Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-JGI_221_v2.0
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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 186 of 202
Found at i:57133419 original size:38 final size:38
Alignment explanation
Indices: 57133376--57133449 Score: 148
Period size: 38 Copynumber: 1.9 Consensus size: 38
57133366 CAAACAATTT
57133376 GTTTGTTACTAAGGTGGTATTATATGATTTTAGTATTA
1 GTTTGTTACTAAGGTGGTATTATATGATTTTAGTATTA
57133414 GTTTGTTACTAAGGTGGTATTATATGATTTTAGTAT
1 GTTTGTTACTAAGGTGGTATTATATGATTTTAGTAT
57133450 AAATTTATAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.26, C:0.03, G:0.22, T:0.50
Consensus pattern (38 bp):
GTTTGTTACTAAGGTGGTATTATATGATTTTAGTATTA
Found at i:57140625 original size:18 final size:18
Alignment explanation
Indices: 57140604--57140639 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
57140594 AAAAAAATCA
57140604 AATTAAAAAAAAAAAAGG
1 AATTAAAAAAAAAAAAGG
* *
57140622 AATTAAAAGAAACAAAGG
1 AATTAAAAAAAAAAAAGG
57140640 GTTTACCTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.72, C:0.03, G:0.14, T:0.11
Consensus pattern (18 bp):
AATTAAAAAAAAAAAAGG
Found at i:57141363 original size:16 final size:17
Alignment explanation
Indices: 57141344--57141377 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
57141334 ATTTTTACTT
57141344 TTAAT-AAAATATATAA
1 TTAATGAAAATATATAA
57141360 TTAATGGAAAATATATAA
1 TTAAT-GAAAATATATAA
57141378 ATATTTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
18 11 0.69
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (17 bp):
TTAATGAAAATATATAA
Found at i:57141631 original size:20 final size:21
Alignment explanation
Indices: 57141602--57141643 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
57141592 AAAGTCATTG
*
57141602 TAAATACATT-AATTATATTA
1 TAAATACATTAAATAATATTA
*
57141622 TAAATGCATTAAATAATATTA
1 TAAATACATTAAATAATATTA
57141643 T
1 T
57141644 TGTTTTGAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (21 bp):
TAAATACATTAAATAATATTA
Found at i:57142496 original size:68 final size:68
Alignment explanation
Indices: 57142415--57142561 Score: 190
Period size: 68 Copynumber: 2.2 Consensus size: 68
57142405 ATACAAAACT
* * * *
57142415 AAAGTTTATGTATAGGATTGTGTCACAG-GCGACATATTTCTAACCCCGTGACAATCGCGA-GTT
1 AAAGTTTATGTATAGCATCGTGTCA-AGAGCCACAGATTTCTAACCCCGTGACAATCGC-ACGTT
57142478 CAATC
64 CAATC
* * * *
57142483 AAAGTTCATGTATAGCATCGTGTCATGAGCCACAGATTTCTAACCCTGTGACAATTGCACGTTCA
1 AAAGTTTATGTATAGCATCGTGTCAAGAGCCACAGATTTCTAACCCCGTGACAATCGCACGTTCA
57142548 ATC
66 ATC
57142551 AAAGTTTATGT
1 AAAGTTTATGT
57142562 GCAGTTTTGA
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
67 2 0.03
68 66 0.97
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (68 bp):
AAAGTTTATGTATAGCATCGTGTCAAGAGCCACAGATTTCTAACCCCGTGACAATCGCACGTTCA
ATC
Found at i:57143216 original size:23 final size:22
Alignment explanation
Indices: 57143190--57143232 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
57143180 TAATATTTTA
57143190 AAGAAATGTAAAATTTATATGGT
1 AAGAAAT-TAAAATTTATATGGT
* *
57143213 AAGAAGTTTAAATTTATATG
1 AAGAAATTAAAATTTATATG
57143233 ATAACAAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.47, C:0.00, G:0.16, T:0.37
Consensus pattern (22 bp):
AAGAAATTAAAATTTATATGGT
Found at i:57145646 original size:25 final size:25
Alignment explanation
Indices: 57145590--57145664 Score: 93
Period size: 25 Copynumber: 3.1 Consensus size: 25
57145580 ACTATTAAAT
*
57145590 AGAGAGAACTAAAGTGCT-AT-A-C
1 AGAGAGCACTAAAGTGCTAATAATC
* *
57145612 AGAGAACACTAATGTGCTAATAATC
1 AGAGAGCACTAAAGTGCTAATAATC
*
57145637 AGAGAGCACTAACGTGCTAATAATC
1 AGAGAGCACTAAAGTGCTAATAATC
57145662 AGA
1 AGA
57145665 AAGTGCGCTA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
22 15 0.33
23 2 0.04
24 1 0.02
25 27 0.60
ACGTcount: A:0.44, C:0.16, G:0.20, T:0.20
Consensus pattern (25 bp):
AGAGAGCACTAAAGTGCTAATAATC
Found at i:57150425 original size:25 final size:25
Alignment explanation
Indices: 57150397--57150469 Score: 65
Period size: 25 Copynumber: 2.9 Consensus size: 25
57150387 ACTCTCTCTC
*
57150397 GAGCTATATAACAGGAAGCTCATGT
1 GAGCTATATAACAGGAAGCTCATCT
* * * *
57150422 GAGCCATGTAACGGGAAGCTTATCT
1 GAGCTATATAACAGGAAGCTCATCT
* * * *
57150447 GGGTTGTATAATAGGAAGCTCAT
1 GAGCTATATAACAGGAAGCTCAT
57150470 AAGAGCCATA
Statistics
Matches: 35, Mismatches: 13, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.26
Consensus pattern (25 bp):
GAGCTATATAACAGGAAGCTCATCT
Found at i:57150544 original size:25 final size:25
Alignment explanation
Indices: 57150496--57150661 Score: 99
Period size: 25 Copynumber: 6.6 Consensus size: 25
57150486 AAGCTCATAT
* * *
57150496 GAGCCAATAA-CGGGTAGCTCCGAA
1 GAGCCATTAATCGGGAAGTTCCGAA
*
57150520 GAGCCATTAATCAGGAAGTTCCGAA
1 GAGCCATTAATCGGGAAGTTCCGAA
* * **
57150545 TAGTCA-TATATCGGGAAGTT-TAAA
1 GAGCCATTA-ATCGGGAAGTTCCGAA
* * *
57150569 TGAGCCAAT-ATCGGGAAGCTCCGGA
1 -GAGCCATTAATCGGGAAGTTCCGAA
** *
57150594 GAGCCATTAATTAGGAAGTTCACAAA
1 GAGCCATTAATCGGGAAGTTC-CGAA
* * *
57150620 AAGCCTTTAATCGGGAAGCTCACGAA
1 GAGCCATTAATCGGGAAGTTC-CGAA
57150646 GAGCCA-TATATCGGGA
1 GAGCCATTA-ATCGGGA
57150662 CGCTCATAAA
Statistics
Matches: 105, Mismatches: 29, Indels: 14
0.71 0.20 0.09
Matches are distributed among these distances:
24 30 0.29
25 41 0.39
26 34 0.32
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.20
Consensus pattern (25 bp):
GAGCCATTAATCGGGAAGTTCCGAA
Found at i:57150650 original size:26 final size:25
Alignment explanation
Indices: 57150578--57150667 Score: 74
Period size: 26 Copynumber: 3.5 Consensus size: 25
57150568 ATGAGCCAAT
*
57150578 ATCGGGAAGCTC-CGGAGAGCCATTA
1 ATCGGGAAGCTCACGAAGAGCC-TTA
** * * *
57150603 ATTAGGAAGTTCACAAAAAGCCTTTA
1 ATCGGGAAGCTCACGAAGAGCC-TTA
*
57150629 ATCGGGAAGCTCACGAAGAGCCATA
1 ATCGGGAAGCTCACGAAGAGCCTTA
*
57150654 TATCGGGACGCTCA
1 -ATCGGGAAGCTCA
57150668 TAAAAGTTGT
Statistics
Matches: 49, Mismatches: 14, Indels: 3
0.74 0.21 0.05
Matches are distributed among these distances:
25 11 0.22
26 38 0.78
ACGTcount: A:0.33, C:0.22, G:0.26, T:0.19
Consensus pattern (25 bp):
ATCGGGAAGCTCACGAAGAGCCTTA
Found at i:57152868 original size:108 final size:109
Alignment explanation
Indices: 57152653--57152871 Score: 363
Period size: 110 Copynumber: 2.0 Consensus size: 109
57152643 AATGATCGTA
57152653 AAACAATAAGAAAAGAAAAATAAAACACATAGATTTTACGTGGAAACCCTTTTGGGAAAAAAACC
1 AAACAATAAGAAAAGAAAAATAAAACACATAGATTTTACGTGGAAACCCTTTTGGG-AAAAAACC
*
57152718 ATGGGCTGAGTAGAAGAAATTCACTAATGTTGAAAACTGAATGAT
65 ATAGGCTGAGTAGAAGAAATTCACTAATGTTGAAAACTGAATGAT
*
57152763 AAACAATAAGAAAAGAAAAATAAAACATATAGATTTTACGTGGAAACCCTTTTGGG-AAAAACCA
1 AAACAATAAGAAAAGAAAAATAAAACACATAGATTTTACGTGGAAACCCTTTTGGGAAAAAACCA
*
57152827 TAGGCAATG-G-AGAAGAAATTCACTAATGTTGAAATCTGAATGAT
66 TAGGC--TGAGTAGAAGAAATTCACTAATGTTGAAAACTGAATGAT
57152871 A
1 A
57152872 TAATATGAGT
Statistics
Matches: 104, Mismatches: 3, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
108 46 0.44
109 1 0.01
110 57 0.55
ACGTcount: A:0.48, C:0.11, G:0.18, T:0.22
Consensus pattern (109 bp):
AAACAATAAGAAAAGAAAAATAAAACACATAGATTTTACGTGGAAACCCTTTTGGGAAAAAACCA
TAGGCTGAGTAGAAGAAATTCACTAATGTTGAAAACTGAATGAT
Found at i:57173804 original size:2 final size:2
Alignment explanation
Indices: 57173797--57173833 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
57173787 TTTTTATTTC
* *
57173797 TA TA TA TA TA TA TA TA TA TA TG TA TA TC TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
57173834 GCATTATGCT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:57176685 original size:21 final size:21
Alignment explanation
Indices: 57176636--57176682 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
57176626 TAAAAAATTA
57176636 TAAAAATATATCAAATTATTT
1 TAAAAATATATCAAATTATTT
* * *
57176657 TTAAAATATTTTAAATT-TTT
1 TAAAAATATATCAAATTATTT
57176677 TAAAAA
1 TAAAAA
57176683 ATAGTTAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (21 bp):
TAAAAATATATCAAATTATTT
Found at i:57177256 original size:25 final size:23
Alignment explanation
Indices: 57177207--57177251 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
57177197 GATTTGTATT
57177207 TTTTCAAGAGAAAAAATTTAATG
1 TTTTCAAGAGAAAAAATTTAATG
*
57177230 TTTTCAGGAGAAAAAATTTAAT
1 TTTTCAAGAGAAAAAATTTAAT
57177252 TTGTTATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.47, C:0.04, G:0.13, T:0.36
Consensus pattern (23 bp):
TTTTCAAGAGAAAAAATTTAATG
Found at i:57180219 original size:13 final size:13
Alignment explanation
Indices: 57180201--57180225 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
57180191 AGTAAATGTA
57180201 AAAAAAGAAAAAG
1 AAAAAAGAAAAAG
57180214 AAAAAAGAAAAA
1 AAAAAAGAAAAA
57180226 CAATAAAGCA
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:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAAAG
Found at i:57182763 original size:19 final size:19
Alignment explanation
Indices: 57182722--57182764 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
57182712 TTTTTCATAT
*
57182722 TAATTATTGTATCTTATTT
1 TAATTATTGTATCTTATTA
*
57182741 TAATTATTTTATC-TATTAA
1 TAATTATTGTATCTTATT-A
57182760 TAATT
1 TAATT
57182765 TAACCTCATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (19 bp):
TAATTATTGTATCTTATTA
Found at i:57185634 original size:13 final size:14
