Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 44 of 206
Found at i:12584965 original size:16 final size:16
Alignment explanation
Indices: 12584938--12585007 Score: 86
Period size: 16 Copynumber: 4.4 Consensus size: 16
12584928 TTAATTTGCT
* *
12584938 ATTACACATCTATTCC
1 ATTACACCTCTAATCC
* *
12584954 ATTATACCTCTAATTC
1 ATTACACCTCTAATCC
12584970 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
*
12584986 AATACACCTCTAATCC
1 ATTACACCTCTAATCC
*
12585002 AATACA
1 ATTACA
12585008 GCGAACCAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.36, C:0.31, G:0.00, T:0.33
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:12585231 original size:6 final size:7
Alignment explanation
Indices: 12585216--12585240 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
12585206 TATATAATTA
12585216 TTTTGTT
1 TTTTGTT
12585223 TTTTGTT
1 TTTTGTT
12585230 TTTTGTT
1 TTTTGTT
12585237 TTTT
1 TTTT
12585241 TCATCTTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (7 bp):
TTTTGTT
Found at i:12588120 original size:13 final size:13
Alignment explanation
Indices: 12588102--12588126 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12588092 AAAACCCACA
12588102 TTTTAAATAAGAT
1 TTTTAAATAAGAT
12588115 TTTTAAATAAGA
1 TTTTAAATAAGA
12588127 CTTACTGTAA
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:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (13 bp):
TTTTAAATAAGAT
Found at i:12613499 original size:30 final size:30
Alignment explanation
Indices: 12613463--12613521 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
12613453 CTTGCAAACT
*
12613463 TACTTCCCTCTGGTAAGTCTCTTCTTTCCC
1 TACTTCCCTCTGGTAAGTCTCTTCATTCCC
12613493 TACTTCCCTCTGGTAAGTCTCTTCATTCC
1 TACTTCCCTCTGGTAAGTCTCTTCATTCC
12613522 GAGGTCTTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.12, C:0.36, G:0.10, T:0.42
Consensus pattern (30 bp):
TACTTCCCTCTGGTAAGTCTCTTCATTCCC
Found at i:12615479 original size:2 final size:2
Alignment explanation
Indices: 12615472--12615509 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
12615462 TTACAGCAGC
12615472 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
12615510 TTAGAGATTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12618232 original size:23 final size:23
Alignment explanation
Indices: 12618206--12618304 Score: 189
Period size: 23 Copynumber: 4.3 Consensus size: 23
12618196 ATAAGTGCCA
12618206 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
12618229 CACTGATATGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
12618252 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
12618275 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
12618298 CACTGAT
1 CACTGAT
12618305 CAATAACACT
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 74 1.00
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.23
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:12619901 original size:28 final size:28
Alignment explanation
Indices: 12619861--12619938 Score: 129
Period size: 28 Copynumber: 2.8 Consensus size: 28
12619851 TGGTCATACG
12619861 ACCATATTGTAACGGTCAGATTCCAACA
1 ACCATATTGTAACGGTCAGATTCCAACA
*
12619889 ACCATGTTGTAACGGTCAGATTCCAACA
1 ACCATATTGTAACGGTCAGATTCCAACA
* *
12619917 ACCATATTGTAATGGTAAGATT
1 ACCATATTGTAACGGTCAGATT
12619939 TTTGCATTAC
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 46 1.00
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.28
Consensus pattern (28 bp):
ACCATATTGTAACGGTCAGATTCCAACA
Found at i:12621028 original size:3 final size:3
Alignment explanation
Indices: 12621020--12621085 Score: 114
Period size: 3 Copynumber: 21.7 Consensus size: 3
12621010 ATTAGTTTGC
12621020 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
12621068 TATT TGT TAT TAT TAT TA
1 TA-T TAT TAT TAT TAT TA
12621086 ATCTTGTAAT
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
3 58 0.97
4 2 0.03
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:12627132 original size:26 final size:26
Alignment explanation
Indices: 12627103--12627174 Score: 101
Period size: 26 Copynumber: 2.8 Consensus size: 26
12627093 AATTTTCTCG
12627103 AAATTTTACTGGAGGTAAAATCGTCA
1 AAATTTTACTGGAGGTAAAATCGTCA
* *
12627129 AAATTTTACTGGGGGTAAAATTGTCA
1 AAATTTTACTGGAGGTAAAATCGTCA
* *
12627155 ACATTTTATTGGA-GTAAAAT
1 AAATTTTACTGGAGGTAAAAT
12627175 TGGGATGAGA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
25 7 0.17
26 34 0.83
ACGTcount: A:0.38, C:0.08, G:0.19, T:0.35
Consensus pattern (26 bp):
AAATTTTACTGGAGGTAAAATCGTCA
Found at i:12633788 original size:19 final size:19
Alignment explanation
Indices: 12633736--12633790 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
12633726 TCAAGGTAAT
12633736 AATAAAAATGTAAATAAATA
1 AATAAAAATGTAAA-AAATA
* * *
12633756 AATAAAATTTTAAAAAATT
1 AATAAAAATGTAAAAAATA
*
12633775 TATAAAAATGTAAAAA
1 AATAAAAATGTAAAAA
12633791 GATATGTACA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (19 bp):
AATAAAAATGTAAAAAATA
Found at i:12634001 original size:24 final size:26
Alignment explanation
Indices: 12633954--12634015 Score: 65
Period size: 24 Copynumber: 2.4 Consensus size: 26
12633944 AGAAAATATG
**
12633954 AAATATAAGAAATATATATTTATAAT
1 AAATATAAGAAATATATACATATAAT
*
12633980 AAATA-AAG-AATATATACATATATGT
1 AAATATAAGAAATATATACATATA-AT
12634005 AAATTATAAGA
1 AAA-TATAAGA
12634016 TATAATAAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
24 12 0.41
25 7 0.24
26 7 0.24
27 3 0.10
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.34
Consensus pattern (26 bp):
AAATATAAGAAATATATACATATAAT
Found at i:12634170 original size:2 final size:2
Alignment explanation
Indices: 12634163--12634187 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12634153 TAGGTAAATA
12634163 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 A
12634188 ACTTAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12634936 original size:19 final size:19
Alignment explanation
Indices: 12634908--12634980 Score: 56
Period size: 19 Copynumber: 3.5 Consensus size: 19
12634898 ACCCAATTAC
*
12634908 CCAACTCAATTACTATTTA
1 CCAACCCAATTACTATTTA
* *
12634927 CCAACCCAATAATCTAAAGTCTA
1 CCAACCCAATTA-CT--A-TTTA
*
12634950 CCCAAACCCAATTACCATTTA
1 -CC-AACCCAATTACTATTTA
12634971 CCAACCCAAT
1 CCAACCCAAT
12634981 AAAACAAACA
Statistics
Matches: 42, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
19 18 0.43
20 4 0.10
21 3 0.07
22 2 0.05
23 3 0.07
24 3 0.07
25 9 0.21
ACGTcount: A:0.40, C:0.34, G:0.01, T:0.25
Consensus pattern (19 bp):
CCAACCCAATTACTATTTA
Found at i:12635446 original size:16 final size:16
Alignment explanation
Indices: 12635421--12635480 Score: 102
Period size: 16 Copynumber: 3.8 Consensus size: 16
12635411 TTTTACTGCA
* *
12635421 CTTTTTCTAATTCATT
1 CTTTTCCTAAATCATT
12635437 CTTTTCCTAAATCATT
1 CTTTTCCTAAATCATT
12635453 CTTTTCCTAAATCATT
1 CTTTTCCTAAATCATT
12635469 CTTTTCCTAAAT
1 CTTTTCCTAAAT
12635481 TAACCCCAAG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 42 1.00
ACGTcount: A:0.23, C:0.23, G:0.00, T:0.53
Consensus pattern (16 bp):
CTTTTCCTAAATCATT
Found at i:12637350 original size:41 final size:41
Alignment explanation
Indices: 12637289--12637477 Score: 258
Period size: 41 Copynumber: 4.6 Consensus size: 41
12637279 AATTTAAACA
* *
12637289 GATTCACTGGCACTTCA-CCTGCTAGGCTTATAGACTGATTC
1 GATTCACCGGCACTT-AGCCTGCTAGGCTTATAGCCTGATTC
* *
12637330 -AGTTCACCGGCACTTAACCTGCTAGGCTTAGAGCCTGATTC
1 GA-TTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTC
*
12637371 -AGTTCACCGGCACTTAGCCTGCTAGGCTTATAGCTTGATTC
1 GA-TTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTC
*
12637412 GAATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTC
1 GATTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTC
* *
12637453 GAATCACCGACACTTAGCCTGCTAG
1 GATTCACCGGCACTTAGCCTGCTAG
12637478 ACGTAAAGTC
Statistics
Matches: 136, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
40 2 0.01
41 133 0.98
42 1 0.01
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.28
Consensus pattern (41 bp):
GATTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTC
Found at i:12637501 original size:82 final size:82
Alignment explanation
Indices: 12637332--12637510 Score: 202
Period size: 82 Copynumber: 2.2 Consensus size: 82
12637322 ACTGATTCAG
* * *
12637332 TTCACCGGCACTTAACCTGCTAGGCTTAGAGCCTGATTCAGTTCACCGGCACTTAGCCTGCTAGG
1 TTCACCGGCACTTAACCTGCTAGGCTTAGAGCCTGATTCAGATCACCGACACTTAGCCTGCTAGA
* * * **
12637397 CTTATAGCTTGATTCGA
66 CGTAAAGCTCGAAACGA
* * *
12637414 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTC-GAATCACCGACACTTAGCCTGCTAG
1 TTCACCGGCACTTAACCTGCTAGGCTTAGAGCCTGATTCAG-ATCACCGACACTTAGCCTGCTAG
12637478 ACGTAAAG-TCCGAAAC-A
65 ACGTAAAGCT-CGAAACGA
*
12637495 TTTCACCGGCAATTAA
1 -TTCACCGGCACTTAA
12637511 TCTGATTGGT
Statistics
Matches: 80, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
81 3 0.04
82 77 0.96
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.26
Consensus pattern (82 bp):
TTCACCGGCACTTAACCTGCTAGGCTTAGAGCCTGATTCAGATCACCGACACTTAGCCTGCTAGA
CGTAAAGCTCGAAACGA
Found at i:12639481 original size:25 final size:28
Alignment explanation
Indices: 12639453--12639506 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 28
12639443 TTTTGTTTTT
12639453 ATTATAATAA-CATTAT-AAT-ATATAA
1 ATTATAATAACCATTATAAATAATATAA
* *
12639478 ATTATTATAACCTTTATAAATAATATAA
1 ATTATAATAACCATTATAAATAATATAA
12639506 A
1 A
12639507 AACTATATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 9 0.38
26 5 0.21
27 3 0.12
28 7 0.29
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.41
Consensus pattern (28 bp):
ATTATAATAACCATTATAAATAATATAA
Found at i:12640006 original size:22 final size:22
Alignment explanation
Indices: 12639966--12640007 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
12639956 ACGCGAAAAT
*
12639966 AAAAAAATCAAACAAAAAAAGA
1 AAAAAAATCAAAAAAAAAAAGA
12639988 AAAAAAAT-AAAAAATAAAAA
1 AAAAAAATCAAAAAA-AAAAA
12640008 TTTCACCTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.86, C:0.05, G:0.02, T:0.07
Consensus pattern (22 bp):
AAAAAAATCAAAAAAAAAAAGA
Found at i:12640376 original size:31 final size:31
Alignment explanation
Indices: 12640318--12640376 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 31
12640308 GTTTATGTTG
* *
12640318 TTGGCCTGTTGGGCTAGGTTTTGGTTAGATT
1 TTGGCCTGTTGGGCTAGGGTTTAGTTAGATT
* * *
12640349 TTGGGCTGTTGGGTTTGGGTTTAGTTAG
1 TTGGCCTGTTGGGCTAGGGTTTAGTTAG
12640377 GTTTGAGTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 23 1.00
