Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 135709677
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: 135709677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 414 of 438
Found at i:128533226 original size:7 final size:7
Alignment explanation
Indices: 128533214--128533245 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
128533204 AAAAAGTAGT
128533214 CTGTCTC
1 CTGTCTC
128533221 CTGTCTC
1 CTGTCTC
128533228 CTGTCTC
1 CTGTCTC
128533235 CTGTCTC
1 CTGTCTC
128533242 CTGT
1 CTGT
128533246 TTATATATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.00, C:0.41, G:0.16, T:0.44
Consensus pattern (7 bp):
CTGTCTC
Found at i:128533985 original size:16 final size:16
Alignment explanation
Indices: 128533964--128534012 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 16
128533954 TCTGACACCT
128533964 TTTTATTTTCTTTTTC
1 TTTTATTTTCTTTTTC
*
128533980 TTTTATTTTCATATTTC
1 TTTTATTTTC-TTTTTC
*
128533997 TTTTTTTTTACTTTTT
1 TTTTATTTT-CTTTTT
128534013 TATTTTTGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 10 0.36
17 17 0.61
18 1 0.04
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTATTTTCTTTTTC
Found at i:128533996 original size:17 final size:16
Alignment explanation
Indices: 128533964--128534018 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
128533954 TCTGACACCT
*
128533964 TTTTATTTTCTTTTTC
1 TTTTATTTTCTATTTC
128533980 TTTTATTTTCATATTTC
1 TTTTATTTTC-TATTTC
*
128533997 TTTT-TTTT-TACTT-
1 TTTTATTTTCTATTTC
128534010 TTTTATTTT
1 TTTTATTTT
128534019 TGTTCCTTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
13 4 0.11
14 8 0.23
16 14 0.40
17 9 0.26
ACGTcount: A:0.11, C:0.09, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTATTTTCTATTTC
Found at i:128534016 original size:22 final size:22
Alignment explanation
Indices: 128533963--128534017 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 22
128533953 TTCTGACACC
128533963 TTTTTATTTTCTTTTTCTTTTAT
1 TTTTTA-TTTCTTTTTCTTTTAT
*
128533986 TTTCATATTTCTTTTT-TTTTACT
1 TTT-TTATTTCTTTTTCTTTTA-T
128534009 TTTTTATTT
1 TTTTTATTT
128534018 TTGTTCCTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
22 10 0.36
23 16 0.57
24 2 0.07
ACGTcount: A:0.11, C:0.09, G:0.00, T:0.80
Consensus pattern (22 bp):
TTTTTATTTCTTTTTCTTTTAT
Found at i:128534052 original size:9 final size:9
Alignment explanation
Indices: 128534033--128534111 Score: 72
Period size: 9 Copynumber: 8.8 Consensus size: 9
128534023 CCTTAATAAA
128534033 TTTTA-TTT
1 TTTTATTTT
128534041 TTTTATTTT
1 TTTTATTTT
*
128534050 TTTTACTTT
1 TTTTATTTT
*
128534059 TTTGATTTT
1 TTTTATTTT
* *
128534068 TTTT-CTTA
1 TTTTATTTT
*
128534076 TTTCATTTT
1 TTTTATTTT
*
128534085 GTTTATTTT
1 TTTTATTTT
128534094 GTTTTATTTT
1 -TTTTATTTT
128534104 TTATTATT
1 TT-TTATT
128534112 AACTTTAAAA
Statistics
Matches: 55, Mismatches: 12, Indels: 6
0.75 0.16 0.08
Matches are distributed among these distances:
8 10 0.18
9 32 0.58
10 13 0.24
ACGTcount: A:0.13, C:0.04, G:0.04, T:0.80
Consensus pattern (9 bp):
TTTTATTTT
Found at i:128534084 original size:48 final size:49
Alignment explanation
Indices: 128533998--128534103 Score: 126
Period size: 48 Copynumber: 2.2 Consensus size: 49
128533988 TCATATTTCT
128533998 TTTTTTTTACTTTTTTATTTTTGTTCCTTAATAAATTTTATTT-TTTTA
1 TTTTTTTTACTTTTTTATTTTTGTTCCTTAATAAATTTTATTTATTTTA
* * ** * *
128534046 TTTTTTTTACTTTTTTGATTTTT-TTTCTTATTTCATTTTGTTTATTTTG