Alignment explanation
Indices: 57185613--57185645 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
57185603 GTTAAGCCAT
*
57185613 ATATTTATTTTA-A
1 ATATATATTTTATA
57185626 ATATATATTTTATA
1 ATATATATTTTATA
57185640 ATATAT
1 ATATAT
57185646 TTATTTTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
ATATATATTTTATA
Found at i:57186129 original size:32 final size:31
Alignment explanation
Indices: 57186067--57186131 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
57186057 GTCATTTTTA
*** *
57186067 TCGCTTTCCAATGAGAAAAAATTTTGATTTG
1 TCGCTTTCCAATGAGAAAAAAACATAATTTG
57186098 TCGCTTTCCAATGAGAAAAAAAACATAATTTG
1 TCGCTTTCCAATGAG-AAAAAAACATAATTTG
57186130 TC
1 TC
57186132 ATTCTCCCAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 15 0.52
32 14 0.48
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (31 bp):
TCGCTTTCCAATGAGAAAAAAACATAATTTG
Found at i:57186651 original size:56 final size:55
Alignment explanation
Indices: 57186566--57186672 Score: 169
Period size: 56 Copynumber: 1.9 Consensus size: 55
57186556 TTATATATTG
* *
57186566 CAAATTAATTATTCATGAGCACTATTCAAATTAAAAGTGATGATTTATCATCTTA
1 CAAATTAATTATTCATAAACACTATTCAAATTAAAAGTGATGATTTATCATCTTA
* *
57186621 CAAATTTAATTGTTCATAAACACTATTCAAATTAAAATTGATGATTTATCAT
1 CAAA-TTAATTATTCATAAACACTATTCAAATTAAAAGTGATGATTTATCAT
57186673 TCAATGAATA
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
55 4 0.09
56 43 0.91
ACGTcount: A:0.41, C:0.12, G:0.07, T:0.39
Consensus pattern (55 bp):
CAAATTAATTATTCATAAACACTATTCAAATTAAAAGTGATGATTTATCATCTTA
Found at i:57187514 original size:15 final size:15
Alignment explanation
Indices: 57187494--57187530 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
57187484 GATCATGGAT
57187494 CAAGTCCATGAATTA
1 CAAGTCCATGAATTA
57187509 CAAGTCCATGAATTA
1 CAAGTCCATGAATTA
57187524 CAAGTCC
1 CAAGTCC
57187531 TTGTAAGCAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.38, C:0.24, G:0.14, T:0.24
Consensus pattern (15 bp):
CAAGTCCATGAATTA
Found at i:57202229 original size:16 final size:16
Alignment explanation
Indices: 57202208--57202240 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
57202198 TAGGTATTAC
57202208 TTTTGATAAATTTTAT
1 TTTTGATAAATTTTAT
57202224 TTTTGATAAATTTTAT
1 TTTTGATAAATTTTAT
57202240 T
1 T
57202241 GACAATGACG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (16 bp):
TTTTGATAAATTTTAT
Found at i:57202734 original size:15 final size:15
Alignment explanation
Indices: 57202714--57202744 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
57202704 TTCCCTCCAA
57202714 CCCCAAACTCAACTC
1 CCCCAAACTCAACTC
57202729 CCCCAAACTCAACTC
1 CCCCAAACTCAACTC
57202744 C
1 C
57202745 AACACTAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.55, G:0.00, T:0.13
Consensus pattern (15 bp):
CCCCAAACTCAACTC
Found at i:57205442 original size:24 final size:25
Alignment explanation
Indices: 57205400--57205447 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
57205390 AGGTGCTTTT
*
57205400 TCAGCAGCTACAGTCACAT-TTTAA
1 TCAGCAGCAACAGTCACATGTTTAA
57205424 TCAGCAGCAACAG-CTACATGTTTA
1 TCAGCAGCAACAGTC-ACATGTTTA
57205448 CACATTGTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 1 0.05
24 16 0.76
25 4 0.19
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.27
Consensus pattern (25 bp):
TCAGCAGCAACAGTCACATGTTTAA
Found at i:57209407 original size:63 final size:63
Alignment explanation
Indices: 57209284--57209410 Score: 166
Period size: 63 Copynumber: 2.0 Consensus size: 63
57209274 GTAAATAGTA
* * **
57209284 AGTCACACGGCCTGGACACACGCCCATGTCTCTAGCCTATGTGGTCCCTAATGGTGAACAGTG
1 AGTCACACGGCCTGGACACACGCCCATGTCTCTAGCCCATGTGGTCCCTAATAGCAAACAGTG
* * * *
57209347 AGTCACACGGCCTGGACACACG-CCAGTGTTTTTGGCCCGTGTGGTCCCTAATAGCAAACAGTG
1 AGTCACACGGCCTGGACACACGCCCA-TGTCTCTAGCCCATGTGGTCCCTAATAGCAAACAGTG
57209410 A
1 A
57209411 ACCACACAGT
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
62 3 0.05
63 52 0.95
ACGTcount: A:0.23, C:0.29, G:0.26, T:0.22
Consensus pattern (63 bp):
AGTCACACGGCCTGGACACACGCCCATGTCTCTAGCCCATGTGGTCCCTAATAGCAAACAGTG
Found at i:57209986 original size:2 final size:2
Alignment explanation
Indices: 57209979--57210021 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
57209969 AGAGCCTAAA
* *
57209979 AT AT AT AT AT AT AT AT TT AT AT AT A- AT AT A- AA 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
57210019 AT A
1 AT A
57210022 GGATTGTAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:57212143 original size:20 final size:21
Alignment explanation
Indices: 57212118--57212157 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
57212108 TAATTCATAA
57212118 TTTTTTAA-AAAATATAAAAT
1 TTTTTTAATAAAATATAAAAT
*
57212138 TTTTTTAATAAAATTTAAAA
1 TTTTTTAATAAAATATAAAA
57212158 ACTATTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TTTTTTAATAAAATATAAAAT
Found at i:57214245 original size:27 final size:26
Alignment explanation
Indices: 57214177--57214249 Score: 69
Period size: 27 Copynumber: 2.7 Consensus size: 26
57214167 AAAATCATAA
*
57214177 AAATATAAAAATAATT-GAAATATATAC
1 AAAT-TAAAAAT-ATTATAAATATATAC
*
57214204 AAATTAAAAATATTATAAATGATATAT
1 AAATTAAAAATATTATAAAT-ATATAC
*
57214231 AAATTATTAAA-ATTATAAA
1 AAATTA-AAAATATTATAAA
57214250 AAATTGCAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
25 3 0.08
26 11 0.28
27 23 0.57
28 3 0.08
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (26 bp):
AAATTAAAAATATTATAAATATATAC
Found at i:57214251 original size:9 final size:9
Alignment explanation
Indices: 57214164--57214251 Score: 56
Period size: 9 Copynumber: 9.8 Consensus size: 9
57214154 ATATTTTATA
*
57214164 ATAAAAATC
1 ATAAAAATT
57214173 ATAAAAA-T
1 ATAAAAATT
*
57214181 ATAAAAATA
1 ATAAAAATT
**
57214190 ATTGAAATAT
1 ATAAAAAT-T
*
57214200 ATACAAATT
1 ATAAAAATT
57214209 A-AAAATATT
1 ATAAAA-ATT
*
57214218 ATAAATGA-T
1 ATAAA-AATT
*
57214227 ATATAAATT
1 ATAAAAATT
*
57214236 ATTAAAATT
1 ATAAAAATT
57214245 ATAAAAA
1 ATAAAAA
57214252 ATTGCAAAAA
Statistics
Matches: 59, Mismatches: 14, Indels: 12
0.69 0.16 0.14
Matches are distributed among these distances:
8 11 0.19
9 38 0.64
10 10 0.17
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (9 bp):
ATAAAAATT
Found at i:57214336 original size:20 final size:20
Alignment explanation
Indices: 57214307--57214354 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
57214297 TACAAAAAAT
*
57214307 AAAAAT-TTTAAAATTATGA
1 AAAAATATTTAAAAATATGA
*
57214326 AAAAATATTTAAAAATATGG
1 AAAAATATTTAAAAATATGA
*
57214346 AAAATTATT
1 AAAAATATT
57214355 AAAGTTGTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 6 0.24
20 19 0.76
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.35
Consensus pattern (20 bp):
AAAAATATTTAAAAATATGA
Found at i:57214356 original size:19 final size:19
Alignment explanation
Indices: 57214294--57214357 Score: 60
Period size: 20 Copynumber: 3.4 Consensus size: 19
57214284 TAAAAATATA
*
57214294 TATTACAAAAAAT-AAAAAT
1 TATTA-AAAATATGAAAAAT
* *
57214313 T-TTAAAATTATGAAAAAA
1 TATTAAAAATATGAAAAAT
*
57214331 TATTTAAAAATATGGAAAAT
1 TA-TTAAAAATATGAAAAAT
57214351 TATTAAA
1 TATTAAA
57214358 GTTGTTAATG
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
17 5 0.14
18 9 0.25
19 6 0.17
20 16 0.44
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.33
Consensus pattern (19 bp):
TATTAAAAATATGAAAAAT
Found at i:57218727 original size:17 final size:17
Alignment explanation
Indices: 57218705--57218740 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
57218695 TATTTTATAT
57218705 TAAAAATAATACAAATA
1 TAAAAATAATACAAATA
57218722 TAAAAATAATACAAATA
1 TAAAAATAATACAAATA
57218739 TA
1 TA
57218741 TACAAATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (17 bp):
TAAAAATAATACAAATA
Found at i:57218763 original size:26 final size:27
Alignment explanation
Indices: 57218701--57218781 Score: 85
Period size: 26 Copynumber: 3.0 Consensus size: 27
57218691 ATAATATTTT
57218701 ATATTAAAAATA-ATACAAATATAAAA
1 ATATTAAAAATATATACAAATATAAAA
* * *
57218727 ATAATACAAATATATACAAAT-TTAAA
1 ATATTAAAAATATATACAAATATAAAA
* * *
57218753 ATATTATAAATTTATAAAAATATATAAA
1 ATATTAAAAATATATACAAATATA-AAA
57218781 A
1 A
57218782 GGACAAAAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
26 31 0.70
27 9 0.20
28 4 0.09
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (27 bp):
ATATTAAAAATATATACAAATATAAAA
Found at i:57218781 original size:9 final size:9
Alignment explanation
Indices: 57218707--57218827 Score: 60
Period size: 9 Copynumber: 13.3 Consensus size: 9
57218697 TTTTATATTA
57218707 AAAATA-AT
1 AAAATATAT
57218715 ACAAATATA-
1 A-AAATATAT
57218724 AAAATA-AT
1 AAAATATAT
57218732 ACAAATATAT
1 A-AAATATAT
57218742 ACAAAT-T-T
1 A-AAATATAT
57218750 AAAATAT-T
1 AAAATATAT
*
57218758 ATAAATTTAT
1 A-AAATATAT
57218768 AAAAATATAT
1 -AAAATATAT
* *
57218778 AAAAGGACA-
1 AAAA-TATAT
57218787 AAAA-ATAT
1 AAAATATAT
*
57218795 AAAACATATT
1 AAAATATA-T
*
57218805 ATAAATGAAAT
1 A-AAAT-ATAT
57218816 AAAATATAT
1 AAAATATAT
57218825 AAA
1 AAA
57218828 TTTTTAGAAA
Statistics
Matches: 90, Mismatches: 8, Indels: 29
0.71 0.06 0.23
Matches are distributed among these distances:
7 7 0.08
8 16 0.18
9 34 0.38
10 25 0.28
11 6 0.07
12 2 0.02
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.28
Consensus pattern (9 bp):