ACGTcount: A:0.08, C:0.07, G:0.39, T:0.46
Consensus pattern (31 bp):
TTGGCCTGTTGGGCTAGGGTTTAGTTAGATT
Found at i:12658259 original size:23 final size:25
Alignment explanation
Indices: 12658223--12658268 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
12658213 CAAATCCTTA
*
12658223 ATAAATTATATAAA-AATATTTTTT
1 ATAAAGTATATAAATAATATTTTTT
*
12658247 ATAAAGTA-ATAAATATTATTTT
1 ATAAAGTATATAAATAATATTTT
12658269 AAAATGTGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (25 bp):
ATAAAGTATATAAATAATATTTTTT
Found at i:12658992 original size:14 final size:14
Alignment explanation
Indices: 12658969--12658999 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
12658959 TTATCACTGC
12658969 AAAAAAAAAAAAAG
1 AAAAAAAAAAAAAG
*
12658983 AAAAAGAAAAAAAG
1 AAAAAAAAAAAAAG
12658997 AAA
1 AAA
12659000 CCCATTATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAAAG
Found at i:12660309 original size:20 final size:20
Alignment explanation
Indices: 12660270--12660309 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
12660260 ATAAATAATT
*
12660270 TTTTATATCTTATTTTTTTA
1 TTTTATATCTTATATTTTTA
12660290 TTTTATATCGTTA-ATTTTTA
1 TTTTATATC-TTATATTTTTA
12660310 AGTTCAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.70
Consensus pattern (20 bp):
TTTTATATCTTATATTTTTA
Found at i:12670365 original size:20 final size:20
Alignment explanation
Indices: 12670322--12670365 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
12670312 AATACCCAAT
*
12670322 GTATCGATACATAACATAAG
1 GTATCGATACATAACATAAA
* * *
12670342 GTATCGATACTTACCTTAAA
1 GTATCGATACATAACATAAA
12670362 GTAT
1 GTAT
12670366 TTTACCACTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.32
Consensus pattern (20 bp):
GTATCGATACATAACATAAA
Found at i:12673891 original size:13 final size:13
Alignment explanation
Indices: 12673875--12673908 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
12673865 ATTGGAGTTT
12673875 AAAATAAATTAAA
1 AAAATAAATTAAA
**
12673888 AAAACGAATTAAA
1 AAAATAAATTAAA
12673901 AAAATAAA
1 AAAATAAA
12673909 AAAAACTTAA
Statistics
Matches: 17, Mismatches: 4, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.18
Consensus pattern (13 bp):
AAAATAAATTAAA
Found at i:12673901 original size:23 final size:24
Alignment explanation
Indices: 12673873--12673935 Score: 76
Period size: 22 Copynumber: 2.7 Consensus size: 24
12673863 AAATTGGAGT
12673873 TTAAAATAAATTAAAAAAAC-GAA
1 TTAAAATAAATTAAAAAAACTGAA
* *
12673896 TTAAAA-AAATAAAAAAAACTTAA
1 TTAAAATAAATTAAAAAAACTGAA
*
12673919 TTGAAAATACATTAAAA
1 TT-AAAATAAATTAAAA
12673936 GGCGGAGGGG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
22 12 0.36
23 10 0.30
24 4 0.12
25 7 0.21
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.24
Consensus pattern (24 bp):
TTAAAATAAATTAAAAAAACTGAA
Found at i:12675523 original size:20 final size:20
Alignment explanation
Indices: 12675500--12675538 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
12675490 TGCTTGTTCT
12675500 AAAGTATCAATACTTTATGG
1 AAAGTATCAATACTTTATGG
**
12675520 AAAGTATCGGTACTTTATG
1 AAAGTATCAATACTTTATG
12675539 ATGGTATCAA
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:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (20 bp):
AAAGTATCAATACTTTATGG
Found at i:12676497 original size:126 final size:125
Alignment explanation
Indices: 12676346--12676575 Score: 329
Period size: 126 Copynumber: 1.8 Consensus size: 125
12676336 AAAGTTTAAG
* * ***
12676346 GGGTTGAGGGAGTAAAATTTTGGGGGAGAATATTAAAAAAAATTGGGGGGAGGGGGATGGGTTTG
1 GGGTTGAAGGAGTAAAATTTGGGGGGAGAATATTAAAAAAAA-T--GGGGAGGAAAATGGGTTTG
*
12676411 GGGTAGAAGGG-GGGTGGGATGG-GAGGGAGTAAAAGTTTTGGGGGGGAAAAAAAAGTTTTGA
63 GGGTAGAAGGGAGGGTGGGATGGAGAGGGAATAAAAGTTTTGGGGGGGAAAAAAAAGTTTTGA
* * *
12676472 GGGTTGAATGAGTAAAATTTGGGGGGGGGATATTAAAAAAAATGGGGAGGAAAATGGGTTTGGGG
1 GGGTTGAAGGAGTAAAATTTGGGGGGAGAATATTAAAAAAAATGGGGAGGAAAATGGGTTTGGGG
*
12676537 TAGAAGGGAGGGTGGGATGGAGGGGGAATAAAAGTTTTG
66 TAGAAGGGAGGGTGGGATGGAGAGGGAATAAAAGTTTTG
12676576 ATAGGAAAGT
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
123 27 0.29
124 11 0.12
125 17 0.18
126 37 0.40
ACGTcount: A:0.32, C:0.00, G:0.46, T:0.22
Consensus pattern (125 bp):
GGGTTGAAGGAGTAAAATTTGGGGGGAGAATATTAAAAAAAATGGGGAGGAAAATGGGTTTGGGG
TAGAAGGGAGGGTGGGATGGAGAGGGAATAAAAGTTTTGGGGGGGAAAAAAAAGTTTTGA
Found at i:12676600 original size:30 final size:30
Alignment explanation
Indices: 12676560--12676644 Score: 136
Period size: 30 Copynumber: 2.9 Consensus size: 30
12676550 GGGATGGAGG
*
12676560 GGGAATAAAAGTTTTGATAGGAAAGTGGGA
1 GGGAGTAAAAGTTTTGATAGGAAAGTGGGA
*
12676590 GGGAGTAAAAGTTTTGATCGGAAAGTGGGA
1 GGGAGTAAAAGTTTTGATAGGAAAGTGGGA
*
12676620 GGGAGTAAAAGTTTTG-GAGGAAAGT
1 GGGAGTAAAAGTTTTGATAGGAAAGT
12676645 AAAGAGGTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 7 0.14
30 44 0.86
ACGTcount: A:0.36, C:0.01, G:0.39, T:0.24
Consensus pattern (30 bp):
GGGAGTAAAAGTTTTGATAGGAAAGTGGGA
Found at i:12682224 original size:21 final size:21
Alignment explanation
Indices: 12682198--12682239 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
12682188 CTGTTAGACC
12682198 AACTTGGATATAAAGTATGTT
1 AACTTGGATATAAAGTATGTT
*
12682219 AACTTGGATCTAAAGTATGTT
1 AACTTGGATATAAAGTATGTT
12682240 CTTTTACTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.07, G:0.19, T:0.38
Consensus pattern (21 bp):
AACTTGGATATAAAGTATGTT
Found at i:12684136 original size:20 final size:22
Alignment explanation
Indices: 12684111--12684155 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
12684101 ATTAAAAAAT
12684111 AATGAA-TTACAAAA-TATATA
1 AATGAAGTTACAAAACTATATA
* *
12684131 AATGAAGTTATAAAACTATTTA
1 AATGAAGTTACAAAACTATATA
12684153 AAT
1 AAT
12684156 TTATATAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 6 0.29
21 7 0.33
22 8 0.38
ACGTcount: A:0.56, C:0.04, G:0.07, T:0.33
Consensus pattern (22 bp):
AATGAAGTTACAAAACTATATA
Found at i:12684490 original size:14 final size:15
Alignment explanation
Indices: 12684466--12684495 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
12684456 ACTTAAATTA
12684466 TAATAATTTAAATAT
1 TAATAATTTAAATAT
12684481 TAAT-ATTTAAATAT
1 TAATAATTTAAATAT
12684495 T
1 T
12684496 GATGAGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TAATAATTTAAATAT
Found at i:12684683 original size:17 final size:17
Alignment explanation
Indices: 12684663--12684701 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
12684653 CTAATGTCTT
*
12684663 ATTAAAGCTAATAAAAA
1 ATTAAAGATAATAAAAA
* *
12684680 ATTAAATATATTAAAAA
1 ATTAAAGATAATAAAAA
12684697 ATTAA
1 ATTAA
12684702 CATGTGATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (17 bp):
ATTAAAGATAATAAAAA
Found at i:12686427 original size:2 final size:2
Alignment explanation
Indices: 12686420--12686449 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
12686410 TCATCCAAAC
12686420 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
12686450 ACTCAGAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:12694287 original size:20 final size:20
Alignment explanation
Indices: 12694258--12694312 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
12694248 ACTAGGAAGG
*
12694258 GGTATTGATAATTTTTTAAA
1 GGTATTGATACTTTTTTAAA
* * *
12694278 GGTATCGATACTTTGTTAAG
1 GGTATTGATACTTTTTTAAA
12694298 GGTATTGATACTTTT
1 GGTATTGATACTTTT
12694313 GATTTTTGTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.27, C:0.05, G:0.20, T:0.47
Consensus pattern (20 bp):
GGTATTGATACTTTTTTAAA
Found at i:12694402 original size:20 final size:20
Alignment explanation
Indices: 12694379--12694425 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
12694369 ATGGGTATCA
12694379 ATACTTTGA-AGAAGGTATTG
1 ATACTTTGATA-AAGGTATTG
* *
12694399 ATACTTTTATAAGGGTATTG
1 ATACTTTGATAAAGGTATTG
12694419 ATACTTT
1 ATACTTT
12694426 TGATTTTTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.32, C:0.06, G:0.19, T:0.43
Consensus pattern (20 bp):
ATACTTTGATAAAGGTATTG
Found at i:12694457 original size:114 final size:113
Alignment explanation
Indices: 12694276--12694536 Score: 292
Period size: 114 Copynumber: 2.3 Consensus size: 113
12694266 TAATTTTTTA
*
12694276 AAGGTATCGATACTTTGTTAAGGGTATTGATACTTTTGATTTTTGTTCAATTTTCCAAAACATCG
1 AAGGTATCGATACTTTGTTAAGGGTATTGATACTTTTGATTTTTGCTCAATTTTCCAAAACATCG
* *
12694341 AAGCTCAAATTGGTATCGATACCAGGTCATGGGTATCAATACTTTGAAG
66 AAGCTCAAATTGGTATCAATACCAAG-CATGGGTATCAATACTTTGAAG
* * * * * *
12694390 AAGGTATTGATACTTT-TATAAGGGTATTGATACTTTTGATTTTTGCTCTATTTT-TATGATCTT
1 AAGGTATCGATACTTTGT-TAAGGGTATTGATACTTTTGATTTTTGCTCAATTTTCCA-AAACAT
** ** * ***
12694453 CGAAGCTCATTTTGGTATCAATACCAAGCATGGGTATGGATACTTGGTTC
64 CGAAGCTCAAATTGGTATCAATACCAAGCATGGGTATCAATACTTTGAAG
* * * *
12694503 AAGGTATCGATACCTTATTGAGGGTATCGATACT
1 AAGGTATCGATACTTTGTTAAGGGTATTGATACT
12694537 ATGGTCCTTA
Statistics
Matches: 123, Mismatches: 21, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
113 46 0.37
114 77 0.63
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.39
Consensus pattern (113 bp):
AAGGTATCGATACTTTGTTAAGGGTATTGATACTTTTGATTTTTGCTCAATTTTCCAAAACATCG
AAGCTCAAATTGGTATCAATACCAAGCATGGGTATCAATACTTTGAAG
Found at i:12701144 original size:42 final size:42
Alignment explanation
Indices: 12701031--12701147 Score: 118
Period size: 42 Copynumber: 2.9 Consensus size: 42
12701021 CTCATTGGAT
* * * *
12701031 AATTCGAAGTAATAATTTGACACCCAGTGTCTCATCG-GTTA
1 AATTCGAAATAGTAAATTGACACCCAGTGTCTCATCGAATTA
* * **
12701072 AA-CCG--A-AGTAAATTGGCACCCAGTACCTCATCGAATTA
1 AATTCGAAATAGTAAATTGACACCCAGTGTCTCATCGAATTA
*
12701110 AATTCGAAATAGTAAATTGACACCCAATGTCTCATCGA
1 AATTCGAAATAGTAAATTGACACCCAGTGTCTCATCGA
12701148 CTCGAAGTCG
Statistics
Matches: 58, Mismatches: 13, Indels: 9
0.73 0.16 0.11
Matches are distributed among these distances:
37 22 0.38
38 5 0.09
39 2 0.03
40 2 0.03
41 3 0.05
42 24 0.41
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.26
Consensus pattern (42 bp):
AATTCGAAATAGTAAATTGACACCCAGTGTCTCATCGAATTA
Found at i:12701289 original size:13 final size:13
Alignment explanation
Indices: 12701271--12701296 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12701261 TTCATTTCAT
12701271 TTCAATATATATA
1 TTCAATATATATA
12701284 TTCAATATATATA
1 TTCAATATATATA
12701297 CCAATTCAAT
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:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
TTCAATATATATA
Found at i:12701303 original size:17 final size:14
Alignment explanation
