Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 127 of 279
Found at i:40414517 original size:73 final size:71
Alignment explanation
Indices: 40414382--40414517 Score: 227
Period size: 73 Copynumber: 1.9 Consensus size: 71
40414372 TATCTTCAGT
* * *
40414382 GTTATATTTATTTTGATTTTTATCTCTAAGTCAAAGCTTTTTTTGACTTAAAATGTTTTCTTTTT
1 GTTATATTTATTTTGATTTTTATCTCTAAGCCAAACCTTTTTTTGACTTAAAATGTTGTCTTTTT
40414447 TTGGCA
66 TTGGCA
40414453 GTTATATTTATTTTGATTTTTGATCTCTAAGCCAAACCTTTCTTTTGACTTAAAATGTTGTCTTT
1 GTTATATTTATTTTGATTTTT-ATCTCTAAGCCAAACCTTT-TTTTGACTTAAAATGTTGTCTTT
40414518 AGTTTTTGGT
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
71 21 0.35
72 17 0.28
73 22 0.37
ACGTcount: A:0.23, C:0.12, G:0.11, T:0.54
Consensus pattern (71 bp):
GTTATATTTATTTTGATTTTTATCTCTAAGCCAAACCTTTTTTTGACTTAAAATGTTGTCTTTTT
TTGGCA
Found at i:40416863 original size:12 final size:12
Alignment explanation
Indices: 40416846--40416872 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
40416836 GAAAGAAAAT
40416846 GGGGTGTTTCTC
1 GGGGTGTTTCTC
40416858 GGGGTGTTTCTC
1 GGGGTGTTTCTC
40416870 GGG
1 GGG
40416873 CTTCGACGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.15, G:0.48, T:0.37
Consensus pattern (12 bp):
GGGGTGTTTCTC
Found at i:40424127 original size:17 final size:16
Alignment explanation
Indices: 40424107--40424142 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
40424097 AAGAACAATT
*
40424107 AACAAAAATGAACTAGA
1 AACAAAAATAAACTA-A
40424124 AACAAAAATAAACTAA
1 AACAAAAATAAACTAA
40424140 AAC
1 AAC
40424143 TAATATTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.69, C:0.14, G:0.06, T:0.11
Consensus pattern (16 bp):
AACAAAAATAAACTAA
Found at i:40426973 original size:52 final size:48
Alignment explanation
Indices: 40426954--40427156 Score: 265
Period size: 46 Copynumber: 4.3 Consensus size: 48
40426944 TGACAAGTGG
* *
40426954 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
40427000 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGA
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC-A---A
* *
40427052 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
** *
40427098 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
40427144 AAAGTGATAAGTG
1 AAAGTGATAAGTG
40427157 GCTACACTTA
Statistics
Matches: 144, Mismatches: 7, Indels: 12
0.88 0.04 0.07
Matches are distributed among these distances:
46 100 0.69
52 44 0.31
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (48 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
Found at i:40427008 original size:98 final size:98
Alignment explanation
Indices: 40426888--40427156 Score: 457
Period size: 98 Copynumber: 2.7 Consensus size: 98
40426878 TTTGAGTACT
*
40426888 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
40426953 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
**
40426986 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
40427051 AAAAGTGATAAGTGATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
* *
40427084 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGAC-AAGT
*
40427149 GATAAGTG
65 GAAAAGTG
40427157 GCTACACTTA
Statistics
Matches: 160, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
98 149 0.93
99 11 0.07
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.28
Consensus pattern (98 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
Found at i:40427164 original size:37 final size:37
Alignment explanation
Indices: 40427120--40427265 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
40427110 GATAGCTTTA
*
40427120 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
40427157 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
40427194 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
40427231 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
40427266 ATCATACGTA
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 11 0.11
36 4 0.04
37 89 0.86
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:40430039 original size:21 final size:22
Alignment explanation
Indices: 40430007--40430060 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 22
40429997 GCTTCTGTTT
*
40430007 AACTC-ATATGAGATTCCGTTC
1 AACTCTATATGAGATTCCGTTA
* *
40430028 AACTCTAT-TGAGCTTCTGTTA
1 AACTCTATATGAGATTCCGTTA
40430049 AACTCT-TATGAG
1 AACTCTATATGAG
40430061 TTTTCGTTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 1 0.04
21 25 0.89
22 2 0.07
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (22 bp):
AACTCTATATGAGATTCCGTTA
Found at i:40430059 original size:42 final size:42
Alignment explanation
Indices: 40429995--40430075 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
40429985 TAGCTCTTAC
*
40429995 GAGCTTCTGTTTAACTCATATGAGATTCCGTTCAACTCTATT
1 GAGCTTCTGTTAAACTCATATGAGATTCCGTTCAACTCTATT
* * * *
40430037 GAGCTTCTGTTAAACTCTTATGAGTTTTCGTTCAGCTCT
1 GAGCTTCTGTTAAACTCATATGAGATTCCGTTCAACTCT
40430076 TACAAGTTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.21, C:0.21, G:0.16, T:0.42
Consensus pattern (42 bp):
GAGCTTCTGTTAAACTCATATGAGATTCCGTTCAACTCTATT
Found at i:40430117 original size:21 final size:21
Alignment explanation
Indices: 40430093--40430168 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 21
40430083 TTATGTTTAA
*
40430093 CTTCTGTTTAGCTCTTATAAG
1 CTTCTGTTCAGCTCTTATAAG
* *
40430114 CTTCTATTCAACTCTTA-AGAG
1 CTTCTGTTCAGCTCTTATA-AG
* * * *
40430135 TTTCTGTTAAGCTATTATGAG
1 CTTCTGTTCAGCTCTTATAAG
40430156 CTTCTGTTCAGCT
1 CTTCTGTTCAGCT
40430169 TGCGAGCTTC
Statistics
Matches: 42, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
20 1 0.02
21 41 0.98
ACGTcount: A:0.21, C:0.20, G:0.14, T:0.45
Consensus pattern (21 bp):
CTTCTGTTCAGCTCTTATAAG
Found at i:40440344 original size:29 final size:28
Alignment explanation
Indices: 40440295--40440358 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 28
40440285 AAATTACATT
* *
40440295 AAAAATAAAGAAGAGA-GAAAAACATAGA
1 AAAAAAAAAGAAGAGACAAAAAACATA-A
40440323 GAAAAAAAAAGAA-AGTACAAAAAACATAA
1 -AAAAAAAAAGAAGAG-ACAAAAAACATAA
40440352 AAAAAAA
1 AAAAAAA
40440359 GTTAAATTGC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
28 9 0.29
29 13 0.42
30 9 0.29
ACGTcount: A:0.77, C:0.05, G:0.12, T:0.06
Consensus pattern (28 bp):
AAAAAAAAAGAAGAGACAAAAAACATAA
Found at i:40457859 original size:129 final size:128
Alignment explanation
Indices: 40457624--40457859 Score: 339
Period size: 129 Copynumber: 1.8 Consensus size: 128
40457614 NNNNNNNNNN
40457624 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGAACACGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGAACACGCTGAGGTAATTTCAATTTCT
* *
40457689 GTTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTACTTTTTC
66 GTTGTTTT-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTTTTAATTTCTACTTTTTC
* * * ** * *
40457753 AAAATCAGCTCATATTGCTAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGAACACGCTGAGGTAATTTCAA-TTTC
**
40457818 TGTGTGTTTT-AATTTCAACTCATATTGCGAGAGGTGAGTTGA
65 TGT-TGTTTTAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
40457860 GCCTCGGGTC
Statistics
Matches: 94, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
129 83 0.88
130 6 0.06
131 5 0.05
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.36
Consensus pattern (128 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGAACACGCTGAGGTAATTTCAATTTCT
GTTGTTTTAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTTTTAATTTCTACTTTTTC
Found at i:40459145 original size:10 final size:10
Alignment explanation
Indices: 40459132--40459190 Score: 91
Period size: 10 Copynumber: 5.7 Consensus size: 10
40459122 TCGATTTCCA
40459132 TATACATATC
1 TATACATATC
40459142 TATACATATC
1 TATACATATC
*
40459152 TATACATTTCC
1 TATACATAT-C
40459163 ATATACATATC
1 -TATACATATC
40459174 TATACATATC
1 TATACATATC
40459184 TATACAT
1 TATACAT
40459191 TTTCTTTCAT
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
10 35 0.78
11 2 0.04
12 8 0.18
ACGTcount: A:0.39, C:0.20, G:0.00, T:0.41
Consensus pattern (10 bp):
TATACATATC
Found at i:40459166 original size:32 final size:32
Alignment explanation
Indices: 40459125--40459192 Score: 136
Period size: 32 Copynumber: 2.1 Consensus size: 32
40459115 TTTTCTTTCG
40459125 ATTTCCATATACATATCTATACATATCTATAC
1 ATTTCCATATACATATCTATACATATCTATAC
40459157 ATTTCCATATACATATCTATACATATCTATAC
1 ATTTCCATATACATATCTATACATATCTATAC
40459189 ATTT
1 ATTT
40459193 TCTTTCATCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.37, C:0.21, G:0.00, T:0.43
Consensus pattern (32 bp):
ATTTCCATATACATATCTATACATATCTATAC
Found at i:40461370 original size:30 final size:31
Alignment explanation
Indices: 40461336--40461395 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
40461326 AGATAAAAGA
40461336 GTCACTTAAC-TT-TAGAAAAATGACAAATCG
1 GTCAC-TAACATTATAGAAAAATGACAAATCG
* *
40461366 GTCACTAACATTATCGAAAAGTGACAAATC
1 GTCACTAACATTATAGAAAAATGACAAATC
40461396 AGCTGCCCAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 4 0.15
30 7 0.27
31 15 0.58
ACGTcount: A:0.43, C:0.18, G:0.13, T:0.25
Consensus pattern (31 bp):
GTCACTAACATTATAGAAAAATGACAAATCG
Found at i:40473575 original size:24 final size:24
Alignment explanation
Indices: 40473548--40473599 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
40473538 TTAGTAAGTC
*
40473548 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
40473572 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
40473596 AAAT
1 AAAT
40473600 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:40475545 original size:24 final size:24
Alignment explanation
Indices: 40475518--40475569 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
40475508 TTAGTAAGTC
*
40475518 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
40475542 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
40475566 AAAT
1 AAAT
40475570 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:40501334 original size:6 final size:6
Alignment explanation
Indices: 40501323--40501357 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
40501313 AAAAACCTAG
*
40501323 AAAGAA AAAGAA AAA-AA AAAGAA AAAGAA ATAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
40501358 GAATTCAGCC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (6 bp):
AAAGAA
Found at i:40515210 original size:6 final size:6
Alignment explanation
Indices: 40515201--40515231 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
40515191 CCGAAGCCGG
*
40515201 AACAGT AACAGT AACAGT AACAGT AGCAGT A
1 AACAGT AACAGT AACAGT AACAGT AACAGT A
40515232 CGGTACACAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.48, C:0.16, G:0.19, T:0.16
Consensus pattern (6 bp):
AACAGT
Found at i:40515274 original size:53 final size:53
Alignment explanation
Indices: 40515216--40515333 Score: 175
Period size: 53 Copynumber: 2.2 Consensus size: 53
40515206 TAACAGTAAC
* * *
40515216 AGTAACAGTAGCAGTACGGTACACAGAGTACCTCATAGGAACAAATCTAGAAT
1 AGTAACAATAACAGTACGATACACAGAGTACCTCATAGGAACAAATCTAGAAT
* *
40515269 AGTAACAATAACAGTACGATACACAGAGTACCTCATCGGAACAAATCT-GAAAC
1 AGTAACAATAACAGTACGATACACAGAGTACCTCATAGGAACAAATCTAG-AAT
40515322 AGTAACAATAAC
1 AGTAACAATAAC
40515334 GGTAACAGCA
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
52 1 0.02
53 58 0.98
ACGTcount: A:0.45, C:0.20, G:0.17, T:0.18
Consensus pattern (53 bp):
AGTAACAATAACAGTACGATACACAGAGTACCTCATAGGAACAAATCTAGAAT
Found at i:40516464 original size:21 final size:24
Alignment explanation
Indices: 40516426--40516502 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 24
40516416 TTCTTTAGTT
*
40516426 TATATATATATATATAAAATATAA
1 TATATATATATATATAAAACATAA
40516450 TATA-ATATA-AT-TAAAACATAA
1 TATATATATATATATAAAACATAA
* * * *
40516471 AATATCTTTATTATATAATAATATAA
1 TATATATATA-TATATAA-AACATAA
