAAAGATTCTAGAACCTT
3814523 AAACCCTAGT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.32, C:0.09, G:0.14, T:0.45
Consensus pattern (40 bp):
ATATTAGAATATTTTGCTATTAAAGATTCTAGAACCTTTA
Found at i:3818915 original size:28 final size:27
Alignment explanation
Indices: 3818845--3818915 Score: 70
Period size: 27 Copynumber: 2.6 Consensus size: 27
3818835 TTTTTCATCA
*
3818845 TAACAATTATATTTTTTAACATGACGTG
1 TAACAATTA-ATTTTTTAAAATGACGTG
* * ** *
3818873 CAATAGCTAAATTTTTAAAATGACGTG
1 TAACAATTAATTTTTTAAAATGACGTG
3818900 TAACAATTACATTTTT
1 TAACAATTA-ATTTTT
3818916 CAACATAGCA
Statistics
Matches: 31, Mismatches: 11, Indels: 2
0.70 0.25 0.05
Matches are distributed among these distances:
27 21 0.68
28 10 0.32
ACGTcount: A:0.38, C:0.11, G:0.10, T:0.41
Consensus pattern (27 bp):
TAACAATTAATTTTTTAAAATGACGTG
Found at i:3818964 original size:40 final size:40
Alignment explanation
Indices: 3818915--3818992 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 40
3818905 ATTACATTTT
* *
3818915 TCAACATAGCATTTAACAATTAAATCTTT-AACATGGTGCA
1 TCAACATAGCATGTAACAACTAAAT-TTTCAACATGGTGCA
* *
3818955 TCAATATAGCGTGTAACAACTAAATTTTCAACATGGTG
1 TCAACATAGCATGTAACAACTAAATTTTCAACATGGTG
3818993 TATAATAACT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 3 0.09
40 30 0.91
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (40 bp):
TCAACATAGCATGTAACAACTAAATTTTCAACATGGTGCA
Found at i:3818993 original size:25 final size:25
Alignment explanation
Indices: 3818965--3819021 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 25
3818955 TCAATATAGC
3818965 GTGTAACAACTAAATTTTCAACATG
1 GTGTAACAACTAAATTTTCAACATG
* * *
3818990 GTGTATAATAACTTAATTTTTAACATG
1 GTG--TAACAACTAAATTTTCAACATG
3819017 GTGTA
1 GTGTA
3819022 TAATAATTAC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 5 0.19
27 22 0.81
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.39
Consensus pattern (25 bp):
GTGTAACAACTAAATTTTCAACATG
Found at i:3819002 original size:27 final size:27
Alignment explanation
Indices: 3818972--3819042 Score: 99
Period size: 27 Copynumber: 2.7 Consensus size: 27
3818962 AGCGTGTAAC
3818972 AACTAAATTTTCAACATGGTGTATAAT
1 AACTAAATTTTCAACATGGTGTATAAT
* *
3818999 AACTTAATTTTTAACATGGTGTATAAT
1 AACTAAATTTTCAACATGGTGTATAAT
* *
3819026 AATTACA-TTTCAACATG
1 AACTAAATTTTCAACATG
3819043 ACGTGTAACA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
26 9 0.24
27 29 0.76
ACGTcount: A:0.39, C:0.11, G:0.10, T:0.39
Consensus pattern (27 bp):
AACTAAATTTTCAACATGGTGTATAAT
Found at i:3819055 original size:26 final size:25
Alignment explanation
Indices: 3819026--3819076 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
3819016 GGTGTATAAT
3819026 AATTACATTTCAACATGACGTGTAAC
1 AATTA-ATTTCAACATGACGTGTAAC
* *
3819052 AATTATTTTCAATATGACGTGTAAC
1 AATTAATTTCAACATGACGTGTAAC
3819077 CATCAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 18 0.78
26 5 0.22
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (25 bp):
AATTAATTTCAACATGACGTGTAAC
Found at i:3820054 original size:23 final size:23
Alignment explanation