AAAATATAT
Found at i:57219215 original size:8 final size:8
Alignment explanation
Indices: 57219202--57219251 Score: 64
Period size: 8 Copynumber: 6.1 Consensus size: 8
57219192 ACAAAAAAAT
57219202 ATTATAAA
1 ATTATAAA
57219210 ATTATAAA
1 ATTATAAA
57219218 ATTATAAA
1 ATTATAAA
** *
57219226 AAAATATTA
1 ATTATA-AA
57219235 ATTATAAA
1 ATTATAAA
57219243 ATTATAAA
1 ATTATAAA
57219251 A
1 A
57219252 AAATATTTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
8 30 0.86
9 5 0.14
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
ATTATAAA
Found at i:57219243 original size:25 final size:25
Alignment explanation
Indices: 57219209--57219258 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
57219199 AATATTATAA
57219209 AATTATAAAATTATAAAAAAATATT
1 AATTATAAAATTATAAAAAAATATT
57219234 AATTATAAAATTATAAAAAAATATT
1 AATTATAAAATTATAAAAAAATATT
57219259 TAAAAGTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (25 bp):
AATTATAAAATTATAAAAAAATATT
Found at i:57219960 original size:2 final size:2
Alignment explanation
Indices: 57219955--57219997 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
57219945 AATTAAGCCC
57219955 TA 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 TA
57219997 T
1 T
57219998 TTTGCATTCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:57222125 original size:3 final size:3
Alignment explanation
Indices: 57222117--57222222 Score: 108
Period size: 3 Copynumber: 35.0 Consensus size: 3
57222107 AAAGTTGACG
57222117 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * *
57222165 TCA TCA TTTA TCA TCT- TTA CTA TTA TTA TTA ATA TTA -AA GTTA TTA
1 TTA TTA -TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
*
57222211 TTA TTA TCA TTA
1 TTA TTA TTA TTA
57222223 CATTTATATT
Statistics
Matches: 86, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
2 2 0.02
3 81 0.94
4 3 0.03
ACGTcount: A:0.34, C:0.06, G:0.01, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:57223096 original size:109 final size:110
Alignment explanation
Indices: 57222883--57223104 Score: 322
Period size: 109 Copynumber: 2.0 Consensus size: 110
57222873 TCAAAAAGGG
* *
57222883 AAAAATTTTCAAATAAGGCAATGTTTCGCATTTGGAAATTCGAGAAAAACGTGCCCTAAGGTGCT
1 AAAAATTTTAAAATAAGGCAATGTTTCGCATTTGGAAATTCGAGAAAAACATGCCCTAAGGTGCT
* ** *
57222948 GGGTGTCAATTTTTCTCGTTCAATCCAATGGCTTAATATCCTTTT
66 GGGTGTCAATTTTTCTCGTTCAATCCAATAGCCAAATATCCTCTT
* * *
57222993 AAAAATTTTAAAATAAGGCAATGTTTTGCATTTGGAAATTCG-GGAAAACATGCCCTGAGGTGCT
1 AAAAATTTTAAAATAAGGCAATGTTTCGCATTTGGAAATTCGAGAAAAACATGCCCTAAGGTGCT
**
57223057 GGGTGTCGTTTTTTCTCGTTCAA-CCAAATAGCCAAATATCCTCTT
66 GGGTGTCAATTTTTCTCGTTCAATCC-AATAGCCAAATATCCTCTT
57223102 AAA
1 AAA
57223105 TTTTAATTCA
Statistics
Matches: 100, Mismatches: 11, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
108 2 0.02
109 58 0.58
110 40 0.40
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Consensus pattern (110 bp):
AAAAATTTTAAAATAAGGCAATGTTTCGCATTTGGAAATTCGAGAAAAACATGCCCTAAGGTGCT
GGGTGTCAATTTTTCTCGTTCAATCCAATAGCCAAATATCCTCTT
Found at i:57229463 original size:2 final size:2
Alignment explanation
Indices: 57229456--57229495 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
57229446 AATACAATTC
57229456 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
57229496 GAAAAGCATG
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):
AT
Found at i:57229645 original size:2 final size:2
Alignment explanation
Indices: 57229638--57229672 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
57229628 CCCTGTTTGA
57229638 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
57229673 ATACAATAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:57235631 original size:17 final size:17
Alignment explanation
Indices: 57235596--57235635 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
57235586 ACTTTCTTTC
*
57235596 TTTCTTCTTCTTCTGTT
1 TTTCTTTTTCTTCTGTT
57235613 TTTCTTTTTCTT-T-TT
1 TTTCTTTTTCTTCTGTT
57235628 TTT-TTTTT
1 TTTCTTTTT
57235636 TTTTGAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 5 0.23
15 5 0.23
16 1 0.05
17 11 0.50
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (17 bp):
TTTCTTTTTCTTCTGTT
Found at i:57236987 original size:29 final size:31
Alignment explanation
Indices: 57236949--57237008 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
57236939 GGGTTGGGAG
*
57236949 GGGAGAGGAGTAAAAGTTTT-AGGGGAAAGT
1 GGGAGAGGAGTAAAAGTTTTGAGGGAAAAGT
57236979 GGGA-AGGAGTAAAAGTTTTGAGGGAAAAGT
1 GGGAGAGGAGTAAAAGTTTTGAGGGAAAAGT
57237009 AAAAAGGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 15 0.54
30 13 0.46
ACGTcount: A:0.38, C:0.00, G:0.42, T:0.20
Consensus pattern (31 bp):
GGGAGAGGAGTAAAAGTTTTGAGGGAAAAGT
Found at i:57237640 original size:63 final size:64
Alignment explanation
Indices: 57237507--57237643 Score: 170
Period size: 63 Copynumber: 2.2 Consensus size: 64
57237497 GGTCTAATTT
* * * * *
57237507 GCAAACAGT-AAGTCACACGGCCTGGACACATGCCCGTGTCTCTAGCCTATGTGGTCCTTAATG
1 GCAAACAGTGAAGTCACACGGCCTAGACACATGCCAGTGTCTCTAGCCCATGTGGTCCCTAATA
** * * *
57237570 GTGAACAGTGAA-TCACACGGCCTAGACACGTGCCAGTGTCTCTGGCCCGTGTGGTCCCTAATA
1 GCAAACAGTGAAGTCACACGGCCTAGACACATGCCAGTGTCTCTAGCCCATGTGGTCCCTAATA
57237633 GCAAACAGTGA
1 GCAAACAGTGA
57237644 GCCACATGGT
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
63 59 0.97
64 2 0.03
ACGTcount: A:0.25, C:0.28, G:0.26, T:0.22
Consensus pattern (64 bp):
GCAAACAGTGAAGTCACACGGCCTAGACACATGCCAGTGTCTCTAGCCCATGTGGTCCCTAATA
Found at i:57243650 original size:2 final size:2
Alignment explanation
Indices: 57243643--57243681 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
57243633 GAATTGAAAT
57243643 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
57243682 CTTATTTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:57244797 original size:2 final size:2
Alignment explanation
Indices: 57244790--57244832 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
57244780 CCCTGTTTGA
57244790 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
57244832 A
1 A
57244833 GAATTTTNNN
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:57252398 original size:13 final size:13
Alignment explanation
Indices: 57252380--57252456 Score: 118
Period size: 13 Copynumber: 5.9 Consensus size: 13
57252370 AGTTCTTCAT
57252380 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
57252393 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
*
57252406 TGCTTTTCAGAAG
1 TGCTTTTGAGAAG
57252419 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
*
57252432 TGATTTTGAGAAG
1 TGCTTTTGAGAAG
* *
57252445 TACTTTTTAGAA
1 TGCTTTTGAGAA
57252457 ATTTGAGTGT
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 58 1.00
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (13 bp):
TGCTTTTGAGAAG
Found at i:57253297 original size:21 final size:24
Alignment explanation
Indices: 57253264--57253310 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 24
57253254 CCTTTAGATT
*
57253264 AAATGTTTGAGAA-TATAAAA-CA
1 AAATATTTGAGAATTATAAAAGCA
57253286 AAATATTT-AGAATTATAAAAGCA
1 AAATATTTGAGAATTATAAAAGCA
57253309 AA
1 AA
57253311 CATAGTTTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 4 0.18
22 14 0.64
23 4 0.18
ACGTcount: A:0.57, C:0.04, G:0.11, T:0.28
Consensus pattern (24 bp):
AAATATTTGAGAATTATAAAAGCA
Found at i:57261004 original size:16 final size:18
Alignment explanation
Indices: 57260973--57261009 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
57260963 AAAATAATAC
57260973 AAATATATACAAATTT-T
1 AAATATATACAAATTTAT
*
57260990 AAATAT-TATAAATTTAT
1 AAATATATACAAATTTAT
57261007 AAA
1 AAA
57261010 AACATATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (18 bp):
AAATATATACAAATTTAT
Found at i:57262158 original size:14 final size:14
Alignment explanation
Indices: 57262139--57262175 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
57262129 AAAATTATCC
57262139 CTCCTTTTATTCAT
1 CTCCTTTTATTCAT
57262153 CTCC-TTTATTCAT
1 CTCCTTTTATTCAT
*
57262166 -TCCTATTATT
1 CTCCTTTTATT
57262176 TCCTTCATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
12 3 0.14
13 14 0.67
14 4 0.19
ACGTcount: A:0.16, C:0.27, G:0.00, T:0.57
Consensus pattern (14 bp):
CTCCTTTTATTCAT
Found at i:57268718 original size:3 final size:3
Alignment explanation
Indices: 57268710--57268743 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
57268700 CAAATATTAA
57268710 GAT GAT GAT GAT GAT GAT GATT G-T GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GA-T GAT GAT GAT GAT G
57268744 GTGCAATACT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 25 0.86
4 2 0.07
ACGTcount: A:0.29, C:0.00, G:0.35, T:0.35
Consensus pattern (3 bp):
GAT
Found at i:57271304 original size:2 final size:2
Alignment explanation
Indices: 57271297--57271337 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
57271287 TTCATAGCAA
57271297 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
57271338 AATCAGATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:57275447 original size:147 final size:147
Alignment explanation
Indices: 57275178--57275618 Score: 580
Period size: 147 Copynumber: 3.0 Consensus size: 147
57275168 AGTTTTGAAC
* * * * * * * *
57275178 CCAAGTCGACTATAGTTCAGCATGGCATTTCATCAAACAATT-TAGATGCAGAAAACGTAATGAA