1 TTTTTTTTACTTTTTT-ATTTTTGTTCCTTAATAAATTTTATTTATTTTA
128534095 TTTTATTTT
1 TTTT-TTTT
128534104 TTATTATTAA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
48 31 0.63
49 14 0.29
50 4 0.08
ACGTcount: A:0.14, C:0.06, G:0.04, T:0.76
Consensus pattern (49 bp):
TTTTTTTTACTTTTTTATTTTTGTTCCTTAATAAATTTTATTTATTTTA
Found at i:128534108 original size:17 final size:16
Alignment explanation
Indices: 128534033--128534108 Score: 64
Period size: 17 Copynumber: 4.4 Consensus size: 16
128534023 CCTTAATAAA
128534033 TTTTATTTTTTTATTTT
1 TTTTA-TTTTTTATTTT
128534050 TTTTACTTTTTTGATTTT
1 TTTTA-TTTTTT-ATTTT
* *
128534068 TTTTCTTATTTCATTTT
1 TTTTATT-TTTTATTTT
*
128534085 GTTTATTTTGTT-TTATT
1 TTTTATTTT-TTATT-TT
128534102 TTTTATT
1 TTTTATT
128534109 ATTAACTTTA
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
16 4 0.08
17 32 0.67
18 12 0.25
ACGTcount: A:0.12, C:0.04, G:0.04, T:0.80
Consensus pattern (16 bp):
TTTTATTTTTTATTTT
Found at i:128534156 original size:29 final size:29
Alignment explanation
Indices: 128534121--128534183 Score: 117
Period size: 29 Copynumber: 2.2 Consensus size: 29
128534111 TAACTTTAAA
128534121 ATGATATAATATAATATACTTTTTTAATT
1 ATGATATAATATAATATACTTTTTTAATT
*
128534150 ATGATATAATATAATATATTTTTTTAATT
1 ATGATATAATATAATATACTTTTTTAATT
128534179 ATGAT
1 ATGAT
128534184 TGGTTTATCT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (29 bp):
ATGATATAATATAATATACTTTTTTAATT
Found at i:128535094 original size:9 final size:8
Alignment explanation
Indices: 128535041--128535117 Score: 55
Period size: 9 Copynumber: 8.9 Consensus size: 8
128535031 TTTTAAAGTT
128535041 AATAATAAA
1 AATAA-AAA
128535050 AATAAAACAA
1 AAT-AAA-AA
128535060 AATAAACAA
1 AATAAA-AA
* *
128535069 AATGAAAT
1 AATAAAAA
*
128535077 AAGAAAAA
1 AATAAAAA
128535085 AATCAAAAA
1 AAT-AAAAA
*
128535094 AGTAAAAAA
1 AAT-AAAAA
128535103 AATAAAAA
1 AATAAAAA
*
128535111 GATAAAA
1 AATAAAA
128535118 TTTATTAAGG
Statistics
Matches: 55, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
8 19 0.35
9 29 0.53
10 7 0.13
ACGTcount: A:0.78, C:0.04, G:0.05, T:0.13
Consensus pattern (8 bp):
AATAAAAA
Found at i:128535166 original size:17 final size:17
Alignment explanation
Indices: 128535144--128535203 Score: 83
Period size: 17 Copynumber: 3.8 Consensus size: 17
128535134 ATAAAAAAGT
128535144 AAAATAAAAGAAATATG
1 AAAATAAAAGAAATATG
128535161 AAAATAAAAG-AA-A--
1 AAAATAAAAGAAATATG
*
128535174 AAAACAAAAGAAATATG
1 AAAATAAAAGAAATATG
128535191 AAAATAAAAGAAA
1 AAAATAAAAGAAA
128535204 AAGAAAACAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
13 9 0.24
14 2 0.05
15 2 0.05
16 2 0.05
17 22 0.59
ACGTcount: A:0.77, C:0.02, G:0.10, T:0.12
Consensus pattern (17 bp):
AAAATAAAAGAAATATG
Found at i:128535217 original size:17 final size:17
Alignment explanation
Indices: 128535128--128535215 Score: 69
Period size: 17 Copynumber: 5.4 Consensus size: 17
128535118 TTTATTAAGG
* *
128535128 AACAAAATAAAAAAGTAA
1 AACAAAAGAAATAAG-AA
* *
128535146 AATAAAAGAAATATGAA
1 AACAAAAGAAATAAGAA
*
128535163 AATAAAAG--A-AA-AA
1 AACAAAAGAAATAAGAA
*
128535176 AACAAAAGAAATATGAA
1 AACAAAAGAAATAAGAA
*
128535193 AATAAAAGAAA-AAGAA
1 AACAAAAGAAATAAGAA
128535209 AACAAAA
1 AACAAAA
128535216 AGGTGTCAGC
Statistics
Matches: 56, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
13 9 0.16
14 1 0.02
15 2 0.04
16 11 0.20
17 22 0.39
18 11 0.20