Indices: 3820011--3820054 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
3820001 ACATCTAACC
* *
3820011 TTTTAAAAATAGTTGCTTAAAAG
1 TTTTAAAAATAGTTACCTAAAAG
*
3820034 TTTTGAAAATAGTTACCTAAA
1 TTTTAAAAATAGTTACCTAAA
3820055 TGCCTTTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.39
Consensus pattern (23 bp):
TTTTAAAAATAGTTACCTAAAAG
Found at i:3820292 original size:30 final size:30
Alignment explanation
Indices: 3820258--3820316 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
3820248 TTATTCTTGA
*
3820258 GATAAAGTTGCATTTGGTTTAATAAAATGG
1 GATAAAGTTGCATTTGGTTCAATAAAATGG
*
3820288 GATAAAGTTGCATTTGGTTCAATGAAATG
1 GATAAAGTTGCATTTGGTTCAATAAAATG
3820317 ATTATTCTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.36, C:0.05, G:0.24, T:0.36
Consensus pattern (30 bp):
GATAAAGTTGCATTTGGTTCAATAAAATGG
Found at i:3820648 original size:45 final size:44
Alignment explanation
Indices: 3820545--3820693 Score: 182
Period size: 45 Copynumber: 3.4 Consensus size: 44
3820535 GAAATGAAAA
* * *
3820545 TATTTA-AATATTATTTAACTATAATAAATATTAT-AAGCATAT
1 TATTTATATTATTATTTAACTATAATAAATGTTATAAAGAATAT
*
3820587 TATTTCATATTATTATTTCAA-TATAATAAATGTAATAAAGAATAT
1 TATTT-ATATTATTATTT-AACTATAATAAATGTTATAAAGAATAT
* *
3820632 TATTTAGTATTNTTATTTAACTAGAATAAATGTTATAAAGAATAT
1 TATTTA-TATTATTATTTAACTATAATAAATGTTATAAAGAATAT
3820677 TATTTA-A-TATTATTTAA
1 TATTTATATTATTATTTAA
3820694 ATTTAATGAA
Statistics
Matches: 93, Mismatches: 8, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
42 14 0.15
43 2 0.02
44 25 0.27
45 52 0.56
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.46
Consensus pattern (44 bp):
TATTTATATTATTATTTAACTATAATAAATGTTATAAAGAATAT
Found at i:3825978 original size:42 final size:40
Alignment explanation
Indices: 3825918--3826001 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 40
3825908 ATTTGAAATA
3825918 TATATATATATATATAGATTTAA-TTTTTAATTATATATTGT
1 TATATATATATATATAGA--TAATTTTTTAATTATATATTGT
3825959 TNATATATATATATATAGATAATTTTTTTAATTATATATTGT
1 T-ATATATATATATATAGATAA-TTTTTTAATTATATATTGT
3826001 T
1 T
3826002 GGTATTATAA
Statistics
Matches: 40, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
40 3 0.08
41 1 0.03
42 36 0.90
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (40 bp):
TATATATATATATATAGATAATTTTTTAATTATATATTGT
Found at i:3832470 original size:44 final size:44
Alignment explanation
Indices: 3832422--3832510 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
3832412 AGACTTCCAG
3832422 CCATTTTGTTTCAGTTTTTTCTGTGTTGCTGCTTTAAGTGGCTT
1 CCATTTTGTTTCAGTTTTTTCTGTGTTGCTGCTTTAAGTGGCTT
3832466 CCATTTTGTTTCAGTTTTTTCTGTGTTGCTGCTTTAAGTGGCTT
1 CCATTTTGTTTCAGTTTTTTCTGTGTTGCTGCTTTAAGTGGCTT
3832510 C
1 C
3832511 TATGCACACT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.09, C:0.17, G:0.20, T:0.54
Consensus pattern (44 bp):
CCATTTTGTTTCAGTTTTTTCTGTGTTGCTGCTTTAAGTGGCTT
Found at i:3835926 original size:66 final size:66
Alignment explanation
Indices: 3835873--3835999 Score: 191
Period size: 66 Copynumber: 1.9 Consensus size: 66
3835863 ATTGTTGTAG