1 CCAAGTCGACAATAGTTCAGCCTGACATTTCATCAAAC-ATTGGAGATGCTGAAAATGCAATCAA
* *
57275242 GGAAGATAACCTGACATCTCAACTTAAGGAGGAGGTTACTGAAATGGATGATTCTGGGGTTGTGG
65 GGAAGATAACCTGACATCTGAACTTAAGGAGGAGGTTACCGAAATGGATGATTCTGGGGTTGTGG
*
57275307 AAGTTAAAGTTAATGTAG
130 AAGATAAAGTTAATGTAG
* * * ** *
57275325 CGAAGTCTACAATAGTTCAGCCTGACATTTCATCGAACATTGGAGATGCTGAAGGTGCAATTAAG
1 CCAAGTCGACAATAGTTCAGCCTGACATTTCATCAAACATTGGAGATGCTGAAAATGCAATCAAG
* * *
57275390 GAAGATAACCTAACATCTGAACTTAAGGAGGAGGTTACCGAAATGGATGATTCTGGGGTTGTAGC
66 GAAGATAACCTGACATCTGAACTTAAGGAGGAGGTTACCGAAATGGATGATTCTGGGGTTGTGGA
57275455 AGATAAAGTTAATGTAG
131 AGATAAAGTTAATGTAG
* * ** *
57275472 CCAAGTGGACGATAGTTCAGTGTGGCATTTCATCAAACATTGGAGATGCTGAAAATGCAATCAAG
1 CCAAGTCGACAATAGTTCAGCCTGACATTTCATCAAACATTGGAGATGCTGAAAATGCAATCAAG
* * * * *
57275537 GAAGATAACCTGACGTCTGAACTTAAGGAGGAGGTCACCGAAAGGGTTGATTCCT-TGGTTGTGG
66 GAAGATAACCTGACATCTGAACTTAAGGAGGAGGTTACCGAAATGGATGATT-CTGGGGTTGTGG
57275601 AAGATAAAGTTAATGTAG
130 AAGATAAAGTTAATGTAG
57275619 AAAAGAAAGA
Statistics
Matches: 254, Mismatches: 38, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
146 3 0.01
147 249 0.98
148 2 0.01
ACGTcount: A:0.34, C:0.14, G:0.26, T:0.26
Consensus pattern (147 bp):
CCAAGTCGACAATAGTTCAGCCTGACATTTCATCAAACATTGGAGATGCTGAAAATGCAATCAAG
GAAGATAACCTGACATCTGAACTTAAGGAGGAGGTTACCGAAATGGATGATTCTGGGGTTGTGGA
AGATAAAGTTAATGTAG
Found at i:57281154 original size:16 final size:16
Alignment explanation
Indices: 57281097--57281161 Score: 62
Period size: 16 Copynumber: 4.1 Consensus size: 16
57281087 AGACTCAGGC
57281097 TTTTC-CAAACTCAAA
1 TTTTCTCAAACTCAAA
*** **
57281112 TTTTCTCGGTCTCGAGC
1 TTTTCTCAAACTC-AAA
57281129 TTTT-TCAAACTCAAA
1 TTTTCTCAAACTCAAA
57281144 TTTTCTCAAACTCAAA
1 TTTTCTCAAACTCAAA
57281160 TT
1 TT
57281162 ATTACGAGCA
Statistics
Matches: 37, Mismatches: 10, Indels: 5
0.71 0.19 0.10
Matches are distributed among these distances:
15 10 0.27
16 22 0.59
17 5 0.14
ACGTcount: A:0.29, C:0.25, G:0.06, T:0.40
Consensus pattern (16 bp):
TTTTCTCAAACTCAAA
Found at i:57288897 original size:17 final size:17
Alignment explanation
Indices: 57288840--57288897 Score: 55
Period size: 18 Copynumber: 3.4 Consensus size: 17
57288830 ACACCATTAA
*
57288840 AAATAATAAAAAT-TAC
1 AAATAATAAAAATATAT
**
57288856 AAATTTTAAAAATATAAT
1 AAATAATAAAAATAT-AT
* *
57288874 ATATAATAAAATTATAT
1 AAATAATAAAAATATAT
57288891 AAATAAT
1 AAATAAT
57288898 TTAATATTTG
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
16 11 0.34
17 9 0.28
18 12 0.38
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (17 bp):
AAATAATAAAAATATAT
Found at i:57291667 original size:25 final size:25
Alignment explanation
Indices: 57291639--57291688 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
57291629 ATTTGGCCAT
57291639 TAAACTATTTGAAAGTTTTCATTTA
1 TAAACTATTTGAAAGTTTTCATTTA
57291664 TAAACTATTTGAAAGTTTTCATTTA
1 TAAACTATTTGAAAGTTTTCATTTA
57291689 AGTTATTGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.48
Consensus pattern (25 bp):
TAAACTATTTGAAAGTTTTCATTTA
Found at i:57292674 original size:2 final size:2
Alignment explanation
Indices: 57292667--57292705 Score: 62
Period size: 2 Copynumber: 19.5 Consensus size: 2
57292657 AAATATGTGT
57292667 TA TA TA TA TA TA TA TA TA TA TA TA TA TGA T- TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA T
57292706 GATTCGAGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 32 0.91
3 2 0.06
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:57292706 original size:12 final size:12
Alignment explanation
Indices: 57292673--57292709 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
57292663 GTGTTATATA
57292673 TATATATAT-AT
1 TATATATATGAT
57292684 ATATATATATGAT
1 -TATATATATGAT
57292697 TATATATATGAT
1 TATATATATGAT
57292709 T
1 T
57292710 CGAGTAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 22 0.92
13 2 0.08
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.51
Consensus pattern (12 bp):
TATATATATGAT
Found at i:57293239 original size:9 final size:9
Alignment explanation
Indices: 57293225--57293259 Score: 52
Period size: 10 Copynumber: 3.7 Consensus size: 9
57293215 AAAGATGTAA
57293225 TTAAAATAT
1 TTAAAATAT
57293234 TTAAAAATAT
1 TT-AAAATAT
57293244 TTAAAATAAT
1 TTAAAAT-AT
57293254 TTAAAA
1 TTAAAA
57293260 CGAGCATCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 7 0.29
10 17 0.71
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (9 bp):
TTAAAATAT
Found at i:57295503 original size:20 final size:18
Alignment explanation
Indices: 57295469--57295511 Score: 59
Period size: 20 Copynumber: 2.3 Consensus size: 18
57295459 TATAAAAAAT
*
57295469 AAATATAAAAAATTATAG
1 AAATATAAAAAATTATAA
57295487 AAATAGTAAAAATATTATAA
1 AAATA-TAAAAA-ATTATAA
57295507 AAATA
1 AAATA
57295512 CTTTTCAGTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.23
19 6 0.27
20 11 0.50
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (18 bp):
AAATATAAAAAATTATAA
Found at i:57295699 original size:16 final size:17
Alignment explanation
Indices: 57295672--57295703 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
57295662 GTCCGGCCCG
57295672 TTTTTAATTAAAATTAT
1 TTTTTAATTAAAATTAT
57295689 TTTTTAA-TAAAATTA
1 TTTTTAATTAAAATTA
57295704 AAACTAATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTTTAATTAAAATTAT
Found at i:57295705 original size:22 final size:22
Alignment explanation
Indices: 57295677--57295725 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
57295667 GCCCGTTTTT
* * *
57295677 AATTAAAATTATTTTTTAATAA
1 AATTAAAACTAATTGTTAATAA
*
57295699 AATTAAAACTAATTGTTATTAA
1 AATTAAAACTAATTGTTAATAA
57295721 AATTA
1 AATTA
57295726 GTTGTTGCTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (22 bp):
AATTAAAACTAATTGTTAATAA
Found at i:57295833 original size:9 final size:9
Alignment explanation
Indices: 57295821--57295848 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
57295811 ATTATCAAAT
57295821 TATTAATTG
1 TATTAATTG
57295830 TATTAATTG
1 TATTAATTG
57295839 TATTAATTG
1 TATTAATTG
57295848 T
1 T
57295849 TATAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:57296620 original size:24 final size:24
Alignment explanation
Indices: 57296578--57296623 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
57296568 GTAAAGTATT
*
57296578 AAAATAAAAAATTATTATATTTTA
1 AAAATAAAAAAATATTATATTTTA
57296602 AAAATAAAAAAA-ATATATATTT
1 AAAATAAAAAAATAT-TATATTT
57296624 AATATATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (24 bp):
AAAATAAAAAAATATTATATTTTA
Found at i:57297892 original size:30 final size:31
Alignment explanation
Indices: 57297853--57297918 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
57297843 TAACAGCTTG
*
57297853 ATGAATTAAAT-AAAAAATTTGAATACTTTA
1 ATGACTTAAATGAAAAAATTTGAATACTTTA
* ** *
57297883 GTGACTTAAATGAAAACTTTTGAATAGTTTA
1 ATGACTTAAATGAAAAAATTTGAATACTTTA
57297914 ATGAC
1 ATGAC
57297919 CATTTTGTAA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
30 9 0.31
31 20 0.69
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.36
Consensus pattern (31 bp):
ATGACTTAAATGAAAAAATTTGAATACTTTA
Found at i:57300809 original size:302 final size:301
Alignment explanation
Indices: 57300257--57301002 Score: 1152
Period size: 302 Copynumber: 2.5 Consensus size: 301
57300247 CCAATGAAAA
** * * * *
57300257 AGGAAAATT-ATGGTTTCTTTTATG-TTTCCTTAGCAGGATGTATGCAAAAAGGCAATCTGCTAG
1 AGGAAAATTCATGGTTTCTTTTATGTTTTGGTT-GCAGGGTTTGTTCAAAAAGGCAATCTGCTAG
** * * * * *
57300320 GCATAAAACCCAAG---CAGAAACAACTGAATATGTAATT-GAGGTAGATGATACAAAATCTTTT
65 GTTTAAAGCCCAAGAACCTGAAACTACTGAATATAT-GTTCGAGGTAGATGATACAAAATCTTTT
* *
57300381 GATTCTACCTGTGATGATAAGGTCCATGAGAGTGGCCCTTCTGATATCAAACCAGTCCAAGCCAA
129 GATTCTACCTGTGATGATAACGTCCATGAGAGTGGCCCTTCTGATATCAAACCAGTCCAAACCAA
57300446 GGAGGGGATTGACAACAAAAGGTTTTTGTACATTTCTTATTGCTTAGTGCAAATTATTTTCAATA
194 GGAGGGGATTGACAACAAAAGGTTTTTGTACATTTCTTATTGCTTAGTGCAAATTATTTTCAATA
57300511 ACAGTGTAGTC-TTTAACTTTTTTGTTTGAAAACTTCAGTGAC
259 ACAGTGTAGTCTTTTAACTTTTTTGTTTGAAAACTTCAGTGAC
*
57300553 AGAGTAAAATTCATGGTTTCTTTTATGTTTTGGTTGCAGGGTTTGTTCAAGAAGGCAATCTGCTA
1 AG-G-AAAATTCATGGTTTCTTTTATGTTTTGGTTGCAGGGTTTGTTCAAAAAGGCAATCTGCTA
57300618 GGTTTAAAGCCCAAGAACCTGAAACTACTGAATATATGTTCGAGGTAGATGATACAAAATCTTTT
64 GGTTTAAAGCCCAAGAACCTGAAACTACTGAATATATGTTCGAGGTAGATGATACAAAATCTTTT
* *
57300683 GATTCTACCCGTGATGATAACGTCCATGGGAGTGGCCCTTCTGATATCAAACCAGTCCAAACCAA
129 GATTCTACCTGTGATGATAACGTCCATGAGAGTGGCCCTTCTGATATCAAACCAGTCCAAACCAA
57300748 GGAGGGGATTGACAACAAAAGGTTTTTGTACATTTCTTATTGCTTAGTGCAAATTATTTTCAATA
194 GGAGGGGATTGACAACAAAAGGTTTTTGTACATTTCTTATTGCTTAGTGCAAATTATTTTCAATA
57300813 ACAGTGTAGTCTTTTAACTTTTTTGTTTGAAAACTTCAGTGAC
259 ACAGTGTAGTCTTTTAACTTTTTTGTTTGAAAACTTCAGTGAC
* *
57300856 AGGAAAATTCATGGGTTTTTTTTTATGTTTTGGTTGCAGGGTTTGTTTAAAAAGGCAATCTGCTA
1 AGGAAAATTCAT-GG-TTTCTTTTATGTTTTGGTTGCAGGGTTTGTTCAAAAAGGCAATCTGCTA
*
57300921 GGTTTAAAGCCCAAGAACCTGAAACTACTGAATATATGTGCGAGGTAGATG---CAAAATCTTTT
64 GGTTTAAAGCCCAAGAACCTGAAACTACTGAATATATGTTCGAGGTAGATGATACAAAATCTTTT
* * *
57300983 GCTCCTATCTGTGATGATAA
129 GATTCTACCTGTGATGATAA
57301003 GGTGTGTAAA
Statistics
Matches: 413, Mismatches: 26, Indels: 18
0.90 0.06 0.04
Matches are distributed among these distances:
296 2 0.00
297 1 0.00
298 6 0.01
299 52 0.13
300 32 0.08
301 11 0.03
302 180 0.44