ACGTcount: A:0.77, C:0.03, G:0.09, T:0.10
Consensus pattern (17 bp):
AACAAAAGAAATAAGAA
Found at i:128535587 original size:12 final size:13
Alignment explanation
Indices: 128535559--128535587 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
128535549 TTATTTTAGG
128535559 TTTTTAAAATTAC
1 TTTTTAAAATTAC
128535572 TTTTTAAAATTA-
1 TTTTTAAAATTAC
128535584 TTTT
1 TTTT
128535588 AGTTATGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.25
13 12 0.75
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTTTAAAATTAC
Found at i:128538255 original size:9 final size:9
Alignment explanation
Indices: 128538241--128538273 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
128538231 AATGAAGGAA
128538241 TTGAGAGAG
1 TTGAGAGAG
128538250 TTGAGAGAG
1 TTGAGAGAG
*
128538259 TTGAGAGAA
1 TTGAGAGAG
128538268 TTGAGA
1 TTGAGA
128538274 ATTTAAAGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.39, T:0.24
Consensus pattern (9 bp):
TTGAGAGAG
Found at i:128538423 original size:2 final size:2
Alignment explanation
Indices: 128538410--128538456 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
128538400 TTCAACTCAA
* *
128538410 AC AC AC AT AC AC AC AC AC AC AT AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
128538452 AC AC A
1 AC AC A
128538457 TATATATATA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.45, G:0.00, T:0.04
Consensus pattern (2 bp):
AC
Found at i:128538429 original size:14 final size:14
Alignment explanation
Indices: 128538410--128538456 Score: 85
Period size: 14 Copynumber: 3.4 Consensus size: 14
128538400 TTCAACTCAA
128538410 ACACACATACACAC
1 ACACACATACACAC
128538424 ACACACATACACAC
1 ACACACATACACAC
*
128538438 ACACACACACACAC
1 ACACACATACACAC
128538452 ACACA
1 ACACA
128538457 TATATATATA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 32 1.00
ACGTcount: A:0.51, C:0.45, G:0.00, T:0.04
Consensus pattern (14 bp):
ACACACATACACAC
Found at i:128544172 original size:14 final size:15
Alignment explanation
Indices: 128544153--128544182 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
128544143 GAAGGGATAC
128544153 TTTGTTT-TTTCTTT
1 TTTGTTTGTTTCTTT
128544167 TTTGTTTGTTTCTTT
1 TTTGTTTGTTTCTTT
128544182 T
1 T
128544183 ATTAGATCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.00, C:0.07, G:0.10, T:0.83
Consensus pattern (15 bp):
TTTGTTTGTTTCTTT
Found at i:128552140 original size:15 final size:15
Alignment explanation
Indices: 128552120--128552152 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
128552110 AATCCTTTAA
128552120 AAATTA-TAAAAATAT
1 AAATTATTAAAAAT-T
128552135 AAATTATTAAAAATT
1 AAATTATTAAAAATT
128552150 AAA
1 AAA
128552153 ATTTCATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AAATTATTAAAAATT
Found at i:128557504 original size:3 final size:3
Alignment explanation
Indices: 128557496--128557530 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
128557486 TTGCAGTCCT
128557496 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
128557531 TGTTTAACTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:128559388 original size:6 final size:5
Alignment explanation
Indices: 128559345--128559393 Score: 64
Period size: 5 Copynumber: 9.6 Consensus size: 5
128559335 TCATTTTTTT
*
128559345 TTTCA TTTCA TTTCA TTTC- TTCCA TTTCA TTTACA TTTCTA TTTCA TTT
1 TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTT-CA TTTC-A TTTCA TTT