* * * *
3835873 GTTGTGGTTGAGCCTTGAAAAACCACCTTGGGTTTTAGTTTAGCCCGTGAAAAACTAGTGTGAAA
1 GTTGTAGTTGAGCCTTGAAAAACCACCTTGGGTTTTAGTTGAGCCCATGAAAAACCAGTGTGAAA
3835938 A
66 A
* * *
3835939 GTTGTAGTTGAGCCTTGGAAAACCACTTTGGGTTTTAGTTGAGCCCATGAAAAACTAGTGT
1 GTTGTAGTTGAGCCTTGAAAAACCACCTTGGGTTTTAGTTGAGCCCATGAAAAACCAGTGT
3836000 AAAGGTTTTG
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 56 1.00
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (66 bp):
GTTGTAGTTGAGCCTTGAAAAACCACCTTGGGTTTTAGTTGAGCCCATGAAAAACCAGTGTGAAA
A
Found at i:3835981 original size:31 final size:31
Alignment explanation
Indices: 3835879--3835993 Score: 95
Period size: 32 Copynumber: 3.5 Consensus size: 31
3835869 GTAGGTTGTG
*
3835879 GTTGAGCCTTGAAAAACCACCTTGGGTTTTA
1 GTTGAGCCTTGAAAAACCACTTTGGGTTTTA
* * * * * * *
3835910 GTTTAGCCCGTGAAAAACTAGTGTGAAAAGTTGTA
1 GTTGAG-CCTTGAAAAACCACTTTG---GGTTTTA
*
3835945 GTTGAGCCTTGGAAAACCACTTTGGGTTTTA
1 GTTGAGCCTTGAAAAACCACTTTGGGTTTTA
*
3835976 GTTGAGCCCATGAAAAAC
1 GTTGAG-CCTTGAAAAAC
3835994 TAGTGTAAAG
Statistics
Matches: 61, Mismatches: 18, Indels: 9
0.69 0.20 0.10
Matches are distributed among these distances:
31 16 0.26
32 22 0.36
34 13 0.21
35 10 0.16
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.30
Consensus pattern (31 bp):
GTTGAGCCTTGAAAAACCACTTTGGGTTTTA
Found at i:3843538 original size:58 final size:57
Alignment explanation
Indices: 3843448--3843567 Score: 188
Period size: 58 Copynumber: 2.1 Consensus size: 57
3843438 CATAATCATC
* *
3843448 CAAAGTAGTTTGCATGTGATAGATTTATTTTATGCAATTTAATAAATG-CTATGCAATG
1 CAAAGTAGTATGCATCTGATAGATTTATTTTATGCAATTTAATAAATGTC-ATGC-ATG
*
3843506 CAAAGTAGTATGCATCTGATAGATTTATTTTATGCGATTTAATAAATGTCATGCATG
1 CAAAGTAGTATGCATCTGATAGATTTATTTTATGCAATTTAATAAATGTCATGCATG
3843563 CAAAG
1 CAAAG
3843568 ATGAGATCCT
Statistics
Matches: 58, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
57 8 0.14
58 49 0.84
59 1 0.02
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (57 bp):
CAAAGTAGTATGCATCTGATAGATTTATTTTATGCAATTTAATAAATGTCATGCATG
Found at i:3852866 original size:20 final size:20
Alignment explanation
Indices: 3852841--3852879 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3852831 TAATGAATGT
* *
3852841 TTGATGATGATTGATAATAC
1 TTGATGATAATTGAGAATAC
3852861 TTGATGATAATTGAGAATA
1 TTGATGATAATTGAGAATA
3852880 GTGCTTAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.21, T:0.38
Consensus pattern (20 bp):
TTGATGATAATTGAGAATAC
Found at i:3855481 original size:66 final size:65
Alignment explanation
Indices: 3855411--3855558 Score: 215
Period size: 66 Copynumber: 2.3 Consensus size: 65
3855401 TCATTGTTGT
* *
3855411 AGGTTATGGTTGAGCCTTGAAAAACCACCTTGGGTTTTTGTTTAGCCCGTGAAAAACTAGTGTAA
1 AGGTTATGGTTGAGCCTTGAAAAACCACCTTGGGTTTTAGTTGAGCCCGTGAAAAACTAGTGT-A
3855476 A
65 A
* * * *
3855477 AGGTTGTGGTTGAGCCTTGGAAAACCACTTTGGGTTTTAGTTGAGTCCGTGAAAAACTAGTGTAA
1 AGGTTATGGTTGAGCCTTGAAAAACCACCTTGGGTTTTAGTTGAGCCCGTGAAAAACTAGTGTAA
* *
3855542 AGGTTTTGGCTGAGCCT
1 AGGTTATGGTTGAGCCT
3855559 GCGAAAAGCC
Statistics