40516497 TA-ATAT
1 TATATAT
40516503 GCTAAACATA
Statistics
Matches: 41, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
21 12 0.29
22 5 0.12
23 5 0.12
24 6 0.15
25 6 0.15
26 7 0.17
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (24 bp):
TATATATATATATATAAAACATAA
Found at i:40526309 original size:61 final size:61
Alignment explanation
Indices: 40526200--40526317 Score: 164
Period size: 61 Copynumber: 1.9 Consensus size: 61
40526190 AAATGATTTT
* * ** * *
40526200 AAATTTTTAGAGTTAGGACTAAATTGACAGGTTTTGTAAGTATGGAGGGCCAAATTTATTA
1 AAATTTTTAGAGTTAGAACTAAAATGACAAATTTTATAAGCATGGAGGGCCAAATTTATTA
* *
40526261 AAATTTTTAGAGTTAGAACTAAAATGACAAATTTTATAAGCATTGAGGGCTAAATTT
1 AAATTTTTAGAGTTAGAACTAAAATGACAAATTTTATAAGCATGGAGGGCCAAATTT
40526318 GTTGAATTTT
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 49 1.00
ACGTcount: A:0.38, C:0.07, G:0.19, T:0.36
Consensus pattern (61 bp):
AAATTTTTAGAGTTAGAACTAAAATGACAAATTTTATAAGCATGGAGGGCCAAATTTATTA
Found at i:40527627 original size:42 final size:42
Alignment explanation
Indices: 40527568--40527653 Score: 154
Period size: 42 Copynumber: 2.0 Consensus size: 42
40527558 GCCCGACCCG
40527568 TATCCAAAGAAGGATCCGCGCACTTCCCATCATTGGGATATT
1 TATCCAAAGAAGGATCCGCGCACTTCCCATCATTGGGATATT
* *
40527610 TATCCAAGGAAGGATCCGCGCACTTCCCATTATTGGGATATT
1 TATCCAAAGAAGGATCCGCGCACTTCCCATCATTGGGATATT
40527652 TA
1 TA
40527654 CGCGTTGGGT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (42 bp):
TATCCAAAGAAGGATCCGCGCACTTCCCATCATTGGGATATT
Found at i:40528037 original size:29 final size:29
Alignment explanation
Indices: 40528004--40528061 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
40527994 CGCTTGTATA
40528004 ATATTGTATTCGTATTGTATTATTCTATG
1 ATATTGTATTCGTATTGTATTATTCTATG
40528033 ATATTGTATTCGTATTGTATTATTCTATG
1 ATATTGTATTCGTATTGTATTATTCTATG
40528062 CTCTATGTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.24, C:0.07, G:0.14, T:0.55
Consensus pattern (29 bp):
ATATTGTATTCGTATTGTATTATTCTATG
Found at i:40532193 original size:38 final size:39
Alignment explanation
Indices: 40532109--40532243 Score: 116
Period size: 39 Copynumber: 3.4 Consensus size: 39
40532099 ACCAATATGG
*
40532109 CACCCAGTGCCTCATCGGATAGTTCGAAGTAATAGTTGA
1 CACCCAGTGCCTCATCGGATAGTCCGAAGTAATAGTTGA
* * *
40532148 CACCCAGTGTCTCATCGGCCTAG-CCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-ATAGTCCGAAGTAATAGTTGA
* * * *
40532186 TACCCAGTACCTCATCGAATCTA-TCCGAAGAAATA-TAGTGA
1 CACCCAGTGCCTCATCGGA--TAGTCCGAAGTAATAGT--TGA
*
40532227 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
40532244 ACTCGAGGTC
Statistics
Matches: 75, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
38 19 0.25
39 36 0.48
40 4 0.05
41 16 0.21
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGGATAGTCCGAAGTAATAGTTGA
Found at i:40542024 original size:89 final size:89
Alignment explanation
Indices: 40541859--40542059 Score: 242
Period size: 89 Copynumber: 2.3 Consensus size: 89
40541849 CTACGAATTT
* *
40541859 TGGCAAATCTTATCTTCCTGAAGTAGCAGTGAAGCGGATCAAAGCCACTAACCTTATCTCCTTGA
1 TGGCAAATCTTATCTTCCTGAAGTAGCAGTGAAGCAGATCAAAGCCACTAACCTTATCTCCTCGA
* *
40541924 AGTTGCAATGGAATAGACTGAAGA
66 AGATACAATGGAATAGACTGAAGA
* * * * *
40541948 TGGCGAATCTTGTCTTCCTGAAGTTGCAGTGAAGTAGATCGAAGCCACTAACCTTATCTCCTCGA
1 TGGCAAATCTTATCTTCCTGAAGTAGCAGTGAAGCAGATCAAAGCCACTAACCTTATCTCCTCGA
* * **
40542013 AGATACGATGGAGTAGGTTGAAG-
66 AGATACAATGGAATAGACTGAAGA
** * *
40542036 TTACAAATCTTATCTCCCTAAAGT
1 TGGCAAATCTTATCTTCCTGAAGT
40542060 TGTAGCGGGG
Statistics
Matches: 93, Mismatches: 19, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
88 18 0.19
89 75 0.81
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.28
Consensus pattern (89 bp):
TGGCAAATCTTATCTTCCTGAAGTAGCAGTGAAGCAGATCAAAGCCACTAACCTTATCTCCTCGA
AGATACAATGGAATAGACTGAAGA
Found at i:40542198 original size:41 final size:41
Alignment explanation
Indices: 40542141--40542292 Score: 259
Period size: 41 Copynumber: 3.7 Consensus size: 41
40542131 ATTACAAATA
*
40542141 TTATCTCTCTGAAGTTGCAGTAGAGCAGATCAAAACAAGTC
1 TTATCTCTCTGAAGTTGCAGTAGAGCAGATCAAAATAAGTC
40542182 TTATCTCTCTGAAGTTGCAGTAGAGCAGATCAAAATAAGTC
1 TTATCTCTCTGAAGTTGCAGTAGAGCAGATCAAAATAAGTC
* *
40542223 TTATCTTTCTGAAGTTGCAGTAGAGCAAATCAAAATAAGTC
1 TTATCTCTCTGAAGTTGCAGTAGAGCAGATCAAAATAAGTC
* *
40542264 TTATCTCCCTGAAGTTGCAGTAGAACAGA
1 TTATCTCTCTGAAGTTGCAGTAGAGCAGA
40542293 CTGGAGATGG
Statistics
Matches: 104, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 104 1.00
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (41 bp):
TTATCTCTCTGAAGTTGCAGTAGAGCAGATCAAAATAAGTC
Found at i:40543156 original size:10 final size:9
Alignment explanation
Indices: 40543115--40543156 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
40543105 AGTTTCATTC
40543115 TCTTTTTTT
1 TCTTTTTTT
40543124 CTCTTTTTTT
1 -TCTTTTTTT
*
40543134 TCTTTATTT
1 TCTTTTTTT
*
40543143 T-TTTATTT
1 TCTTTTTTT
40543151 TCTTTT
1 TCTTTT
40543157 CTTCTAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
8 8 0.28
9 12 0.41
10 9 0.31
ACGTcount: A:0.05, C:0.12, G:0.00, T:0.83
Consensus pattern (9 bp):
TCTTTTTTT
Found at i:40543156 original size:22 final size:23
Alignment explanation
Indices: 40543117--40543159 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
40543107 TTTCATTCTC
* *
40543117 TTTTTTTCTCTTTTTTTTCTTTA
1 TTTTTTTATCTTTCTTTTCTTTA
40543140 TTTTTTTAT-TTTCTTTTCTT
1 TTTTTTTATCTTTCTTTTCTT
40543160 CTAAAATCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.05, C:0.12, G:0.00, T:0.84
Consensus pattern (23 bp):
TTTTTTTATCTTTCTTTTCTTTA
Found at i:40544079 original size:3 final size:3
Alignment explanation
Indices: 40544064--40544163 Score: 87
Period size: 3 Copynumber: 31.7 Consensus size: 3
40544054 ATCATTACTG
*
40544064 TTA TTA GTA TTA TTA TTA TT- TTA TTCA TTA GTCTA TTTA GTTA TCTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA -T-TA -TTA -TTA T-TA
** *
40544111 TTCA TT- TGC TTA ATA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
40544156 TTA TTA TT
1 TTA TTA TT
40544164 GTCTTACGAA
Statistics
Matches: 81, Mismatches: 9, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
2 3 0.04
3 60 0.74
4 15 0.19
5 3 0.04
ACGTcount: A:0.29, C:0.05, G:0.04, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:40544490 original size:21 final size:22
Alignment explanation
Indices: 40544454--40544499 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
40544444 TTTAACCCCT
* *
40544454 TTTATATATCATTTTTGAATTA
1 TTTATATATCATTTTTAAACTA
*
40544476 TTTATAT-TTATTTTTAAACTA
1 TTTATATATCATTTTTAAACTA
40544497 TTT
1 TTT
40544500 TTCATAGACT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.63
Consensus pattern (22 bp):
TTTATATATCATTTTTAAACTA
Found at i:40551428 original size:43 final size:42
Alignment explanation
Indices: 40551374--40552072 Score: 227
Period size: 44 Copynumber: 16.5 Consensus size: 42
40551364 ATCTGTTTCT
40551374 CTACTGCTTAGGGTGTTAAGATCTGTAAATTTAGCCTGTTACC
1 CTACTGCTTAGGG-GTTAAGATCTGTAAATTTAGCCTGTTACC
* * * ** * * *
40551417 CTACTGTTTAGGGGTTAAG-GCTTGTCACCTTCGATCTGTTTCC
1 CTACTGCTTAGGGGTTAAGATC-TGTAAATTTAG-CCTGTTACC
40551460 CTACTGCTTAGGGGGTTTAAGATCTGTAAATCTTCAGCCTGTTACC
1 CTACTGCTTA-GGGG-TTAAGATCTGTAAAT-TT-AGCCTGTTACC
* * ** * * *
40551506 CTACTGCTTAGGGGTTTAAG-GCTTGTCACCTTCGATCTGTTTCC
1 CTACTGCTTAGGGG-TTAAGATC-TGTAAATTTAG-CCTGTTACC
* *
40551550 CTACTGTTTA--GG----G-TCTGTAAATTTAACCTGTTACC
1 CTACTGCTTAGGGGTTAAGATCTGTAAATTTAGCCTGTTACC
* ** * * **
40551585 CTACTGCTTAGGGGTTTAAG-GCT-TATCGTCTTTGATCTGTTTTC
1 CTACTGCTTAGGGG-TTAAGATCTGTA-AAT-TTAG-CCTGTTACC
* * *
40551629 CTACTGTTTA--GG----G-TCTGTAAATTTAACATGTTACC
1 CTACTGCTTAGGGGTTAAGATCTGTAAATTTAGCCTGTTACC
* * * ** * *
40551664 CCACTGCTTAAGGGTTTAAG-GCT-TATCGTCTTTGACCTGTTTCC
1 CTACTGCTT-AGGGGTTAAGATCTGTA-AAT-TTAG-CCTGTTACC
*
40551708 CTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTACC
1 CTACTGCTTA-GGGGTTAAGATCTGTAAATTTAGCCTGTTACC
** ** * ** * * *
40551751 CTACTGCTTAGGGGTTTAAGGCCCATCAGCTTCGATCTGCT-CC
1 CTACTGCTTAGGGG-TTAAGATCTGTAAATTTAG-CCTGTTACC
* * *
40551794 ACTACTGCTTAGGGAGATAAAATC--TACAATTTGGCCTGTTACC
1 -CTACTGCTTAGGG-GTTAAGATCTGTA-AATTTAGCCTGTTACC
* ** * * *
40551837 CTACTGCTTAGGGGTTTAAGACCCT-T-CGTCTTCGATCTGCT-CC
1 CTACTGCTTAGGGG-TTAAGA-TCTGTAAAT-TTAG-CCTGTTACC
* * * *
40551880 ACTACTGCTTAGGGAGATAAGATCTG-CAA-TTCGATCTGTTACC
1 -CTACTGCTTAGGG-GTTAAGATCTGTAAATTTAG-CCTGTTACC
* * ** * * *
40551923 CTACTACTTAGGGGTTTAAGACCCT-T-CGTCTTCGATCTGTTTCC
1 CTACTGCTTAGGGG-TTAAGA-TCTGTAAAT-TTAG-CCTGTTACC
* *
40551967 CTACTGCTTAGGGGGTTAAGATCTAG-AAATTCAGCCTATTACC
1 CTACTGCTTA-GGGGTTAAGATCT-GTAAATTTAGCCTGTTACC
40552010 CTACTGCTTAGGGGTTTAAGATCTGTAAATTTAGCCTGTTACC
1 CTACTGCTTAGGGG-TTAAGATCTGTAAATTTAGCCTGTTACC
40552053 CTACTGCTTAGGGGGTTAAG
1 CTACTGCTTA-GGGGTTAAG
40552073 GCTTGTGGAT
Statistics
Matches: 475, Mismatches: 120, Indels: 122
0.66 0.17 0.17
Matches are distributed among these distances:
35 28 0.06
36 9 0.02
37 8 0.02
38 3 0.01
41 7 0.01
42 84 0.18
43 139 0.29
44 141 0.30
45 33 0.07
46 22 0.05
47 1 0.00
ACGTcount: A:0.20, C:0.22, G:0.21, T:0.36
Consensus pattern (42 bp):
CTACTGCTTAGGGGTTAAGATCTGTAAATTTAGCCTGTTACC
Found at i:40551456 original size:86 final size:87
Alignment explanation
Indices: 40551326--40552029 Score: 733
Period size: 86 Copynumber: 8.3 Consensus size: 87
40551316 TTCAGCTTGG
** * *
40551326 TACCCTACTGCTTAGGGGTTTAAGGCACATCGTCTTCGATCTGTTTCTCTACTGCTTAGGGTGTT
1 TACCCTACTGCTTAGGGGTTTAAGGCTTATCGTCTTCGATCTGTTTCCCTACTGCTTAGGGGGTT
40551391 AAGATCTGTAAATTTAGCCTGT
66 AAGATCTGTAAATTTAGCCTGT
* * **
40551413 TACCCTACTGTTTAGGGG-TTAAGGCTTGTCACCTTCGATCTGTTTCCCTACTGCTTAGGGGGTT
1 TACCCTACTGCTTAGGGGTTTAAGGCTTATCGTCTTCGATCTGTTTCCCTACTGCTTAGGGGG-T
40551477 TAAGATCTGTAAATCTTCAGCCTGT
65 TAAGATCTGTAAAT-TT-AGCCTGT
* ** *
40551502 TACCCTACTGCTTAGGGGTTTAAGGCTTGTCACCTTCGATCTGTTTCCCTACTGTTTA---GG--
1 TACCCTACTGCTTAGGGGTTTAAGGCTTATCGTCTTCGATCTGTTTCCCTACTGCTTAGGGGGTT
*
40551562 --G-TCTGTAAATTTAACCTGT
66 AAGATCTGTAAATTTAGCCTGT
* * *
40551581 TACCCTACTGCTTAGGGGTTTAAGGCTTATCGTCTTTGATCTGTTTTCCTACTGTTTA---GG--
1 TACCCTACTGCTTAGGGGTTTAAGGCTTATCGTCTTCGATCTGTTTCCCTACTGCTTAGGGGGTT
* *
40551641 --G-TCTGTAAATTTAACATGT
66 AAGATCTGTAAATTTAGCCTGT
* * * *
40551660 TACCCCACTGCTTAAGGGTTTAAGGCTTATCGTCTTTGACCTGTTTCCCTACTGCTTAGGGGGTT
1 TACCCTACTGCTTAGGGGTTTAAGGCTTATCGTCTTCGATCTGTTTCCCTACTGCTTAGGGGGTT
*
40551725 AAGATCTGTAAATTCAGCCTGT
66 AAGATCTGTAAATTTAGCCTGT
** * *
40551747 TACCCTACTGCTTAGGGGTTTAAGGCCCATCAG-CTTCGATCTG-CTCCACTACTGCTTAGGGAG
1 TACCCTACTGCTTAGGGGTTTAAGGCTTATC-GTCTTCGATCTGTTTCC-CTACTGCTTAGGGGG
* * *
40551810 ATAAAATC--TACAATTTGGCCTGT
64 TTAAGATCTGTA-AATTTAGCCTGT
* * * *
40551833 TACCCTACTGCTTAGGGGTTTAAGACCCT-TCGTCTTCGATCTG-CTCCACTACTGCTTAGGGAG
1 TACCCTACTGCTTAGGGGTTTAAG-GCTTATCGTCTTCGATCTGTTTCC-CTACTGCTTAGGGGG
* * * *
40551896 ATAAGATCTG-CAA-TTCGATCTGT
64 TTAAGATCTGTAAATTTAG-CCTGT
* * *
40551919 TACCCTACTACTTAGGGGTTTAAGACCCT-TCGTCTTCGATCTGTTTCCCTACTGCTTAGGGGGT
1 TACCCTACTGCTTAGGGGTTTAAG-GCTTATCGTCTTCGATCTGTTTCCCTACTGCTTAGGGGGT
* *
40551983 TAAGATCTAG-AAATTCAGCCTAT
65 TAAGATCT-GTAAATTTAGCCTGT
40552006 TACCCTACTGCTTAGGGGTTTAAG
1 TACCCTACTGCTTAGGGGTTTAAG
40552030 ATCTGTAAAT
Statistics
Matches: 541, Mismatches: 53, Indels: 46
0.85 0.08 0.07
Matches are distributed among these distances:
79 132 0.24
80 2 0.00
81 9 0.02
82 3 0.01
85 6 0.01
86 184 0.34
87 138 0.26
88 5 0.01
89 24 0.04
90 38 0.07
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.36
Consensus pattern (87 bp):
TACCCTACTGCTTAGGGGTTTAAGGCTTATCGTCTTCGATCTGTTTCCCTACTGCTTAGGGGGTT
AAGATCTGTAAATTTAGCCTGT
Found at i:40551607 original size:79 final size:79
Alignment explanation