303 129 0.31
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (301 bp):
AGGAAAATTCATGGTTTCTTTTATGTTTTGGTTGCAGGGTTTGTTCAAAAAGGCAATCTGCTAGG
TTTAAAGCCCAAGAACCTGAAACTACTGAATATATGTTCGAGGTAGATGATACAAAATCTTTTGA
TTCTACCTGTGATGATAACGTCCATGAGAGTGGCCCTTCTGATATCAAACCAGTCCAAACCAAGG
AGGGGATTGACAACAAAAGGTTTTTGTACATTTCTTATTGCTTAGTGCAAATTATTTTCAATAAC
AGTGTAGTCTTTTAACTTTTTTGTTTGAAAACTTCAGTGAC
Found at i:57303157 original size:13 final size:13
Alignment explanation
Indices: 57303139--57303163 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
57303129 CATCTTCTTC
57303139 GTTTGGTACAGGA
1 GTTTGGTACAGGA
57303152 GTTTGGTACAGG
1 GTTTGGTACAGG
57303164 TACGGGTTTG
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:0.20, C:0.08, G:0.40, T:0.32
Consensus pattern (13 bp):
GTTTGGTACAGGA
Found at i:57303859 original size:14 final size:15
Alignment explanation
Indices: 57303828--57303860 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
57303818 AGAAACATTT
*
57303828 GAATTAAAAATGTTA
1 GAATTAAAAATGTGA
57303843 GAATTAAAAATG-GA
1 GAATTAAAAATGTGA
57303857 GAAT
1 GAAT
57303861 ATTAGAGGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.55, C:0.00, G:0.18, T:0.27
Consensus pattern (15 bp):
GAATTAAAAATGTGA
Found at i:57304589 original size:13 final size:13
Alignment explanation
Indices: 57304571--57304596 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
57304561 TCGACATTGA
57304571 AATCGATTTGGCT
1 AATCGATTTGGCT
57304584 AATCGATTTGGCT
1 AATCGATTTGGCT
57304597 TACCTTAGCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.38
Consensus pattern (13 bp):
AATCGATTTGGCT
Found at i:57305323 original size:22 final size:22
Alignment explanation
Indices: 57305298--57305369 Score: 65
Period size: 22 Copynumber: 3.2 Consensus size: 22
57305288 ACAATTTTCA
57305298 TTATTTATAGCAAATTAAAGAG
1 TTATTTATAGCAAATTAAAGAG
* *** * *
57305320 TTATTAATTTAAAATTCTATATA-
1 TTATTTATAGCAAA-T-TAAAGAG
57305343 TTATTTATAGCAAATTAAAGAG
1 TTATTTATAGCAAATTAAAGAG
57305365 TTATT
1 TTATT
57305370 AATTTAAAAG
Statistics
Matches: 35, Mismatches: 12, Indels: 6
0.66 0.23 0.11
Matches are distributed among these distances:
21 4 0.11
22 16 0.46
23 11 0.31
24 4 0.11
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.44
Consensus pattern (22 bp):
TTATTTATAGCAAATTAAAGAG
Found at i:57307974 original size:15 final size:15
Alignment explanation
Indices: 57307954--57307985 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
57307944 CAAAAAGGAT
57307954 GATGACAACGATGAC
1 GATGACAACGATGAC
*
57307969 GATGACGACGATGAC
1 GATGACAACGATGAC
57307984 GA
1 GA
57307986 CGAGGTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.38, C:0.19, G:0.31, T:0.12
Consensus pattern (15 bp):
GATGACAACGATGAC
Found at i:57308864 original size:20 final size:20
Alignment explanation
Indices: 57308839--57308879 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
57308829 TTGGTCAAAG
*
57308839 AAAGGTTAAATTCTGTTCTT
1 AAAGGTTAAATTCTATTCTT
57308859 AAAGGTTAAATTCTATTCTT
1 AAAGGTTAAATTCTATTCTT
57308879 A
1 A
57308880 GTCTTCTACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.44
Consensus pattern (20 bp):
AAAGGTTAAATTCTATTCTT
Found at i:57309078 original size:16 final size:16
Alignment explanation
Indices: 57309049--57309092 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 16
57309039 AGCAAATTAG
57309049 CAATTAATACAATTAATA
1 CAATTAAT--AATTAATA
57309067 CAATTAATAATTAATA
1 CAATTAATAATTAATA
*
57309083 AAATTAATAA
1 CAATTAATAA
57309093 AATTAATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 17 0.68
18 8 0.32
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (16 bp):
CAATTAATAATTAATA
Found at i:57309101 original size:9 final size:9
Alignment explanation
Indices: 57309050--57309101 Score: 72
Period size: 9 Copynumber: 6.0 Consensus size: 9
57309040 GCAAATTAGC
*
57309050 AATTAATAC
1 AATTAATAA
*
57309059 AATTAATAC
1 AATTAATAA
57309068 AATTAAT--
1 AATTAATAA
57309075 AATTAATAA
1 AATTAATAA
57309084 AATTAATAA
1 AATTAATAA
57309093 AATTAATAA
1 AATTAATAA
57309102 TTTGATAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.17
9 34 0.83
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.35
Consensus pattern (9 bp):
AATTAATAA
Found at i:57309112 original size:25 final size:25
Alignment explanation
Indices: 57309050--57309103 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
57309040 GCAAATTAGC
* *
57309050 AATTAATACAATTAATACAATTAAT
1 AATTAATAAAATTAATAAAATTAAT
57309075 AATTAATAAAATTAATAAAATTAAT
1 AATTAATAAAATTAATAAAATTAAT
57309100 AATT
1 AATT
57309104 TGATAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (25 bp):
AATTAATAAAATTAATAAAATTAAT
Found at i:57309218 original size:22 final size:21
Alignment explanation
Indices: 57309188--57309237 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
57309178 TTACTACCAA
* * *
57309188 TTAAATTTAATAACAATTAGTT
1 TTAATTTTAATAA-AAATAATT
*
57309210 TTAATTTTATTAAAAATAATT
1 TTAATTTTAATAAAAATAATT
57309231 TTAATTT
1 TTAATTT
57309238 AAAAACGGGC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 13 0.54
22 11 0.46
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (21 bp):
TTAATTTTAATAAAAATAATT
Found at i:57309524 original size:38 final size:34
Alignment explanation
Indices: 57309471--57309541 Score: 88
Period size: 37 Copynumber: 2.0 Consensus size: 34
57309461 CAGTCTATTT
57309471 TATTATTAAAATAAATGATAATATAAAAAGTATTTTA
1 TATTATTAAAATAAAT-ATAA-ATAAAAA-TATTTTA
* *
57309508 TATTTTTATAAATAAATTTAAATAAAAATATTTT
1 TATTATTA-AAATAAATATAAATAAAAATATTTT
57309542 TAATTTATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
35 6 0.19
36 7 0.23
37 10 0.32
38 8 0.26
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (34 bp):
TATTATTAAAATAAATATAAATAAAAATATTTTA
Found at i:57312710 original size:28 final size:28
Alignment explanation
Indices: 57312678--57312738 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
57312668 TATAACCACT
*
57312678 TTTTATTAT-ATTTTCAATTTGTGTATTG
1 TTTTAGTATAATTTT-AATTTGTGTATTG
* * *
57312706 TTTTAGTATAATTTTTATTTGTTTCTTG
1 TTTTAGTATAATTTTAATTTGTGTATTG
57312734 TTTTA
1 TTTTA
57312739 ATATTTATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 23 0.82
29 5 0.18
ACGTcount: A:0.20, C:0.03, G:0.10, T:0.67
Consensus pattern (28 bp):
TTTTAGTATAATTTTAATTTGTGTATTG
Found at i:57317585 original size:32 final size:33
Alignment explanation
Indices: 57317544--57317608 Score: 123
Period size: 32 Copynumber: 2.0 Consensus size: 33
57317534 ATTGAAGAAA
57317544 AAGAATTCAGCACAATTGAAG-AAAAAAATCAT
1 AAGAATTCAGCACAATTGAAGAAAAAAAATCAT
57317576 AAGAATTCAGCACAATTGAAGAAAAAAAATCAT
1 AAGAATTCAGCACAATTGAAGAAAAAAAATCAT
57317609 TCTCTTTAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 21 0.66
33 11 0.34
ACGTcount: A:0.57, C:0.12, G:0.12, T:0.18
Consensus pattern (33 bp):
AAGAATTCAGCACAATTGAAGAAAAAAAATCAT
Found at i:57319373 original size:19 final size:20
Alignment explanation
Indices: 57319340--57319377 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
57319330 TGGTTGTGAG
*
57319340 AAATGAAAAAGATTTTTTTA
1 AAATGAAAAACATTTTTTTA
57319360 AAAT-AAAAACATTTTTTT
1 AAATGAAAAACATTTTTTT
57319378 CCTAAATGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (20 bp):
AAATGAAAAACATTTTTTTA
Found at i:57320130 original size:22 final size:21
Alignment explanation
Indices: 57320105--57320146 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
57320095 TTTATTATTG
*
57320105 AATAAATTAAAAAAATATTTTT
1 AATAAAAT-AAAAAATATTTTT
*
57320127 AATAAAATATAAAATATTTT
1 AATAAAATAAAAAATATTTT
57320147 CTTTCACCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
AATAAAATAAAAAATATTTTT
Found at i:57321247 original size:55 final size:53
Alignment explanation
Indices: 57321196--57321353 Score: 155
Period size: 54 Copynumber: 2.9 Consensus size: 53
57321186 TAAAATTTAA
*
57321196 ATTTATTATTATATTTTT-AAGATATTTATTTATTTTTATATATTTTTAAATTT
1 ATTTATTATTAT-TTTTTCAAAATATTTATTTATTTTTATATATTTTTAAATTT
57321249 -TGTATATTATTATTTTTGGTCCAAAATA-TT-TTTATTTTTATATATATTTTTAAATTT
1 AT-T-TATTATTATTTTT--T-CAAAATATTTATTTA-TTTT-TATATATTTTTAAATTT
* * *
57321306 A-TTATTATGTATTTTTTGAAAATGTTTATGTTTTTTTTATATATTTTT
1 ATTTATTAT-TATTTTTTCAAAATATTTAT-TTATTTTTATATATTTTT
57321354 TTTGCATTTT
Statistics
Matches: 88, Mismatches: 4, Indels: 25
0.75 0.03 0.21
Matches are distributed among these distances:
52 1 0.01
53 10 0.11
54 23 0.26
55 16 0.18
56 16 0.18
57 22 0.25
ACGTcount: A:0.29, C:0.01, G:0.05, T:0.65
Consensus pattern (53 bp):
ATTTATTATTATTTTTTCAAAATATTTATTTATTTTTATATATTTTTAAATTT
Found at i:57321256 original size:27 final size:29
Alignment explanation
Indices: 57321196--57321261 Score: 73
Period size: 27 Copynumber: 2.3 Consensus size: 29
57321186 TAAAATTTAA
*
57321196 ATTTATTATTATATTTTTAAGATATTTATTT
1 ATTT-TTA-TATATTTTTAAGATATTTATAT
*
57321227 ATTTTTATATATTTTTAA-AT-TTTGTAT
1 ATTTTTATATATTTTTAAGATATTTATAT
*
57321254 ATTATTAT
1 ATTTTTAT
57321262 TTTTGGTCCA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 12 0.38
28 2 0.06
29 11 0.34
30 3 0.09
31 4 0.12
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (29 bp):
ATTTTTATATATTTTTAAGATATTTATAT
Found at i:57321278 original size:57 final size:53
Alignment explanation
Indices: 57321191--57321353 Score: 160
Period size: 56 Copynumber: 3.1 Consensus size: 53