Matches: 74, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
65 17 0.23
66 57 0.77
ACGTcount: A:0.26, C:0.14, G:0.28, T:0.32
Consensus pattern (65 bp):
AGGTTATGGTTGAGCCTTGAAAAACCACCTTGGGTTTTAGTTGAGCCCGTGAAAAACTAGTGTAA
Found at i:3857066 original size:15 final size:15
Alignment explanation
Indices: 3857036--3857065 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
3857026 TTTTATTAAA
3857036 ATTTAATATTTTTTT
1 ATTTAATATTTTTTT
3857051 ATTTGAATATTTTTT
1 ATTT-AATATTTTTT
3857066 AATTGTTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (15 bp):
ATTTAATATTTTTTT
Found at i:3858627 original size:29 final size:30
Alignment explanation
Indices: 3858583--3858643 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 30
3858573 CTAAATATTT
*
3858583 AAATGAAGCATTTTTTTATTAAAATTAAGA
1 AAATGAAGCACTTTTTTATTAAAATTAAGA
*
3858613 AAATGAAGC-CTTTTTTATTAAAGTTAAGA
1 AAATGAAGCACTTTTTTATTAAAATTAAGA
3858642 AA
1 AA
3858644 GAGTAAATGA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 20 0.69
30 9 0.31
ACGTcount: A:0.46, C:0.05, G:0.11, T:0.38
Consensus pattern (30 bp):
AAATGAAGCACTTTTTTATTAAAATTAAGA
Found at i:3859045 original size:3 final size:3
Alignment explanation
Indices: 3858988--3859057 Score: 51
Period size: 3 Copynumber: 24.0 Consensus size: 3
3858978 AATAAGTACA
* * *
3858988 TAT T-T TAT TAAT TAT T-T TAT T-T T-T TAT ATAT TTT TAA TAT AAT
1 TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT
3859031 TAAT TA- TAT TAT TAT TAT TAT TAT TAT
1 T-AT TAT TAT TAT TAT TAT TAT TAT TAT
3859058 AAAATTACGA
Statistics
Matches: 54, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
2 10 0.19
3 35 0.65
4 9 0.17
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:3861034 original size:2 final size:2
Alignment explanation
Indices: 3861027--3861059 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3861017 TGGGGCTCAC
3861027 AT AT AT AT AT AT AT AT -T 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
3861060 TCATCTCATT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:3861048 original size:15 final size:15
Alignment explanation
Indices: 3861028--3861057 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3861018 GGGGCTCACA
3861028 TATATATATATATAT
1 TATATATATATATAT
3861043 TATATATATATATAT
1 TATATATATATATAT
3861058 ATTCATCTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATATATATATATAT
Found at i:3861049 original size:17 final size:17
Alignment explanation
Indices: 3861027--3861060 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
3861017 TGGGGCTCAC
3861027 ATATATATATATATATT
1 ATATATATATATATATT
3861044 ATATATATATATATATT
1 ATATATATATATATATT
3861061 CATCTCATTT
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:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATATATATATATATATT
Found at i:3862086 original size:17 final size:15
Alignment explanation
Indices: 3862064--3862111 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
3862054 TTGTGTATTT
3862064 TATATAAATGAATAATA
1 TATATAAA-G-ATAATA
*
3862081 TATATAAAGTTAATA
1 TATATAAAGATAATA
*
3862096 TATATAAAGTTAATA