Indices: 40551482--40551979 Score: 378
Period size: 79 Copynumber: 6.0 Consensus size: 79
40551472 GGGTTTAAGA
* * *
40551482 TCTGTAAATCTTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCTTGTCACCTTCGATCTGTT
1 TCTGTAAAT-TT-AACCTGTTACCCTACTGCTTAGGGGTTTAAGGCTTATCATCTTCGATCTGTT
*
40551547 TCCCTACTGTTTAGGG
64 TCCCTACTGCTTAGGG
* * *
40551563 TCTGTAAATTTAACCTGTTACCCTACTGCTTAGGGGTTTAAGGCTTATCGTCTTTGATCTGTTTT
1 TCTGTAAATTTAACCTGTTACCCTACTGCTTAGGGGTTTAAGGCTTATCATCTTCGATCTGTTTC
*
40551628 CCTACTGTTTAGGG
66 CCTACTGCTTAGGG
* * * * * *
40551642 TCTGTAAATTTAACATGTTACCCCACTGCTTAAGGGTTTAAGGCTTATCGTCTTTGACCTGTTTC
1 TCTGTAAATTTAACCTGTTACCCTACTGCTTAGGGGTTTAAGGCTTATCATCTTCGATCTGTTTC
40551707 CCTACTGCTTAGGGGGTTAAG
66 CCTACTGCTTA---GG----G
* * ** * *
40551728 ATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCAGCTTCGATCTG-CT
1 -TCTGTAAATTTAACCTGTTACCCTACTGCTTAGGGGTTTAAGGCTTATCATCTTCGATCTGTTT
40551792 CCACTACTGCTTAGGGAG
65 CC-CTACTGCTTA-GG-G
* * ** * * *
40551810 ATAAAATCTACAATTTGGCCTGTTACCCTACTGCTTAGGGGTTTAAGACCCT-TCGTCTTCGATC
1 -T---CTGTA-AATTTAACCTGTTACCCTACTGCTTAGGGGTTTAAG-GCTTATCATCTTCGATC
*
40551874 TG-CTCCACTACTGCTTAGGG
60 TGTTTCC-CTACTGCTTAGGG
* * * * * *
40551894 --AGATAAGATCTGCAATTCGATCTGTTACCCTACTACTTAGGGGTTTAAGACCCT-TCGTCTTC
1 TCTG-TAA-AT-T-TAA--C---CTGTTACCCTACTGCTTAGGGGTTTAAG-GCTTATCATCTTC
40551956 GATCTGTTTCCCTACTGCTTAGGG
56 GATCTGTTTCCCTACTGCTTAGGG
40551980 GGTTAAGATC
Statistics
Matches: 354, Mismatches: 39, Indels: 43
0.81 0.09 0.10
Matches are distributed among these distances:
78 1 0.00
79 136 0.38
80 3 0.01
81 9 0.03
82 6 0.02
83 1 0.00
84 1 0.00
85 8 0.02
86 124 0.35
87 65 0.18
ACGTcount: A:0.20, C:0.24, G:0.20, T:0.36
Consensus pattern (79 bp):
TCTGTAAATTTAACCTGTTACCCTACTGCTTAGGGGTTTAAGGCTTATCATCTTCGATCTGTTTC
CCTACTGCTTAGGG
Found at i:40552055 original size:86 final size:85
Alignment explanation
Indices: 40551657--40552072 Score: 416
Period size: 86 Copynumber: 4.8 Consensus size: 85
40551647 AAATTTAACA
* * * * *
40551657 TGTTACCCCACTGCTTAAGGGTTTAAG--GCTTATCGTCTTTGACCTGTTTCCCTACTGCTTAGG
1 TGTTACCCTACTGCTTAGGGGTTTAAGACCCTTA--GTCTTCGATCTG-TTCCCTACTGCTTAGG
40551720 GGGTTAAGATCTGTAAATTCAGCC
63 GGGTTAAGATCTG-AAATTCAGCC
* * *
40551744 TGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCAG-CTTCGATCTGCTCCACTACTGCTTAGGG
1 TGTTACCCTACTGCTTAGGGGTTTAAGACCC-TTAGTCTTCGATCTGTTCC-CTACTGCTTAGGG
* * * **
40551808 AGATAAAATCT-ACAATTTGGCC
64 GGTTAAGATCTGA-AATTCAGCC
* * *
40551830 TGTTACCCTACTGCTTAGGGGTTTAAGACCCTTCGTCTTCGATCTGCTCCACTACTGCTTAGGGA
1 TGTTACCCTACTGCTTAGGGGTTTAAGACCCTTAGTCTTCGATCTGTTCC-CTACTGCTTAGGGG
* * *
40551895 GATAAGATCTGCAATTC-GATC
65 GTTAAGATCTGAAATTCAG-CC
* *
40551916 TGTTACCCTACTACTTAGGGGTTTAAGACCCTTCGTCTTCGATCTGTTTCCCTACTGCTTAGGGG
1 TGTTACCCTACTGCTTAGGGGTTTAAGACCCTTAGTCTTCGATCTG-TTCCCTACTGCTTAGGGG
40551981 GTTAAGATCTAGAAATTCAGCC
65 GTTAAGATCT-GAAATTCAGCC
* * * * *
40552003 TATTACCCTACTGCTTAGGGGTTTAAGA-TCTGTAAAT-TTAG-CCTGTTACCCTACTGCTTAGG
1 TGTTACCCTACTGCTTAGGGGTTTAAGACCCT-T-AGTCTTCGATCTGTT-CCCTACTGCTTAGG
40552065 GGGTTAAG
63 GGGTTAAG
40552073 GCTTGTGGAT
Statistics
Matches: 283, Mismatches: 32, Indels: 29
0.82 0.09 0.08
Matches are distributed among these distances:
85 6 0.02
86 177 0.63
87 94 0.33
88 3 0.01
89 1 0.00
90 2 0.01
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.34
Consensus pattern (85 bp):
TGTTACCCTACTGCTTAGGGGTTTAAGACCCTTAGTCTTCGATCTGTTCCCTACTGCTTAGGGGG
TTAAGATCTGAAATTCAGCC
Found at i:40552059 original size:172 final size:172
Alignment explanation
Indices: 40551326--40552065 Score: 431
Period size: 173 Copynumber: 4.3 Consensus size: 172
40551316 TTCAGCTTGG
* * * ** * * * * *
40551326 TACCCTACTGCTTAGGGGTTTAAGGCACATCGTCTTCGATCTGTTTCTCTACTGCTTAGGGTGTT
1 TACCCTACTGCTTAGGGGTTTAAGACCCTTAATCTTAGACCTG-TTCCCTACTGCTTAGGGAGAT
* ** * *** *
40551391 AAGATCTGTAAATTTAGCCTGTTACCCTACTGTTTAGGGG-TTAAGGCTTGTCACCTTCGATCTG
65 AAGATCTGTAAATTCAGCCTGTTACCCTACTACTTAGGGGTTTAAGACCCATCAGCTTCGATCTG
* * * * * *
40551455 TTTCC-CTACTGCTTAGGGGGTTTAAGATCTGTAAATCTTCAGCCTGT
130 -CTCCACTACTGCTTAGGGAG-ATAAAATC--TAAA-ATTCAGCCTAT
* * * * * * *
40551502 TACCCTACTGCTTAGGGGTTTAAG-GCTTGTCACCTTCGATCTGTTTCCCTACTGTTTA--G-G-
1 TACCCTACTGCTTAGGGGTTTAAGACCCT-TAATCTTAGACCTG-TTCCCTACTGCTTAGGGAGA
* * * * ** *
40551562 ---G-TCTGTAAATTTAACCTGTTACCCTACTGCTTAGGGGTTTAAGGCTTATC-GTCTTTGATC
64 TAAGATCTGTAAATTCAGCCTGTTACCCTACTACTTAGGGGTTTAAGACCCATCAG-CTTCGATC
* * * * * * * * *
40551622 TGTTTTC-CTACTGTTTA-GG-G-T---CTGT-AAATTTAACATGT
128 TG-CTCCACTACTGCTTAGGGAGATAAAATCTAAAATTCAGCCTAT
* * * * * *
40551660 TACCCCACTGCTTAAGGGTTTAAG--GCTTATCGTCTTTGACCTGTTTCCCTACTGCTTAGGGGG
1 TACCCTACTGCTTAGGGGTTTAAGACCCTTA--ATCTTAGACCTG-TTCCCTACTGCTTAGGGAG
* * *
40551723 TTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCAGCTTCGATC
63 ATAAGATCTGTAAATTCAGCCTGTTACCCTACTACTTAGGGGTTTAAGACCCATCAGCTTCGATC
* ** *
40551788 TGCTCCACTACTGCTTAGGGAGATAAAATCTACAATTTGGCCTGT
128 TGCTCCACTACTGCTTAGGGAGATAAAATCTAAAATTCAGCCTAT
** * * *
40551833 TACCCTACTGCTTAGGGGTTTAAGACCCTTCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGAT
1 TACCCTACTGCTTAGGGGTTTAAGACCCTTAATCTTAGACCTGTTCC-CTACTGCTTAGGGAGAT
* * *
40551898 AAGATCTG-CAATTC-GATCTGTTACCCTACTACTTAGGGGTTTAAGACCCTTC-GTCTTCGATC
65 AAGATCTGTAAATTCAG-CCTGTTACCCTACTACTTAGGGGTTTAAGACCCATCAG-CTTCGATC
* * * *
40551960 TGTTTCC-CTACTGCTTAGGGGGTTAAGATCTAGAAATTCAGCCTAT
128 TG-CTCCACTACTGCTTAGGGAGATAAAATCTA-AAATTCAGCCTAT
*
40552006 TACCCTACTGCTTAGGGGTTTAAGA-TCTGTAAAT-TTAG-CCTGTTACCCTACTGCTTAGGG
1 TACCCTACTGCTTAGGGGTTTAAGACCCT-T-AATCTTAGACCTGTT-CCCTACTGCTTAGGG
40552066 GGTTAAGGCT
Statistics
Matches: 459, Mismatches: 73, Indels: 68
0.76 0.12 0.11
Matches are distributed among these distances:
156 1 0.00
157 1 0.00
158 51 0.11
159 2 0.00
160 2 0.00
161 1 0.00
162 1 0.00
165 4 0.01
166 63 0.14
167 4 0.01
168 37 0.08
169 35 0.08
171 2 0.00
172 93 0.20
173 108 0.24
174 2 0.00
175 3 0.01
176 49 0.11
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.36
Consensus pattern (172 bp):
TACCCTACTGCTTAGGGGTTTAAGACCCTTAATCTTAGACCTGTTCCCTACTGCTTAGGGAGATA
AGATCTGTAAATTCAGCCTGTTACCCTACTACTTAGGGGTTTAAGACCCATCAGCTTCGATCTGC
TCCACTACTGCTTAGGGAGATAAAATCTAAAATTCAGCCTAT
Found at i:40553042 original size:52 final size:53
Alignment explanation
Indices: 40552940--40553053 Score: 185
Period size: 52 Copynumber: 2.2 Consensus size: 53
40552930 GCATAGCTCG
* *
40552940 AAATGAATAAATTAATCAAAGATTGCAAATGCCATAAGAAAGAAATTAACTCA
1 AAATGAATAAATTAATCAAAGATAGCAAATGCAATAAGAAAGAAATTAACTCA
* *
40552993 AAATGAATAAGTTAATCAAAGATAGC-AATGCAATAAGAAGGAAATTAACTCA
1 AAATGAATAAATTAATCAAAGATAGCAAATGCAATAAGAAAGAAATTAACTCA
40553045 AAATGAATA
1 AAATGAATA
40553054 TAGCAAATTC
Statistics
Matches: 57, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
52 33 0.58
53 24 0.42
ACGTcount: A:0.55, C:0.10, G:0.13, T:0.22
Consensus pattern (53 bp):
AAATGAATAAATTAATCAAAGATAGCAAATGCAATAAGAAAGAAATTAACTCA
Found at i:40555075 original size:23 final size:27
Alignment explanation
Indices: 40555049--40555103 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 27
40555039 GTATCTATTT
40555049 TTATTGATT-TATGG-AAAT-TATA-A
1 TTATTGATTATATGGAAAATATATATA
*
40555072 TTATT-ATTATTTGGAAAATATATATA
1 TTATTGATTATATGGAAAATATATATA
40555098 TTATTG
1 TTATTG
40555104 TAGTTGAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 3 0.12
23 9 0.35
24 4 0.15
25 4 0.15
26 6 0.23
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (27 bp):
TTATTGATTATATGGAAAATATATATA
Found at i:40557483 original size:60 final size:59
Alignment explanation
Indices: 40557416--40557554 Score: 174
Period size: 60 Copynumber: 2.3 Consensus size: 59
40557406 CCAACTGTGT
40557416 TGATATGGGCAAGGCCCAATATA-TCTCG-ACTTGTAATAGGGCTACGGCCCAGATTAATAC
1 TGATATGGGCAAGGCCCAATATACTCT-GTAC-TGTAA-AGGGCTACGGCCCAGATTAATAC
* * * * *
40557476 TGATATGGGCTAGGCCCAGTATACTCTGTTACTGTAAGGGGCTATGGCCCAGATTAATAT
1 TGATATGGGCAAGGCCCAATATACTCTG-TACTGTAAAGGGCTACGGCCCAGATTAATAC
40557536 TGATATGGGCTAAGGCCCA
1 TGATATGGGC-AAGGCCCA
40557555 GTTAACATTA
Statistics
Matches: 69, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
60 52 0.75
61 15 0.22
62 2 0.03
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (59 bp):
TGATATGGGCAAGGCCCAATATACTCTGTACTGTAAAGGGCTACGGCCCAGATTAATAC
Found at i:40558513 original size:510 final size:510
Alignment explanation
Indices: 40557554--40558574 Score: 1997
Period size: 510 Copynumber: 2.0 Consensus size: 510
40557544 GCTAAGGCCC
*
40557554 AGTTAACATTAAATTCTGAATAGGGCTTAGGCCCAGTAAAGCTTGAACTGATTTGGACTTTGGTT
1 AGTTAACATTAAATTCTGAATAGGGCTTAGACCCAGTAAAGCTTGAACTGATTTGGACTTTGGTT
40557619 GGGATACTTTACACACTGAGTTTTCCAAACTCACCCCCCCTTTTTCCCATCTTTGCAGGTGAGCC
66 GGGATACTTTACACACTGAGTTTTCCAAACTCACCCCCCCTTTTTCCCATCTTTGCAGGTGAGCC
*
40557684 TTATATCGATGGACTTGGAGCTGGGCGGGATTCAGAGTGGCCACGAAGATTAAGTTTTGTTTTCT
131 TTAGATCGATGGACTTGGAGCTGGGCGGGATTCAGAGTGGCCACGAAGATTAAGTTTTGTTTTCT
*
40557749 TTAAAATAAGTTTCGCATTTATTATTTTAATTATTTTTATTCTGGTTAAAGTTGTAATAAGGCCG
196 TTAAAATAAGTTTCACATTTATTATTTTAATTATTTTTATTCTGGTTAAAGTTGTAATAAGGCCG
40557814 CTCTTTTTATTATTTTTAATATTTTGGGTTATTAAATTGGTTAGCTCTAGGGCGCGTTTTATAAA
261 CTCTTTTTATTATTTTTAATATTTTGGGTTATTAAATTGGTTAGCTCTAGGGCGCGTTTTATAAA
40557879 AGTTACTTATTTTTAAAATATCACGATAACCGAGCAAAGCTTCCGCAACGTAAATGCTTTCAAAG
326 AGTTACTTATTTTTAAAATATCACGATAACCGAGCAAAGCTTCCGCAACGTAAATGCTTTCAAAG
40557944 GAAATAAATATTTTAAATAGACTTAAACTTAATTTGTTGTTCGTGGACAAGTAATAAGCTTAAAG
391 GAAATAAATATTTTAAATAGACTTAAACTTAATTTGTTGTTCGTGGACAAGTAATAAGCTTAAAG
40558009 TGTGGCAATGGATGTATGCATGTCTAGGATTGGATCATGGAAGAGCTAGGTACTT
456 TGTGGCAATGGATGTATGCATGTCTAGGATTGGATCATGGAAGAGCTAGGTACTT
*
40558064 AGTTAACATTAAATTCTGAATAGGGCTTAGACCCAGTAAAGCTTGAACTGATTTGGGCTTTGGTT
1 AGTTAACATTAAATTCTGAATAGGGCTTAGACCCAGTAAAGCTTGAACTGATTTGGACTTTGGTT
40558129 GGGATACTTTACACACTGAGTTTTCCAAACTCACCCCCCCTTTTTCCCATCTTTGCAGGTGAGCC
66 GGGATACTTTACACACTGAGTTTTCCAAACTCACCCCCCCTTTTTCCCATCTTTGCAGGTGAGCC
40558194 TTAGATCGATGGACTTGGAGCTGGGCGGGATTCAGAGTGGCCACGAAGATTAAGTTTTGTTTTCT
131 TTAGATCGATGGACTTGGAGCTGGGCGGGATTCAGAGTGGCCACGAAGATTAAGTTTTGTTTTCT
40558259 TTAAAATAAGTTTCACATTTATTATTTTAATTATTTTTATTCTGGTTAAAGTTGTAATAAGGCCG
196 TTAAAATAAGTTTCACATTTATTATTTTAATTATTTTTATTCTGGTTAAAGTTGTAATAAGGCCG
40558324 CTCTTTTTATTATTTTTAATATTTTGGGTTATTAAATTGGTTAGCTCTAGGGCGCGTTTTATAAA
261 CTCTTTTTATTATTTTTAATATTTTGGGTTATTAAATTGGTTAGCTCTAGGGCGCGTTTTATAAA
*
40558389 AGTTACTTATTTTTAAAATATCACGATAACCGAGCAAAGCTTCCGCAACGTAAATGTTTTCAAAG
326 AGTTACTTATTTTTAAAATATCACGATAACCGAGCAAAGCTTCCGCAACGTAAATGCTTTCAAAG
40558454 GAAATAAATATTTTAAATAGACTTAAACTTAATTTGTTGTTCGTGGACAAGTAATAAGCTTAAAG
391 GAAATAAATATTTTAAATAGACTTAAACTTAATTTGTTGTTCGTGGACAAGTAATAAGCTTAAAG
40558519 TGTGGCAATGGATGTATGCATGTCTAGGATTGGATCATGGAAGAGCTAGGTACTT
456 TGTGGCAATGGATGTATGCATGTCTAGGATTGGATCATGGAAGAGCTAGGTACTT
40558574 A
1 A
40558575 AGCAGTCTAA
Statistics
Matches: 506, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
510 506 1.00
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.37
Consensus pattern (510 bp):
AGTTAACATTAAATTCTGAATAGGGCTTAGACCCAGTAAAGCTTGAACTGATTTGGACTTTGGTT
GGGATACTTTACACACTGAGTTTTCCAAACTCACCCCCCCTTTTTCCCATCTTTGCAGGTGAGCC
TTAGATCGATGGACTTGGAGCTGGGCGGGATTCAGAGTGGCCACGAAGATTAAGTTTTGTTTTCT
TTAAAATAAGTTTCACATTTATTATTTTAATTATTTTTATTCTGGTTAAAGTTGTAATAAGGCCG
CTCTTTTTATTATTTTTAATATTTTGGGTTATTAAATTGGTTAGCTCTAGGGCGCGTTTTATAAA
AGTTACTTATTTTTAAAATATCACGATAACCGAGCAAAGCTTCCGCAACGTAAATGCTTTCAAAG
GAAATAAATATTTTAAATAGACTTAAACTTAATTTGTTGTTCGTGGACAAGTAATAAGCTTAAAG
TGTGGCAATGGATGTATGCATGTCTAGGATTGGATCATGGAAGAGCTAGGTACTT
Found at i:40567965 original size:17 final size:17
Alignment explanation
Indices: 40567923--40567965 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