Indices: 12701271--12701323 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 14
12701261 TTCATTTCAT
*
12701271 TTCAAT-ATATATA
1 TTCAATAATATAAA
12701284 TTCAATATATATACCAA
1 TTCAATA-ATATA--AA
12701301 TTCAATCAATATAAA
1 TTCAAT-AATATAAA
12701316 TTCAATAA
1 TTCAATAA
12701324 ATTCATCACA
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
13 6 0.18
14 2 0.06
15 13 0.38
17 12 0.35
18 1 0.03
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (14 bp):
TTCAATAATATAAA
Found at i:12701319 original size:15 final size:16
Alignment explanation
Indices: 12701272--12701321 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 16
12701262 TCATTTCATT
*
12701272 TCAATATATATATTCAA
1 TCAATATACA-ATTCAA
12701289 T-ATATATACCAATTCAA
1 TCA-ATATA-CAATTCAA
12701306 TCAATATA-AATTCAA
1 TCAATATACAATTCAA
12701321 T
1 T
12701322 AAATTCATCA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
15 8 0.28
16 1 0.03
17 18 0.62
18 2 0.07
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (16 bp):
TCAATATACAATTCAA
Found at i:12704693 original size:41 final size:41
Alignment explanation
Indices: 12704583--12704697 Score: 149
Period size: 41 Copynumber: 2.8 Consensus size: 41
12704573 TGGACCTTCT
* *
12704583 AGGGCTTTAGAGGCATTTTTAAAAAAGCGTCGCTAATGCTC
1 AGGGCTTTAGCGGCATTTTTAAAAAAGCGCCGCTAATGCTC
* * ** *
12704624 AGAGCTTTAGCGGTATTTTCCAAGAAGCGCCGCTAATGCTC
1 AGGGCTTTAGCGGCATTTTTAAAAAAGCGCCGCTAATGCTC
* *
12704665 GGGGCTTTAGCGGCGTTTTTAAAAAAGCGCCGC
1 AGGGCTTTAGCGGCATTTTTAAAAAAGCGCCGC
12704698 AAAAATATTT
Statistics
Matches: 60, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
41 60 1.00
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (41 bp):
AGGGCTTTAGCGGCATTTTTAAAAAAGCGCCGCTAATGCTC
Found at i:12705118 original size:7 final size:7
Alignment explanation
Indices: 12705108--12705159 Score: 68
Period size: 7 Copynumber: 7.3 Consensus size: 7
12705098 ATTTTAAGGT
*
12705108 TTATAGA
1 TTATGGA
12705115 TTATGGAA
1 TTATGG-A
*
12705123 TTAGGGA
1 TTATGGA
12705130 TTATGGA
1 TTATGGA
12705137 TTATGGA
1 TTATGGA
12705144 TTATGGA
1 TTATGGA
*
12705151 TTAGGGA
1 TTATGGA
12705158 TT
1 TT
12705160 CTGGTTTAAG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
7 34 0.85
8 6 0.15
ACGTcount: A:0.31, C:0.00, G:0.29, T:0.40
Consensus pattern (7 bp):
TTATGGA
Found at i:12705133 original size:22 final size:21
Alignment explanation
Indices: 12705108--12705153 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
12705098 ATTTTAAGGT
12705108 TTATAGATTATGGAATTAGGGA
1 TTATAGATTATGG-ATTAGGGA
* *
12705130 TTATGGATTATGGATTATGGA
1 TTATAGATTATGGATTAGGGA
12705151 TTA
1 TTA
12705154 GGGATTCTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.33, C:0.00, G:0.26, T:0.41
Consensus pattern (21 bp):
TTATAGATTATGGATTAGGGA
Found at i:12705144 original size:14 final size:14
Alignment explanation
Indices: 12705113--12705159 Score: 76
Period size: 14 Copynumber: 3.3 Consensus size: 14
12705103 AAGGTTTATA
12705113 GATTATGGAATTAGG
1 GATTATGG-ATTAGG
*
12705128 GATTATGGATTATG
1 GATTATGGATTAGG
12705142 GATTATGGATTAGG
1 GATTATGGATTAGG
12705156 GATT
1 GATT
12705160 CTGGTTTAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
14 22 0.73
15 8 0.27
ACGTcount: A:0.30, C:0.00, G:0.32, T:0.38
Consensus pattern (14 bp):
GATTATGGATTAGG
Found at i:12709116 original size:14 final size:14
Alignment explanation
Indices: 12709081--12709113 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
12709071 TAACTTTTGA
12709081 ATTTTAATTGTGTT
1 ATTTTAATTGTGTT
12709095 A-TTTAATT-TGTT
1 ATTTTAATTGTGTT
12709107 ATTTTAA
1 ATTTTAA
12709114 ATTCTAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 5 0.28
13 12 0.67
14 1 0.06
ACGTcount: A:0.27, C:0.00, G:0.09, T:0.64
Consensus pattern (14 bp):
ATTTTAATTGTGTT
Found at i:12709234 original size:24 final size:22
Alignment explanation
Indices: 12709206--12709249 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
12709196 AATTTAAAAA
12709206 ATAAAACATAATATAATATTTATC
1 ATAAAA-ATAA-ATAATATTTATC
*
12709230 ATAAAAATAAATATTATTTA
1 ATAAAAATAAATAATATTTA
12709250 ATTAAAACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 4 0.21
24 6 0.32
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.39
Consensus pattern (22 bp):
ATAAAAATAAATAATATTTATC
Found at i:12709333 original size:43 final size:43
Alignment explanation
Indices: 12709280--12709500 Score: 217
Period size: 43 Copynumber: 5.1 Consensus size: 43
12709270 AGGTTATATT
* * *
12709280 TTTAGCAGCGTTTTTTGCAAAAACGTCGCTAAAGGTCATGGTC
1 TTTAGCAGCGTTTGTGGCAAAAACGCCGCTAAAGGTCATGGTC
* * * *
12709323 TTTAACAGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCAGCGTTTGTGGCAAAAACGCCGCTAAAGGTCATGGTC
* * * * * *
12709366 TTTAGCGGCGTTTGTGGGAGAAATGCCGCCAAAGGTCTTGGTC
1 TTTAGCAGCGTTTGTGGCAAAAACGCCGCTAAAGGTCATGGTC
* * * * * * *
12709409 TTTAGCGGCGTTTGTGGGAGAAGCGCCACCAAAGGTCTTGGTC
1 TTTAGCAGCGTTTGTGGCAAAAACGCCGCTAAAGGTCATGGTC
* * * * *
12709452 TTTAGCGGCGTTTGTGGGAGAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCAGCGTTTGTGGCAAAAACGCCGCTAAAGGTCATGGTC
12709495 TTTAGC
1 TTTAGC
12709501 GGCATTTTTT
Statistics
Matches: 160, Mismatches: 18, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 160 1.00
ACGTcount: A:0.20, C:0.19, G:0.32, T:0.29
Consensus pattern (43 bp):
TTTAGCAGCGTTTGTGGCAAAAACGCCGCTAAAGGTCATGGTC
Found at i:12709501 original size:43 final size:43
Alignment explanation
Indices: 12709306--12709503 Score: 315
Period size: 43 Copynumber: 4.6 Consensus size: 43
12709296 GCAAAAACGT
* * * *
12709306 CGCTAAAGGTCATGGTCTTTAACAGCGTTTGTGGGAAAAGCGC
1 CGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAGAAGCGC
**
12709349 CGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAGAAATGC
1 CGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAGAAGCGC
*
12709392 CGCCAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAGAAGCGC
1 CGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAGAAGCGC
* *
12709435 CACCAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAGAAGCGC
1 CGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAGAAGCGC
12709478 CGCTAAAGGTCTTGGTCTTTAGCGGC
1 CGCTAAAGGTCTTGGTCTTTAGCGGC
12709504 ATTTTTTTCG
Statistics
Matches: 143, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 143 1.00
ACGTcount: A:0.19, C:0.20, G:0.34, T:0.27
Consensus pattern (43 bp):
CGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAGAAGCGC
Found at i:12712028 original size:45 final size:45
Alignment explanation
Indices: 12711964--12712089 Score: 225
Period size: 45 Copynumber: 2.8 Consensus size: 45
12711954 TGGTGGTGGC
*
12711964 GGAGGAGCTCCATATGAAGGATAGCCAGAAAAAGATTGGGGCGAT
1 GGAGGAGCTCCATACGAAGGATAGCCAGAAAAAGATTGGGGCGAT
*
12712009 GGAGGAGCTCCATACGAAGGATAGCCAGAAAAAGATTGGGGTGAT
1 GGAGGAGCTCCATACGAAGGATAGCCAGAAAAAGATTGGGGCGAT
*
12712054 GGAGGAGCTCCATACGAAGGATAGCCAGAAAGAGAT
1 GGAGGAGCTCCATACGAAGGATAGCCAGAAAAAGAT
12712090 GGTGATGGCA
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 78 1.00
ACGTcount: A:0.37, C:0.14, G:0.35, T:0.14
Consensus pattern (45 bp):
GGAGGAGCTCCATACGAAGGATAGCCAGAAAAAGATTGGGGCGAT
Found at i:12717902 original size:4 final size:4
Alignment explanation
Indices: 12717895--12717926 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
12717885 CAATCATAGC
12717895 AAAT AAAT AAAT AAAT AAAT AAAT AAACT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA-T AAA
12717927 GTATAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:12718144 original size:10 final size:11
Alignment explanation
Indices: 12718113--12718155 Score: 50
Period size: 12 Copynumber: 3.7 Consensus size: 11
12718103 CGTGAATTAC
*
12718113 AAAATATTTAT
1 AAAATATATAT
12718124 AAAATATATAT
1 AAAATATATAT
*
12718135 AAAAATATATTTT
1 -AAAATATA-TAT
12718148 AAAATATA
1 AAAATATA
12718156 AAGGATAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 10 0.36
12 16 0.57
13 2 0.07
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
AAAATATATAT
Found at i:12718403 original size:16 final size:16
Alignment explanation
Indices: 12718382--12718420 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
12718372 TGAATTATAA
*
12718382 AAAAATAA-AGTAAGAT
1 AAAAATAACA-TAAAAT
12718398 AAAAATAACATAAAAT
1 AAAAATAACATAAAAT
12718414 AAAAATA
1 AAAAATA
12718421 TATATATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 20 0.95
17 1 0.05
ACGTcount: A:0.74, C:0.03, G:0.05, T:0.18
Consensus pattern (16 bp):
AAAAATAACATAAAAT
Found at i:12718605 original size:3 final size:3
Alignment explanation
Indices: 12718597--12718699 Score: 79
Period size: 3 Copynumber: 34.3 Consensus size: 3
12718587 AAGCTATTAT
* *
12718597 ATA ATA ATA ATA ATA ATA AT- ATG ATA AGTA ATA ATG AT- ATAA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA AT-A ATA
* * * *
12718642 ATA ATA ATA ATA ATA ATA AAA GATG ATA AT- ATA TTA AAA ATA ATGA
1 ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA AT-A
*
12718688 AGA A-A ATA ATA A
1 ATA ATA ATA ATA A
12718700 AAATGCTAAA
Statistics
Matches: 81, Mismatches: 11, Indels: 16
0.75 0.10 0.15
Matches are distributed among these distances:
2 8 0.10
3 65 0.80
4 8 0.10
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:12718683 original size:42 final size:44
Alignment explanation
Indices: 12718597--12718699 Score: 115
Period size: 42 Copynumber: 2.4 Consensus size: 44
12718587 AAGCTATTAT
* *
12718597 ATAATAATAATAATAATAATATGATAAGTAATAATGATATAAATA
1 ATAATAATAATAATAATAATAAGATAAGTAATAAT-ATAAAAATA
*
12718642 ATAATAATAATAATAATAA-AAGATGA-TAAT-ATATTAAAAATA
1 ATAATAATAATAATAATAATAAGATAAGTAATAATA-TAAAAATA
*
12718684 ATGAAGAA-AATAATAA
1 AT-AATAATAATAATAA
12718700 AAATGCTAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
41 1 0.02
42 19 0.37
43 8 0.15
44 5 0.10
45 19 0.37
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (44 bp):
ATAATAATAATAATAATAATAAGATAAGTAATAATATAAAAATA
Found at i:12718684 original size:39 final size:44
Alignment explanation
Indices: 12718597--12718701 Score: 123
Period size: 45 Copynumber: 2.5 Consensus size: 44
12718587 AAGCTATTAT
*
12718597 ATAATAATAATAATAATAATATGATAAGTAATAATGATATAAATA
1 ATAATAATAATAATAATAA-AAGATAAGTAATAATGATATAAATA
*
12718642 ATAATAATAATAATAATAAAAGATGA-TAAT-AT-AT-TAAA-A
1 ATAATAATAATAATAATAAAAGATAAGTAATAATGATATAAATA
*
12718681 ATAATGAAGAA-AATAATAAAA
1 ATAAT-AATAATAATAATAAAA
12718702 ATGCTAAAAA
Statistics
Matches: 56, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
39 16 0.29
40 8 0.14
41 2 0.04
42 2 0.04
43 4 0.07
44 5 0.09
45 19 0.34