1 TATATAAAGATAATA
3862111 T
1 T
3862112 TATTCATAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 21 0.70
16 1 0.03
17 8 0.27
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (15 bp):
TATATAAAGATAATA
Found at i:3862096 original size:13 final size:15
Alignment explanation
Indices: 3862076--3862111 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
3862066 TATAAATGAA
3862076 TAATATATATAAAGT
1 TAATATATATAAAGT
3862091 TAATATATATAAAGT
1 TAATATATATAAAGT
3862106 TAATAT
1 TAATAT
3862112 TATTCATAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.42
Consensus pattern (15 bp):
TAATATATATAAAGT
Found at i:3862509 original size:14 final size:14
Alignment explanation
Indices: 3862490--3862518 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3862480 TAAGACACCT
3862490 ACATTTTTCTACCA
1 ACATTTTTCTACCA
3862504 ACATTTTTCTACCA
1 ACATTTTTCTACCA
3862518 A
1 A
3862519 AGATGTTTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.28, G:0.00, T:0.41
Consensus pattern (14 bp):
ACATTTTTCTACCA
Found at i:3863524 original size:22 final size:22
Alignment explanation
Indices: 3863481--3863525 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
3863471 TCGATTCGAT
*
3863481 TTTAATTATTTTTAAATATAAA
1 TTTAATTATATTTAAATATAAA
*
3863503 TTTAATTA-ATTTAATTATTAAA
1 TTTAATTATATTTAAATA-TAAA
3863525 T
1 T
3863526 ATTTAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TTTAATTATATTTAAATATAAA
Found at i:3866583 original size:19 final size:19
Alignment explanation
Indices: 3866559--3866596 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
3866549 CCATTTGACT
3866559 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
3866578 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
3866597 GTTTAGAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.32, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATGATTTGAG
Found at i:3867346 original size:20 final size:20
Alignment explanation
Indices: 3867333--3867389 Score: 114
Period size: 20 Copynumber: 2.9 Consensus size: 20
3867323 TTTTGGTGCG
3867333 AAAATACGAATTTTTGCGCA
1 AAAATACGAATTTTTGCGCA
3867353 AAAATACGAATTTTTGCGCA
1 AAAATACGAATTTTTGCGCA
3867373 AAAATACGAATTTTTGC
1 AAAATACGAATTTTTGC
3867390 TCAACATATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.32
Consensus pattern (20 bp):
AAAATACGAATTTTTGCGCA
Found at i:3871450 original size:60 final size:60
Alignment explanation
Indices: 3871325--3871452 Score: 166
Period size: 60 Copynumber: 2.1 Consensus size: 60
3871315 AGAGTTTTTT
* * * * * *
3871325 GCTGCAGCGAAATTGTAACCCAGAAATAGAAGGTTTCTCGCTGCAGCGAGATTCAATCTC
1 GCTGCAGCAAAATTGCAACCCAGAAACAAAAAGTTTCTCGCTGCAGCGAGAATCAATCTC
* * * *
3871385 ACTGCAGCAAAATTGCAACCCAGAAACAAAAAGTTTCTTGCTGCAGCGAGAATGAATTTC
1 GCTGCAGCAAAATTGCAACCCAGAAACAAAAAGTTTCTCGCTGCAGCGAGAATCAATCTC
3871445 GCTGCAGC
1 GCTGCAGC
3871453 GAGAAGCTAT
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
60 57 1.00
ACGTcount: A:0.33, C:0.23, G:0.22, T:0.22
Consensus pattern (60 bp):
GCTGCAGCAAAATTGCAACCCAGAAACAAAAAGTTTCTCGCTGCAGCGAGAATCAATCTC