40567913 GGATTCGTCA
40567923 TTTGGCGAATTCCAAGT
1 TTTGGCGAATTCCAAGT
* * *
40567940 TCTGACGAATTTCAAGT
1 TTTGGCGAATTCCAAGT
40567957 TTTGGCGAA
1 TTTGGCGAA
40567966 CTCTAAGGTT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.35
Consensus pattern (17 bp):
TTTGGCGAATTCCAAGT
Found at i:40573521 original size:22 final size:22
Alignment explanation
Indices: 40573493--40573538 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
40573483 TAAAAGNAAG
* *
40573493 AAGAAAAGAGGAAGAAG-AAAGA
1 AAGAAAA-AAGAAAAAGAAAAGA
40573515 AAGAAAAAAGAAAAAGAAAAGA
1 AAGAAAAAAGAAAAAGAAAAGA
40573537 AA
1 AA
40573539 TAATAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (22 bp):
AAGAAAAAAGAAAAAGAAAAGA
Found at i:40573525 original size:18 final size:18
Alignment explanation
Indices: 40573504--40573538 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
40573494 AGAAAAGAGG
40573504 AAGAAGAAAG-AAAGAAAA
1 AAGAA-AAAGAAAAGAAAA
40573522 AAGAAAAAGAAAAGAAA
1 AAGAAAAAGAAAAGAAA
40573539 TAATAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (18 bp):
AAGAAAAAGAAAAGAAAA
Found at i:40573832 original size:20 final size:19
Alignment explanation
Indices: 40573803--40573855 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
40573793 CCCAGCAGAG
40573803 AAAA-AAAAAGAAAACAAA
1 AAAAGAAAAAGAAAACAAA
**
40573821 AAGAAGAAAAAGAGAAGGAAA
1 AA-AAGAAAAAGA-AAACAAA
40573842 AAAAGAAAAA-AAAA
1 AAAAGAAAAAGAAAA
40573856 AGAGGTTCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
18 4 0.14
19 3 0.10
20 15 0.52
21 7 0.24
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (19 bp):
AAAAGAAAAAGAAAACAAA
Found at i:40573856 original size:11 final size:11
Alignment explanation
Indices: 40573803--40573858 Score: 67
Period size: 11 Copynumber: 5.0 Consensus size: 11
40573793 CCCAGCAGAG
40573803 AAAAAAAAAGA
1 AAAAAAAAAGA
*
40573814 AAACAAAAAGA
1 AAAAAAAAAGA
* *
40573825 AGAAAAAGAGA
1 AAAAAAAAAGA
*
40573836 AGGAAAAAAAGA
1 A-AAAAAAAAGA
40573848 AAAAAAAAAGA
1 AAAAAAAAAGA
40573859 GGTTCAATTC
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
11 28 0.74
12 10 0.26
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAGA
Found at i:40574237 original size:18 final size:18
Alignment explanation
Indices: 40574181--40574314 Score: 75
Period size: 17 Copynumber: 7.5 Consensus size: 18
40574171 AAAATTGTAA
* *
40574181 TTTCAATAATCCTCGTGCT
1 TTTCAAAAATCTTCGTG-T
*
40574200 TTT-AAAAAT-TCTCATG-
1 TTTCAAAAATCT-TCGTGT
40574216 TTTCAAAAATCTTCGTGT
1 TTTCAAAAATCTTCGTGT
* *
40574234 TTTCAAAATTC-TAGTG-
1 TTTCAAAAATCTTCGTGT
* *
40574250 TTTCAAAAATTTTCTTGT
1 TTTCAAAAATCTTCGTGT
*
40574268 TTTCAGAAAAAATTTTCGTGT
1 TTTC---AAAAATCTTCGTGT
* *
40574289 TTT-ATAAAT-TTCCGTAT
1 TTTCAAAAATCTT-CGTGT
40574306 TTTCAAAAA
1 TTTCAAAAA
40574315 AANNNNNNNN
Statistics
Matches: 90, Mismatches: 14, Indels: 23
0.71 0.11 0.18
Matches are distributed among these distances:
16 14 0.16
17 29 0.32
18 28 0.31
19 3 0.03
21 16 0.18
ACGTcount: A:0.31, C:0.14, G:0.09, T:0.46
Consensus pattern (18 bp):
TTTCAAAAATCTTCGTGT
Found at i:40574252 original size:34 final size:34
Alignment explanation
Indices: 40574181--40574272 Score: 114
Period size: 34 Copynumber: 2.7 Consensus size: 34
40574171 AAAATTGTAA
* * *
40574181 TTTCAATAATCCTCGTGCTTTTAAAAATTCTCATG
1 TTTCAAAAATCTTCGTG-TTTTCAAAATTCTCATG
40574216 TTTCAAAAATCTTCGTGTTTTCAAAATTCT-AGTG
1 TTTCAAAAATCTTCGTGTTTTCAAAATTCTCA-TG
* *
40574250 TTTCAAAAATTTTCTTGTTTTCA
1 TTTCAAAAATCTTCGTGTTTTCA
40574273 GAAAAAATTT
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
33 1 0.02
34 35 0.69
35 15 0.29
ACGTcount: A:0.28, C:0.16, G:0.09, T:0.47
Consensus pattern (34 bp):
TTTCAAAAATCTTCGTGTTTTCAAAATTCTCATG
Found at i:40574255 original size:16 final size:16
Alignment explanation
Indices: 40574204--40574257 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
40574194 CGTGCTTTTA
40574204 AAAATTCTCA-TGTTTC
1 AAAATTCT-AGTGTTTC
* *
40574220 AAAAATCTTCGTGTTTTC
1 AAAATTC-TAGTG-TTTC
40574238 AAAATTCTAGTGTTTC
1 AAAATTCTAGTGTTTC
40574254 AAAA
1 AAAA
40574258 ATTTTCTTGT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
16 14 0.45
17 7 0.23
18 10 0.32
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (16 bp):
AAAATTCTAGTGTTTC
Found at i:40574609 original size:18 final size:17
Alignment explanation
Indices: 40574505--40574731 Score: 144
Period size: 17 Copynumber: 13.4 Consensus size: 17
40574495 ATCCATTTTC
* *
40574505 CAAAATTTTTAGTGTCTT
1 CAAAAATTTTCGTGT-TT
*
40574523 CTAAAAATTTTTGTGTTT
1 C-AAAAATTTTCGTGTTT
40574541 CAAAAATTTTCGT-TTT
1 CAAAAATTTTCGTGTTT
*
40574557 CAAAAATTTCCGTGTTT
1 CAAAAATTTTCGTGTTT
40574574 CAAAAATTTTCGTGTTT
1 CAAAAATTTTCGTGTTT
*
40574591 TAAAAATTTTCGTGTTTT
1 CAAAAATTTTCGTG-TTT
* * *
40574609 TAAAAATTCTCGTATTT
1 CAAAAATTTTCGTGTTT
*
40574626 --TAAATTTT--T-TTT
1 CAAAAATTTTCGTGTTT
* **
40574638 AAGAAAAAAATT-GTGTTT
1 --CAAAAATTTTCGTGTTT
* * *
40574656 CAAAAAAATGTCTTGTTT
1 C-AAAAATTTTCGTGTTT
* * *
40574674 TAAAAATTCTCGTTTTT
1 CAAAAATTTTCGTGTTT
* *
40574691 CAAAAAATGTCGTGTTT
1 CAAAAATTTTCGTGTTT
**
40574708 TGAAAATTTTCGTGTTTT
1 CAAAAATTTTCGTG-TTT
40574726 CAAAAA
1 CAAAAA
40574732 AAAAATCTCG
Statistics
Matches: 165, Mismatches: 32, Indels: 24
0.75 0.14 0.11
Matches are distributed among these distances:
12 3 0.02
13 1 0.01
15 6 0.04
16 20 0.12
17 89 0.54
18 34 0.21
19 12 0.07
ACGTcount: A:0.33, C:0.09, G:0.11, T:0.47
Consensus pattern (17 bp):
CAAAAATTTTCGTGTTT
Found at i:40574743 original size:39 final size:38
Alignment explanation
Indices: 40574692--40574820 Score: 124
Period size: 39 Copynumber: 3.4 Consensus size: 38
40574682 CTCGTTTTTC
*
40574692 AAAAAATGTCGTGTTTTGAAAATTTTCGTGTTTTCAAAA
1 AAAAAATCTCGTGTTTT-AAAATTTTCGTGTTTTCAAAA
*
40574731 AAAAAATCTCGTGTTTCATAAATTTT-G-GTTTT-AAAA
1 AAAAAATCTCGTGTTTTA-AAATTTTCGTGTTTTCAAAA
* * * *
40574767 AAAATAT-T-ATGTCTTAAAATTCTCGTGTTTTCAAAA
1 AAAAAATCTCGTGTTTTAAAATTTTCGTGTTTTCAAAA
*
40574803 CAAGAAATTCTCGTGTTT
1 -AA-AAAATCTCGTGTTT
40574821 CAATCGGATC
Statistics
Matches: 71, Mismatches: 11, Indels: 15
0.73 0.11 0.15
Matches are distributed among these distances:
33 6 0.08
34 6 0.08
35 6 0.08
36 14 0.20
37 7 0.10
38 5 0.07
39 23 0.32
40 4 0.06
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.41
Consensus pattern (38 bp):
AAAAAATCTCGTGTTTTAAAATTTTCGTGTTTTCAAAA
Found at i:40574762 original size:73 final size:72
Alignment explanation
Indices: 40574657--40574823 Score: 181
Period size: 73 Copynumber: 2.3 Consensus size: 72
40574647 ATTGTGTTTC
* * * ** * * * *
40574657 AAAAAAATGTCTTGTTTTAAAAATTCTCGTTTTTCAAAAAATGTCGTGTTTTGAAAATTTTCGTG
1 AAAAAAATCTCGTGTTTCAAAAATTCTCGTTTTAAAAAAAATATCATGTCTT-AAAATTCTCGTG
40574722 TTTTCAAA
65 TTTTCAAA
* * * *
40574730 AAAAAAATCTCGTGTTTCATAAATTTTGGTTTTAAAAAAAATATTATGTCTTAAAATTCTCGTGT
1 AAAAAAATCTCGTGTTTCAAAAATTCTCGTTTTAAAAAAAATATCATGTCTTAAAATTCTCGTGT
40574795 TTTCAAA
66 TTTCAAA
*
40574802 ACAAGAAATTCTCGTGTTTCAA
1 A-AA-AAAATCTCGTGTTTCAA
40574824 TCGGATCACG
Statistics
Matches: 77, Mismatches: 15, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
72 20 0.26
73 42 0.55
74 15 0.19
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.41
Consensus pattern (72 bp):
AAAAAAATCTCGTGTTTCAAAAATTCTCGTTTTAAAAAAAATATCATGTCTTAAAATTCTCGTGT
TTTCAAA
Found at i:40576446 original size:21 final size:22
Alignment explanation
Indices: 40576402--40576448 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
40576392 ATTAATATTT
*
40576402 TAATATATTACATCATTAAATA
1 TAATATATTAAATCATTAAATA
* *
40576424 TAATATTTTAAAT-ATTTAATA
1 TAATATATTAAATCATTAAATA
40576445 TAAT
1 TAAT
40576449 TTAATATAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (22 bp):
TAATATATTAAATCATTAAATA
Found at i:40576455 original size:31 final size:30
Alignment explanation
Indices: 40576394--40576457 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
40576384 ATTGAATTAT
*
40576394 TAATATTTTAATATATTACATCATTAAATA
1 TAATATTTTAATATATTACATAATTAAATA
* *
40576424 TAATATTTTAA-ATATTTAATATAATTTAATA
1 TAATATTTTAATATA-TT-ACATAATTAAATA
40576455 TAA
1 TAA
40576458 AAATAATTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 3 0.10
30 13 0.45
31 13 0.45
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (30 bp):
TAATATTTTAATATATTACATAATTAAATA
Found at i:40576684 original size:16 final size:16
Alignment explanation
Indices: 40576663--40576693 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
40576653 TGAATTAATG
40576663 ATTACAAATCTATTCC
1 ATTACAAATCTATTCC
40576679 ATTACAAATCTATTC
1 ATTACAAATCTATTC
40576694 GATTTCAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.23, G:0.00, T:0.39
Consensus pattern (16 bp):
ATTACAAATCTATTCC
Found at i:40579115 original size:16 final size:18
Alignment explanation
Indices: 40579090--40579122 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
40579080 TTTTATAATC
40579090 TTTTAGAAAAA-TATTTT
1 TTTTAGAAAAATTATTTT
40579107 TTTTA-AAAAATTATTT
1 TTTTAGAAAAATTATTT
40579123 GAAAATGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (18 bp):
TTTTAGAAAAATTATTTT
Found at i:40579154 original size:21 final size:22
Alignment explanation
Indices: 40579105--40579155 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 22
40579095 GAAAAATATT
40579105 TTTTTTAAAAAATTATTTGAAAA
1 TTTTTT-AAAAATTATTTGAAAA
*
40579128 TGTTTTAAAAATT-TTTG-AAA
1 TTTTTTAAAAATTATTTGAAAA
40579148 TCTTTTTA
1 T-TTTTTA
40579156 CTAAGTGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 4 0.16
21 9 0.36
22 7 0.28
23 5 0.20
ACGTcount: A:0.39, C:0.02, G:0.06, T:0.53
Consensus pattern (22 bp):
TTTTTTAAAAATTATTTGAAAA
Found at i:40579491 original size:15 final size:15
Alignment explanation
Indices: 40579471--40579505 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
40579461 TTTAAATACC
40579471 AACAATC-CTCTTTAT
1 AACAATCAC-CTTTAT
40579486 AACAATCACCTTTAT
1 AACAATCACCTTTAT
40579501 AACAA
1 AACAA
40579506 CCAAATATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 18 0.95
16 1 0.05
ACGTcount: A:0.43, C:0.26, G:0.00, T:0.31
Consensus pattern (15 bp):
AACAATCACCTTTAT
Found at i:40580202 original size:12 final size:12
Alignment explanation
Indices: 40580185--40580216 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
40580175 TAGATAGAAA
40580185 AAGAAATTATTG
1 AAGAAATTATTG
40580197 AAGAAATTATTG
1 AAGAAATTATTG
40580209 AAGAAATT
1 AAGAAATT
40580217 GGGTAAAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.16, T:0.31
Consensus pattern (12 bp):
AAGAAATTATTG
Found at i:40585674 original size:85 final size:85
Alignment explanation
Indices: 40585573--40585740 Score: 327
Period size: 85 Copynumber: 2.0 Consensus size: 85
40585563 TCCTCATTTT
*
40585573 TCTAATTTAATTTTAATATTATTTATAATATCATATTTTATTATTGTTGTATTTTTATTAATAGT
1 TCTAACTTAATTTTAATATTATTTATAATATCATATTTTATTATTGTTGTATTTTTATTAATAGT
40585638 TCATTATTATCATTTTATTA
66 TCATTATTATCATTTTATTA
40585658 TCTAACTTAATTTTAATATTATTTATAATATCATATTTTATTATTGTTGTATTTTTATTAATAGT
1 TCTAACTTAATTTTAATATTATTTATAATATCATATTTTATTATTGTTGTATTTTTATTAATAGT
40585723 TCATTATTATCATTTTAT
66 TCATTATTATCATTTTAT
40585741 AGTATATATA
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 82 1.00
ACGTcount: A:0.32, C:0.05, G:0.04, T:0.60
Consensus pattern (85 bp):
TCTAACTTAATTTTAATATTATTTATAATATCATATTTTATTATTGTTGTATTTTTATTAATAGT
TCATTATTATCATTTTATTA
Found at i:40585911 original size:21 final size:21
Alignment explanation
Indices: 40585873--40585912 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
40585863 CCTCCTTTTA
*
40585873 ATATTATGTATATATTTTGAT
1 ATATTACGTATATATTTTGAT
* *
40585894 ATATTACGTGTATGTTTTG
1 ATATTACGTATATATTTTG
40585913 TTTCGTATAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.03, G:0.15, T:0.55