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.30
Consensus pattern (44 bp):
ATAATAATAATAATAATAAAAGATAAGTAATAATGATATAAATA
Found at i:12719389 original size:15 final size:14
Alignment explanation
Indices: 12719371--12719409 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
12719361 TCGAAAATAT
*
12719371 GAAAAGAAAAAATG
1 GAAAAGAAAAAACG
12719385 AGAAAA-AAAAAACG
1 -GAAAAGAAAAAACG
12719399 GAAAAGAAAAA
1 GAAAAGAAAAA
12719410 GAACAACAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 5 0.23
14 12 0.55
15 5 0.23
ACGTcount: A:0.77, C:0.03, G:0.18, T:0.03
Consensus pattern (14 bp):
GAAAAGAAAAAACG
Found at i:12723940 original size:41 final size:41
Alignment explanation
Indices: 12723879--12723958 Score: 142
Period size: 41 Copynumber: 2.0 Consensus size: 41
12723869 TGATCGAATG
*
12723879 TAATACAGACTTTACATCTAGCAGGTTTGATGCCGGTGAAA
1 TAATACAGACTTTACATCTAGCAGGTTTAATGCCGGTGAAA
*
12723920 TAATACAGACTTTACGTCTAGCAGGTTTAATGCCGGTGA
1 TAATACAGACTTTACATCTAGCAGGTTTAATGCCGGTGA
12723959 TACATTTCGG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (41 bp):
TAATACAGACTTTACATCTAGCAGGTTTAATGCCGGTGAAA
Found at i:12723980 original size:41 final size:41
Alignment explanation
Indices: 12723880--12723985 Score: 122
Period size: 41 Copynumber: 2.6 Consensus size: 41
12723870 GATCGAATGT
* * * *
12723880 AATACAGACTTTACATCTAGCAGGTTTGATGCCGGTGAAAT
1 AATACAGACTATACGTCTAGCAGGTTTAATGCCGGTGAAAC
* *
12723921 AATACAGACTTTACGTCTAGCAGGTTTAATGCCGGTGATAC
1 AATACAGACTATACGTCTAGCAGGTTTAATGCCGGTGAAAC
* * * *
12723962 ATTTCGGACTATAGGTCTAGCAGG
1 AATACAGACTATACGTCTAGCAGG
12723986 CTAAAGGCCG
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 56 1.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (41 bp):
AATACAGACTATACGTCTAGCAGGTTTAATGCCGGTGAAAC
Found at i:12730720 original size:9 final size:9
Alignment explanation
Indices: 12730701--12730737 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
12730691 TGAGTTTTTG
*
12730701 AATTTGAAT
1 AATTCGAAT
*
12730710 AACTCGAAT
1 AATTCGAAT
12730719 AATTCGAAT
1 AATTCGAAT
12730728 AATTCGAAT
1 AATTCGAAT
12730737 A
1 A
12730738 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:12732956 original size:43 final size:43
Alignment explanation
Indices: 12732891--12733035 Score: 150
Period size: 43 Copynumber: 3.4 Consensus size: 43
12732881 CCTAGATATA
* * * **
12732891 GTCTTACATGTAATCTCGTATCGATGCCAATAGCCCAGCCATG
1 GTCTTACACGAAATCTCATATCGATGCCAATAGCCCAGAAATG
* *
12732934 GTCTTACACGAAATCACATATCGATGCCAAT-GTCCCAGAAACG
1 GTCTTACACGAAATCTCATATCGATGCCAATAG-CCCAGAAATG
* * * **
12732977 GTGTTACACGAAGTCTCATATCGATGCC-ATATCCCAGATGTG
1 GTCTTACACGAAATCTCATATCGATGCCAATAGCCCAGAAATG
*
12733019 GTCTTACACGTAATCTC
1 GTCTTACACGAAATCTC
12733036 GATAACCCTA
Statistics
Matches: 83, Mismatches: 17, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
42 24 0.29
43 59 0.71
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.27
Consensus pattern (43 bp):
GTCTTACACGAAATCTCATATCGATGCCAATAGCCCAGAAATG
Found at i:12740167 original size:21 final size:22
Alignment explanation
Indices: 12740136--12740180 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
12740126 ACCCTAAAAA
12740136 TAATATTATTAAAAGAAATAAT
1 TAATATTATTAAAAGAAATAAT
*
12740158 TAAT-TTATTAAAAGAAATCAT
1 TAATATTATTAAAAGAAATAAT
12740179 TA
1 TA
12740181 TAAATTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (22 bp):
TAATATTATTAAAAGAAATAAT
Found at i:12748748 original size:174 final size:174
Alignment explanation
Indices: 12748416--12748749 Score: 399
Period size: 174 Copynumber: 1.9 Consensus size: 174
12748406 TTGTGACTCA
* * * *
12748416 TGAGGTGGAAAAGGTAGAGAGAGGGCAATGCAGGAGCAAGGAAAGGAGTGAAAATGTTTATTCAG
1 TGAGGTGGAAAAGGTAGAAAGAGGGCAATGCAGGAGCAAGGAAAGGACTGAAAAGGTTTACTCAG
* * * * * * *
12748481 GTAGAGTAACTAGATCACGAAGTTCAATCCATCCTTCCATGTCTGAGAGTGGGCCTTCAGGTACA
66 GTAGAGTAACAAGATCAAGAAGTTCAATCCAACCTTCAAAGTCTGAAAATGGGCCTTCAGGTACA
*
12748546 GGCAACGACTCCTTTGTTGCAAAGCAGGATAATGTTGTCAGTAG
131 GGAAACGACTCCTTTGTTGCAAAGCAGGATAATGTTGTCAGTAG
12748590 TGAGGTGGAAAAAGG-AGAAAGAGTGG-AATGCAGGAGCAAGGAAAGGACTGAAAAGGTTTACTC
1 TGAGGTGG-AAAAGGTAGAAAGAG-GGCAATGCAGGAGCAAGGAAAGGACTGAAAAGGTTTACTC
* * * * * *
12748653 TGGTCGAGTCACAAGATCAAGAGGTTC-AGCTCAACCTTCAAAGTCT-ATAAATGGGCTTTCAGG
64 AGGTAGAGTAACAAGATCAAGAAGTTCAATC-CAACCTTCAAAGTCTGA-AAATGGGCCTTCAGG
* * *
12748716 TGCAGGAAAC-ACTTCTTCTGTTGCTAAGCAGGAT
127 TACAGGAAACGACTCCTT-TGTTGCAAAGCAGGAT
12748750 GGTGTGGTAC
Statistics
Matches: 134, Mismatches: 21, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
173 9 0.07
174 117 0.87
175 8 0.06
ACGTcount: A:0.33, C:0.16, G:0.29, T:0.22
Consensus pattern (174 bp):
TGAGGTGGAAAAGGTAGAAAGAGGGCAATGCAGGAGCAAGGAAAGGACTGAAAAGGTTTACTCAG
GTAGAGTAACAAGATCAAGAAGTTCAATCCAACCTTCAAAGTCTGAAAATGGGCCTTCAGGTACA
GGAAACGACTCCTTTGTTGCAAAGCAGGATAATGTTGTCAGTAG
Found at i:12755252 original size:5 final size:5
Alignment explanation
Indices: 12755242--12755279 Score: 76
Period size: 5 Copynumber: 7.6 Consensus size: 5
12755232 CAGAGTGAAC
12755242 ATGTG ATGTG ATGTG ATGTG ATGTG ATGTG ATGTG ATG
1 ATGTG ATGTG ATGTG ATGTG ATGTG ATGTG ATGTG ATG
12755280 ATGTTGGAGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.21, C:0.00, G:0.39, T:0.39
Consensus pattern (5 bp):
ATGTG
Found at i:12758815 original size:119 final size:119
Alignment explanation
Indices: 12758596--12758841 Score: 388
Period size: 119 Copynumber: 2.1 Consensus size: 119
12758586 TTTCTGTTGC
* *
12758596 TTGAATACTTACAATGTATATACTTCCATTTGTAGCAATCCCTTCTGGTAAGTTATTGATCTAGA
1 TTGAATACTTACAATGTATATACTT-C-TTTGTAGCAATCCCTTCTGGTAAGTTATTCATCCAGA
**
12758661 AAGGTTGATCAAGCTAGAAAACATGGGAACAATGAATCAGAATCCAGTGACAAAAAA
64 AAGGTTGATCAAGCTAGAAAACAAAGGAACAATGAATCAGAAT-CAGTGACAAAAAA
* *
12758718 TTGAGTACTTACAATGTATATAC-T-TTTGTTGCAATCCCTTCTGGTAAGTTTATTCATCCAGAA
1 TTGAATACTTACAATGTATATACTTCTTTGTAGCAATCCCTTCTGGTAAG-TTATTCATCCAGAA
12758781 AGGTTGATCAAGCTAGAAAACAAAGGAACAATGAATCAGAATCAGTGACAAAAAA
65 AGGTTGATCAAGCTAGAAAACAAAGGAACAATGAATCAGAATCAGTGACAAAAAA
12758836 TTGAAT
1 TTGAAT
12758842 CAGCATTTTA
Statistics
Matches: 116, Mismatches: 7, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
118 41 0.35
119 52 0.45
121 1 0.01
122 22 0.19
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (119 bp):
TTGAATACTTACAATGTATATACTTCTTTGTAGCAATCCCTTCTGGTAAGTTATTCATCCAGAAA
GGTTGATCAAGCTAGAAAACAAAGGAACAATGAATCAGAATCAGTGACAAAAAA
Found at i:12759939 original size:21 final size:21
Alignment explanation
Indices: 12759913--12759954 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
12759903 AGAAGGACAT
12759913 CCAAGTTGCTACTCAACTTGG
1 CCAAGTTGCTACTCAACTTGG
12759934 CCAAGTTGCTACTCAACTTGG
1 CCAAGTTGCTACTCAACTTGG
12759955 GGAGGCAGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.29
Consensus pattern (21 bp):
CCAAGTTGCTACTCAACTTGG
Found at i:12763384 original size:99 final size:92
Alignment explanation
Indices: 12763245--12763443 Score: 220
Period size: 94 Copynumber: 2.1 Consensus size: 92
12763235 ATAAATACAA
*
12763245 ATATATCAAATAAATTAGTTTAAAATAAAATATATTTAACACAATGATAAATATAAAAAATATAT
1 ATATAT-AAATAAATAAGTTTAAAATAAAATATATTTAACACAAT-A-AAATATAAAAAATAT-T
12763310 AATTTTATTATATAATTACATATTTATTAATTT
62 --TTTTATTATATAATTACATATTTATTAATTT
* * * * *
12763343 ATATATAAATAAATAAGTTATTAATTAAAA-ATACTTTTAACATAATAATATATATAAAATATTT
1 ATATATAAATAAATAAGTT-TAAAATAAAATATA--TTTAACACAATAAAATATAAAAAATATTT
* * *
12763407 TTTATTTTATAATTATATATTTATTATTTT
63 TTTATTATATAATTACATATTTATTAATTT
*
12763437 ATTTATA
1 ATATATA
12763444 TAAAATTGGC
Statistics
Matches: 88, Mismatches: 10, Indels: 10
0.81 0.09 0.09
Matches are distributed among these distances:
94 34 0.39
96 1 0.01
97 28 0.32
98 15 0.17
99 10 0.11
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (92 bp):
ATATATAAATAAATAAGTTTAAAATAAAATATATTTAACACAATAAAATATAAAAAATATTTTTT
ATTATATAATTACATATTTATTAATTT
Found at i:12763442 original size:20 final size:21
Alignment explanation
Indices: 12763401--12763445 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
12763391 TATATATAAA
*
12763401 ATATTTTTTATTTTATAATTAT
1 ATATTTATTATTTTAT-ATTAT
12763423 ATATTTATTATTTTAT-TTAT
1 ATATTTATTATTTTATATTAT
12763443 ATA
1 ATA
12763446 AAATTGGCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 7 0.32
22 15 0.68
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
ATATTTATTATTTTATATTAT
Found at i:12763784 original size:21 final size:21
Alignment explanation
Indices: 12763759--12763836 Score: 95
Period size: 21 Copynumber: 3.6 Consensus size: 21
12763749 ATCTTCGAGG
12763759 ATATGTAATCTTAAATATGAT
1 ATATGTAATCTTAAATATGAT
* *
12763780 ATATGCAATCTTAGATATGAT
1 ATATGTAATCTTAAATATGAT
12763801 ATATGTAATCTTAGAAGATATGAT
1 ATATGTAATCTT--AA-ATATGAT
*
12763825 -TTTGTAATCTTA
1 ATATGTAATCTTA
12763837 GAGATTTAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
21 31 0.63
23 11 0.22
24 7 0.14
ACGTcount: A:0.38, C:0.06, G:0.13, T:0.42
Consensus pattern (21 bp):
ATATGTAATCTTAAATATGAT
Found at i:12763848 original size:22 final size:23
Alignment explanation
Indices: 12763804--12763848 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
12763794 ATATGATATA
*
12763804 TGTAATCTTAGAAGATATGATTT
1 TGTAATCTTAGAAGATATAATTT
*
12763827 TGTAATCTTAG-AGATTTAATTT
1 TGTAATCTTAGAAGATATAATTT
12763849 GTAGATACCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (23 bp):
TGTAATCTTAGAAGATATAATTT
Found at i:12764454 original size:46 final size:46
Alignment explanation
Indices: 12764401--12764555 Score: 125
Period size: 46 Copynumber: 3.2 Consensus size: 46
12764391 TTTTTAAGTT
*
12764401 TATATATGTAATTATTATTTTTATGATTTATATATTTATTACCTTA
1 TATATATGTAATTATTATTTTTATGATTTATATATTTATTAACTTA
* * *
12764447 TATATATGTACGTATATATATATATTAT-ACTTTCTATACATATTT-TATAATTTCTA
1 TATATATGTA-AT-TAT-TAT-TTTTATGA--TT-TAT--ATATTTAT-TAA-CT-TA
* * *
12764503 TATATATATAATTATTATCTTTATGATCTATATATTTATTAACTTA
1 TATATATGTAATTATTATTTTTATGATTTATATATTTATTAACTTA
12764549 TATATAT
1 TATATAT
12764556 ATATGTACGT
Statistics
Matches: 85, Mismatches: 10, Indels: 28
0.69 0.08 0.23
Matches are distributed among these distances:
46 19 0.22
47 2 0.02
48 12 0.14
49 5 0.06
50 8 0.09
51 3 0.04
52 7 0.08
53 5 0.06
54 11 0.13
55 2 0.02
56 11 0.13
ACGTcount: A:0.35, C:0.06, G:0.03, T:0.55
Consensus pattern (46 bp):
TATATATGTAATTATTATTTTTATGATTTATATATTTATTAACTTA
Found at i:12764484 original size:20 final size:20
Alignment explanation
Indices: 12764461--12764616 Score: 84