128559394 AAATTTAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
4 3 0.08
5 26 0.67
6 10 0.26
ACGTcount: A:0.18, C:0.20, G:0.00, T:0.61
Consensus pattern (5 bp):
TTTCA
Found at i:128559432 original size:18 final size:18
Alignment explanation
Indices: 128559409--128559452 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
128559399 TAATTATTTC
*
128559409 TCATTTCAGTTTTTTTTT
1 TCATTTCAGTTTTTGTTT
128559427 TCATTTCAGTTTTTGTTT
1 TCATTTCAGTTTTTGTTT
128559445 TCATTTCA
1 TCATTTCA
128559453 ATTTATAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.14, C:0.14, G:0.07, T:0.66
Consensus pattern (18 bp):
TCATTTCAGTTTTTGTTT
Found at i:128559559 original size:28 final size:27
Alignment explanation
Indices: 128559507--128559564 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
128559497 TCATCATTCT
128559507 ATTTCATTTCATTATAAATTACATTTC
1 ATTTCATTTCATTATAAATTACATTTC
* *
128559534 ATTTCATATTCATT-TAATTTTTCATTTC
1 ATTTCAT-TTCATTATAA-ATTACATTTC
128559562 ATT
1 ATT
128559565 AATTTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 10 0.37
28 17 0.63
ACGTcount: A:0.29, C:0.14, G:0.00, T:0.57
Consensus pattern (27 bp):
ATTTCATTTCATTATAAATTACATTTC
Found at i:128559572 original size:17 final size:18
Alignment explanation
Indices: 128559535--128559571 Score: 60
Period size: 16 Copynumber: 2.2 Consensus size: 18
128559525 TTACATTTCA
128559535 TTTCATATTCATTTAATT
1 TTTCATATTCATTTAATT
128559553 TTTCAT-TTCA-TTAATT
1 TTTCATATTCATTTAATT
128559569 TTT
1 TTT
128559572 TTTCACATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.47
17 4 0.21
18 6 0.32
ACGTcount: A:0.24, C:0.11, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTCATATTCATTTAATT
Found at i:128559663 original size:20 final size:17
Alignment explanation
Indices: 128559638--128559677 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 17
128559628 ATAGTCTCAT
128559638 TTCAATTTATCTTTTTTCAA
1 TTCAATTT-T-TTTTTT-AA
128559658 TTCAATTTTTTTTTTAA
1 TTCAATTTTTTTTTTAA
128559675 TTC
1 TTC
128559678 GTTTCATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 6 0.30
19 1 0.05
20 8 0.40
ACGTcount: A:0.23, C:0.12, G:0.00, T:0.65
Consensus pattern (17 bp):
TTCAATTTTTTTTTTAA
Found at i:128559901 original size:111 final size:111
Alignment explanation
Indices: 128559698--128559900 Score: 275
Period size: 112 Copynumber: 1.8 Consensus size: 111
128559688 TATTATTAAA
* * * *
128559698 TGTACTTGGTGTCAGCCATTACATGTCCAACACCCAATTTTTTTTTTAAAATACACTGATGCCAG
1 TGTACTTGGTGGCAGCCATTACATGGCCAACACCAAAGTTTTTTTTTAAAATACACTGATGCCAG
*
128559763 CCATCAGTGTTCCAAAATAAAAAAAAATATATTGAAAGCCGAAAAT
66 CCATCAGTGTCCCAAAATAAAAAAAAATATATTGAAAGCCGAAAAT
* *
128559809 TGTACTTGGTGGC-GACCATTACATGGCCAACACTCAAAAGTTTTTTTTT-AAATACACTGGTGT
1 TGTACTTGGTGGCAG-CCATTACATGGCCAACAC-C-AAAGTTTTTTTTTAAAATACACTGATGC
* * *
128559872 CGGTCATCAGTGTCCCAAAGTAAAAAAAA
63 CAGCCATCAGTGTCCCAAAATAAAAAAAA
128559901 TGTGCCTTGG
Statistics
Matches: 79, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
110 1 0.01
111 29 0.37
112 38 0.48
113 11 0.14
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (111 bp):
TGTACTTGGTGGCAGCCATTACATGGCCAACACCAAAGTTTTTTTTTAAAATACACTGATGCCAG
CCATCAGTGTCCCAAAATAAAAAAAAATATATTGAAAGCCGAAAAT
Found at i:128561243 original size:5 final size:5
Alignment explanation
Indices: 128561233--128561285 Score: 54
Period size: 5 Copynumber: 10.0 Consensus size: 5