Found at i:3871568 original size:21 final size:21
Alignment explanation
Indices: 3871542--3871587 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
3871532 ACCCGAGAGT
3871542 TTCTCGCTGCAGCGAAAATGA
1 TTCTCGCTGCAGCGAAAATGA
3871563 TTCTCGCTGCAGCGAAAATGA
1 TTCTCGCTGCAGCGAAAATGA
3871584 TTCT
1 TTCT
3871588 TACTACAGCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (21 bp):
TTCTCGCTGCAGCGAAAATGA
Found at i:3871596 original size:21 final size:21
Alignment explanation
Indices: 3871542--3871598 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
3871532 ACCCGAGAGT
* *
3871542 TTCTCGCTGCAGCGAAAATGA
1 TTCTCACTACAGCGAAAATGA
* *
3871563 TTCTCGCTGCAGCGAAAATGA
1 TTCTCACTACAGCGAAAATGA
*
3871584 TTCTTACTACAGCGA
1 TTCTCACTACAGCGA
3871599 GAAACAGGGC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.26
Consensus pattern (21 bp):
TTCTCACTACAGCGAAAATGA
Found at i:3871932 original size:41 final size:41
Alignment explanation
Indices: 3871847--3871950 Score: 113
Period size: 41 Copynumber: 2.5 Consensus size: 41
3871837 TAGCTCATGC
** *
3871847 GCACTCCCTACTCGCACATGGTTAGGTCATCACCGAGTTTT
1 GCACTCCCTACTCGCACATAATTAGGTCATCACCGAGTTAT
*
3871888 GCACTCCCTACTCGCACATAATTGGGTCATC-CTCG-GCTTAT
1 GCACTCCCTACTCGCACATAATTAGGTCATCAC-CGAG-TTAT
*
3871929 GCACACTCCTTACTCGCACATA
1 G--CACTCCCTACTCGCACATA
3871951 GTCGAGTCAA
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
40 2 0.04
41 34 0.63
43 18 0.33
ACGTcount: A:0.21, C:0.35, G:0.16, T:0.28
Consensus pattern (41 bp):
GCACTCCCTACTCGCACATAATTAGGTCATCACCGAGTTAT
Found at i:3875615 original size:12 final size:12
Alignment explanation
Indices: 3875598--3875649 Score: 54
Period size: 12 Copynumber: 4.4 Consensus size: 12
3875588 CTCTTCTCTC
3875598 AAAAAAATTAAA-
1 AAAAAAA-TAAAG
3875610 AAAAAAATAAAG
1 AAAAAAATAAAG
3875622 AAAAAAA-AAAG
1 AAAAAAATAAAG
* * *
3875633 AAAGAGAGAAAG
1 AAAAAAATAAAG
3875645 AAAAA
1 AAAAA
3875650 CGTGCAAAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
11 13 0.37
12 22 0.63
ACGTcount: A:0.83, C:0.00, G:0.12, T:0.06
Consensus pattern (12 bp):
AAAAAAATAAAG
Found at i:3875625 original size:15 final size:15
Alignment explanation
Indices: 3875607--3875637 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3875597 CAAAAAAATT
*
3875607 AAAAAAAAAATAAAG
1 AAAAAAAAAAGAAAG
3875622 AAAAAAAAAAGAAAG
1 AAAAAAAAAAGAAAG
3875637 A
1 A
3875638 GAGAAAGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.87, C:0.00, G:0.10, T:0.03
Consensus pattern (15 bp):
AAAAAAAAAAGAAAG
Found at i:3875642 original size:19 final size:19
Alignment explanation
Indices: 3875607--3875649 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
3875597 CAAAAAAATT
*
3875607 AAAAAAAAAATAAAGAAA-
1 AAAAAAAAAAGAAAGAAAG
*
3875625 AAAAAAAGAAAGAGAGAAAG
1 AAAAAAA-AAAGAAAGAAAG
3875645 AAAAA
1 AAAAA
3875650 CGTGCAAAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 7 0.33
19 9 0.43
20 5 0.24
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (19 bp):
AAAAAAAAAAGAAAGAAAG
Found at i:3878148 original size:22 final size:22
Alignment explanation