Period size: 20 Copynumber: 7.6 Consensus size: 20
12764451 TATGTACGTA
*
12764461 TATATATATATTATACTTTC
1 TATATATATATTATAATTTC
* *
12764481 TATACATATTTTATAATTTC
1 TATATATATATTATAATTTC
* *
12764501 TATATATATATAATTATTATC
1 TATATATATATTATAATT-TC
* * * *
12764522 TTTATGATCTATATATTTATTAAC
1 TATAT-ATATAT-TA-TAATT-TC
*
12764546 T-TATATATA-TAT-ATGTAC
1 TATATATATATTATAAT-TTC
* *
12764564 GTATATATGTATTATATTTTC
1 -TATATATATATTATAATTTC
** *
12764585 TATCCATATTTTATAATTTC
1 TATATATATATTATAATTTC
*
12764605 TATATGTATATT
1 TATATATATATT
12764617 TTTCTTTATT
Statistics
Matches: 103, Mismatches: 24, Indels: 18
0.71 0.17 0.12
Matches are distributed among these distances:
18 4 0.04
19 3 0.03
20 63 0.61
21 11 0.11
22 10 0.10
23 4 0.04
24 8 0.08
ACGTcount: A:0.35, C:0.08, G:0.03, T:0.54
Consensus pattern (20 bp):
TATATATATATTATAATTTC
Found at i:12764511 original size:104 final size:104
Alignment explanation
Indices: 12764401--12764616 Score: 319
Period size: 104 Copynumber: 2.1 Consensus size: 104
12764391 TTTTTAAGTT
* * * *
12764401 TATATATGTAATTATTATTTTTATGATTTATATATTTATTACCTTATATATATGTACGTA-TATA
1 TATATAT-TAATTATTATCTTTATGATCTATATATTTATTAACTTATATATATATACGTACTATA
12764465 TATATATTATACTTTCTATACATATTTTATAATTTCTATA
65 TATATATTATACTTTCTATACATATTTTATAATTTCTATA
*
12764505 TATATA-TAATTATTATCTTTATGATCTATATATTTATTAACTTATATATATATATGTACGTATA
1 TATATATTAATTATTATCTTTATGATCTATATATTTATTAACTTATATATATATACGTAC-TATA
* * *
12764569 TATGTATTATATTTTCTATCCATATTTTATAATTTCTATA
65 TATATATTATACTTTCTATACATATTTTATAATTTCTATA
*
12764609 TGTATATT
1 TATATATT
12764617 TTTCTTTATT
Statistics
Matches: 100, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
102 47 0.47
104 52 0.52
105 1 0.01
ACGTcount: A:0.34, C:0.07, G:0.04, T:0.55
Consensus pattern (104 bp):
TATATATTAATTATTATCTTTATGATCTATATATTTATTAACTTATATATATATACGTACTATAT
ATATATTATACTTTCTATACATATTTTATAATTTCTATA
Found at i:12764515 original size:102 final size:103
Alignment explanation
Indices: 12764401--12764615 Score: 324
Period size: 102 Copynumber: 2.1 Consensus size: 103
12764391 TTTTTAAGTT
* * * * *
12764401 TATATATGTAATTATTATTTTTATGATTTATATATTTATTACCTTATATATATGTACGTA-TATA
1 TATATATATAATTATTATCTTTATGATCTATATATTTATTAACTTATATATATATACGTACTATA
12764465 TATATATTATACTTTCTATACATATTTTATAATTTCTA
66 TATATATTATACTTTCTATACATATTTTATAATTTCTA
*
12764503 TATATATATAATTATTATCTTTATGATCTATATATTTATTAACTTATATATATATATGTACGTAT
1 TATATATATAATTATTATCTTTATGATCTATATATTTATTAACTTATATATATATACGTAC-TAT
* * *
12764568 ATATGTATTATATTTTCTATCCATATTTTATAATTTCTA
65 ATATATATTATACTTTCTATACATATTTTATAATTTCTA
*
12764607 TATGTATAT
1 TATATATAT
12764616 TTTTCTTTAT
Statistics
Matches: 101, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
102 54 0.53
104 47 0.47
ACGTcount: A:0.34, C:0.07, G:0.04, T:0.54
Consensus pattern (103 bp):
TATATATATAATTATTATCTTTATGATCTATATATTTATTAACTTATATATATATACGTACTATA
TATATATTATACTTTCTATACATATTTTATAATTTCTA
Found at i:12764541 original size:24 final size:22
Alignment explanation
Indices: 12764501--12764559 Score: 73
Period size: 24 Copynumber: 2.6 Consensus size: 22
12764491 TTATAATTTC
* *
12764501 TATATATATATAATTATTATCTT
1 TATATATATATATTTATTAAC-T
*
12764524 TATGATCTATATATTTATTAACT
1 TAT-ATATATATATTTATTAACT
12764547 TATATATATATAT
1 TATATATATATAT
12764560 GTACGTATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
22 9 0.29
23 7 0.23
24 15 0.48
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.54
Consensus pattern (22 bp):
TATATATATATATTTATTAACT
Found at i:12764761 original size:24 final size:24
Alignment explanation
Indices: 12764699--12764761 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 24
12764689 ATATATTATG
* * * *
12764699 TATTTTCTTTTCTTTATTTTTTTA
1 TATTTTTTTTTATTTATGTTTTCA
* * *
12764723 TATGTTTGTTGATTTATGTTTTCA
1 TATTTTTTTTTATTTATGTTTTCA
12764747 TATTTTTTTTTATTT
1 TATTTTTTTTTATTT
12764762 TGCTCATTTA
Statistics
Matches: 29, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.14, C:0.05, G:0.06, T:0.75
Consensus pattern (24 bp):
TATTTTTTTTTATTTATGTTTTCA
Found at i:12768866 original size:5 final size:6
Alignment explanation
Indices: 12768851--12768901 Score: 81
Period size: 6 Copynumber: 9.0 Consensus size: 6
12768841 AAAGTGATAA
12768851 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG -AAAAG -AAAAG -AAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
12768896 AAAAAG
1 AAAAAG
12768902 GAGAGGCCAA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
5 15 0.34
6 29 0.66
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:12770182 original size:44 final size:44
Alignment explanation
Indices: 12770129--12770768 Score: 589
Period size: 44 Copynumber: 14.5 Consensus size: 44
12770119 GAAAAAATAA
* * *
12770129 ATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGATAGCAG
1 ATCTTGTCTTCCTATATTGGTAG-GAAGTAGATCGAAGATAGCAG
* *
12770173 ATCCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGAT-GCAG
1 ATCTTGTCTTCCTATATTGGTAGGAAGTAGATCGAAGATAGCAG
* * * *
12770216 ATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAAAAAGCAG
1 ATCTTGTCTTCCTATATTGGTAG-GAAGTAGATCGAAGATAGCAG
* * * * *
12770261 ATCTTGTCTTCATGTATTGG-CGTGAAGTAAATCAAAGATAGCAG
1 ATCTTGTCTTCCTATATTGGTAG-GAAGTAGATCGAAGATAGCAG
* * * * * *
12770305 GTCCTATTTTCCTATATTGGTAGGAAGTGGATCGAAGAT-GTAG
1 ATCTTGTCTTCCTATATTGGTAGGAAGTAGATCGAAGATAGCAG
* * * * * *
12770348 AGCTTATCTTCCCATATTGGTAGCCAAGTATATCGAAGAAAGCAG
1 ATCTTGTCTTCCTATATTGGTAG-GAAGTAGATCGAAGATAGCAG
* * * *
12770393 ATCTTGTCCTCATGTATTGG-CGTGAAGTAGATCGAAGATAGCAG
1 ATCTTGTCTTCCTATATTGGTAG-GAAGTAGATCGAAGATAGCAG
* *
12770437 ATCCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGAT-GCAG
1 ATCTTGTCTTCCTATATTGGTAGGAAGTAGATCGAAGATAGCAG
* * * *
12770480 ATCTTGGCTTCCGATATTGGTGGCGAAGTAGATCGAAGAAAGCAG
1 ATCTTGTCTTCCTATATTGGTAG-GAAGTAGATCGAAGATAGCAG
* * * *
12770525 ATCTTATCTTCATGTATTGG-CGAGAAGTAGATCGAAGATAGCAG
1 ATCTTGTCTTCCTATATTGGTAG-GAAGTAGATCGAAGATAGCAG
* * *
12770569 ATCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGAT-GCAG
1 ATCTTGTCTTCCTATATTGGTAGGAAGTAGATCGAAGATAGCAG
* * * * *
12770612 ATCTTATCTTCCCATATTGGTGGCGAAATAGATCGAAGAAAGCAG
1 ATCTTGTCTTCCTATATTGGTAG-GAAGTAGATCGAAGATAGCAG
* * *
12770657 ATCTTGTCTTCATATACTGGT-GGCAAAGTAGATCGAAGAAAGCAG
1 ATCTTGTCTTCCTATATTGGTAGG--AAGTAGATCGAAGATAGCAG
* * * * *
12770702 ATCTTATCTTCATGTATTGG-CGTGAAGTAGATCGAATATAGCAG
1 ATCTTGTCTTCCTATATTGGTAG-GAAGTAGATCGAAGATAGCAG
* *
12770746 ATCATGTCTTCTTATATTGGTAG
1 ATCTTGTCTTCCTATATTGGTAG
12770769 TAAAGTGGAC
Statistics
Matches: 481, Mismatches: 98, Indels: 33
0.79 0.16 0.05
Matches are distributed among these distances:
43 93 0.19
44 267 0.56
45 120 0.25
46 1 0.00
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.30
Consensus pattern (44 bp):
ATCTTGTCTTCCTATATTGGTAGGAAGTAGATCGAAGATAGCAG
Found at i:12770358 original size:132 final size:132
Alignment explanation
Indices: 12770129--12770766 Score: 920
Period size: 132 Copynumber: 4.8 Consensus size: 132
12770119 GAAAAAATAA
*
12770129 ATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATATTGGT
1 ATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTATCTTCCTATATTGGT
* *
12770194 AGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAAAAAGC
66 AGGAAGTGGATCGAAGATGCAGATCTTATCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGC
12770259 AG
131 AG
* * * *
12770261 ATCTTGTCTTCATGTATTGGCGTGAAGTAAATCAAAGATAGCAGGTCCTATTTTCCTATATTGGT
1 ATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTATCTTCCTATATTGGT
* * * * *
12770326 AGGAAGTGGATCGAAGATGTAGAGCTTATCTTCCCATATTGGTAGCCAAGTATATCGAAGAAAGC
66 AGGAAGTGGATCGAAGATGCAGATCTTATCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGC
12770391 AG
131 AG
* *
12770393 ATCTTGTCCTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATATTGGT
1 ATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTATCTTCCTATATTGGT
** *
12770458 AGGAAGTGGATCGAAGATGCAGATCTTGGCTTCCGATATTGGTGGCGAAGTAGATCGAAGAAAGC
66 AGGAAGTGGATCGAAGATGCAGATCTTATCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGC
12770523 AG
131 AG
* *
12770525 ATCTTATCTTCATGTATTGGCGAGAAGTAGATCGAAGATAGCAGATCCTATCTTCCTATATTGGT
1 ATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTATCTTCCTATATTGGT
*
12770590 AGGAAGTGGATCGAAGATGCAGATCTTATCTTCCCATATTGGTGGCGAAATAGATCGAAGAAAGC
66 AGGAAGTGGATCGAAGATGCAGATCTTATCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGC
12770655 AG
131 AG
* * * * * * *
12770657 ATCTTGTCTTCATATACTGGTG-GCAAAGTAGATCGAAGAAAGCAGATCTTATCTTCATGTATTG
1 ATCTTGTCTTCATGTATTGGCGTG--AAGTAGATCGAAGATAGCAGATCCTATCTTCCTATATTG
* * * * * **
12770721 G-CGTGAAGTAGATCGAATATAGCAGATCATGTCTTCTTATATTGGT
64 GTAG-GAAGTGGATCGAAGAT-GCAGATCTTATCTTCCCATATTGGT
12770767 AGTAAAGTGG
Statistics
Matches: 453, Mismatches: 49, Indels: 6
0.89 0.10 0.01
Matches are distributed among these distances:
131 1 0.00
132 381 0.84
133 50 0.11
134 21 0.05
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (132 bp):
ATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTATCTTCCTATATTGGT
AGGAAGTGGATCGAAGATGCAGATCTTATCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGC
AG
Found at i:12770694 original size:177 final size:177
Alignment explanation
Indices: 12770373--12770799 Score: 538
Period size: 177 Copynumber: 2.4 Consensus size: 177
12770363 ATTGGTAGCC
* * * * * * * * *
12770373 AAGTATATCGAAGAAAGCAGATCTTGTCCTCATGTATTGG-CGTGAAGTAGATCGAAGATAGCAG
1 AAGTAGATCGAAGATAGCAGATCATATCTTCCTATATTGGTAGTGAAGTGGATCGAAGATAGCAG
* * * * * * * *
12770437 ATCCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGGCTTCCGATATTGGTG
66 ATCTTATCTTCCCATATTGGTAGGAAATAGATCGAAGAAGCAGATCTTGGCTTCAGATACTGGTG
*
12770502 GCGAAGTAGATCGAAGAAAGCAGATCTTATCTTCATGTATTGGCGAG
131 GCAAAGTAGATCGAAGAAAGCAGATCTTATCTTCATGTATTGGCGAG
*
12770549 AAGTAGATCGAAGATAGCAGATCCTATCTTCCTATATTGGTAG-GAAGTGGATCGAAGAT-GCAG
1 AAGTAGATCGAAGATAGCAGATCATATCTTCCTATATTGGTAGTGAAGTGGATCGAAGATAGCAG
* * *
12770612 ATCTTATCTTCCCATATTGGTGGCGAAATAGATCGAAGAAAGCAGATCTTGTCTTCATATACTGG
66 ATCTTATCTTCCCATATTGGTAG-GAAATAGATCGAAG-AAGCAGATCTTGGCTTCAGATACTGG
*
12770677 TGGCAAAGTAGATCGAAGAAAGCAGATCTTATCTTCATGTATTGGCGTG
129 TGGCAAAGTAGATCGAAGAAAGCAGATCTTATCTTCATGTATTGGCGAG
* * * * *
12770726 AAGTAGATCGAATATAGCAGATCATGTCTTCTTATATTGGTAGTAAAGTGGA-CAGAAGATGGCA
1 AAGTAGATCGAAGATAGCAGATCATATCTTCCTATATTGGTAGTGAAGTGGATC-GAAGATAGCA
*
12770790 AATCTTATCT
65 GATCTTATCT
12770800 CCCTGAAGTT
Statistics
Matches: 217, Mismatches: 28, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
175 23 0.11