128561223 TAGGAAGATA
*
128561233 TTATT TTATTT TTATTT TTGTTT TTATT TGT-TT TTATT TTATT TTATT
1 TTATT TTA-TT TTA-TT TT-ATT TTATT T-TATT TTATT TTATT TTATT
128561281 TTATT
1 TTATT
128561286 ATTAAATTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
4 1 0.02
5 26 0.62
6 15 0.36
ACGTcount: A:0.15, C:0.00, G:0.04, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:128563103 original size:53 final size:53
Alignment explanation
Indices: 128562962--128563112 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
128562952 ATAAGTGCGC
* **
128562962 CCGTTTAAGACCATAGCTGGGCTATGGCATCGGTGCAATGTGATAATGTGACT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
*
128563015 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGATT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
* *
128563068 CCGTATAAGACCAT-GTCTGGGATATGGCTTCGGTATGATATGTGA
1 CCGTATAAGACCATAG-CTGGGCTATGGCATCGGTAT-A-ATGTGA
128563113 ACCGTGTAAG
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:0.26, C:0.17, G:0.28, T:0.30
Consensus pattern (53 bp):
CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
Found at i:128570522 original size:53 final size:53
Alignment explanation
Indices: 128570456--128570596 Score: 201
Period size: 53 Copynumber: 2.7 Consensus size: 53
128570446 ATAAGTGCGC
* *
128570456 CCGTTTAAGACCATAACTGGGCTATGGCATCGGTGCAATGTGATAATGTGACT
1 CCGTATAAGACCATAACTGGGCTATGGCATCGGTACAATGTGATAATGTGACT
* * *
128570509 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGATT
1 CCGTATAAGACCATAACTGGGCTATGGCATCGGTACAATGTGATAATGTGACT
** * *
128570562 CCGTATAAGACCATGTCTGGGATATGGCTTCGGTA
1 CCGTATAAGACCATAACTGGGCTATGGCATCGGTA
128570597 TGATATGTGA
Statistics
Matches: 79, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 79 1.00
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.29
Consensus pattern (53 bp):
CCGTATAAGACCATAACTGGGCTATGGCATCGGTACAATGTGATAATGTGACT
Found at i:128577662 original size:20 final size:20
Alignment explanation
Indices: 128577639--128577699 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
128577629 TAAAATCTAT
128577639 TAGTCATAATTTCAATCCAA
1 TAGTCATAATTTCAATCCAA
* * *
128577659 TAGTTA-AGATTTC--TTC-T
1 TAGTCATA-ATTTCAATCCAA
128577676 TAGTCATAATTTCAATCCAA
1 TAGTCATAATTTCAATCCAA
128577696 TAGT
1 TAGT
128577700 TAAGATTTCT
Statistics
Matches: 30, Mismatches: 6, Indels: 10
0.65 0.13 0.22
Matches are distributed among these distances:
17 10 0.33
18 3 0.10
19 3 0.10
20 14 0.47
ACGTcount: A:0.34, C:0.16, G:0.08, T:0.41
Consensus pattern (20 bp):
TAGTCATAATTTCAATCCAA
Found at i:128577688 original size:37 final size:37
Alignment explanation
Indices: 128577638--128577714 Score: 154
Period size: 37 Copynumber: 2.1 Consensus size: 37
128577628 TTAAAATCTA
128577638 TTAGTCATAATTTCAATCCAATAGTTAAGATTTCTTC
1 TTAGTCATAATTTCAATCCAATAGTTAAGATTTCTTC
128577675 TTAGTCATAATTTCAATCCAATAGTTAAGATTTCTTC
1 TTAGTCATAATTTCAATCCAATAGTTAAGATTTCTTC
128577712 TTA
1 TTA
128577715 CTTTTCAATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.32, C:0.16, G:0.08, T:0.44
Consensus pattern (37 bp):
TTAGTCATAATTTCAATCCAATAGTTAAGATTTCTTC
Found at i:128577707 original size:20 final size:20
Alignment explanation
Indices: 128577647--128577708 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
128577637 ATTAGTCATA
128577647 ATTTCAATCCAATAGTTAAG
1 ATTTCAATCCAATAGTTAAG
* * *
128577667 ATTTC--TTC-TTAGTCATA-