Consensus pattern (21 bp):
ATATTACGTATATATTTTGAT
Found at i:40590593 original size:22 final size:22
Alignment explanation
Indices: 40590565--40590608 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
40590555 TACAATAATG
40590565 ACATGGAATTCATACTTGCTAA
1 ACATGGAATTCATACTTGCTAA
40590587 ACATGGAATTCATACTTGCTAA
1 ACATGGAATTCATACTTGCTAA
40590609 TTAGTACATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (22 bp):
ACATGGAATTCATACTTGCTAA
Found at i:40592269 original size:68 final size:68
Alignment explanation
Indices: 40592160--40592294 Score: 270
Period size: 68 Copynumber: 2.0 Consensus size: 68
40592150 CGATCCTGAC
40592160 TTTGCATTGATGCGTTCAAAGACACATTGGAAATTGGTTTTAGTGAATGGATTGAAGGTTTTGCA
1 TTTGCATTGATGCGTTCAAAGACACATTGGAAATTGGTTTTAGTGAATGGATTGAAGGTTTTGCA
40592225 TGA
66 TGA
40592228 TTTGCATTGATGCGTTCAAAGACACATTGGAAATTGGTTTTAGTGAATGGATTGAAGGTTTTGCA
1 TTTGCATTGATGCGTTCAAAGACACATTGGAAATTGGTTTTAGTGAATGGATTGAAGGTTTTGCA
40592293 TG
66 TG
40592295 GAAATTGAAA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 67 1.00
ACGTcount: A:0.27, C:0.09, G:0.27, T:0.37
Consensus pattern (68 bp):
TTTGCATTGATGCGTTCAAAGACACATTGGAAATTGGTTTTAGTGAATGGATTGAAGGTTTTGCA
TGA
Found at i:40593409 original size:49 final size:49
Alignment explanation
Indices: 40593351--40593473 Score: 138
Period size: 54 Copynumber: 2.4 Consensus size: 49
40593341 ATGTAAATAT
* **
40593351 TCATTTATTAGTTTACGTATAATGTAATGAAAAAGACTAATCCCATTAA
1 TCATTTATTAATTTACGTATAATGTAATGAAAAAGACTAATCCCAACAA
* * * *
40593400 TCTTTTATTAATTTACGTATTTCTTAATGTAATGAGAGAGACTAATCCCAACAT
1 TCATTTATTAATTTACGTA-----TAATGTAATGAAAAAGACTAATCCCAACAA
40593454 TCATTTATTAATTTACGTAT
1 TCATTTATTAATTTACGTAT
40593474 TTAAAATATA
Statistics
Matches: 61, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
49 18 0.30
54 43 0.70
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (49 bp):
TCATTTATTAATTTACGTATAATGTAATGAAAAAGACTAATCCCAACAA
Found at i:40593447 original size:54 final size:54
Alignment explanation
Indices: 40593370--40593475 Score: 158
Period size: 54 Copynumber: 2.0 Consensus size: 54
40593360 AGTTTACGTA
** *
40593370 TAATGTAATGAAAAAGACTAATCCCATTAATCTTTTATTAATTTACGTATTTCT
1 TAATGTAATGAAAAAGACTAATCCCAACAATCATTTATTAATTTACGTATTTCT
* * *
40593424 TAATGTAATGAGAGAGACTAATCCCAACATTCATTTATTAATTTACGTATTT
1 TAATGTAATGAAAAAGACTAATCCCAACAATCATTTATTAATTTACGTATTT
40593476 AAAATATATG
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 46 1.00
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.41
Consensus pattern (54 bp):
TAATGTAATGAAAAAGACTAATCCCAACAATCATTTATTAATTTACGTATTTCT
Found at i:40594543 original size:23 final size:23
Alignment explanation
Indices: 40594516--40594599 Score: 125
Period size: 23 Copynumber: 3.7 Consensus size: 23
40594506 CAACTCTTTG
40594516 AAGGCATCACAGAATGTGCCACA
1 AAGGCATCACAGAATGTGCCACA
40594539 AAGGCATCACAGAATGTGCCACA
1 AAGGCATCACAGAATGTGCCACA
* * *
40594562 AATGCACCACA-AAAGATGCCACA
1 AAGGCATCACAGAATG-TGCCACA
40594585 AAGGCATCACAGAAT
1 AAGGCATCACAGAAT
40594600 ACGCCACGAA
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
22 3 0.06
23 48 0.91
24 2 0.04
ACGTcount: A:0.43, C:0.26, G:0.19, T:0.12
Consensus pattern (23 bp):
AAGGCATCACAGAATGTGCCACA
Found at i:40594605 original size:23 final size:23
Alignment explanation
Indices: 40594516--40594612 Score: 122
Period size: 23 Copynumber: 4.2 Consensus size: 23
40594506 CAACTCTTTG
*
40594516 AAGGCATCACAGAATGTGCCACA
1 AAGGCATCACAGAATATGCCACA
*
40594539 AAGGCATCACAGAATGTGCCACA
1 AAGGCATCACAGAATATGCCACA
* * * *
40594562 AATGCACCACAAAAGATGCCACA
1 AAGGCATCACAGAATATGCCACA
* *
40594585 AAGGCATCACAGAATACGCCACG
1 AAGGCATCACAGAATATGCCACA
40594608 AAGGC
1 AAGGC
40594613 TTTCCAGAGG
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 63 1.00
ACGTcount: A:0.41, C:0.28, G:0.21, T:0.10
Consensus pattern (23 bp):
AAGGCATCACAGAATATGCCACA
Found at i:40597608 original size:69 final size:69
Alignment explanation
Indices: 40597497--40598382 Score: 1763
Period size: 69 Copynumber: 12.8 Consensus size: 69
40597487 AGTGTGCTCT
40597497 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGCCTGATATGAAATACCATGG
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGCCTGATATGAAATACCATGG
40597562 CAAC
66 CAAC
40597566 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGCCTGATATGAAATACCATGG
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGCCTGATATGAAATACCATGG
40597631 CAAC
66 CAAC
40597635 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGCCTGATATGAAATACCATGG
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGCCTGATATGAAATACCATGG
40597700 CAAC
66 CAAC
40597704 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGCCTGATATGAAATACCATGG
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGCCTGATATGAAATACCATGG
40597769 CAAC
66 CAAC
40597773 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGCCTGATATGAAATACCATGG
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGCCTGATATGAAATACCATGG
40597838 CAAC
66 CAAC
40597842 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGCCTGATATGAAATACCATGG
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGCCTGATATGAAATACCATGG
40597907 CAAC
66 CAAC
40597911 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGCCTGATATGAAATACCATGG
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGCCTGATATGAAATACCATGG
40597976 CAAC
66 CAAC
40597980 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGCCTGATATGAAATACCATGG
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGCCTGATATGAAATACCATGG
40598045 CAAC
66 CAAC
40598049 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGCCTGATATGAAATACCATGG
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGCCTGATATGAAATACCATGG
40598114 CAAC
66 CAAC
40598118 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGCCTGATATGAAATACCATGG
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGCCTGATATGAAATACCATGG
40598183 CAAC
66 CAAC
40598187 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGCCTGATATGAAATACCATGG
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGCCTGATATGAAATACCATGG
40598252 CAAC
66 CAAC
40598256 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGCCTGATATGAAATACCATGG
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGCCTGATATGAAATACCATGG
40598321 CAAC
66 CAAC
*
40598325 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAAT
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGCCTGATATGAAAT
40598383 GTGTAAGACC
Statistics
Matches: 816, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 816 1.00
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.23
Consensus pattern (69 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGCCTGATATGAAATACCATGG
CAAC
Found at i:40598362 original size:46 final size:46
Alignment explanation
Indices: 40598312--40598406 Score: 190
Period size: 46 Copynumber: 2.1 Consensus size: 46
40598302 CTGATATGAA
40598312 ATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAG
1 ATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAG
40598358 ATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAG
1 ATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAG
40598404 ATA
1 ATA
40598407 AAGACACTAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.24
Consensus pattern (46 bp):
ATACCATGGCAACCTGATATGAAATGTGTAAGACCATGGTTGAAAG
Found at i:40649081 original size:19 final size:19
Alignment explanation
Indices: 40649059--40649096 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
40649049 AGTTTTCAAT
40649059 TATTGTAAATT-TTTTTTAA
1 TATT-TAAATTATTTTTTAA
*
40649078 TATTTACATTATTTTTTAA
1 TATTTAAATTATTTTTTAA
40649097 AATACTGTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.63
Consensus pattern (19 bp):
TATTTAAATTATTTTTTAA
Found at i:40652850 original size:18 final size:18
Alignment explanation
Indices: 40652827--40652869 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
40652817 GAATAGGTTT
*
40652827 TTAATTAAACTATTTT-AA
1 TTAATTAAA-AATTTTAAA
40652845 TTAATTAAAAATTTTAAA
1 TTAATTAAAAATTTTAAA
40652863 TTAATTA
1 TTAATTA
40652870 CACGTTGAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (18 bp):
TTAATTAAAAATTTTAAA
Found at i:40668444 original size:126 final size:127
Alignment explanation
Indices: 40668196--40668552 Score: 500
Period size: 126 Copynumber: 2.8 Consensus size: 127
40668186 GAGAGGTCTG
* * *
40668196 TTTTAGGTCAGACGCACTGTTGTCAATCTGAGGTTGCTCCAAATCATCCATTAATGAAGAGGAAG
1 TTTTATGTCAGATGTACTGTTGTCAATCTGAGGTTGCTCCAAATCATCCATT-A-GAAGAGGAAG
* * * * *
40668261 TTGGCTGGCATGCCTCAAACTTAAAGTCGGCTGTATCGTAGGTAATCCGATTCTCTTCACCCTC
64 TTGGCTGGCATGCCTCGAACTTAAAGTCAGCTGCATCGTAGATAATCAGATTCTCTTCACCCTC
* * *
40668325 TTTTATGTCAGATTTACTGTTGTCAATCTGAGGTTTCTCCAAATCATCCATTA-AAGAGGATGTT
1 TTTTATGTCAGATGTACTGTTGTCAATCTGAGGTTGCTCCAAATCATCCATTAGAAGAGGAAGTT
* * *
40668389 GGCTGGCAAGCCTCGAACTTAAAGTCAGTTGCATTGTAGATAATCAGATTCTCTTCACCCTC
66 GGCTGGCATGCCTCGAACTTAAAGTCAGCTGCATCGTAGATAATCAGATTCTCTTCACCCTC
*
40668451 TTTTATGTCAGATGTACTGTTGTCAATCTGAGGTTGCTCCAAATCATCCATTACTGTAGAGGAAG
1 TTTTATGTCAGATGTACTGTTGTCAATCTGAGGTTGCTCCAAATCATCCATTA--GAAGAGGAAG
* * **
40668516 TTGTCTGGCATGCCTCGAACTTAGAGTTGGCTGCATC
64 TTGGCTGGCATGCCTCGAACTTAAAGTCAGCTGCATC
40668553 ATGGGCGATC
Statistics
Matches: 200, Mismatches: 25, Indels: 6
0.87 0.11 0.03
Matches are distributed among these distances:
126 115 0.57
128 1 0.00
129 84 0.42
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (127 bp):
TTTTATGTCAGATGTACTGTTGTCAATCTGAGGTTGCTCCAAATCATCCATTAGAAGAGGAAGTT
GGCTGGCATGCCTCGAACTTAAAGTCAGCTGCATCGTAGATAATCAGATTCTCTTCACCCTC
Found at i:40668897 original size:28 final size:28
Alignment explanation
Indices: 40668865--40668920 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
40668855 GTATACATAG
40668865 TTTGACAGATGCCAACATATAGTTAAAA
1 TTTGACAGATGCCAACATATAGTTAAAA
*
40668893 TTTGATAGATGCCAACATATAGTTAAAA
1 TTTGACAGATGCCAACATATAGTTAAAA
40668921 GAAAGAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.30
Consensus pattern (28 bp):
TTTGACAGATGCCAACATATAGTTAAAA
Found at i:40672429 original size:25 final size:25
Alignment explanation
Indices: 40672411--40672458 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
40672401 AATTTAGTAT
*
40672411 TTTTA-TTGTTTTAAGAATTTAATCA
1 TTTTACTTGATTTAA-AATTTAATCA
40672436 TTTTACTTGATTTAAAATTTAAT
1 TTTTACTTGATTTAAAATTTAAT
40672459 TGATAACATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 13 0.62
26 8 0.38
ACGTcount: A:0.33, C:0.04, G:0.06, T:0.56
Consensus pattern (25 bp):
TTTTACTTGATTTAAAATTTAATCA
Found at i:40680604 original size:5 final size:5
Alignment explanation
Indices: 40680594--40680665 Score: 64
Period size: 5 Copynumber: 14.8 Consensus size: 5
40680584 TGTTAAAAAA
* *
40680594 ATATT ATATT ATAGTA ATGATT ATGTT -T-TT ATATT ATATT ATTATT
1 ATATT ATATT ATA-TT AT-ATT ATATT ATATT ATATT ATATT A-TATT
40680640 A-A-T ATATT ATATT ATATT ATA-T ATAT
1 ATATT ATATT ATATT ATATT ATATT ATAT
40680666 ACATAAAACA
Statistics
Matches: 56, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
3 4 0.07
4 8 0.14
5 32 0.57
6 11 0.20
7 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (5 bp):
ATATT
Found at i:40680647 original size:19 final size:19
Alignment explanation
Indices: 40680623--40680665 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
40680613 ATTATGTTTT
40680623 TATATTATATTATTATTA-A
1 TATATTATATTA-TATTATA
40680642 TATATTATATTATATTATA
1 TATATTATATTATATTATA
40680661 TATAT
1 TATAT
40680666 ACATAAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TATATTATATTATATTATA
Found at i:40680697 original size:19 final size:19
Alignment explanation
Indices: 40680670--40680710 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