176 60 0.28
177 109 0.50
178 13 0.06
179 12 0.06
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (177 bp):
AAGTAGATCGAAGATAGCAGATCATATCTTCCTATATTGGTAGTGAAGTGGATCGAAGATAGCAG
ATCTTATCTTCCCATATTGGTAGGAAATAGATCGAAGAAGCAGATCTTGGCTTCAGATACTGGTG
GCAAAGTAGATCGAAGAAAGCAGATCTTATCTTCATGTATTGGCGAG
Found at i:12771170 original size:19 final size:19
Alignment explanation
Indices: 12771146--12771218 Score: 101
Period size: 19 Copynumber: 3.7 Consensus size: 19
12771136 AATCTTCGAG
*
12771146 GATATGTAATCTTAGATAT
1 GATATGCAATCTTAGATAT
12771165 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
12771184 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
* *
12771205 GATACGTAATCTTA
1 GATATGCAATCTTA
12771219 AAAGATATGA
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
19 30 0.61
21 19 0.39
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:12771192 original size:21 final size:21
Alignment explanation
Indices: 12771147--12771208 Score: 101
Period size: 21 Copynumber: 3.0 Consensus size: 21
12771137 ATCTTCGAGG
*
12771147 ATATGTAATCTTAGATATG--
1 ATATGCAATCTTAGATATGAT
12771166 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
12771187 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
12771208 A
1 A
12771209 CGTAATCTTA
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
19 18 0.45
21 22 0.55
ACGTcount: A:0.39, C:0.08, G:0.15, T:0.39
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:12771866 original size:20 final size:22
Alignment explanation
Indices: 12771833--12771890 Score: 77
Period size: 20 Copynumber: 2.8 Consensus size: 22
12771823 TATATATATG
*
12771833 TACATATATATTATACTTTCTA
1 TACATATATATTATAATTTCTA
12771855 TACATAT-T-TTATAATTTCTA
1 TACATATATATTATAATTTCTA
*
12771875 TATATATATA-TATAAT
1 TACATATATATTATAAT
12771891 CATTATCTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 17 0.53
21 8 0.25
22 7 0.22
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.52
Consensus pattern (22 bp):
TACATATATATTATAATTTCTA
Found at i:12771896 original size:100 final size:102
Alignment explanation
Indices: 12771779--12771987 Score: 314
Period size: 100 Copynumber: 2.0 Consensus size: 102
12771769 TTTTTAAGTT
* * * * *
12771779 TATATATGTAATTATTATTTTTATAATTTATATATTTATTACCTTATATATATGTAC-ATATA-T
1 TATATATATAATCATTATCTTTATAATCTATATATTTATTAACTTATATATATGTACGATATAGT
12771842 ATTATACTTTCTATACATATTTTATAATTTCTATATA
66 ATTATACTTTCTATACATATTTTATAATTTCTATATA
*
12771879 TATATATATAATCATTATCTTTATGATCTATATATTTATTAACTTATATATATGTACGTATATAT
1 TATATATATAATCATTATCTTTATAATCTATATATTTATTAACTTATATATATGTACG-ATATA-
* *
12771944 GTATTATACTTTCTATCCATATTTTATAATTTCTATATG
64 GTATTATACTTTCTATACATATTTTATAATTTCTATATA
12771983 TATAT
1 TATAT
12771988 TTTTCTTTAT
Statistics
Matches: 97, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
100 51 0.53
102 5 0.05
104 41 0.42
ACGTcount: A:0.35, C:0.08, G:0.03, T:0.54
Consensus pattern (102 bp):
TATATATATAATCATTATCTTTATAATCTATATATTTATTAACTTATATATATGTACGATATAGT
ATTATACTTTCTATACATATTTTATAATTTCTATATA
Found at i:12771915 original size:52 final size:50
Alignment explanation
Indices: 12771823--12771987 Score: 145
Period size: 52 Copynumber: 3.2 Consensus size: 50
12771813 TTTATTACCT
* * ** * *
12771823 TATATATATGTACATATATATTATACTTTCTATACATATTTTATAATTTC
1 TATATATATATATATATGCATTATACTTTATATCCATATTTTATAATTTC
* * *
12771873 TATATATATATATATAAT-CATTAT-CTTTATGATCTATATATTTATTAACTTA
1 TATATATATATATAT-ATGCATTATACTTTAT-ATCCATAT-TTTA-TAATTTC
* * *
12771925 TATATATGTACGTATATATGTATTATACTTTCTATCCATATTTTATAATTTC
1 TATATATATA--TATATATGCATTATACTTTATATCCATATTTTATAATTTC
*
12771977 TATATGTATAT
1 TATATATATAT
12771988 TTTTCTTTAT
Statistics
Matches: 91, Mismatches: 16, Indels: 16
0.74 0.13 0.13
Matches are distributed among these distances:
49 5 0.05
50 25 0.27
51 6 0.07
52 27 0.30
53 6 0.07
54 17 0.19
55 5 0.05
ACGTcount: A:0.35, C:0.09, G:0.04, T:0.52
Consensus pattern (50 bp):
TATATATATATATATATGCATTATACTTTATATCCATATTTTATAATTTC
Found at i:12771981 original size:54 final size:52
Alignment explanation
Indices: 12771823--12771981 Score: 170
Period size: 50 Copynumber: 3.1 Consensus size: 52
12771813 TTTATTACCT
*
12771823 TATATATATGTAC-ATATA-TATTATACTTTCTATACATATTTTATAATTTC
1 TATATATATGTACTATATATTATTATACTTTCTATCCATATTTTATAATTTC
* * * * *
12771873 TATATATATATA-TATA-ATCATTAT-CTTTATGATCTATATATTTATTAA-CT-
1 TATATATATGTACTATATATTATTATACTTTCT-ATCCATAT-TTTA-TAATTTC
12771923 TATATATATGTACGTATATATGTATTATACTTTCTATCCATATTTTATAATTTC
1 TATATATATGTAC-TATATAT-TATTATACTTTCTATCCATATTTTATAATTTC
12771977 TATAT
1 TATAT
12771982 GTATATTTTT
Statistics
Matches: 86, Mismatches: 11, Indels: 20
0.74 0.09 0.17
Matches are distributed among these distances:
49 6 0.07
50 36 0.42
51 5 0.06
52 10 0.12
53 7 0.08
54 17 0.20
55 5 0.06
ACGTcount: A:0.35, C:0.09, G:0.03, T:0.52
Consensus pattern (52 bp):
TATATATATGTACTATATATTATTATACTTTCTATCCATATTTTATAATTTC
Found at i:12772137 original size:24 final size:24
Alignment explanation
Indices: 12772082--12772137 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
12772072 ATGTACTTTC
* * *
12772082 TTTTCTTTATTTTTTTATATGTTT
1 TTTTATTTATGTTTTCATATGTTT
* * *
12772106 GTTGATTTATGTTTTCATATTTTT
1 TTTTATTTATGTTTTCATATGTTT
12772130 TTTTATTT
1 TTTTATTT
12772138 TGCTCATTTA
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.14, C:0.04, G:0.07, T:0.75
Consensus pattern (24 bp):
TTTTATTTATGTTTTCATATGTTT
Found at i:12781895 original size:9 final size:8
Alignment explanation
Indices: 12781852--12781908 Score: 51
Period size: 8 Copynumber: 6.5 Consensus size: 8
12781842 TTTTTATTAA
*
12781852 AAAATTAT
1 AAAATTTT
*
12781860 AAAATATT
1 AAAATTTT
12781868 AAAATTATAT
1 AAAATT-T-T
12781878 AAAATTTT
1 AAAATTTT
12781886 AAAGATTTT
1 AAA-ATTTT
12781895 ATAAATTTAT
1 A-AAATTT-T
12781905 AAAA
1 AAAA
12781909 AAATAGCTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
8 15 0.37
9 15 0.37
10 11 0.27
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (8 bp):
AAAATTTT
Found at i:12781900 original size:18 final size:18
Alignment explanation
Indices: 12781856--12781908 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
12781846 TATTAAAAAA
*
12781856 TTATAAAATATTAAAATT
1 TTATAAAATTTTAAAATT
*
12781874 ATATAAAATTTTAAAGATT
1 TTATAAAATTTTAAA-ATT
12781893 TTAT-AAATTTATAAAA
1 TTATAAAATTT-TAAAA
12781909 AAATAGCTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 20 0.67
19 10 0.33
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (18 bp):
TTATAAAATTTTAAAATT
Found at i:12782156 original size:9 final size:9
Alignment explanation
Indices: 12782134--12782423 Score: 130
Period size: 9 Copynumber: 30.9 Consensus size: 9
12782124 ATTTTCTCAT
12782134 AAAATTATCAA
1 AAAATTAT--A
12782145 AAAATTATA
1 AAAATTATA
12782154 AAAA--ATA
1 AAAATTATA
*
12782161 ATAAGTTATA
1 A-AAATTATA
*
12782171 AATATTATA
1 AAAATTATA
*
12782180 AAAAATATA
1 AAAATTATA
* *
12782189 CAAATTTTA
1 AAAATTATA
*
12782198 ATAAATT-TT
1 A-AAATTATA
12782207 AAAATTAATA
1 AAAATT-ATA
*
12782217 AAACATATTTA
1 AAA-AT-TATA
*
12782228 AAATTTTATA
1 AAA-ATTATA
*
12782238 AAAACGTATA
1 AAAA-TTATA
*
12782248 AAAATTCTTA
1 AAAATT-ATA
12782258 AAAACTTATA
1 AAAA-TTATA
*
12782268 AAAGATCATA
1 AAA-ATTATA
12782278 AAAATTATA
1 AAAATTATA
*
12782287 AATAATAATA
1 AA-AATTATA
*
12782297 AACATTAT-
1 AAAATTATA
*
12782305 TAAA-TATTA
1 AAAATTA-TA
12782314 AAAA-TATTA
1 AAAATTA-TA
12782323 AAAATTGATA
1 AAAATT-ATA
*
12782333 TAAATTTATA
1 -AAAATTATA
12782343 AAAATTATA
1 AAAATTATA
*
12782352 AAATCTTATA
1 AAA-ATTATA
12782362 AATAA-TATA
1 AA-AATTATA
12782371 AAAATCTA-A
1 AAAAT-TATA
*
12782380 CAAATTAT-
1 AAAATTATA
* *
12782388 AAAATCATT
1 AAAATTATA
* *
12782397 AAAATTGTT
1 AAAATTATA
*
12782406 AAAAGTATA
1 AAAATTATA
12782415 TAAAATTAT
1 -AAAATTAT
12782424 TTTTTTTTAA
Statistics
Matches: 213, Mismatches: 41, Indels: 51
0.70 0.13 0.17
Matches are distributed among these distances:
7 6 0.03
8 20 0.09
9 85 0.40
10 75 0.35
11 26 0.12
12 1 0.00
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (9 bp):
AAAATTATA
Found at i:12782157 original size:20 final size:19
Alignment explanation
Indices: 12782134--12782391 Score: 119
Period size: 19 Copynumber: 13.6 Consensus size: 19
12782124 ATTTTCTCAT
12782134 AAAATTATCAAAAAATTATA
1 AAAATTAT-AAAAAATTATA
* *
12782154 AAAA--ATAATAAGTTATA
1 AAAATTATAAAAAATTATA
*
12782171 AATATTATAAAAAA-TATA
1 AAAATTATAAAAAATTATA
* * * *
12782189 CAAATTTTAATAAATT-TT
1 AAAATTATAAAAAATTATA
12782207 AAAATTAATAAAACATATT-TA
1 AAAATT-ATAAAA-A-ATTATA
* **
12782228 AAATTTTATAAAAACGTATA
1 AAA-ATTATAAAAAATTATA
* *
12782248 AAAATTCTTAAAAACTTATA
1 AAAATT-ATAAAAAATTATA
*
12782268 AAAGATCAT-AAAAATTATA
1 AAA-ATTATAAAAAATTATA
* *
12782287 AATAATAAT-AAACATTAT-
1 AA-AATTATAAAAAATTATA
* *
12782305 TAAA-TATTAAAAA-TATTA
1 AAAATTATAAAAAATTA-TA
* *
12782323 AAAATTGATATAAATTTATA
1 AAAATT-ATAAAAAATTATA
**
12782343 AAAATTATAAAATCTTATA
1 AAAATTATAAAAAATTATA
12782362 AATAA-TAT-AAAAATCTA-A
1 AA-AATTATAAAAAAT-TATA
*
12782380 CAAATTATAAAA
1 AAAATTATAAAA
12782392 TCATTAAAAT
Statistics
Matches: 179, Mismatches: 38, Indels: 43
0.69 0.15 0.17
Matches are distributed among these distances:
16 4 0.02
17 21 0.12
18 35 0.20
19 58 0.32
20 42 0.23
21 17 0.09
22 2 0.01
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (19 bp):
AAAATTATAAAAAATTATA
Found at i:12782344 original size:29 final size:27
Alignment explanation
Indices: 12782282--12782354 Score: 76
Period size: 29 Copynumber: 2.6 Consensus size: 27
12782272 ATCATAAAAA
*
12782282 TTATAAATAATAATAAACATTATTAAAT
1 TTATAAA-AATAATAAAAATTATTAAAT
* *
12782310 AT-TAAAAATATTAAAAATTGATATAAAT
1 TTATAAAAATAATAAAAATT-AT-TAAAT
*
12782338 TTATAAAAATTATAAAA
1 TTATAAAAATAATAAAA
12782355 TCTTATAAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
26 11 0.31
27 6 0.17
28 7 0.19
29 12 0.33
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (27 bp):
TTATAAAAATAATAAAAATTATTAAAT
Found at i:12782393 original size:17 final size:17
Alignment explanation
Indices: 12782344--12782393 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 17
12782334 AAATTTATAA
* *
12782344 AAATTATAAAATCTTAT
1 AAATTATAAAATCTAAC
12782361 AAATAATATAAAAATCTAAC
1 AAAT--TAT-AAAATCTAAC
12782381 AAATTATAAAATC
1 AAATTATAAAATC
12782394 ATTAAAATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
17 10 0.36
18 3 0.11
19 3 0.11
20 12 0.43
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (17 bp):
AAATTATAAAATCTAAC