1 ATTTCAATCCAATAGTTA-AG
128577684 ATTTCAATCCAATAGTTAAG
1 ATTTCAATCCAATAGTTAAG
128577704 ATTTC
1 ATTTC
128577709 TTCTTACTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 10
0.66 0.13 0.21
Matches are distributed among these distances:
17 10 0.32
18 3 0.10
19 3 0.10
20 15 0.48
ACGTcount: A:0.34, C:0.16, G:0.08, T:0.42
Consensus pattern (20 bp):
ATTTCAATCCAATAGTTAAG
Found at i:128588402 original size:3 final size:3
Alignment explanation
Indices: 128588348--128588384 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
128588338 ACAATAACTA
128588348 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
128588385 GAACATCCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:128595596 original size:19 final size:19
Alignment explanation
Indices: 128595572--128595626 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 19
128595562 CAATGCCTTT
128595572 TTTGCATTAATTTCATTCA
1 TTTGCATTAATTTCATTCA
128595591 TTTGCATTACATTTCA-TCA
1 TTTGCATTA-ATTTCATTCA
*
128595610 TATGCATTAAGTTTCAT
1 TTTGCATTAA-TTTCAT
128595627 AAAAAAGACC
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
18 1 0.03
19 25 0.78
20 6 0.19
ACGTcount: A:0.27, C:0.16, G:0.07, T:0.49
Consensus pattern (19 bp):
TTTGCATTAATTTCATTCA
Found at i:128597392 original size:48 final size:48
Alignment explanation
Indices: 128597314--128597540 Score: 207
Period size: 48 Copynumber: 4.9 Consensus size: 48
128597304 CACATGGTAG
* * *
128597314 GATGCCAATGCCATATCCCCGATATGGTCTTACATGGGATCACATATC
1 GATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATC
* * ** * *
128597362 GATGCCAATGCCATGTCCCAAACATAGTCTTACATGGGATCGTAGATT
1 GATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATC
* * *
128597410 GATGCCAATGCTATGTCTCAGACACGGTCTTACATGGGATCACATATC
1 GATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATC
* * * * ** *
128597458 GATGTCGAT---A-G-CCCAG-CTATTGTCTTACACGAAATTACATATC
1 GATGCCAATGCCATGTCCCAGAC-ATGGTCTTACATGGGATCACATATC
* *
128597501 GATGCCAAAGCAATGTCCCAGACAT-GTCTTACATGGGATC
1 GATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATC
128597541 GTACATAACC
Statistics
Matches: 138, Mismatches: 34, Indels: 15
0.74 0.18 0.08
Matches are distributed among these distances:
42 1 0.01
43 29 0.21
44 1 0.01
45 1 0.01
46 1 0.01
47 12 0.09
48 92 0.67
49 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.27
Consensus pattern (48 bp):
GATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATC
Found at i:128599235 original size:23 final size:25
Alignment explanation
Indices: 128599209--128599255 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
128599199 TATCATTCAT
*
128599209 TTCATTATAT-CA-ATATTTTATGC
1 TTCATCATATCCATATATTTTATGC
*
128599232 TTCATCATTTCCATATATTTTATG
1 TTCATCATATCCATATATTTTATG
128599256 TATATTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.40
24 2 0.10
25 10 0.50
ACGTcount: A:0.28, C:0.15, G:0.04, T:0.53
Consensus pattern (25 bp):
TTCATCATATCCATATATTTTATGC
Found at i:128599576 original size:46 final size:47
Alignment explanation
Indices: 128599516--128599643 Score: 188
Period size: 46 Copynumber: 2.8 Consensus size: 47
128599506 TTTGACGTGA
* * *
128599516 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACTATGGTCTTACTCATTTTCATGTCACGT
*
128599562 TGCCATGGTATCTTTCAACTATGGTCTTATTC-TTTTCATGTCACGT
1 TGCCATGGTATCTTTCAACTATGGTCTTACTCATTTTCATGTCACGT
* *