Indices: 3878123--3878176 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
3878113 AGATCATTTT
*
3878123 TATATTTTTATTATCA-ATAAAA
1 TATATTTTT-TAATCATATAAAA
*
3878145 TATATTTTTTAATCATTTAAAA
1 TATATTTTTTAATCATATAAAA
3878167 TATTATTTTT
1 TA-TATTTTT
3878177 CATTGTATCG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 5 0.18
22 16 0.57
23 7 0.25
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (22 bp):
TATATTTTTTAATCATATAAAA
Found at i:3882176 original size:18 final size:18
Alignment explanation
Indices: 3882153--3882208 Score: 67
Period size: 18 Copynumber: 3.0 Consensus size: 18
3882143 TTTGTAATGT
3882153 TATAATTAAAATAAAATA
1 TATAATTAAAATAAAATA
*
3882171 TATAATATAAAAATAAAAAA
1 TATAAT-T-AAAATAAAATA
* *
3882191 TAAAAATAAAATAAAATA
1 TATAATTAAAATAAAATA
3882209 AAAGAAATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
18 16 0.50
19 2 0.06
20 14 0.44
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (18 bp):
TATAATTAAAATAAAATA
Found at i:3882189 original size:26 final size:26
Alignment explanation
Indices: 3882160--3882342 Score: 105
Period size: 26 Copynumber: 7.0 Consensus size: 26
3882150 TGTTATAATT
3882160 AAAATAAAATATATAATATAAAAATAA
1 AAAATAAAATATATAATATAAAAAT-A
*
3882187 AAAATAAAA-ATA-AA-ATAAAATAAA
1 AAAATAAAATATATAATATAAAA-ATA
* ***
3882211 AGAAATTAAATTTATATAATATAGGTA-A
1 A-AAA-TAAA-ATATATAATATAAAAATA
* *
3882239 AAAATTAAA-ATATAATATATAATATA
1 AAAATAAAATATATAATATA-AAAATA
** *
3882265 AAAA-ATTATAT-TAAAAATAAAAATA
1 AAAATAAAATATAT-AATATAAAAATA
* *
3882290 AAAATATAATATTATAATA-AAAAATG
1 AAAATAAAATA-TATAATATAAAAATA
3882316 AAAATAAAATATATGACAT-TAAAAATA
1 AAAATAAAATATAT-A-ATATAAAAATA
3882343 TATTTAAGAG
Statistics
Matches: 120, Mismatches: 19, Indels: 34
0.69 0.11 0.20
Matches are distributed among these distances:
24 18 0.15
25 22 0.18
26 44 0.37
27 24 0.20
28 6 0.05
29 3 0.03
30 3 0.03
ACGTcount: A:0.68, C:0.01, G:0.03, T:0.28
Consensus pattern (26 bp):
AAAATAAAATATATAATATAAAAATA
Found at i:3882293 original size:13 final size:13
Alignment explanation
Indices: 3882160--3882201 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
3882150 TGTTATAATT
*
3882160 AAAATAAAATATAT
1 AAAATAAAA-ATAA
*
3882174 AATATAAAAATAA
1 AAAATAAAAATAA
3882187 AAAATAAAAATAA
1 AAAATAAAAATAA
3882200 AA
1 AA
3882202 TAAAATAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
13 17 0.68
14 8 0.32
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (13 bp):
AAAATAAAAATAA
Found at i:3882311 original size:31 final size:33
Alignment explanation
Indices: 3882245--3882329 Score: 93
Period size: 32 Copynumber: 2.6 Consensus size: 33
3882235 GTAAAAAATT
* * * * *
3882245 AAAATATAATATATAATATAAAAAATTAT-ATTA
1 AAAATA-AAAATAAAATATATAATATTATAATAA
3882278 AAAATAAAAATAAAA-ATATAATATTATAATAA
1 AAAATAAAAATAAAATATATAATATTATAATAA
*
3882310 AAAATGAAAATAAAATATAT
1 AAAATAAAAATAAAATATAT
3882330 GACATTAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
31 10 0.23
32 24 0.55
33 10 0.23
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (33 bp):
AAAATAAAAATAAAATATATAATATTATAATAA
Done.