Found at i:12783475 original size:27 final size:27
Alignment explanation
Indices: 12783445--12783600 Score: 98
Period size: 29 Copynumber: 5.9 Consensus size: 27
12783435 AGTTTATGTT
12783445 TTTTATAAGTTTTTATAATTTATTAT-A
1 TTTTATAAGTTTTTATAATTT-TTATAA
** * *
12783472 TTTT-TTTGTTTTTTTATATTTTTGTAA
1 TTTTATAAGTTTTTATA-ATTTTTATAA
*
12783499 TGTTTATAAGTTTTTATATTTTTTTATAA
1 T-TTTATAAGTTTTTATA-ATTTTTATAA
*
12783528 TTTTTATAAGTTTATATCAA-TTTTA-AA
1 -TTTTATAAGTTTTTAT-AATTTTTATAA
*
12783555 TTTTA-AA--TTTT-TAATATTTAATAA
1 TTTTATAAGTTTTTATAAT-TTTTATAA
* *
12783579 ATTTAT-A-TTTTTATAAATTTTA
1 TTTTATAAGTTTTTATAATTTTTA
12783601 ATGATTTTTA
Statistics
Matches: 101, Mismatches: 16, Indels: 26
0.71 0.11 0.18
Matches are distributed among these distances:
21 2 0.02
22 1 0.01
23 7 0.07
24 7 0.07
25 10 0.10
26 20 0.20
27 12 0.12
28 8 0.08
29 32 0.32
30 2 0.02
ACGTcount: A:0.31, C:0.01, G:0.04, T:0.64
Consensus pattern (27 bp):
TTTTATAAGTTTTTATAATTTTTATAA
Found at i:12783475 original size:29 final size:28
Alignment explanation
Indices: 12783444--12783558 Score: 105
Period size: 29 Copynumber: 4.1 Consensus size: 28
12783434 AAGTTTATGT
12783444 TTTTTATAAGTTTTTATAATTTATTAT-A
1 TTTTTATAAGTTTTTATAATTT-TTATAA
* * *
12783472 TTTTT-T-TGTTTTTTTATATTTTTGTAA
1 TTTTTATAAGTTTTTATA-ATTTTTATAA
* *
12783499 TGTTTATAAGTTTTTATATTTTTTTATAA
1 TTTTTATAAGTTTTTATA-ATTTTTATAA
*
12783528 TTTTTATAAGTTTATATCAA-TTTTA-AA
1 TTTTTATAAGTTTTTAT-AATTTTTATAA
12783555 TTTT
1 TTTT
12783559 AAATTTTTAA
Statistics
Matches: 71, Mismatches: 11, Indels: 11
0.76 0.12 0.12
Matches are distributed among these distances:
26 11 0.15
27 16 0.23
28 11 0.15
29 32 0.45
30 1 0.01
ACGTcount: A:0.27, C:0.01, G:0.05, T:0.67
Consensus pattern (28 bp):
TTTTTATAAGTTTTTATAATTTTTATAA
Found at i:12783493 original size:9 final size:9
Alignment explanation
Indices: 12783437--12783535 Score: 60
Period size: 9 Copynumber: 10.7 Consensus size: 9
12783427 TTTAAAAAAG
*
12783437 TTTATGTTT
1 TTTATATTT
*
12783446 TTTATAAGTT
1 TTTAT-ATTT
12783456 TTTATAATTT
1 TTTAT-ATTT
*
12783466 ATTATATTT
1 TTTATATTT
*
12783475 TTT-TGTTTT
1 TTTAT-ATTT
12783484 TTTATATTT
1 TTTATATTT
*
12783493 TTGTA-A-TG
1 TT-TATATTT
*
12783501 TTTATAAGTT
1 TTTAT-ATTT
12783511 TTTATATTTT
1 TTTATA-TTT
*
12783521 TTTATAATT
1 TTTATATTT
12783530 TTTATA
1 TTTATA
12783536 AGTTTATATC
Statistics
Matches: 71, Mismatches: 11, Indels: 16
0.72 0.11 0.16
Matches are distributed among these distances:
7 2 0.03
8 4 0.06
9 33 0.46
10 32 0.45
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.70
Consensus pattern (9 bp):
TTTATATTT
Found at i:12783536 original size:9 final size:9
Alignment explanation
Indices: 12783444--12783611 Score: 86
Period size: 10 Copynumber: 18.8 Consensus size: 9
12783434 AAGTTTATGT
12783444 TTTTTATAA
1 TTTTTATAA
12783453 GTTTTTATAA
1 -TTTTTATAA
12783463 TTTATTAT-A
1 TTT-TTATAA
**
12783472 TTTTT-TTG
1 TTTTTATAA
*
12783480 TTTTTTTATA
1 TTTTTATA-A
*
12783490 TTTTTGTAA
1 TTTTTATAA
*
12783499 TGTTTATAA
1 TTTTTATAA
*
12783508 GTTTTTATATT
1 -TTTTTATA-A
12783519 TTTTTATAA
1 TTTTTATAA
12783528 TTTTTATAA
1 TTTTTATAA
*
12783537 GTTTATATCAA
1 -TTTTTAT-AA
12783548 -TTTTA-AA
1 TTTTTATAA
12783555 -TTTTA-AA
1 TTTTTATAA
12783562 -TTTT-TAA
1 TTTTTATAA
*
12783569 TATTTAATAA
1 T-TTTTATAA
*
12783579 -ATTTAT-A
1 TTTTTATAA
12783586 TTTTTATAAA
1 TTTTTAT-AA
* *
12783596 TTTTAATGA
1 TTTTTATAA
12783605 TTTTTAT
1 TTTTTAT
12783612 GAGAAAATGT
Statistics
Matches: 125, Mismatches: 18, Indels: 31
0.72 0.10 0.18
Matches are distributed among these distances:
7 17 0.14
8 16 0.13
9 39 0.31
10 51 0.41
11 2 0.02
ACGTcount: A:0.31, C:0.01, G:0.04, T:0.64
Consensus pattern (9 bp):
TTTTTATAA
Found at i:12783541 original size:37 final size:37
Alignment explanation
Indices: 12783443--12783558 Score: 121
Period size: 38 Copynumber: 3.1 Consensus size: 37
12783433 AAAGTTTATG
* *
12783443 TTTTTTATAAGTTTTTATAA-TTTATTATATTTTTTTGT
1 TTTTTTATAA-TTTTTATAAGTTTA-TATATTTTTATAT
*
12783481 TTTTTTAT-ATTTTTGTAATGTTTATA-AGTTTTTATAT
1 TTTTTTATAATTTTTATAA-GTTTATATA-TTTTTATAT
* *
12783518 TTTTTTATAATTTTTATAAGTTTATATCAATTTTAAAT
1 TTTTTTATAATTTTTATAAGTTTATAT-ATTTTTATAT
12783556 TTT
1 TTT
12783559 AAATTTTTAA
Statistics
Matches: 66, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
36 9 0.14
37 25 0.38
38 31 0.47
39 1 0.02
ACGTcount: A:0.27, C:0.01, G:0.05, T:0.67
Consensus pattern (37 bp):
TTTTTTATAATTTTTATAAGTTTATATATTTTTATAT
Found at i:12783931 original size:19 final size:19
Alignment explanation
Indices: 12783866--12783951 Score: 60
Period size: 19 Copynumber: 4.7 Consensus size: 19
12783856 AAAATCGTAT
* *
12783866 AAAACTAATAAAAATCCAT-
1 AAAACTTATAAAAA-CTATA
12783885 AAAACTTATAAATAA-TA-A
1 AAAACTTATAAA-AACTATA
12783903 AAAA--TA-AAAAA-TATA
1 AAAACTTATAAAAACTATA
* *
12783918 ATAAATTTATAAAAACTATT
1 A-AAACTTATAAAAACTATA
12783938 AAAACTTATAAAAA
1 AAAACTTATAAAAA
12783952 ATCATCTAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 16
0.73 0.05 0.21
Matches are distributed among these distances:
14 4 0.07
15 5 0.09
16 5 0.09
18 7 0.13
19 28 0.51
20 6 0.11
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.27
Consensus pattern (19 bp):
AAAACTTATAAAAACTATA
Found at i:12784359 original size:24 final size:24
Alignment explanation
Indices: 12784332--12784382 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
12784322 TTTCGAGCCA
*
12784332 TTTGA-TTTTTTTCTTTTATGTTCT
1 TTTGACTTTCTTTCTTTT-TGTTCT
*
12784356 TTTGACTTTCTTTCTTTTTTTTCT
1 TTTGACTTTCTTTCTTTTTGTTCT
12784380 TTT
1 TTT
12784383 TTTTTCATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 13 0.54
25 11 0.46
ACGTcount: A:0.06, C:0.12, G:0.06, T:0.76
Consensus pattern (24 bp):
TTTGACTTTCTTTCTTTTTGTTCT
Found at i:12785470 original size:85 final size:86
Alignment explanation
Indices: 12785276--12785619 Score: 433
Period size: 89 Copynumber: 3.9 Consensus size: 86
12785266 ACAATGAGGG
* *
12785276 TTTGTAATTTGTGGGGTGAGAATATGCGGATCAAGTTTTATTTTAGTTTCAGCTTTCGCCTTTTT
1 TTTGTAATTTGTAGGGTGAGAATATGCGAATCAAGTTTTATTTTAGTTTCAGCTTTCGCC-TTTT
12785341 CTTTTTTCATAAACATAAATTTTT
65 CTTTTTTCATAAACAT--ATTTTT
12785365 GTTTGTAATTTGTAGGGTGAGAATATGCGAATCAAGTTTTATTTTAGTTTCAGCTTTCGCCTTTT
1 -TTTGTAATTTGTAGGGTGAGAATATGCGAATCAAGTTTTATTTTAGTTTCAGCTTTCGCCTTTT
*
12785430 CTTTTTTCATAAGCAT-TTTTT
65 CTTTTTTCATAAACATATTTTT
* * *
12785451 TTTGTAATTTGTAGGGTGAGAATATGCGAATCAAGTTTTATTTTGGTTTTAGCTTTTGCCTTCTT
1 TTTGTAATTTGTAGGGTGAGAATATGCGAATCAAGTTTTATTTTAGTTTCAGCTTTCGCCTT-TT
*****
12785516 -TTTTTTCATAAACATAAAAAAAAA
65 CTTTTTTCATAAACAT---ATTTTT
* * * * * * *
12785540 ATTGTAATTTGTGGGGTGAGAATATGAGAATCAATTTTTATTTTGGTTTTAGCTTTTGCCTTTTC
1 TTTGTAATTTGTAGGGTGAGAATATGCGAATCAAGTTTTATTTTAGTTTCAGCTTTCGCCTTTTC
12785605 -TTTTTCATAAACATA
66 TTTTTTCATAAACATA
12785620 AAAAAAAATT
Statistics
Matches: 232, Mismatches: 16, Indels: 17
0.88 0.06 0.06
Matches are distributed among these distances:
85 74 0.32
86 7 0.03
88 16 0.07
89 77 0.33
90 58 0.25
ACGTcount: A:0.25, C:0.10, G:0.17, T:0.48
Consensus pattern (86 bp):
TTTGTAATTTGTAGGGTGAGAATATGCGAATCAAGTTTTATTTTAGTTTCAGCTTTCGCCTTTTC
TTTTTTCATAAACATATTTTT
Found at i:12785573 original size:174 final size:174
Alignment explanation
Indices: 12785276--12785614 Score: 491
Period size: 174 Copynumber: 1.9 Consensus size: 174
12785266 ACAATGAGGG
* * *
12785276 TTTGTAATTTGTGGGGTGAGAATATGCGGATCAAGTTTTATTTTAGTTTCAGCTTTCGCCTTTTT
1 TTTGTAATTTGTAGGGTGAGAATATGCGAATCAAGTTTTATTTTAGTTTCAGCTTTCGCCTTCTT
******* *
12785341 CTTTTTTCATAAACATAAATTTTTGTTTGTAATTTGTAGGGTGAGAATATGCGAATCAAGTTTTA
66 CTTTTTTCATAAACATAAAAAAAAAATTGTAATTTGTAGGGTGAGAATATGAGAATCAAGTTTTA
12785406 TTTTAGTTTCAGCTTTCGCCTTTTCTTTTTTCATAAGCATTTTTT
131 TTTTAGTTTCAGCTTTCGCCTTTTC-TTTTTCATAAGCATTTTTT
* * *
12785451 TTTGTAATTTGTAGGGTGAGAATATGCGAATCAAGTTTTATTTTGGTTTTAGCTTTTGCCTTCTT
1 TTTGTAATTTGTAGGGTGAGAATATGCGAATCAAGTTTTATTTTAGTTTCAGCTTTCGCCTTCTT
* *
12785516 -TTTTTTCATAAACATAAAAAAAAAATTGTAATTTGTGGGGTGAGAATATGAGAATCAATTTTTA
66 CTTTTTTCATAAACATAAAAAAAAAATTGTAATTTGTAGGGTGAGAATATGAGAATCAAGTTTTA
* * *
12785580 TTTTGGTTTTAGCTTTTGCCTTTTCTTTTTCATAA
131 TTTTAGTTTCAGCTTTCGCCTTTTCTTTTTCATAA
12785615 ACATAAAAAA
Statistics
Matches: 145, Mismatches: 19, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
173 10 0.07
174 76 0.52
175 59 0.41
ACGTcount: A:0.24, C:0.10, G:0.17, T:0.49
Consensus pattern (174 bp):
TTTGTAATTTGTAGGGTGAGAATATGCGAATCAAGTTTTATTTTAGTTTCAGCTTTCGCCTTCTT
CTTTTTTCATAAACATAAAAAAAAAATTGTAATTTGTAGGGTGAGAATATGAGAATCAAGTTTTA
TTTTAGTTTCAGCTTTCGCCTTTTCTTTTTCATAAGCATTTTTT
Found at i:12785579 original size:89 final size:89
Alignment explanation
Indices: 12785276--12785630 Score: 434
Period size: 85 Copynumber: 4.0 Consensus size: 89
12785266 ACAATGAGGG
* *
12785276 TTTGTAATTTGTGGGGTGAGAATATGCGGATCAAGTTTTATTTTAGTTTCAGCTTTCGCCTTTTT
1 TTTGTAATTTGTAGGGTGAGAATATGCGAATCAAGTTTTATTTTAGTTTCAGCTTTCGCC-TTTT
******
12785341 CTTTTTTCATAAACATAAATTTTTG
65 CTTTTTTCATAAACATAAAAAAAAA
12785366 TTTGTAATTTGTAGGGTGAGAATATGCGAATCAAGTTTTATTTTAGTTTCAGCTTTCGCCTTTTC
1 TTTGTAATTTGTAGGGTGAGAATATGCGAATCAAGTTTTATTTTAGTTTCAGCTTTCGCCTTTTC
* *****
12785431 TTTTTTCATAAGCAT----TTTTT
66 TTTTTTCATAAACATAAAAAAAAA
* * *
12785451 TTTGTAATTTGTAGGGTGAGAATATGCGAATCAAGTTTTATTTTGGTTTTAGCTTTTGCCTTCTT
1 TTTGTAATTTGTAGGGTGAGAATATGCGAATCAAGTTTTATTTTAGTTTCAGCTTTCGCCTT-TT
12785516 -TTTTTTCATAAACATAAAAAAAAA
65 CTTTTTTCATAAACATAAAAAAAAA
* * * * * * *
12785540 ATTGTAATTTGTGGGGTGAGAATATGAGAATCAATTTTTATTTTGGTTTTAGCTTTTGCCTTTTC
1 TTTGTAATTTGTAGGGTGAGAATATGCGAATCAAGTTTTATTTTAGTTTCAGCTTTCGCCTTTTC
12785605 -TTTTTCATAAACATAAAAAAAAA
66 TTTTTTCATAAACATAAAAAAAAA
12785628 TTT
1 TTT
12785631 AACAAATAGA
Statistics
Matches: 241, Mismatches: 18, Indels: 14
0.88 0.07 0.05
Matches are distributed among these distances:
85 77 0.32
86 2 0.01
88 27 0.11
89 77 0.32
90 58 0.24
ACGTcount: A:0.26, C:0.10, G:0.16, T:0.48
Consensus pattern (89 bp):
TTTGTAATTTGTAGGGTGAGAATATGCGAATCAAGTTTTATTTTAGTTTCAGCTTTCGCCTTTTC
TTTTTTCATAAACATAAAAAAAAA
Found at i:12786288 original size:19 final size:18
Alignment explanation
Indices: 12786227--12786292 Score: 64
Period size: 19 Copynumber: 3.6 Consensus size: 18
12786217 CCAAAAAATG
12786227 AATTTTTATATATTTT-AT
1 AATTTTTATA-ATTTTAAT
* *
12786245 AA-TTTTAAAATTTTATTT
1 AATTTTTATAATTTTA-AT
*
12786263 AAGTTTTATAATTATTAAT
1 AATTTTTATAATT-TTAAT
12786282 AATTTTTATAA
1 AATTTTTATAA
12786293 ATTGTTTAGA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
16 5 0.13
17 6 0.15