128599608 TGCCATGGTATCTTTCAACCATGGTCTTACACATTT
1 TGCCATGGTATCTTTCAACTATGGTCTTACTCATTT
128599644 CATATCAGAG
Statistics
Matches: 73, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
45 5 0.07
46 65 0.89
47 3 0.04
ACGTcount: A:0.19, C:0.23, G:0.15, T:0.44
Consensus pattern (47 bp):
TGCCATGGTATCTTTCAACTATGGTCTTACTCATTTTCATGTCACGT
Found at i:128613399 original size:47 final size:47
Alignment explanation
Indices: 128613345--128613568 Score: 307
Period size: 47 Copynumber: 4.8 Consensus size: 47
128613335 TGGTTGAGCA
128613345 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGGAATG
128613392 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGGAATG
* *
128613439 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGT--AACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGGAA-T--G
* *
128613484 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-CGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGGAATG
* *
128613532 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
128613569 GCGGGTTACA
Statistics
Matches: 160, Mismatches: 7, Indels: 21
0.85 0.04 0.11
Matches are distributed among these distances:
42 2 0.01
43 1 0.01
44 5 0.03
45 1 0.01
46 37 0.23
47 105 0.66
48 3 0.02
50 4 0.03
51 2 0.01
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.30
Consensus pattern (47 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGGAATG
Found at i:128619996 original size:3 final size:3
Alignment explanation
Indices: 128619984--128620048 Score: 112
Period size: 3 Copynumber: 21.3 Consensus size: 3
128619974 CAACAACAAC
*
128619984 AAT AAC AAT AAT AAT AAT AAT AAT AAAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT
128620030 AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT A
128620049 TTATTATTAT
Statistics
Matches: 59, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
3 56 0.95
4 3 0.05
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:128620053 original size:3 final size:3
Alignment explanation
Indices: 128620047--128620076 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
128620037 ATAATAATAA
128620047 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
128620077 AAGAAAAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:128620150 original size:21 final size:21
Alignment explanation
Indices: 128620126--128620201 Score: 70
Period size: 21 Copynumber: 3.7 Consensus size: 21
128620116 ATCTAATTTT
128620126 TAAAAT-A-AATAGATAGATGAA
1 TAAAATAATAATA-ATAGAT-AA
128620147 TAAAATAATAATAATAGATAA
1 TAAAATAATAATAATAGATAA
** *
128620168 TAAAATGGTAATAATA-AAAA
1 TAAAATAATAATAATAGATAA
128620188 TATAAATAA-AATAA
1 TA-AAATAATAATAA
128620202 ATAATGAAAG
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
20 10 0.21
21 26 0.55
22 7 0.15
23 4 0.09
ACGTcount: A:0.66, C:0.00, G:0.08, T:0.26
Consensus pattern (21 bp):
TAAAATAATAATAATAGATAA
Found at i:128620206 original size:27 final size:27
Alignment explanation
Indices: 128620132--128620206 Score: 66
Period size: 26 Copynumber: 2.8 Consensus size: 27
128620122 TTTTTAAAAT
*
128620132 AAATAGATAGAT-GAATAA-AATAATAA
1 AAATAGATA-ATAAAATAATAATAATAA
* **
128620158 TAATAGATAATAAAATGGTAATAATAA
1 AAATAGATAATAAAATAATAATAATAA
*
128620185 AAATATA-AATAAAATAAATAAT
1 AAATAGATAATAAAAT-AATAAT
128620207 GAAAGAAAGT
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
25 2 0.05
26 19 0.50
27 17 0.45
ACGTcount: A:0.65, C:0.00, G:0.08, T:0.27