57321181 TAATATAAAA
*
57321191 TTTAAATTTATTATTA--TA-TTTTT-AAGATATTTATTTATTTTTATATATT
1 TTTAAATTTATTATTATGTATTTTTTCAAAATATTTATTTATTTTTATATATT
*
57321240 TTTAAATTTTGTATATTAT-TATTTTTGGTCCAAAATA-TT-TTTATTTTTATATATATT
1 TTTAAA-TTTAT-TATTATGTATTTTT--T-CAAAATATTTATTTA-TTTT-TATATATT
* * *
57321297 TTTAAATTTATTATTATGTATTTTTTGAAAATGTTTATGTTTTTTTTATATATT
1 TTTAAATTTATTATTATGTATTTTTTCAAAATATTTAT-TTATTTTTATATATT
57321351 TTT
1 TTT
57321354 TTTGCATTTT
Statistics
Matches: 94, Mismatches: 6, Indels: 23
0.76 0.05 0.19
Matches are distributed among these distances:
49 6 0.06
50 4 0.04
51 5 0.05
52 2 0.02
53 9 0.10
54 14 0.15
55 16 0.17
56 19 0.20
57 19 0.20
ACGTcount: A:0.29, C:0.01, G:0.05, T:0.64
Consensus pattern (53 bp):
TTTAAATTTATTATTATGTATTTTTTCAAAATATTTATTTATTTTTATATATT
Found at i:57322954 original size:26 final size:26
Alignment explanation
Indices: 57322918--57322979 Score: 81
Period size: 26 Copynumber: 2.3 Consensus size: 26
57322908 TTAAGATGAC
*
57322918 TATATGAAAATT-TTCAATAAATAAAAA
1 TATAT-AAAATTATTAAAT-AATAAAAA
*
57322945 TATATAAAATTATTAAATATTAAAAA
1 TATATAAAATTATTAAATAATAAAAA
57322971 TATATAAAA
1 TATATAAAA
57322980 ATATAATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
26 22 0.69
27 10 0.31
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (26 bp):
TATATAAAATTATTAAATAATAAAAA
Found at i:57322961 original size:9 final size:10
Alignment explanation
Indices: 57322933--57322984 Score: 58
Period size: 10 Copynumber: 5.6 Consensus size: 10
57322923 GAAAATTTTC
*
57322933 AATAAATAAA
1 AATATATAAA
57322943 AATATAT-AA
1 AATATATAAA
*
57322952 AAT-TAT-TA
1 AATATATAAA
57322960 AATAT-TAAA
1 AATATATAAA
57322969 AATATATAAA
1 AATATATAAA
57322979 AATATA
1 AATATA
57322985 ATTTTTTTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
8 8 0.22
9 12 0.33
10 16 0.44
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
AATATATAAA
Found at i:57331717 original size:29 final size:30
Alignment explanation
Indices: 57331684--57331742 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
57331674 TATGGTTTAA
*
57331684 TGTGCGATTGTATACAT-AAATTTTGATTT
1 TGTGCAATTGTATACATGAAATTTTGATTT
*
57331713 TGTGCAATTTTATACATGAAATTTTGATTT
1 TGTGCAATTGTATACATGAAATTTTGATTT
57331743 GATCCAATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 15 0.56
30 12 0.44
ACGTcount: A:0.29, C:0.07, G:0.15, T:0.49
Consensus pattern (30 bp):
TGTGCAATTGTATACATGAAATTTTGATTT
Found at i:57331751 original size:30 final size:29
Alignment explanation
Indices: 57331694--57331751 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
57331684 TGTGCGATTG
*
57331694 TATACATAAATTTTGATTTTGTGCAATTT
1 TATACATAAATTTTGATTTTGTCCAATTT
57331723 TATACATGAAATTTTGA-TTTGATCCAATT
1 TATACAT-AAATTTTGATTTTG-TCCAATT
57331752 CTTGTAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 11 0.42
30 15 0.58
ACGTcount: A:0.33, C:0.09, G:0.10, T:0.48
Consensus pattern (29 bp):
TATACATAAATTTTGATTTTGTCCAATTT
Found at i:57339879 original size:24 final size:24
Alignment explanation
Indices: 57339852--57339898 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
57339842 ATTGAATTGA
*
57339852 AAACAAATAGGAAAAACAAAACAG
1 AAACAAACAGGAAAAACAAAACAG
** *
57339876 AAACTTACAGGAAGAACAAAACA
1 AAACAAACAGGAAAAACAAAACA
57339899 AACGTGAAAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.66, C:0.15, G:0.13, T:0.06
Consensus pattern (24 bp):
AAACAAACAGGAAAAACAAAACAG
Found at i:57347428 original size:2 final size:2
Alignment explanation
Indices: 57347421--57347471 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
57347411 GTTCCATGTG
57347421 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
57347463 AT AT A- AT AT
1 AT AT AT AT AT
57347472 CAAACTGTCC
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:57348117 original size:48 final size:48
Alignment explanation
Indices: 57348024--57348117 Score: 109
Period size: 48 Copynumber: 2.0 Consensus size: 48
57348014 GCGATTATGA
* * * *
57348024 TGGCTTGACCACCCATATCTGATTCTGGCAGTTTATCTGCATATTTGG
1 TGGCTTGACCACACATATCTAATTCTAGCAGATTATCTGCATATTTGG
* * *
57348072 TGGCTTGATCACACTTATCTAATTCTAGCGGATTA-CTGCACTATTT
1 TGGCTTGACCACACATATCTAATTCTAGCAGATTATCTGCA-TATTT
57348118 CTGACAGCTT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
47 5 0.13
48 33 0.87
ACGTcount: A:0.21, C:0.22, G:0.18, T:0.38
Consensus pattern (48 bp):
TGGCTTGACCACACATATCTAATTCTAGCAGATTATCTGCATATTTGG
Found at i:57350409 original size:12 final size:13
Alignment explanation
Indices: 57350387--57350415 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
57350377 AAAAAAAAAA
57350387 AAGAGAATTCTCT
1 AAGAGAATTCTCT
57350400 AAGA-AATTCTCT
1 AAGAGAATTCTCT
57350412 AAGA
1 AAGA
57350416 CGTCGAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.28
Consensus pattern (13 bp):
AAGAGAATTCTCT
Found at i:57358074 original size:23 final size:22
Alignment explanation
Indices: 57358048--57358097 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
57358038 ATTTTAATTC
57358048 TAAATAATTCAAAAATATATACA
1 TAAATAATTCAAAAATATATA-A
* **
57358071 TAAATATTTTTAAAATATATAA
1 TAAATAATTCAAAAATATATAA
57358093 TAAAT
1 TAAAT
57358098 TATTTATTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 6 0.25
23 18 0.75
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAATAATTCAAAAATATATAA
Found at i:57358101 original size:23 final size:23
Alignment explanation
Indices: 57358059--57358102 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
57358049 AAATAATTCA
57358059 AAAATATATACATAAATATTTTT
1 AAAATATATACATAAATATTTTT
57358082 AAAATATATA-ATAAATTATTT
1 AAAATATATACATAAA-TATTT
57358103 ATTTATATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (23 bp):
AAAATATATACATAAATATTTTT
Found at i:57373632 original size:15 final size:14
Alignment explanation
Indices: 57373594--57373632 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
57373584 AGTAAAATAT
*
57373594 TTTCCGAAAAATGA
1 TTTCTGAAAAATGA
*
57373608 TTTCTAAAAAATGA
1 TTTCTGAAAAATGA
57373622 TTTACTGAAAA
1 TTT-CTGAAAA
57373633 TATTTTCTGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.33
Consensus pattern (14 bp):
TTTCTGAAAAATGA
Found at i:57373681 original size:17 final size:17
Alignment explanation
Indices: 57373659--57373693 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
57373649 AATGAATCTG
57373659 TGTAAAATATTTTATGT
1 TGTAAAATATTTTATGT
57373676 TGTAAAATATTTTATGT
1 TGTAAAATATTTTATGT
57373693 T
1 T
57373694 ATTTGGCAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.54
Consensus pattern (17 bp):
TGTAAAATATTTTATGT
Found at i:57374990 original size:22 final size:24
Alignment explanation
Indices: 57374943--57374992 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 24
57374933 GTTCTCGAAA
57374943 AAACAAAATAATGGATTTTCAAATAT
1 AAACAAAATAATGGATTTT--AATAT
57374969 AAACAAAATAATGG-TTTTATATAT
1 AAACAAAATAATGGATTTTA-ATAT
57374993 TTGCAAATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 1 0.04
24 4 0.17
25 4 0.17
26 14 0.61
ACGTcount: A:0.52, C:0.06, G:0.08, T:0.34
Consensus pattern (24 bp):
AAACAAAATAATGGATTTTAATAT
Found at i:57375142 original size:13 final size:14
Alignment explanation
Indices: 57375117--57375149 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
57375107 TCACTCTTCT
57375117 AAAG-AAAGTCATA
1 AAAGCAAAGTCATA
57375130 AAAGCAAAG-CATA
1 AAAGCAAAGTCATA
57375143 AAAGCAA
1 AAAGCAA
57375150 CTTTTGAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 15 0.79
14 4 0.21
ACGTcount: A:0.64, C:0.12, G:0.15, T:0.09
Consensus pattern (14 bp):
AAAGCAAAGTCATA
Found at i:57380264 original size:5 final size:5
Alignment explanation
Indices: 57380241--57380281 Score: 50
Period size: 5 Copynumber: 8.2 Consensus size: 5
57380231 AAAAAATTTC
57380241 AATA- AATA- AATATT AATAT AATAT AATAT AATAT AAATAT A
1 AATAT AATAT AATA-T AATAT AATAT AATAT AATAT -AATAT A
57380282 TTTTTTTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
4 8 0.24
5 17 0.50
6 9 0.26
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (5 bp):
AATAT
Found at i:57382792 original size:60 final size:60
Alignment explanation
Indices: 57382719--57382837 Score: 238
Period size: 60 Copynumber: 2.0 Consensus size: 60
57382709 ATTCATTTTG
57382719 ATGAACAGCTGATGAATTAACATTTCTCTTACCCTGTTTCCTAGTCAGAATCAGCATCAA
1 ATGAACAGCTGATGAATTAACATTTCTCTTACCCTGTTTCCTAGTCAGAATCAGCATCAA
57382779 ATGAACAGCTGATGAATTAACATTTCTCTTACCCTGTTTCCTAGTCAGAATCAGCATCA
1 ATGAACAGCTGATGAATTAACATTTCTCTTACCCTGTTTCCTAGTCAGAATCAGCATCA
57382838 GTATCTGGAT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.32
Consensus pattern (60 bp):
ATGAACAGCTGATGAATTAACATTTCTCTTACCCTGTTTCCTAGTCAGAATCAGCATCAA
Found at i:57383317 original size:12 final size:12
Alignment explanation
Indices: 57383296--57383337 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
57383286 CAACAGGAAT
*
57383296 GTTTTCATTTTC
1 GTTTTGATTTTC
*
57383308 ATTTTGATTTTC
1 GTTTTGATTTTC
57383320 GTTTTCG-TTTTC
1 GTTTT-GATTTTC
57383332 GTTTTG
1 GTTTTG
57383338 TAGCCACCTG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
11 1 0.04
12 24 0.92
13 1 0.04
ACGTcount: A:0.07, C:0.12, G:0.14, T:0.67
Consensus pattern (12 bp):
GTTTTGATTTTC
Found at i:57383678 original size:19 final size:19
Alignment explanation