40680660 ATATATACAT
* *
40680670 AAAACAAAAGAAAGAATAG
1 AAAAAAAAAGAAAGAAAAG
40680689 AAAAAAAAAGAAAGAAAAG
1 AAAAAAAAAGAAAGAAAAG
40680708 AAA
1 AAA
40680711 CAGAATAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.80, C:0.02, G:0.15, T:0.02
Consensus pattern (19 bp):
AAAAAAAAAGAAAGAAAAG
Found at i:40680698 original size:15 final size:15
Alignment explanation
Indices: 40680675--40680720 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
40680665 TACATAAAAC
*
40680675 AAAAGAAAGAATAGA
1 AAAAAAAAGAATAGA
40680690 AAAAAAAAGAA-AGA
1 AAAAAAAAGAATAGA
*
40680704 AAAGAAACAGAATAGA
1 AAA-AAAAAGAATAGA
40680720 A
1 A
40680721 GAGACGAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
14 6 0.22
15 17 0.63
16 4 0.15
ACGTcount: A:0.76, C:0.02, G:0.17, T:0.04
Consensus pattern (15 bp):
AAAAAAAAGAATAGA
Found at i:40680777 original size:4 final size:4
Alignment explanation
Indices: 40680770--40680797 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
40680760 GAGAAGGAAG
40680770 GAAA GAAA GAAA GAAA GAAA GAAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA
40680798 AAGAAAAAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:40681679 original size:44 final size:45
Alignment explanation
Indices: 40681584--40681717 Score: 162
Period size: 44 Copynumber: 3.0 Consensus size: 45
40681574 ACAGGACAGA
* *
40681584 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
40681630 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * *
40681674 ACAGGAATAATTCATGTAAGTCCATGTTAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
40681718 CAGGATATTG
Statistics
Matches: 75, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
44 37 0.49
45 1 0.01
46 37 0.49
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:40684394 original size:40 final size:40
Alignment explanation
Indices: 40684348--40684430 Score: 139
Period size: 40 Copynumber: 2.1 Consensus size: 40
40684338 GGCTCGTAGG
*
40684348 TTAACTCAAATAATTTAATTGAATCGATTAAATTGATTGA
1 TTAACTCAAATAATTTAATTGAATCGATTAAATTGATTAA
* *
40684388 TTAACTCAACTAATTTAATTGAATCGATTAATTTGATTAA
1 TTAACTCAAATAATTTAATTGAATCGATTAAATTGATTAA
40684428 TTA
1 TTA
40684431 TTTTATGGAT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.42
Consensus pattern (40 bp):
TTAACTCAAATAATTTAATTGAATCGATTAAATTGATTAA
Found at i:40684421 original size:18 final size:18
Alignment explanation
Indices: 40684358--40684421 Score: 56
Period size: 18 Copynumber: 3.3 Consensus size: 18
40684348 TTAACTCAAA
40684358 TAATTTAATTGAATCGAT
1 TAATTTAATTGAATCGAT
* * * *
40684376 TAAATTGATTGATTAACTCAAC
1 TAATTTAATTG---AA-TCGAT
40684398 TAATTTAATTGAATCGAT
1 TAATTTAATTGAATCGAT
40684416 TAATTT
1 TAATTT
40684422 GATTAATTAT
Statistics
Matches: 34, Mismatches: 8, Indels: 8
0.68 0.16 0.16
Matches are distributed among these distances:
18 18 0.53
19 2 0.06
21 2 0.06
22 12 0.35
ACGTcount: A:0.39, C:0.08, G:0.09, T:0.44
Consensus pattern (18 bp):
TAATTTAATTGAATCGAT
Found at i:40692587 original size:18 final size:18
Alignment explanation
Indices: 40692564--40692656 Score: 132
Period size: 18 Copynumber: 5.2 Consensus size: 18
40692554 CCCAACTACT
*
40692564 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
*
40692582 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
*
40692600 GTATACGTAAATAGTACC
1 GTATACGTGAATAGTACC
* *
40692618 GTATACGTAAATAGTGCC
1 GTATACGTGAATAGTACC
*
40692636 GTATACGTGAATAGTATC
1 GTATACGTGAATAGTACC
40692654 GTA
1 GTA
40692657 AACGGTCGTA
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 67 1.00
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:40692616 original size:36 final size:36
Alignment explanation
Indices: 40692564--40692656 Score: 150
Period size: 36 Copynumber: 2.6 Consensus size: 36
40692554 CCCAACTACT
* *
40692564 GTATACGTGAACAGTACCGTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACCGTATACGTAAATAGTGCC
*
40692600 GTATACGTAAATAGTACCGTATACGTAAATAGTGCC
1 GTATACGTGAATAGTACCGTATACGTAAATAGTGCC
*
40692636 GTATACGTGAATAGTATCGTA
1 GTATACGTGAATAGTACCGTA
40692657 AACGGTCGTA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 52 1.00
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (36 bp):
GTATACGTGAATAGTACCGTATACGTAAATAGTGCC
Found at i:40697672 original size:27 final size:27
Alignment explanation
Indices: 40697634--40697688 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
40697624 AATGGAAAAT
40697634 AAGAAAAATTCATTTTTCTTCTTCAAC
1 AAGAAAAATTCATTTTTCTTCTTCAAC
40697661 AAGAAAAATTCATTTTTCTTCTTCAAC
1 AAGAAAAATTCATTTTTCTTCTTCAAC
40697688 A
1 A
40697689 TTTTGTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.38, C:0.18, G:0.04, T:0.40
Consensus pattern (27 bp):
AAGAAAAATTCATTTTTCTTCTTCAAC
Found at i:40707285 original size:21 final size:20
Alignment explanation
Indices: 40707255--40707294 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
40707245 CCGCCACTCT
40707255 TTCTCCCCCTTAC-CCTCCCC
1 TTCTCCCCCTT-CTCCTCCCC
40707275 TTCTCGCCCCTTCTCCTCCC
1 TTCTC-CCCCTTCTCCTCCC
40707295 GAACGCCACG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.03, C:0.62, G:0.03, T:0.33
Consensus pattern (20 bp):
TTCTCCCCCTTCTCCTCCCC
Found at i:40711086 original size:55 final size:55
Alignment explanation
Indices: 40711009--40711118 Score: 211
Period size: 55 Copynumber: 2.0 Consensus size: 55
40710999 GTGCTCCTAC
40711009 CATTTTCCCGTCTGGCCTTGGAGCAGAGTTCTATATGCATAACATGCCACCATAA
1 CATTTTCCCGTCTGGCCTTGGAGCAGAGTTCTATATGCATAACATGCCACCATAA
*
40711064 CATTTTCCCGTCTGGCCTTGGAGCGGAGTTCTATATGCATAACATGCCACCATAA
1 CATTTTCCCGTCTGGCCTTGGAGCAGAGTTCTATATGCATAACATGCCACCATAA
40711119 AAAAAATCCC
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.29
Consensus pattern (55 bp):
CATTTTCCCGTCTGGCCTTGGAGCAGAGTTCTATATGCATAACATGCCACCATAA
Found at i:40716782 original size:57 final size:57
Alignment explanation
Indices: 40716713--40716826 Score: 219
Period size: 57 Copynumber: 2.0 Consensus size: 57
40716703 GTTCTTGCAA
40716713 CTCTTCTTAAATGTAATGTGATGTACAAATTGAGCCTTTTATTAACCTTAGGGGCTG
1 CTCTTCTTAAATGTAATGTGATGTACAAATTGAGCCTTTTATTAACCTTAGGGGCTG
*
40716770 CTCTTCTTAAATGTAATGTGATGTACAAATTGAGCCTTTTATTAACCTTATGGGCTG
1 CTCTTCTTAAATGTAATGTGATGTACAAATTGAGCCTTTTATTAACCTTAGGGGCTG
40716827 GATGAGGTTT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.39
Consensus pattern (57 bp):
CTCTTCTTAAATGTAATGTGATGTACAAATTGAGCCTTTTATTAACCTTAGGGGCTG
Found at i:40726972 original size:18 final size:18
Alignment explanation
Indices: 40726951--40727000 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
40726941 ATTATTATTA
40726951 TTATTTATATATATCATC
1 TTATTTATATATATCATC
*
40726969 TTATTATATATTTAT-ATC
1 TTATT-TATATATATCATC
40726987 TTA-TTATATATATC
1 TTATTTATATATATC
40727001 TATATATCTC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
16 8 0.29
17 1 0.04
18 11 0.39
19 8 0.29
ACGTcount: A:0.34, C:0.08, G:0.00, T:0.58
Consensus pattern (18 bp):
TTATTTATATATATCATC
Found at i:40726974 original size:21 final size:19
Alignment explanation
Indices: 40726948--40727005 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 19
40726938 ATTATTATTA
40726948 TTATTATTTATATATATCATC
1 TTATTA-TTATATATAT-ATC
*
40726969 TTATTA-TATATTTATATC
1 TTATTATTATATATATATC
*
40726987 TTATTATATATATCTATAT
1 TTATTAT-TATATATATAT
40727006 ATCTCTTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
18 9 0.27
19 8 0.24
20 10 0.30
21 6 0.18
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (19 bp):
TTATTATTATATATATATC
Found at i:40730630 original size:9 final size:9
Alignment explanation
Indices: 40730616--40730700 Score: 104
Period size: 9 Copynumber: 9.3 Consensus size: 9
40730606 TCAGGCTCAA
40730616 AAAAAAATC
1 AAAAAAATC
40730625 -AAAAAATC
1 AAAAAAATC
40730633 AAAAAAATC
1 AAAAAAATC
40730642 AAAAAAATC
1 AAAAAAATC
*
40730651 AAAAACAATGAA
1 AAAAA-AAT--C
40730663 AAAAAAATC
1 AAAAAAATC
40730672 AAAAAAAATC
1 -AAAAAAATC
40730682 --AAAAATC
1 AAAAAAATC
40730689 AAAAAAATC
1 AAAAAAATC
40730698 AAA
1 AAA
40730701 GTCAAAATAG
Statistics
Matches: 67, Mismatches: 2, Indels: 14
0.81 0.02 0.17
Matches are distributed among these distances:
7 7 0.10
8 8 0.12
9 32 0.48
10 12 0.18
11 3 0.04
12 5 0.07
ACGTcount: A:0.78, C:0.11, G:0.01, T:0.11
Consensus pattern (9 bp):
AAAAAAATC
Found at i:40730695 original size:10 final size:10
Alignment explanation
Indices: 40730615--40730686 Score: 89
Period size: 10 Copynumber: 7.5 Consensus size: 10
40730605 TTCAGGCTCA
40730615 AAAAAAAATC
1 AAAAAAAATC
40730625 --AAAAAATC
1 AAAAAAAATC
40730633 -AAAAAAATC
1 AAAAAAAATC
40730642 -AAAAAAATC
1 AAAAAAAATC
* *
40730651 AAAAACAATGA
1 AAAAAAAAT-C
40730662 AAAAAAAATC
1 AAAAAAAATC
40730672 AAAAAAAATC
1 AAAAAAAATC
40730682 AAAAA
1 AAAAA
40730687 TCAAAAAAAT
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
8 8 0.15
9 17 0.31
10 22 0.40
11 8 0.15
ACGTcount: A:0.79, C:0.10, G:0.01, T:0.10
Consensus pattern (10 bp):
AAAAAAAATC
Found at i:40730695 original size:30 final size:29
Alignment explanation
Indices: 40730633--40730695 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 29
40730623 TCAAAAAATC
40730633 AAAAAAATCAAAAAAATCAAAAACAATGAA
1 AAAAAAATCAAAAAAATCAAAAACAA-GAA
40730663 AAAAAAATCAAAAAAAATCAAAAATCAA-AA
1 AAAAAAATC-AAAAAAATCAAAAA-CAAGAA
40730693 AAA
1 AAA
40730696 TCAAAGTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
30 14 0.45
31 14 0.45
32 3 0.10
ACGTcount: A:0.79, C:0.10, G:0.02, T:0.10
Consensus pattern (29 bp):
AAAAAAATCAAAAAAATCAAAAACAAGAA
Found at i:40730722 original size:6 final size:6
Alignment explanation
Indices: 40730713--40730747 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
40730703 CAAAATAGGA
*
40730713 AAAAAG AAAAAG AAAAA- AAGAAG AAAAAG AAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
40730748 GAGAGGTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:40730736 original size:17 final size:16
Alignment explanation
Indices: 40730712--40730746 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
40730702 TCAAAATAGG
40730712 AAAAAAGAAAAAGAAA
1 AAAAAAGAAAAAGAAA
40730728 AAAAGAAGAAAAAGAAA
1 AAAA-AAGAAAAAGAAA
40730745 AA
1 AA
40730747 GGAGAGGTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (16 bp):
AAAAAAGAAAAAGAAA
Found at i:40731567 original size:16 final size:18
Alignment explanation
Indices: 40731545--40731591 Score: 80
Period size: 16 Copynumber: 2.7 Consensus size: 18
40731535 GAGTCAAGAA
40731545 AAAAATGAAAAAAAA-TG
1 AAAAATGAAAAAAAATTG
40731562 -AAAATGAAAAAAAATTG
1 AAAAATGAAAAAAAATTG
40731579 AAAAATGAAAAAA
1 AAAAATGAAAAAA
40731592 TAAAAAAGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
16 14 0.50
17 2 0.07
18 12 0.43
ACGTcount: A:0.77, C:0.00, G:0.11, T:0.13
Consensus pattern (18 bp):
AAAAATGAAAAAAAATTG
Found at i:40731573 original size:18 final size:18
Alignment explanation
Indices: 40731545--40731591 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
40731535 GAGTCAAGAA
40731545 AAAAATG-AAAAAAAATG
1 AAAAATGAAAAAAAAATG
*
40731562 -AAAATGAAAAAAAATTG
1 AAAAATGAAAAAAAAATG
40731579 AAAAATGAAAAAA
1 AAAAATGAAAAAA
40731592 TAAAAAAGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 6 0.22
17 9 0.33
18 12 0.44
ACGTcount: A:0.77, C:0.00, G:0.11, T:0.13
Consensus pattern (18 bp):
AAAAATGAAAAAAAAATG
Found at i:40731592 original size:16 final size:17
Alignment explanation
Indices: 40731545--40731591 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
40731535 GAGTCAAGAA
*
40731545 AAAAATGAAAAAAAATG
1 AAAAATGAAAAAAATTG
40731562 -AAAATGAAAAAAAATTG
1 AAAAATG-AAAAAAATTG
40731579 AAAAATGAAAAAA
1 AAAAATGAAAAAA
40731592 TAAAAAAGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 6 0.22
17 15 0.56
18 6 0.22
ACGTcount: A:0.77, C:0.00, G:0.11, T:0.13