18 5 0.13
19 20 0.51
20 3 0.08
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (18 bp):
AATTTTTATAATTTTAAT
Found at i:12786295 original size:10 final size:10
Alignment explanation
Indices: 12786227--12786390 Score: 53
Period size: 10 Copynumber: 16.8 Consensus size: 10
12786217 CCAAAAAATG
12786227 AATTTTTATA
1 AATTTTTATA
*
12786237 TA-TTTTAT-
1 AATTTTTATA
12786245 AA-TTTTA-A
1 AATTTTTATA
*
12786253 AA-TTTTATTT
1 AATTTTTA-TA
*
12786263 AAGTTTTAT-
1 AATTTTTATA
*
12786272 AATTATTA-A
1 AATTTTTATA
12786281 TAATTTTTATA
1 -AATTTTTATA
*
12786292 AATTGTT-TA
1 AATTTTTATA
* *
12786301 GATTTTTTTA
1 AATTTTTATA
*
12786311 CAATTTTTTTA
1 -AATTTTTATA
12786322 TAATTTTTAT-
1 -AATTTTTATA
** *
12786332 GTTTTTTTTCA
1 AATTTTTAT-A
12786343 TAATTTTTATA
1 -AATTTTTATA
* *
12786354 AGTTTATATA
1 AATTTTTATA
*
12786364 AACTTTTA-A
1 AATTTTTATA
*
12786373 TATTTTT-TA
1 AATTTTTATA
12786382 TAATTTTTA
1 -AATTTTTA
12786391 ATTTTTTAAT
Statistics
Matches: 113, Mismatches: 26, Indels: 29
0.67 0.15 0.17
Matches are distributed among these distances:
8 13 0.12
9 32 0.28
10 38 0.34
11 24 0.21
12 6 0.05
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (10 bp):
AATTTTTATA
Found at i:12786316 original size:30 final size:31
Alignment explanation
Indices: 12786282--12786354 Score: 87
Period size: 30 Copynumber: 2.4 Consensus size: 31
12786272 AATTATTAAT
12786282 AATTTTTATAAATTGTTTA-GATTTTTTT-AC
1 AATTTTTATAAATT-TTTATGATTTTTTTCAC
* * *
12786312 AATTTTTTTATAATTTTTATGTTTTTTTTCAT
1 AATTTTTATA-AATTTTTATGATTTTTTTCAC
12786344 AATTTTTATAA
1 AATTTTTATAA
12786355 GTTTATATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
30 13 0.36
31 13 0.36
32 10 0.28
ACGTcount: A:0.29, C:0.03, G:0.04, T:0.64
Consensus pattern (31 bp):
AATTTTTATAAATTTTTATGATTTTTTTCAC
Found at i:12786322 original size:32 final size:32
Alignment explanation
Indices: 12786284--12786350 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 32
12786274 TTATTAATAA
12786284 TTTTTATAAATTGTTTA-GATTTTTTT-ACAATT
1 TTTTTAT-AATT-TTTATGATTTTTTTCACAATT
* *
12786316 TTTTTATAATTTTTATGTTTTTTTTCATAATT
1 TTTTTATAATTTTTATGATTTTTTTCACAATT
12786348 TTT
1 TTT
12786351 ATAAGTTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 4 0.13
31 12 0.39
32 15 0.48
ACGTcount: A:0.24, C:0.03, G:0.04, T:0.69
Consensus pattern (32 bp):
TTTTTATAATTTTTATGATTTTTTTCACAATT
Found at i:12786328 original size:9 final size:9
Alignment explanation
Indices: 12786227--12786408 Score: 84
Period size: 9 Copynumber: 19.0 Consensus size: 9
12786217 CCAAAAAATG
12786227 AATTTTTAT
1 AATTTTTAT
12786236 -ATATTTTAT
1 AAT-TTTTAT
*
12786245 AA-TTTTAA
1 AATTTTTAT
*
12786253 AATTTTATTT
1 AATTTT-TAT
*
12786263 AAGTTTTAT
1 AATTTTTAT
*
12786272 AATTATTAAT
1 AATT-TTTAT
12786282 AATTTTTAT
1 AATTTTTAT
*
12786291 AAATTGTTTAG
1 -AATT-TTTAT
* *
12786302 ATTTTTTTAC
1 A-ATTTTTAT
12786312 AATTTTTTTAT
1 AA--TTTTTAT
12786323 AATTTTTATGT
1 AATTTTTA--T
**
12786334 TTTTTTTCAT
1 AATTTTT-AT
12786344 AATTTTTAT
1 AATTTTTAT
*
12786353 AAGTTTATAT
1 AA-TTTTTAT
*
12786363 AAACTTTTAAT
1 -AA-TTTTTAT
*
12786374 ATTTTTTAT
1 AATTTTTAT
12786383 AATTTTTA-
1 AATTTTTAT
*
12786391 ATTTTTTA-
1 AATTTTTAT
12786399 ATATTTTTAT
1 A-ATTTTTAT
12786409 GAGAAAAAAT
Statistics
Matches: 130, Mismatches: 26, Indels: 33
0.69 0.14 0.17
Matches are distributed among these distances:
8 17 0.13
9 47 0.36
10 38 0.29
11 27 0.21
12 1 0.01
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (9 bp):
AATTTTTAT
Found at i:12797298 original size:24 final size:24
Alignment explanation
Indices: 12797278--12797370 Score: 91
Period size: 24 Copynumber: 3.9 Consensus size: 24
12797268 AAGATTTAGT
* *
12797278 ATTTATGAGTATAATATATTTAAC
1 ATTTATTAATATAATATATTTAAC
* * **
12797302 ATTTATTAATATGGA-AGATTTAGT
1 ATTTATTAATAT-AATATATTTAAC
12797326 ATTTA-TAAGTATAATATATTTAAC
1 ATTTATTAA-TATAATATATTTAAC
*
12797350 ATTTATTAATGTAATATATTT
1 ATTTATTAATATAATATATTT
12797371 GACTTTGATT
Statistics
Matches: 54, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
23 4 0.07
24 46 0.85
25 4 0.07
ACGTcount: A:0.41, C:0.02, G:0.09, T:0.48
Consensus pattern (24 bp):
ATTTATTAATATAATATATTTAAC
Found at i:12797338 original size:48 final size:48
Alignment explanation
Indices: 12797267--12797359 Score: 177
Period size: 48 Copynumber: 1.9 Consensus size: 48
12797257 ATTCTTTCTT
*
12797267 GAAGATTTAGTATTTATGAGTATAATATATTTAACATTTATTAATATG
1 GAAGATTTAGTATTTATAAGTATAATATATTTAACATTTATTAATATG
12797315 GAAGATTTAGTATTTATAAGTATAATATATTTAACATTTATTAAT
1 GAAGATTTAGTATTTATAAGTATAATATATTTAACATTTATTAAT
12797360 GTAATATATT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.41, C:0.02, G:0.11, T:0.46
Consensus pattern (48 bp):
GAAGATTTAGTATTTATAAGTATAATATATTTAACATTTATTAATATG
Found at i:12799204 original size:17 final size:16
Alignment explanation
Indices: 12799169--12799206 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
12799159 AAATAACCTC
12799169 ATATAAAATGTAAAGT
1 ATATAAAATGTAAAGT
12799185 ATATAAATATGTACAA-T
1 ATATAAA-ATGTA-AAGT
12799202 ATATA
1 ATATA
12799207 TATACCATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 7 0.35
17 11 0.55
18 2 0.10
ACGTcount: A:0.55, C:0.03, G:0.08, T:0.34
Consensus pattern (16 bp):
ATATAAAATGTAAAGT
Found at i:12808304 original size:21 final size:21
Alignment explanation
Indices: 12808278--12808318 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
12808268 GAATAGGGCA
* *
12808278 GATGATGATATGGCTGATGAG
1 GATGATGACATGGCGGATGAG
12808299 GATGATGACATGGCGGATGA
1 GATGATGACATGGCGGATGA
12808319 TGGGGAGGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.07, G:0.39, T:0.24
Consensus pattern (21 bp):
GATGATGACATGGCGGATGAG
Found at i:12808328 original size:12 final size:12
Alignment explanation
Indices: 12808313--12808360 Score: 60
Period size: 12 Copynumber: 4.0 Consensus size: 12
12808303 ATGACATGGC
*
12808313 GGATGATGGGGA
1 GGATGATGAGGA
12808325 GGATGATGAGGA
1 GGATGATGAGGA
* *
12808337 TGATGATGAGGG
1 GGATGATGAGGA
*
12808349 GGAGGATGAGGA
1 GGATGATGAGGA
12808361 TGAGGATATA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.54, T:0.17
Consensus pattern (12 bp):
GGATGATGAGGA
Found at i:12808341 original size:24 final size:24
Alignment explanation
Indices: 12808314--12808363 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
12808304 TGACATGGCG
*
12808314 GATGATG-GGGAGGATGATGAGGAT
1 GATGATGAGGG-GGAGGATGAGGAT
12808338 GATGATGAGGGGGAGGATGAGGAT
1 GATGATGAGGGGGAGGATGAGGAT
12808362 GA
1 GA
12808364 GGATATAGCT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 21 0.88
25 3 0.12
ACGTcount: A:0.30, C:0.00, G:0.52, T:0.18
Consensus pattern (24 bp):
GATGATGAGGGGGAGGATGAGGAT
Found at i:12808359 original size:6 final size:6
Alignment explanation
Indices: 12808329--12808367 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
12808319 TGGGGAGGAT
* **
12808329 GATGAG GATGAT GATGAG GGGGAG GATGAG GATGAG GAT
1 GATGAG GATGAG GATGAG GATGAG GATGAG GATGAG GAT
12808368 ATAGCTGAAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.51, T:0.18
Consensus pattern (6 bp):
GATGAG
Found at i:12815592 original size:3 final size:3
Alignment explanation
Indices: 12815586--12815612 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
12815576 GAAAGAAAAA
12815586 AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG
12815613 CTGCCAAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:12815958 original size:30 final size:35
Alignment explanation
Indices: 12815922--12815989 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 35
12815912 TATAACTTTT
12815922 AAAAATTAAA-T-TAAAATT-TTATTA-T-ATTTA
1 AAAAATTAAAGTATAAAATTATTATTATTAATTTA
*
12815952 AAAAATTAAAGTATAAAATTATTTTTATTAATTTA
1 AAAAATTAAAGTATAAAATTATTATTATTAATTTA
12815987 AAA
1 AAA
12815990 TTTTAAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
30 10 0.31
31 1 0.03
32 7 0.22
33 5 0.16
34 1 0.03
35 8 0.25
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (35 bp):
AAAAATTAAAGTATAAAATTATTATTATTAATTTA
Found at i:12819755 original size:41 final size:41
Alignment explanation
Indices: 12819682--12819791 Score: 157
Period size: 41 Copynumber: 2.6 Consensus size: 41
12819672 NNNNNNAAAT
** *
12819682 CTAGCAGGCTAAGTGCCCGGTGATCGGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTG-CCGGTGATATGAATCAGGCTATAAAC
* *
12819724 CTAGCAGGCTACGTGCCGGTGATATGAATCAGGCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGATATGAATCAGGCTATAAAC
12819765 CTAGCAGGCTAAGTGCCGGTGAATATG
1 CTAGCAGGCTAAGTGCCGGTG-ATATG
12819792 TTAAATTATG
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
41 42 0.69
42 19 0.31
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.22
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCGGTGATATGAATCAGGCTATAAAC
Found at i:12823053 original size:41 final size:42
Alignment explanation
Indices: 12822937--12823053 Score: 132
Period size: 41 Copynumber: 2.8 Consensus size: 42
12822927 TTGCATAAAA
* *
12822937 CACCAGCATAAAGCCTGCTAGGCACAAAGCCTG-ATACATTT
1 CACCGGCATAAAGCCTGCTAGGCATAAAGCCTGAATACATTT
* * *
12822978 CACCGGCATAAAGCCTGCTAGACATCAAGTCTGAATTA-A-TT
1 CACCGGCATAAAGCCTGCTAGGCATAAAGCCTGAA-TACATTT
* * *
12823019 CACCGGCATCAAGCCTGCTAGGCATTAGGCCTGAA
1 CACCGGCATAAAGCCTGCTAGGCATAAAGCCTGAA
12823054 AATCTCAGAT
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
41 60 0.94
42 2 0.03
43 2 0.03
ACGTcount: A:0.32, C:0.28, G:0.20, T:0.21
Consensus pattern (42 bp):
CACCGGCATAAAGCCTGCTAGGCATAAAGCCTGAATACATTT
Found at i:12829899 original size:2 final size:2
Alignment explanation
Indices: 12829892--12829941 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
12829882 AATAAGCATG
12829892 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
12829934 TA TA TA TA
1 TA TA TA TA
12829942 GTAATACGTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12830736 original size:41 final size:41
Alignment explanation
Indices: 12830682--12830793 Score: 170
Period size: 41 Copynumber: 2.7 Consensus size: 41
12830672 ATTTTTCAAA
* *
12830682 CTATAAATCTAGCAGGCTAAGTGCCGGTGATCGGAATCAGG
1 CTATAAACCTAGCAGGCTAAGTGCCGGTGATAGGAATCAGG
* * *
12830723 TTATAAACCTAGCAGGCTACGTGCCGGTGATATGAATCAGG
1 CTATAAACCTAGCAGGCTAAGTGCCGGTGATAGGAATCAGG
*
12830764 CTATAAGCCTAGCAGGCTAAGTGCCGGTGA
1 CTATAAACCTAGCAGGCTAAGTGCCGGTGA
12830794 ATATGTTAAA
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 63 1.00
ACGTcount: A:0.29, C:0.21, G:0.29, T:0.22
Consensus pattern (41 bp):
CTATAAACCTAGCAGGCTAAGTGCCGGTGATAGGAATCAGG
Done.