Indices: 57383654--57383695 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
57383644 CACAGAAGTT
57383654 AACAAGAATCTATATATGC
1 AACAAGAATCTATATATGC
*
57383673 AACAAGGATCTATATATGC
1 AACAAGAATCTATATATGC
57383692 AACA
1 AACA
57383696 GACTATGGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.48, C:0.17, G:0.12, T:0.24
Consensus pattern (19 bp):
AACAAGAATCTATATATGC
Found at i:57397639 original size:24 final size:24
Alignment explanation
Indices: 57397612--57397663 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
57397602 AAAGAGCCTA
*
57397612 TAACAGGTAACTCCAAAAATCAAT
1 TAACAGGTAACTCCAAAAAGCAAT
* * * *
57397636 TAACGGGTAGCTCCGAAGAGCAAT
1 TAACAGGTAACTCCAAAAAGCAAT
57397660 TAAC
1 TAAC
57397664 GGGAAGCACA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.42, C:0.21, G:0.17, T:0.19
Consensus pattern (24 bp):
TAACAGGTAACTCCAAAAAGCAAT
Found at i:57397743 original size:26 final size:25
Alignment explanation
Indices: 57397714--57397780 Score: 73
Period size: 26 Copynumber: 2.6 Consensus size: 25
57397704 GCACTAACAA
*
57397714 GAAGCTCATAAAGAGCC-TTTAATCGG
1 GAAGCTCAT-AAGAGCCATATAA-CGG
*
57397740 GAAGCTCACGAAGAGCCATATAACGG
1 GAAGCTCA-TAAGAGCCATATAACGG
*
57397766 GACGCTCATAAGAGC
1 GAAGCTCATAAGAGC
57397781 TACGATGTGC
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
25 6 0.17
26 25 0.71
27 4 0.11
ACGTcount: A:0.36, C:0.22, G:0.25, T:0.16
Consensus pattern (25 bp):
GAAGCTCATAAGAGCCATATAACGG
Found at i:57401505 original size:15 final size:16
Alignment explanation
Indices: 57401475--57401508 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
57401465 TTAAGGAATA
57401475 TTAAAAATGAATTTTTT
1 TTAAAAAT-AATTTTTT
57401492 TTAAAAAT-ATTTTTT
1 TTAAAAATAATTTTTT
57401507 TT
1 TT
57401509 TGATTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
17 8 0.47
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (16 bp):
TTAAAAATAATTTTTT
Found at i:57401928 original size:19 final size:19
Alignment explanation
Indices: 57401904--57401940 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
57401894 TATAATATTT
* *
57401904 TTTTTATAATTTTTAGTAC
1 TTTTTAGAATATTTAGTAC
57401923 TTTTTAGAATATTTAGTA
1 TTTTTAGAATATTTAGTA
57401941 GTTTAATACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.30, C:0.03, G:0.08, T:0.59
Consensus pattern (19 bp):
TTTTTAGAATATTTAGTAC
Found at i:57404425 original size:19 final size:19
Alignment explanation
Indices: 57404403--57404439 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
57404393 TAAAAATTAT
*
57404403 GAAAATTGTTTAAAATATA
1 GAAAATTATTTAAAATATA
*
57404422 GAAAATTATTTGAAATAT
1 GAAAATTATTTAAAATAT
57404440 TATAAAATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.38
Consensus pattern (19 bp):
GAAAATTATTTAAAATATA
Found at i:57407929 original size:44 final size:43
Alignment explanation
Indices: 57407879--57408792 Score: 417
Period size: 44 Copynumber: 20.6 Consensus size: 43
57407869 TCAGAGAGAT
* **
57407879 GAGATCTGCTTTTTTCGATTTACTTCGTGCCAATACATGAAGAC
1 GAGATCTGCTTTTTT-GATCTACTTCACGCCAATACATGAAGAC
* *
57407923 GAGATCTACTTTCTTTGATCTACTTCACGCCAATACGTGAAGAC
1 GAGATCTGCTTT-TTTGATCTACTTCACGCCAATACATGAAGAC
* * * * * * *** *
57407967 AAGATCTGTTTTCTTTAATCTACTCCACCACCAGTATGGGGAGAC
1 GAGATCTGCTTT-TTTGATCTACTTCA-CGCCAATACATGAAGAC
* * * * *
57408012 AAGATCTGCTATCTTTGATCTGCTTCACGGCAGTACATGAAGAC
1 GAGATCTGCT-TTTTTGATCTACTTCACGCCAATACATGAAGAC
* * ** * * * * ***
57408056 AAGACCTGCTTTCTTCAATCCACTCCACCACCAGTATGGGGAA-AC
1 GAGATCTGCTTT-TTTGATCTACTTCA-CGCCAATA-CATGAAGAC
* *
57408101 AAGATCTG-TTGTCTTTGATCTACTTCACGCCAGTACATGAAGAC
1 GAGATCTGCTT-T-TTTGATCTACTTCACGCCAATACATGAAGAC
* * * * * * *** *
57408145 AAAATCTGCTTTCTTCGATCTACTCCACCACCAGTATGGGGAGAC
1 GAGATCTGCTTT-TTTGATCTACTTCA-CGCCAATACATGAAGAC
* *
57408190 AAGATCTG-TTGTCTTTGATCTACTTCACGCCAATACATAAAGAC
1 GAGATCTGCTT-T-TTTGATCTACTTCACGCCAATACATGAAGAC
* * * *
57408234 AATATCTACTTTTTTCGATCTACTTCACGCCAATACATGAAGAT
1 GAGATCTGCTTTTTT-GATCTACTTCACGCCAATACATGAAGAC
* * * * * *
57408278 AAGATCT-ATTATCTTCGATCTACTTCATGTCAATACATGAAGAT
1 GAGATCTGCTT-T-TTTGATCTACTTCACGCCAATACATGAAGAC
* * * * * *
57408322 AAGATCTGCTATCTCTGATCTACTTCATGTCAATACATGAAAAC
1 GAGATCTGCT-TTTTTGATCTACTTCACGCCAATACATGAAGAC
* *** * *
57408366 AAGATCCAATATCTTCGATCTACTTCACGCCAATACATGAAGAC
1 GAGATCTGCT-TTTTTGATCTACTTCACGCCAATACATGAAGAC
* * * *
57408410 AAGATCTACTTTCTTCGATCTACTTCACCACCAATACATGAAGAC
1 GAGATCTGCTTT-TTTGATCTACTTCA-CGCCAATACATGAAGAC
* * * * * ***
57408455 AAGATCTACTTTCTTCGATCTACTTCACCACCAGTATGGGAAGAC
1 GAGATCTGCTTT-TTTGATCTACTTCA-CGCCAATACATGAAGAC
* * *
57408500 AATATCTGCTTTCTTCGATCTACTTCACGCCAATACATGAAGAC
1 GAGATCTGCTTT-TTTGATCTACTTCACGCCAATACATGAAGAC
* * * * *
57408544 AAGATCTGCTTTCTCTGATCTACTTCATGTCAATACATGAAGAA
1 GAGATCTGCTTT-TTTGATCTACTTCACGCCAATACATGAAGAC
* * * * * *
57408588 AAGATC--CATTATCTTCGATCAACTTCATGTCAATACATGAAGAT
1 GAGATCTGC-TT-T-TTTGATCTACTTCACGCCAATACATGAAGAC
* * * * * *
57408632 AAGATCTGCTATCTCTGATCTACTTCATGTCAATATATGAAGAC
1 GAGATCTGCT-TTTTTGATCTACTTCACGCCAATACATGAAGAC
* * * * * * *
57408676 AAGATC--CATTATCTTCGATCTACTTCACCACCAGTATAGGAAGAT
1 GAGATCTGC-TT-T-TTTGATCTACTTCA-CGCCAATACATGAAGAC
* * * * *
57408721 AAGATCTGCTATCTCTGATCTACTTCATGTCAATACATGAAGAC
1 GAGATCTGCT-TTTTTGATCTACTTCACGCCAATACATGAAGAC
*
57408765 AAGATC--CATTATCTTTGATCTACTTCAC
1 GAGATCTGC-TT-T-TTTGATCTACTTCAC
57408793 CACCAGTATG
Statistics
Matches: 695, Mismatches: 141, Indels: 68
0.77 0.16 0.08
Matches are distributed among these distances:
42 5 0.01
43 14 0.02
44 452 0.65
45 214 0.31
46 8 0.01
47 2 0.00
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31
Consensus pattern (43 bp):
GAGATCTGCTTTTTTGATCTACTTCACGCCAATACATGAAGAC
Found at i:57408027 original size:45 final size:45
Alignment explanation
Indices: 57407919--57408213 Score: 249
Period size: 45 Copynumber: 6.6 Consensus size: 45
57407909 CAATACATGA
* * * * * * * *
57407919 AGACGAGATCTACTTTCTTTGATCTACTTCA-CGCCAATACGTGA
1 AGACAAGATCTGCTTTCTTTGATCTACTCCACCACCAGTATGGGG
* *
57407963 AGACAAGATCTGTTTTCTTTAATCTACTCCACCACCAGTATGGGG
1 AGACAAGATCTGCTTTCTTTGATCTACTCCACCACCAGTATGGGG
* * * ** *** *
57408008 AGACAAGATCTGCTATCTTTGATCTGCTTCA-CGGCAGTACATGA
1 AGACAAGATCTGCTTTCTTTGATCTACTCCACCACCAGTATGGGG
* ** *
57408052 AGACAAGACCTGCTTTCTTCAATCCACTCCACCACCAGTATGGGG
1 AGACAAGATCTGCTTTCTTTGATCTACTCCACCACCAGTATGGGG
* * * *** *
57408097 AAACAAGATCTG-TTGTCTTTGATCTACTTCA-CGCCAGTACATGA
1 AGACAAGATCTGCTT-TCTTTGATCTACTCCACCACCAGTATGGGG
* *
57408141 AGACAAAATCTGCTTTCTTCGATCTACTCCACCACCAGTATGGGG
1 AGACAAGATCTGCTTTCTTTGATCTACTCCACCACCAGTATGGGG
57408186 AGACAAGATCTG-TTGTCTTTGATCTACT
1 AGACAAGATCTGCTT-TCTTTGATCTACT
57408214 TCACGCCAAT
Statistics
Matches: 189, Mismatches: 56, Indels: 11
0.74 0.22 0.04
Matches are distributed among these distances:
44 93 0.49
45 96 0.51
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (45 bp):
AGACAAGATCTGCTTTCTTTGATCTACTCCACCACCAGTATGGGG
Found at i:57408027 original size:89 final size:89
Alignment explanation
Indices: 57407880--57408819 Score: 808
Period size: 89 Copynumber: 10.6 Consensus size: 89
57407870 CAGAGAGATG
* * *** * * * *
57407880 AGATCTGCTTTTTTCGATTTACTTC-GTGCCAATACATGAAGACGAGATCTACTTTCTTTGATCT
1 AGATCTGCTTTCTTCGATCTACTTCACCACCAATACAGGAAGACAAGATCTGCTATCTTTGATCT
*
57407944 ACTTCACGCCAATACGTGAAGACA
66 ACTTCACGCCAATACATGAAGACA
* ** * * ** *
57407968 AGATCTGTTTTCTTTAATCTACTCCACCACCAGTATGGGGAGACAAGATCTGCTATCTTTGATCT
1 AGATCTGCTTTCTTCGATCTACTTCACCACCAATACAGGAAGACAAGATCTGCTATCTTTGATCT
* * *
57408033 GCTTCACGGCAGTACATGAAGACA
66 ACTTCACGCCAATACATGAAGACA
* * * * * ** * *
57408057 AGACCTGCTTTCTTCAATCCACTCCACCACCAGTATGGGGAA-ACAAGATCTGTTGTCTTTGATC
1 AGATCTGCTTTCTTCGATCTACTTCACCACCAATA-CAGGAAGACAAGATCTGCTATCTTTGATC
*
57408121 TACTTCACGCCAGTACATGAAGACA
65 TACTTCACGCCAATACATGAAGACA
* * * ** * * *
57408146 AAATCTGCTTTCTTCGATCTACTCCACCACCAGTATGGGGAGACAAGATCTGTTGTCTTTGATCT
1 AGATCTGCTTTCTTCGATCTACTTCACCACCAATACAGGAAGACAAGATCTGCTATCTTTGATCT
*
57408211 ACTTCACGCCAATACATAAAGACA
66 ACTTCACGCCAATACATGAAGACA
* * * * * * ** *
57408235 ATATCTACTTTTTTCGATCTACTTCA-CGCCAATACATGAAGATAAGATCTATTATCTTCGATCT
1 AGATCTGCTTTCTTCGATCTACTTCACCACCAATACAGGAAGACAAGATCTGCTATCTTTGATCT
* * *
57408299 ACTTCATGTCAATACATGAAGATA
66 ACTTCACGCCAATACATGAAGACA
* *** * * *** *
57408323 AGATCTGCTATC-TCTGATCTACTTCA-TGTCAATACATGAAAACAAGATCCAATATCTTCGATC
1 AGATCTGCTTTCTTC-GATCTACTTCACCACCAATACAGGAAGACAAGATCTGCTATCTTTGATC
57408386 TACTTCACGCCAATACATGAAGACA
65 TACTTCACGCCAATACATGAAGACA
* * * * *
57408411 AGATCTACTTTCTTCGATCTACTTCACCACCAATACATGAAGACAAGATCTACTTTCTTCGATCT
1 AGATCTGCTTTCTTCGATCTACTTCACCACCAATACAGGAAGACAAGATCTGCTATCTTTGATCT
* * ***
57408476 ACTTCACCACCAGTATGGGAAGACA
66 ACTTCA-CGCCAATACATGAAGACA
* * * * *
57408501 ATATCTGCTTTCTTCGATCTACTTCA-CGCCAATACATGAAGACAAGATCTGCTTTCTCTGATCT
1 AGATCTGCTTTCTTCGATCTACTTCACCACCAATACAGGAAGACAAGATCTGCTATCTTTGATCT
* * *
57408565 ACTTCATGTCAATACATGAAGAAA
66 ACTTCACGCCAATACATGAAGACA
* *** * * *
57408589 AGATC--CATTATCTTCGATCAACTTCA-TGTCAATACATGAAGATAAGATCTGCTATCTCTGAT
1 AGATCTGC-TT-TCTTCGATCTACTTCACCACCAATACAGGAAGACAAGATCTGCTATCTTTGAT
* * *
57408651 CTACTTCATGTCAATATATGAAGACA
64 CTACTTCACGCCAATACATGAAGACA
* * * *
57408677 AGATC--CATTATCTTCGATCTACTTCACCACCAGTATAGGAAGATAAGATCTGCTATCTCTGAT
1 AGATCTGC-TT-TCTTCGATCTACTTCACCACCAATACAGGAAGACAAGATCTGCTATCTTTGAT