Consensus pattern (17 bp):
AAAAATGAAAAAAATTG
Found at i:40731605 original size:16 final size:16
Alignment explanation
Indices: 40731553--40731605 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
40731543 AAAAAAATGA
* *
40731553 AAAAAAATGAAAATGA
1 AAAAAAATGAAAAAGT
40731569 AAAAAAATTGAAAAA-T
1 AAAAAAA-TGAAAAAGT
* *
40731585 GAAAAAATAAAAAAGT
1 AAAAAAATGAAAAAGT
40731601 AAAAA
1 AAAAA
40731606 TAGAGAGGCT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
15 6 0.20
16 18 0.60
17 6 0.20
ACGTcount: A:0.77, C:0.00, G:0.09, T:0.13
Consensus pattern (16 bp):
AAAAAAATGAAAAAGT
Found at i:40731718 original size:21 final size:21
Alignment explanation
Indices: 40731692--40731736 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
40731682 TCAAATATTA
40731692 ATCAGAATGGGGCATGAAGTG
1 ATCAGAATGGGGCATGAAGTG
* *
40731713 ATCAGATTGGGGCATGCAGTG
1 ATCAGAATGGGGCATGAAGTG
40731734 ATC
1 ATC
40731737 TTGCTATACC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.29, C:0.13, G:0.36, T:0.22
Consensus pattern (21 bp):
ATCAGAATGGGGCATGAAGTG
Found at i:40732876 original size:43 final size:43
Alignment explanation
Indices: 40732827--40732964 Score: 129
Period size: 43 Copynumber: 3.2 Consensus size: 43
40732817 GAAGCAGGTC
40732827 GAAGACACAAACCTTGCCTCTCTCGGTTATGATGGAGCTGGTT
1 GAAGACACAAACCTTGCCTCTCTCGGTTATGATGGAGCTGGTT
* * * * * * *
40732870 GAAGACAAAAGATCTTGCCT-TC-CTG-CATTGACAGCGAAGCAGGTC
1 GAAGACACAA-ACCTTGCCTCTCTCGGTTA-TGA-TG-G-AGCTGGTT
* *
40732915 GAAGACACAAACCTTGCCTCTCTTGGTTGTGATGGAGCTGGTT
1 GAAGACACAAACCTTGCCTCTCTCGGTTATGATGGAGCTGGTT
40732958 GAAGACA
1 GAAGACA
40732965 AAAGATCTTG
Statistics
Matches: 71, Mismatches: 16, Indels: 16
0.69 0.16 0.16
Matches are distributed among these distances:
41 1 0.01
42 5 0.07
43 25 0.35
44 18 0.25
45 18 0.25
46 4 0.06
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.25
Consensus pattern (43 bp):
GAAGACACAAACCTTGCCTCTCTCGGTTATGATGGAGCTGGTT
Found at i:40732887 original size:44 final size:44
Alignment explanation
Indices: 40732839--40732977 Score: 133
Period size: 44 Copynumber: 3.2 Consensus size: 44
40732829 AGACACAAAC
40732839 CTTGCCTCTCTCGGTTATGATGGAGCTGGTTGAAGACAAAAGAT
1 CTTGCCTCTCTCGGTTATGATGGAGCTGGTTGAAGACAAAAGAT
* * * * * * *
40732883 CTTGCCT-TC-CTG-CATTGACAGCGAAGCAGGTCGAAGACACAA-AC
1 CTTGCCTCTCTCGGTTA-TGA-TG-G-AGCTGGTTGAAGACAAAAGAT
* *
40732927 CTTGCCTCTCTTGGTTGTGATGGAGCTGGTTGAAGACAAAAGAT
1 CTTGCCTCTCTCGGTTATGATGGAGCTGGTTGAAGACAAAAGAT
40732971 CTTGCCT
1 CTTGCCT
40732978 TCAGACAATA
Statistics
Matches: 71, Mismatches: 16, Indels: 16
0.69 0.16 0.16
Matches are distributed among these distances:
41 1 0.01
42 5 0.07
43 18 0.25
44 25 0.35
45 18 0.25
46 4 0.06
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.27
Consensus pattern (44 bp):
CTTGCCTCTCTCGGTTATGATGGAGCTGGTTGAAGACAAAAGAT
Found at i:40732948 original size:88 final size:88
Alignment explanation
Indices: 40732791--40733252 Score: 462
Period size: 88 Copynumber: 5.0 Consensus size: 88
40732781 ATGAAGTTGC
* *
40732791 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTA
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTTGGTTG
40732856 TGATGGAGCTGGTTGAAGACAAA
66 TGATGGAGCTGGTTGAAGACAAA
40732879 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTTGGTTG
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTTGGTTG
40732944 TGATGGAGCTGGTTGAAGACAAA
66 TGATGGAGCTGGTTGAAGACAAA
* * * **** ** * ** ***
40732967 AGATCTTGCCTT-CAGACAATAGATCTTGCCTTCCTACATTGACAG-CGAAGCAGGTCGAAGACA
1 AGATCTTGCCTTCCTG-C-ATTGA-C-AGCGAAGC-AGGTCGA-AGAC--A-CA-AACCTTG-C-
* * *
40733030 CAAAC-CTTGCCTCTCTCGGTTGTGATGGAGCTGGTTAAAGACAAC
54 C--TCTCTT---------GGTTGTGATGGAGCTGGTTGAAGACAAA
* *
40733075 AGATCTTGCCTTCCTGCATTGACAGTGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTTGGTTA
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTTGGTTG
* *
40733140 TGATGGAGCTGGTTGAAGAGAAT
66 TGATGGAGCTGGTTGAAGACAAA
* *
40733163 AGATCTTGCCTTCCTACATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTTGGTTG
40733228 TGATGGAGCTGGTTGAAGACAAA
66 TGATGGAGCTGGTTGAAGACAAA
40733251 AG
1 AG
40733253 NNNNNNNNNN
Statistics
Matches: 301, Mismatches: 47, Indels: 52
0.75 0.12 0.13
Matches are distributed among these distances:
87 2 0.01
88 207 0.69
89 4 0.01
90 1 0.00
91 3 0.01
92 5 0.02
93 2 0.01
94 1 0.00
95 2 0.01
96 3 0.01
97 4 0.01
98 2 0.01
99 4 0.01
100 3 0.01
101 2 0.01
102 1 0.00
103 2 0.01
104 5 0.02
105 2 0.01
106 1 0.00
107 4 0.01
108 39 0.13
109 2 0.01
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (88 bp):
AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTTGGTTG
TGATGGAGCTGGTTGAAGACAAA
Found at i:40732985 original size:20 final size:20
Alignment explanation
Indices: 40732960--40732999 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
40732950 AGCTGGTTGA
40732960 AGACAAAAGATCTTGCCTTC
1 AGACAAAAGATCTTGCCTTC
*
40732980 AGACAATAGATCTTGCCTTC
1 AGACAAAAGATCTTGCCTTC
40733000 CTACATTGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.28
Consensus pattern (20 bp):
AGACAAAAGATCTTGCCTTC
Found at i:40733061 original size:108 final size:108
Alignment explanation
Indices: 40732872--40733087 Score: 387
Period size: 108 Copynumber: 2.0 Consensus size: 108
40732862 AGCTGGTTGA
*
40732872 AGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTC
1 AGACAAAAGATCTTGCCTTCCTACATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTC
* *
40732937 TTGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTC
66 TCGGTTGTGATGGAGCTGGTTAAAGACAAAAGATCTTGCCTTC
*
40732980 AGACAATAGATCTTGCCTTCCTACATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTC
1 AGACAAAAGATCTTGCCTTCCTACATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTC
*
40733045 TCGGTTGTGATGGAGCTGGTTAAAGACAACAGATCTTGCCTTC
66 TCGGTTGTGATGGAGCTGGTTAAAGACAAAAGATCTTGCCTTC
40733088 CTGCATTGAC
Statistics
Matches: 103, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
108 103 1.00
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.25
Consensus pattern (108 bp):
AGACAAAAGATCTTGCCTTCCTACATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTC
TCGGTTGTGATGGAGCTGGTTAAAGACAAAAGATCTTGCCTTC
Found at i:40733083 original size:44 final size:44
Alignment explanation
Indices: 40733023--40733249 Score: 155
Period size: 44 Copynumber: 5.2 Consensus size: 44
40733013 GAAGCAGGTC
40733023 GAAGAC-ACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTT
1 GAAGACAACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTT
* * * * ** * * *
40733066 AAAGACAACAGATCTTGCCT-TC-CTGCATTGACAGTGAAGCAGGTC
1 GAAGACAACAAACCTTGCCTCTCTC-G-GTTGTGA-TGGAGCTGGTT
* *
40733111 GAAGAC-ACAAACCTTGCCTCTCTTGGTTATGATGGAGCTGGTT
1 GAAGACAACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTT
* * * * * ** * *
40733154 GAAGAGAATAGATCTTGCCT-TCCTAC-ATTGACA-GCGAAGCAGGTC
1 GAAGACAACAAACCTTGCCTCT-CT-CGGTTGTGATG-G-AGCTGGTT
40733199 GAAGAC-ACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTT
1 GAAGACAACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTT
40733242 GAAGACAA
1 GAAGACAA
40733250 AAGNNNNNNN
Statistics
Matches: 129, Mismatches: 40, Indels: 29
0.65 0.20 0.15
Matches are distributed among these distances:
42 1 0.01
43 36 0.28
44 63 0.49
45 29 0.22
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.25
Consensus pattern (44 bp):
GAAGACAACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTT
Found at i:40735368 original size:18 final size:18
Alignment explanation
Indices: 40735347--40735395 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
40735337 TTATTATAAC
40735347 TATTTATATATATCATCT
1 TATTTATATATATCATCT
*
40735365 TATTATATATTTAT-ATCT
1 TATT-TATATATATCATCT
*
40735383 GA-TTATATATATC
1 TATTTATATATATC
40735396 TATATATCCC
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
16 8 0.31
17 1 0.04
18 9 0.35
19 8 0.31
ACGTcount: A:0.35, C:0.08, G:0.02, T:0.55
Consensus pattern (18 bp):
TATTTATATATATCATCT
Found at i:40746051 original size:37 final size:37
Alignment explanation
Indices: 40745990--40746135 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
40745980 TACGTATGAT
* *
40745990 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
40746025 CACCTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
40746062 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
40746099 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
40746136 TAAAGCTATC
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 9 0.09
36 3 0.03
37 92 0.88
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:40746178 original size:52 final size:52
Alignment explanation
Indices: 40746110--40746989 Score: 1679
Period size: 52 Copynumber: 16.9 Consensus size: 52
40746100 ACTTATCACT
* ** * *
40746110 TTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTTCAC
1 TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATTACTTATCACTTTCCAC
40746162 TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATTACTTATCACTTTCCAC
1 TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATTACTTATCACTTTCCAC
40746214 TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATTACTTATCACTTTCCAC
1 TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATTACTTATCACTTTCCAC
40746266 TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATTACTTATCACTTTCCAC
1 TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATTACTTATCACTTTCCAC
40746318 TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATTACTTATCACTTTCCAC
1 TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATTACTTATCACTTTCCAC
40746370 TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATTACTTATCACTTTCCAC
1 TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATTACTTATCACTTTCCAC
40746422 TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATTACTTATCACTTTCCAC
1 TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATTACTTATCACTTTCCAC
40746474 TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATTACTTATCACTTTCCAC
1 TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATTACTTATCACTTTCCAC
40746526 TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATTACTTATCACTTTCCAC
1 TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATTACTTATCACTTTCCAC
40746578 TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATTACTTATCACTTTCCAC
1 TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATTACTTATCACTTTCCAC
40746630 TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATTACTTATCACTTTCCAC
1 TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATTACTTATCACTTTCCAC
40746682 TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATTACTTATCACTTTCCAC
1 TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATTACTTATCACTTTCCAC
40746734 TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATTACTTATCACTTTCCAC
1 TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATTACTTATCACTTTCCAC
40746786 TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATTACTTATCACTTTCCAC
1 TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATTACTTATCACTTTCCAC
40746838 TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATTACTTATCACTTTCCAC
1 TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATTACTTATCACTTTCCAC
40746890 TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATTACTTATCACTTTCCAC
1 TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATTACTTATCACTTTCCAC
** **
40746942 TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTT
1 TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATTACTTATCACTTT
40746990 GTCACTTGAT
Statistics
Matches: 819, Mismatches: 9, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 819 1.00
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (52 bp):
TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATTACTTATCACTTTCCAC
Found at i:40748718 original size:147 final size:147
Alignment explanation
Indices: 40748451--40748741 Score: 501
Period size: 147 Copynumber: 2.0 Consensus size: 147
40748441 TTGGGTCCTA
* *
40748451 ACTTTATTAAGCAAATTTTGCAATTTTCCAATTTTGCCCTTAATTCTCCTTACTTTCTTGCTGAT
1 ACTTTATTAAGCAAATTTTGCAATATTCCAATTTTGCCCTTAATTATCCTTACTTTCTTGCTGAT
*
40748516 TTCATGCCTCTGCCGTCCAGCCCAAATAGACCTTGGGTCTATTTGCCTTTAAAGCCCTCTTCCTT
66 TTCATGCCTCTGCCGCCCAGCCCAAATAGACCTTGGGTCTATTTGCCTTTAAAGCCCTCTTCCTT
40748581 TTATCATTTAAGCTCTT
131 TTATCATTTAAGCTCTT
* * *
40748598 ACTTTATTAAGTAAATTTTGCAATATTCTAATTTTGCCCTTAATTATCCTTACTTTGTTGCTGAT
1 ACTTTATTAAGCAAATTTTGCAATATTCCAATTTTGCCCTTAATTATCCTTACTTTCTTGCTGAT
* * *
40748663 TTCATGTCTTTGCCGCCCAGCCCAAATAGACCTTGGGTCTATTTGCCTTTTAAGCCCTCTTCCTT
66 TTCATGCCTCTGCCGCCCAGCCCAAATAGACCTTGGGTCTATTTGCCTTTAAAGCCCTCTTCCTT
40748728 TTATCATTTAAGCT
131 TTATCATTTAAGCT
40748742 ATTTAATCAT
Statistics
Matches: 135, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
147 135 1.00
ACGTcount: A:0.21, C:0.25, G:0.11, T:0.43
Consensus pattern (147 bp):
ACTTTATTAAGCAAATTTTGCAATATTCCAATTTTGCCCTTAATTATCCTTACTTTCTTGCTGAT
TTCATGCCTCTGCCGCCCAGCCCAAATAGACCTTGGGTCTATTTGCCTTTAAAGCCCTCTTCCTT
TTATCATTTAAGCTCTT
Found at i:40749760 original size:24 final size:24
Alignment explanation
Indices: 40749733--40749781 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
40749723 ACATAGCTTC
40749733 TTACACTAAGAGTTGTAGCCGGTG
1 TTACACTAAGAGTTGTAGCCGGTG
* * *
40749757 TTACACTAGGAGTTGTCGCTGGTG
1 TTACACTAAGAGTTGTAGCCGGTG
40749781 T
1 T
40749782 CCACGACGGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.20, C:0.16, G:0.31, T:0.33
Consensus pattern (24 bp):
TTACACTAAGAGTTGTAGCCGGTG
Found at i:40750079 original size:9 final size:9
Alignment explanation
Indices: 40750065--40750090 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
40750055 CATGTTCTTT
40750065 GGTGTTTTA
1 GGTGTTTTA
40750074 GGTGTTTTA
1 GGTGTTTTA
40750083 GGTGTTTT
1 GGTGTTTT
40750091 TGGAACCGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.08, C:0.00, G:0.35, T:0.58
Consensus pattern (9 bp):
GGTGTTTTA
Found at i:40750754 original size:32 final size:32
Alignment explanation
Indices: 40750697--40751003 Score: 436
Period size: 32 Copynumber: 9.3 Consensus size: 32
40750687 TGAAATCGTA
40750697 TCTCCTGTTCACATCA-TTCTTGCAGGGAATC
1 TCTCCTGTTCACATCATTTCTTGCAGGGAATC
*
40750728 TCTCCTGTTCACATCATTTCTTGCAGGGAATA
1 TCTCCTGTTCACATCATTTCTTGCAGGGAATC
*
40750760 TTTCCTGTTCACATCATTTCTTGCAGGGAATC
1 TCTCCTGTTCACATCATTTCTTGCAGGGAATC
* *
40750792 TCTCCTGTTCACGCATTATTTTGTTGCAGGGAATC
1 TCTCCTGTTCA--CATCA-TTTCTTGCAGGGAATC
* *
40750827 TCTCCTGTTCACACATTATTTTGTTGCAGGGAATC
1 TCTCCTGTT--CACATCA-TTTCTTGCAGGGAATC
*
40750862 TTTCCTGTTCACATCATTTCTTGCAGGGAATC
1 TCTCCTGTTCACATCATTTCTTGCAGGGAATC
* * *
40750894 TCTCCTGTTCACGGATTATTTTGTTACAGGGAATC
1 TCTCCTGTTCAC--ATCA-TTTCTTGCAGGGAATC
40750929 TCTCCTGTTCACATCATTTCTTGCAGGGAATC
1 TCTCCTGTTCACATCATTTCTTGCAGGGAATC
40750961 TCTCCTGTTCACATCATTTCTTGCAGGGAATC
1 TCTCCTGTTCACATCATTTCTTGCAGGGAATC
40750993 TCTCCTGTTCA
1 TCTCCTGTTCA
40751004 TGTATTATTT
Statistics
Matches: 251, Mismatches: 16, Indels: 17
0.88 0.06 0.06
Matches are distributed among these distances:
31 16 0.06
32 137 0.55
33 9 0.04
34 7 0.03
35 80 0.32
37 2 0.01
ACGTcount: A:0.19, C:0.25, G:0.17, T:0.39
Consensus pattern (32 bp):
TCTCCTGTTCACATCATTTCTTGCAGGGAATC
Found at i:40750875 original size:102 final size:99
Alignment explanation
Indices: 40750716--40751013 Score: 497
Period size: 102 Copynumber: 3.0 Consensus size: 99
40750706 CACATCATTC
*
40750716 TTGCAGGGAATCTCTCCTGTTCACATCATTTCTTGCAGGGAATATTTCCTGTTCACATCATTTCT
1 TTGCAGGGAATCTCTCCTGTTCACATCATTTCTTGCAGGGAATCTTTCCTGTTCACATCATTTCT
40750781 TGCAGGGAATCTCTCCTGTTCACGCATTATTTTG
66 TGCAGGGAATCTCTCCTGTTCACGCATTATTTTG
* *
40750815 TTGCAGGGAATCTCTCCTGTTCACACATTATTTTGTTGCAGGGAATCTTTCCTGTTCACATCATT
1 TTGCAGGGAATCTCTCCTGTT--CACATCA-TTTCTTGCAGGGAATCTTTCCTGTTCACATCATT
*
40750880 TCTTGCAGGGAATCTCTCCTGTTCACGGATTATTTTG
63 TCTTGCAGGGAATCTCTCCTGTTCACGCATTATTTTG
* *
40750917 TTACAGGGAATCTCTCCTGTTCACATCATTTCTTGCAGGGAATCTCTCCTGTTCACATCATTTCT
1 TTGCAGGGAATCTCTCCTGTTCACATCATTTCTTGCAGGGAATCTTTCCTGTTCACATCATTTCT
* *
40750982 TGCAGGGAATCTCTCCTGTTCATGTATTATTT
66 TGCAGGGAATCTCTCCTGTTCACGCATTATTT
40751014 CTTTTTGGAC
Statistics
Matches: 186, Mismatches: 10, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
99 86 0.46
100 6 0.03
101 6 0.03
102 88 0.47
ACGTcount: A:0.19, C:0.24, G:0.17, T:0.40
Consensus pattern (99 bp):
TTGCAGGGAATCTCTCCTGTTCACATCATTTCTTGCAGGGAATCTTTCCTGTTCACATCATTTCT
TGCAGGGAATCTCTCCTGTTCACGCATTATTTTG
Found at i:40750886 original size:67 final size:64
Alignment explanation
Indices: 40750697--40751003 Score: 436
Period size: 67 Copynumber: 4.7 Consensus size: 64
40750687 TGAAATCGTA
*
40750697 TCTCCTGTTCACATCA-TTCTTGCAGGGAATCTCTCCTGTTCACATCATTTCTTGCAGGGAATA
1 TCTCCTGTTCACATCATTTCTTGCAGGGAATCTCTCCTGTTCACATCATTTCTTGCAGGGAATC
* * *
40750760 TTTCCTGTTCACATCATTTCTTGCAGGGAATCTCTCCTGTTCACGCATTATTTTGTTGCAGGGAA
1 TCTCCTGTTCACATCATTTCTTGCAGGGAATCTCTCCTGTTCA--CATCA-TTTCTTGCAGGGAA
40750825 TC
63 TC
* * *
40750827 TCTCCTGTTCACACATTATTTTGTTGCAGGGAATCTTTCCTGTTCACATCATTTCTTGCAGGGAA
1 TCTCCTGTT--CACATCA-TTTCTTGCAGGGAATCTCTCCTGTTCACATCATTTCTTGCAGGGAA
40750892 TC
63 TC
* * *
40750894 TCTCCTGTTCACGGATTATTTTGTTACAGGGAATCTCTCCTGTTCACATCATTTCTTGCAGGGAA
1 TCTCCTGTTCAC--ATCA-TTTCTTGCAGGGAATCTCTCCTGTTCACATCATTTCTTGCAGGGAA
40750959 TC
63 TC
40750961 TCTCCTGTTCACATCATTTCTTGCAGGGAATCTCTCCTGTTCA
1 TCTCCTGTTCACATCATTTCTTGCAGGGAATCTCTCCTGTTCA
40751004 TGTATTATTT
Statistics
Matches: 220, Mismatches: 15, Indels: 17
0.87 0.06 0.07
Matches are distributed among these distances:
63 15 0.07
64 51 0.23
65 6 0.03
66 4 0.02
67 109 0.50
68 4 0.02
69 6 0.03
70 25 0.11
ACGTcount: A:0.19, C:0.25, G:0.17, T:0.39
Consensus pattern (64 bp):
TCTCCTGTTCACATCATTTCTTGCAGGGAATCTCTCCTGTTCACATCATTTCTTGCAGGGAATC
Found at i:40753844 original size:21 final size:22
Alignment explanation
Indices: 40753814--40753858 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
40753804 GAGCAAATTG
40753814 TTGATTCTATTTCCTTTTT-TAT
1 TTGATTCTA-TTCCTTTTTGTAT
*
40753836 TTGA-TCTATTCTTTTTTGTAT
1 TTGATTCTATTCCTTTTTGTAT
40753857 TT
1 TT
40753859 CTCTTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 8 0.38
21 9 0.43
22 4 0.19
ACGTcount: A:0.13, C:0.11, G:0.07, T:0.69
Consensus pattern (22 bp):
TTGATTCTATTCCTTTTTGTAT
Found at i:40755905 original size:35 final size:35
Alignment explanation
Indices: 40755861--40756020 Score: 227
Period size: 35 Copynumber: 4.7 Consensus size: 35
40755851 TTCACTTGTC
* *
40755861 TTTTCTTGCAGGGAATATTTCCTGTTCACGCATTA
1 TTTTGTTGCAGGGAATCTTTCCTGTTCACGCATTA
* *
40755896 TTCTGTTGCAGGGAATCTTTCCTGTTCA--CATCA
1 TTTTGTTGCAGGGAATCTTTCCTGTTCACGCATTA
* *
40755929 -TTTCTTGCAGGGAATCTCTCCTGTTCACGCATTA
1 TTTTGTTGCAGGGAATCTTTCCTGTTCACGCATTA
* *
40755963 TTTTGTTGCAGGGAATCTCTCCTGTTCACACATTA
1 TTTTGTTGCAGGGAATCTTTCCTGTTCACGCATTA
40755998 TTTTGTTGCAGGGAATCTTTCCT
1 TTTTGTTGCAGGGAATCTTTCCT
40756021 TAAATATTTA
Statistics
Matches: 111, Mismatches: 11, Indels: 6
0.87 0.09 0.05
Matches are distributed among these distances:
32 24 0.22
33 4 0.04
34 4 0.04
35 79 0.71
ACGTcount: A:0.18, C:0.23, G:0.18, T:0.41
Consensus pattern (35 bp):
TTTTGTTGCAGGGAATCTTTCCTGTTCACGCATTA
Found at i:40755970 original size:67 final size:69
Alignment explanation
Indices: 40755861--40756020 Score: 243
Period size: 67 Copynumber: 2.3 Consensus size: 69
40755851 TTCACTTGTC
* *
40755861 TTTTCTTGCAGGGAATATTTCCTGTTCACGCATTATTCTGTTGCAGGGAATCTTTCCTGTT-CAC
1 TTTTCTTGCAGGGAATCTTTCCTGTTCACGCATTATTCTGTTGCAGGGAATCTCTCCTGTTACAC
40755925 ATCA
66 ATCA
* *
40755929 -TTTCTTGCAGGGAATCTCTCCTGTTCACGCATTATTTTGTTGCAGGGAATCTCTCCTGTTCACA
1 TTTTCTTGCAGGGAATCTTTCCTGTTCACGCATTATTCTGTTGCAGGGAATCTCTCCTGTT-ACA
*
40755993 CATTA
65 CATCA
*
40755998 TTTTGTTGCAGGGAATCTTTCCT
1 TTTTCTTGCAGGGAATCTTTCCT
40756021 TAAATATTTA
Statistics
Matches: 82, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
67 56 0.68
69 6 0.07
70 20 0.24
ACGTcount: A:0.18, C:0.23, G:0.18, T:0.41
Consensus pattern (69 bp):
TTTTCTTGCAGGGAATCTTTCCTGTTCACGCATTATTCTGTTGCAGGGAATCTCTCCTGTTACAC
ATCA
Found at i:40760240 original size:53 final size:53
Alignment explanation
Indices: 40760159--40760309 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
40760149 CTTACACGGT
* *
40760159 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
40760214 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** *
40760267 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
40760310 GCACACTTAT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:40762853 original size:25 final size:24
Alignment explanation
Indices: 40762778--40762974 Score: 160
Period size: 25 Copynumber: 8.4 Consensus size: 24
40762768 CACTAATGAA
*
40762778 CAGAGAGCACTGAAGTGCT-ATA-
1 CAGAGAGCACTGACGTGCTAATAT
** *
40762800 CAGAGAGCACAAATGTGCT-A-AT
1 CAGAGAGCACTGACGTGCTAATAT
40762822 CAGAGAGCACTGACGTGCTAAATAT
1 CAGAGAGCACTGACGTGCT-AATAT
*
40762847 CAGAGAGCACT-AGCGTGCTAGTAAT
1 CAGAGAGCACTGA-CGTGCTAAT-AT
*
40762872 CAGAGAGCACTGGCGTGCTAAATAT
1 CAGAGAGCACTGACGTGCT-AATAT
** *
40762897 CAGAGAGCACAAATGTGCT-A-AT
1 CAGAGAGCACTGACGTGCTAATAT
* *
40762919 CAGTGAGCACTGGCGTGCTAAATAT
1 CAGAGAGCACTGACGTGCT-AATAT
** *
40762944 CAGAGAGCACAAATGTGCT-A-AT
1 CAGAGAGCACTGACGTGCTAATAT
40762966 CAGAGAGCA
1 CAGAGAGCA
40762975 TGCTGAAGTC
Statistics
Matches: 141, Mismatches: 23, Indels: 22
0.76 0.12 0.12
Matches are distributed among these distances:
21 1 0.01
22 60 0.43
23 2 0.01
24 5 0.04
25 71 0.50
26 2 0.01
ACGTcount: A:0.36, C:0.19, G:0.26, T:0.19
Consensus pattern (24 bp):
CAGAGAGCACTGACGTGCTAATAT
Found at i:40762854 original size:47 final size:47
Alignment explanation
Indices: 40762778--40762974 Score: 283
Period size: 47 Copynumber: 4.2 Consensus size: 47
40762768 CACTAATGAA
*
40762778 CAGAGAGCACTGAAGTGCT--ATA-CAGAGAGCACAAATGTGCTAAT
1 CAGAGAGCACTGACGTGCTAAATATCAGAGAGCACAAATGTGCTAAT
* **
40762822 CAGAGAGCACTGACGTGCTAAATATCAGAGAGCACTAGCGTGCTAGTAAT
1 CAGAGAGCACTGACGTGCTAAATATCAGAGAGCACAAATGTGC---TAAT
*
40762872 CAGAGAGCACTGGCGTGCTAAATATCAGAGAGCACAAATGTGCTAAT
1 CAGAGAGCACTGACGTGCTAAATATCAGAGAGCACAAATGTGCTAAT
* *
40762919 CAGTGAGCACTGGCGTGCTAAATATCAGAGAGCACAAATGTGCTAAT
1 CAGAGAGCACTGACGTGCTAAATATCAGAGAGCACAAATGTGCTAAT
40762966 CAGAGAGCA
1 CAGAGAGCA
40762975 TGCTGAAGTC
Statistics
Matches: 137, Mismatches: 10, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
44 18 0.13
46 3 0.02
47 73 0.53
50 43 0.31
ACGTcount: A:0.36, C:0.19, G:0.26, T:0.19
Consensus pattern (47 bp):
CAGAGAGCACTGACGTGCTAAATATCAGAGAGCACAAATGTGCTAAT
Found at i:40762916 original size:97 final size:94
Alignment explanation
Indices: 40762778--40762953 Score: 289
Period size: 97 Copynumber: 1.8 Consensus size: 94
40762768 CACTAATGAA
40762778 CAGAGAGCACTGAAGTGCTATACAGAGAGCACAAATGTGCTAATCAGAGAGCACTGACGTGCTAA
1 CAGAGAGCACTGAAGTGCTATACAGAGAGCACAAATGTGCTAATCAGAGAGCACTGACGTGCTAA
40762843 ATATCAGAGAGCACTAGCGTGCTAGTAAT
66 ATATCAGAGAGCACTAGCGTGCTAGTAAT
** * *
40762872 CAGAGAGCACTGGCGTGCTAAATATCAGAGAGCACAAATGTGCTAATCAGTGAGCACTGGCGTGC
1 CAGAGAGCACTGAAGTGCT--ATA-CAGAGAGCACAAATGTGCTAATCAGAGAGCACTGACGTGC
40762937 TAAATATCAGAGAGCAC
63 TAAATATCAGAGAGCAC
40762954 AAATGTGCTA
Statistics
Matches: 75, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
94 17 0.23
96 3 0.04
97 55 0.73
ACGTcount: A:0.35, C:0.20, G:0.26, T:0.19
Consensus pattern (94 bp):
CAGAGAGCACTGAAGTGCTATACAGAGAGCACAAATGTGCTAATCAGAGAGCACTGACGTGCTAA
ATATCAGAGAGCACTAGCGTGCTAGTAAT
Done.