* *
57408740 CTACTTCATGTCAATACATGAAGACA
64 CTACTTCACGCCAATACATGAAGACA
* * **
57408766 AGATC--CATTATCTTTGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCT
1 AGATCTGC-TT-TCTTCGATCTACTTCACCACCAATACAGGAAGACAAGATCTGCT
57408820 GCTTTTCAAC
Statistics
Matches: 725, Mismatches: 117, Indels: 19
0.84 0.14 0.02
Matches are distributed among these distances:
86 1 0.00
87 4 0.01
88 274 0.38
89 405 0.56
90 41 0.06
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31
Consensus pattern (89 bp):
AGATCTGCTTTCTTCGATCTACTTCACCACCAATACAGGAAGACAAGATCTGCTATCTTTGATCT
ACTTCACGCCAATACATGAAGACA
Found at i:57408488 original size:310 final size:309
Alignment explanation
Indices: 57407880--57408819 Score: 1084
Period size: 310 Copynumber: 3.0 Consensus size: 309
57407870 CAGAGAGATG
* * ** * * *
57407880 AGATCTGCTTTTTTCGATTTACTTCGTGCCAATACATGAAGACGAGATCTACTTTCTTTGATCTA
1 AGATCTGCTTTCTTCGATCTACTTCACGCCAATACATAAAGACAAGATCTACTTTCTCTGATCTA
* * ** * ** * * *** * *** *
57407945 CTTCACGCCAATACGTGAAGACAAGATCTGTTTTCTTTAATCTACTCCACCACCAGTATGGGGAG
66 CTTCACGCCAATACATGAAGAAAAGATCCATTATCTTCGATCAACTTCA-TGTCAATACATGAAG
* * * * * * * ** * *
57408010 ACAAGATCTGCTATCTTTGATCTGCTTCACGGCAGTACATGAAGACAAGA-CCTGCTTTCTTCAA
130 ATAAGATCTGCTATCTCTGATCTACTTCATGTCAATACATGAAAACAAGATCC-AATATCTTCGA
* * * ** * * *
57408074 TCCACTCCACCACCAGTATGGGGAA-ACAAGATCTGTTGTCTTTGATCTACTTCACGCCAGTACA
194 TCTACTTCACCACCAATA-CAGGAAGACAAGATCTCTT-TCTTCGATCTACTTCACGCCAATACA
* * * *
57408138 TGAAGACAAAATCTGCTTTCTTCGATCTACTCCACCACCAGTATGGGGAGACA
257 TGAAGACAAGATCTACTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACA
* * *
57408191 AGATCTG-TTGTCTTTGATCTACTTCACGCCAATACATAAAGACAATATCTACTTT-TTTCGATC
1 AGATCTGCTT-TCTTCGATCTACTTCACGCCAATACATAAAGACAAGATCTACTTTCTCT-GATC
* * *
57408254 TACTTCACGCCAATACATGAAGATAAGATCTATTATCTTCGATCTACTTCATGTCAATACATGAA
64 TACTTCACGCCAATACATGAAGAAAAGATCCATTATCTTCGATCAACTTCATGTCAATACATGAA
57408319 GATAAGATCTGCTATCTCTGATCTACTTCATGTCAATACATGAAAACAAGATCCAATATCTTCGA
129 GATAAGATCTGCTATCTCTGATCTACTTCATGTCAATACATGAAAACAAGATCCAATATCTTCGA
* * *
57408384 TCTACTTCA-CGCCAATACATGAAGACAAGATCTACTTTCTTCGATCTACTTCACCACCAATACA
194 TCTACTTCACCACCAATACAGGAAGACAAGATCT-CTTTCTTCGATCTACTTCA-CGCCAATACA
57408448 TGAAGACAAGATCTACTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACA
257 TGAAGACAAGATCTACTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACA
* * *
57408501 ATATCTGCTTTCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTCTGATCTA
1 AGATCTGCTTTCTTCGATCTACTTCACGCCAATACATAAAGACAAGATCTACTTTCTCTGATCTA
* *
57408566 CTTCATGTCAATACATGAAGAAAAGATCCATTATCTTCGATCAACTTCATGTCAATACATGAAGA
66 CTTCACGCCAATACATGAAGAAAAGATCCATTATCTTCGATCAACTTCATGTCAATACATGAAGA
* * *
57408631 TAAGATCTGCTATCTCTGATCTACTTCATGTCAATATATGAAGACAAGATCCATTATCTTCGATC
131 TAAGATCTGCTATCTCTGATCTACTTCATGTCAATACATGAAAACAAGATCCAATATCTTCGATC
* * * * * *
57408696 TACTTCACCACCAGTATAGGAAGATAAGATCTGCTATC-TCTGATCTACTTCATGTCAATACATG
196 TACTTCACCACCAATACAGGAAGACAAGATCT-CTTTCTTC-GATCTACTTCACGCCAATACATG
* *
57408760 AAGACAAGATCCA-TTATCTTTGATCTACTTCACCACCAGTATGGGAAGACA
259 AAGACAAGATCTACTT-TCTTCGATCTACTTCACCACCAGTATGGGAAGACA
57408811 AGATCTGCT
1 AGATCTGCT
57408820 GCTTTTCAAC
Statistics
Matches: 542, Mismatches: 76, Indels: 23
0.85 0.12 0.04
Matches are distributed among these distances:
308 3 0.01
309 32 0.06
310 375 0.69
311 132 0.24
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31
Consensus pattern (309 bp):
AGATCTGCTTTCTTCGATCTACTTCACGCCAATACATAAAGACAAGATCTACTTTCTCTGATCTA
CTTCACGCCAATACATGAAGAAAAGATCCATTATCTTCGATCAACTTCATGTCAATACATGAAGA
TAAGATCTGCTATCTCTGATCTACTTCATGTCAATACATGAAAACAAGATCCAATATCTTCGATC
TACTTCACCACCAATACAGGAAGACAAGATCTCTTTCTTCGATCTACTTCACGCCAATACATGAA
GACAAGATCTACTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACA
Found at i:57410134 original size:14 final size:15
Alignment explanation
Indices: 57410106--57410151 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
57410096 AGCCTCTCCA
57410106 TTTTACTTTTCCATT
1 TTTTACTTTTCCATT
*
57410121 TTTTAGTTTT-CA-T
1 TTTTACTTTTCCATT
* *
57410134 TTTCACTTTTTCATT
1 TTTTACTTTTCCATT
57410149 TTT
1 TTT
57410152 CATCTCGTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 9 0.35
14 4 0.15
15 13 0.50
ACGTcount: A:0.13, C:0.15, G:0.02, T:0.70
Consensus pattern (15 bp):
TTTTACTTTTCCATT
Found at i:57411455 original size:33 final size:31
Alignment explanation
Indices: 57411413--57411525 Score: 144
Period size: 33 Copynumber: 3.6 Consensus size: 31
57411403 ATAAAAAGGG
*
57411413 GGTTGCTAAGTGCTGATCCCCCGAACTATTGGT
1 GGTTGCTAAGTGCTGAT-TCCCG-ACTATTGGT
*
57411446 GGTTGCTAAGTGCTGATTCCC--CTA-AGG-
1 GGTTGCTAAGTGCTGATTCCCGACTATTGGT
57411473 GGTTGCTAAGTGCTGATTTCCCGACTCATTGGT
1 GGTTGCTAAGTGCTGA-TTCCCGACT-ATTGGT
57411506 GGTTGCTAAGTGCTGATTCC
1 GGTTGCTAAGTGCTGATTCC
57411526 ACCGTATCTT
Statistics
Matches: 71, Mismatches: 3, Indels: 13
0.82 0.03 0.15
Matches are distributed among these distances:
27 16 0.23
28 7 0.10
29 3 0.04
30 2 0.03
31 1 0.01
32 9 0.13
33 33 0.46
ACGTcount: A:0.17, C:0.22, G:0.28, T:0.33
Consensus pattern (31 bp):
GGTTGCTAAGTGCTGATTCCCGACTATTGGT
Found at i:57411504 original size:60 final size:60
Alignment explanation
Indices: 57411411--57411525 Score: 196
Period size: 60 Copynumber: 1.9 Consensus size: 60
57411401 GAATAAAAAG
57411411 GGGGTTGCTAAGTGCTGATCCCCCGAACTATTGGTGGTTGCTAAGTGCTGATTCCCCTAA
1 GGGGTTGCTAAGTGCTGATCCCCCGAACTATTGGTGGTTGCTAAGTGCTGATTCCCCTAA
**
57411471 GGGGTTGCTAAGTGCTGATTTCCCG-ACTCATTGGTGGTTGCTAAGTGCTGATTCC
1 GGGGTTGCTAAGTGCTGATCCCCCGAACT-ATTGGTGGTTGCTAAGTGCTGATTCC
57411526 ACCGTATCTT
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
59 3 0.06
60 49 0.94
ACGTcount: A:0.17, C:0.22, G:0.30, T:0.32
Consensus pattern (60 bp):
GGGGTTGCTAAGTGCTGATCCCCCGAACTATTGGTGGTTGCTAAGTGCTGATTCCCCTAA
Found at i:57411598 original size:102 final size:102
Alignment explanation
Indices: 57411446--57411671 Score: 371
Period size: 102 Copynumber: 2.2 Consensus size: 102
57411436 AACTATTGGT
* * * * *
57411446 GGTTGCTAAGTGCTGATTCCCCTAAGGGGTTGCTAAGTGCTGATTTCCCGACTCATTGGTGGTTG
1 GGTTGCTAAGTGCTGATTCCCCCAAGGAGTTGCTAAGTGCTAATTCCCCGAATCATTGGTGGTTG
* *
57411511 CTAAGTGCTGATTCCACCGTATCTTAAATGTGAAGGG
66 CTAAGTGCTGATCCCACCGTATCTTAAATGTGAAAGG
*
57411548 GGTTGCTAAGTGTTGATTCCCCCAAGGAGTTGCTAAGTGCTAATTCCCCGAATCATTGGTGGTTG
1 GGTTGCTAAGTGCTGATTCCCCCAAGGAGTTGCTAAGTGCTAATTCCCCGAATCATTGGTGGTTG
*
57411613 CTAAGTGCTGATCCCATCGTATCTTAAATGTGAAAGG
66 CTAAGTGCTGATCCCACCGTATCTTAAATGTGAAAGG
57411650 GGTTGCTAAGTGCTGATTCCCC
1 GGTTGCTAAGTGCTGATTCCCC
57411672 GACTCATTGG
Statistics
Matches: 114, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
102 114 1.00
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.32
Consensus pattern (102 bp):
GGTTGCTAAGTGCTGATTCCCCCAAGGAGTTGCTAAGTGCTAATTCCCCGAATCATTGGTGGTTG
CTAAGTGCTGATCCCACCGTATCTTAAATGTGAAAGG
Found at i:57413772 original size:18 final size:18
Alignment explanation
Indices: 57413749--57413788 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
57413739 TGGTTTGGCA
*
57413749 GAAAAAATCCAAAAGAAT
1 GAAAAAAACCAAAAGAAT
**
57413767 GAAAAAAACGTAAAGAAT
1 GAAAAAAACCAAAAGAAT
57413785 GAAA
1 GAAA
57413789 GAACATTTGC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.68, C:0.07, G:0.15, T:0.10
Consensus pattern (18 bp):
GAAAAAAACCAAAAGAAT
Found at i:57415072 original size:5 final size:5
Alignment explanation
Indices: 57415062--57415087 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
57415052 TGAGCATTCG
57415062 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
57415088 AATTTTCGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:57415558 original size:9 final size:9
Alignment explanation
Indices: 57415541--57415571 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
57415531 TCGAGTTGAT
57415541 TCGAATAAC
1 TCGAATAAC
*
57415550 TCGATTAAC
1 TCGAATAAC
57415559 TCGAATAAC
1 TCGAATAAC
57415568 TCGA
1 TCGA
57415572 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:57416301 original size:19 final size:19
Alignment explanation
Indices: 57416277--57416322 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
57416267 AAAAGTGTCT
* *
57416277 AATGCATATG-ATGTAATG
1 AATGCAAATGCATGAAATG
57416295 AAATGCAAATGCATGAAATG
1 -AATGCAAATGCATGAAATG
57416315 AATGCAAA
1 AATGCAAA
57416323 AAATAGACGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.48, C:0.09, G:0.20, T:0.24
Consensus pattern (19 bp):
AATGCAAATGCATGAAATG
Found at i:57416790 original size:16 final size:16
Alignment explanation
Indices: 57416769--57416803 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
57416759 TTCTATAATG
*
57416769 AAATGCCATGCAGTCA
1 AAATGCCATGCAGCCA
57416785 AAATGCCATGCAGCCA
1 AAATGCCATGCAGCCA
57416801 AAA
1 AAA
57416804 CAAAACATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.43, C:0.26, G:0.17, T:0.14
Consensus pattern (16 bp):
AAATGCCATGCAGCCA
Found at i:57418362 original size:2 final size:2
Alignment explanation
Indices: 57418308--57418354 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
57418298 AATGTATAAG
57418308 TA 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 TA
57418350 -A TA TA
1 TA TA TA
57418355 AGTATATAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Done.