Consensus pattern (27 bp):
AAATAGATAATAAAATAATAATAATAA
Found at i:128620219 original size:17 final size:17
Alignment explanation
Indices: 128620196--128620237 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
128620186 AATATAAATA
128620196 AAATAAATAA-TG-AAAG
1 AAATAAA-AATTGAAAAG
128620212 AAAGTAAAAATTGAAAAG
1 AAA-TAAAAATTGAAAAG
128620230 AAATAAAA
1 AAATAAAA
128620238 GAACAATAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 5 0.22
17 11 0.48
18 7 0.30
ACGTcount: A:0.71, C:0.00, G:0.12, T:0.17
Consensus pattern (17 bp):
AAATAAAAATTGAAAAG
Found at i:128622454 original size:44 final size:44
Alignment explanation
Indices: 128622331--128622469 Score: 127
Period size: 44 Copynumber: 3.2 Consensus size: 44
128622321 AACGTAGCGG
* * * **
128622331 ATCTTATCTCCCTAAAG-TGTAGTGGAGCAAATTAAAGCCACAA
1 ATCTCATCTCCCTGAAGTTGTAGTGGAGCAAATTGAAGTAACAA
* * ** * ** *
128622374 ACCTCATCTCTCTGAAGTTGCGGTGGAGTAGGTTGAAGTTACAA
1 ATCTCATCTCCCTGAAGTTGTAGTGGAGCAAATTGAAGTAACAA
* *
128622418 ATCTCATCTCCCTGATGTTGTAGTGGAGCAAATTGAAGATAACGA
1 ATCTCATCTCCCTGAAGTTGTAGTGGAGCAAATTGAAG-TAACAA
128622463 ATCTCAT
1 ATCTCAT
128622470 TTCTCTAAAG
Statistics
Matches: 72, Mismatches: 22, Indels: 2
0.75 0.23 0.02
Matches are distributed among these distances:
43 13 0.18
44 48 0.67
45 11 0.15
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (44 bp):
ATCTCATCTCCCTGAAGTTGTAGTGGAGCAAATTGAAGTAACAA
Found at i:128622594 original size:95 final size:96
Alignment explanation
Indices: 128622409--128622611 Score: 248
Period size: 95 Copynumber: 2.1 Consensus size: 96
128622399 GAGTAGGTTG
* * * *
128622409 AAGTTACAAATCTCATCTCCCTGATGTTGTAGTGGAGCAAATTGAAGATAACGAATCTCATTTCT
1 AAGTTATAAATCTCATCTCCCTAATGTTGCAGTGGAGCAAATTGAAGATAACGAATCTCATTTCC
128622474 CTAAAGTTGCAATGGAATAGATTAAAGCTAC
66 CTAAAGTTGCAATGGAATAGATTAAAGCTAC
* * * * * * *
128622505 GAGTTATAAATCTTATCTCCCTAAAT-TTGCAGTGGAGTAGATTGAGGAT-GCGAATCTTATTTC
1 AAGTTATAAATCTCATCTCCCT-AATGTTGCAGTGGAGCAAATTGAAGATAACGAATCTCATTTC
* * *
128622568 CCTGAAGTTTCAGTGGAATAGATTAAAGCTAC
65 CCTAAAGTTGCAATGGAATAGATTAAAGCTAC
*
128622600 AAGTCATAAATC
1 AAGTTATAAATC
128622612 CTAAACCCCT
Statistics
Matches: 90, Mismatches: 16, Indels: 3
0.83 0.15 0.03
Matches are distributed among these distances:
95 50 0.56
96 38 0.42
97 2 0.02
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.32
Consensus pattern (96 bp):
AAGTTATAAATCTCATCTCCCTAATGTTGCAGTGGAGCAAATTGAAGATAACGAATCTCATTTCC
CTAAAGTTGCAATGGAATAGATTAAAGCTAC
Found at i:128622644 original size:95 final size:95
Alignment explanation
Indices: 128622460--128622632 Score: 222
Period size: 95 Copynumber: 1.8 Consensus size: 95
128622450 TTGAAGATAA
* * * * *
128622460 CGAATCTCATTTCTCTAAAGTTGCAATGGAATAGATTAAAGCTACGAGTTATAAATCTTATCTCC
1 CGAATCTCATTTCCCTAAAGTTGCAATGGAATAGATTAAAGCTACAAGTCATAAATCTAAACTCC
* *
128622525 CTAAATTTGCAGTGGAGTAGATTGAGGATG
66 CTAAAGTTGCACTGGAGTAGATTGAGGATG
* * * *
128622555 CGAATCTTATTTCCCTGAAGTTTCAGTGGAATAGATTAAAGCTACAAGTCATAAATCCTAAAC-C
1 CGAATCTCATTTCCCTAAAGTTGCAATGGAATAGATTAAAGCTACAAGTCATAAAT-CTAAACTC
*
128622619 CCTGAAGTTGCACT
65 CCTAAAGTTGCACT
128622633 AGGATGGATT
Statistics
Matches: 65, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
95 61 0.94
96 4 0.06
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (95 bp):
CGAATCTCATTTCCCTAAAGTTGCAATGGAATAGATTAAAGCTACAAGTCATAAATCTAAACTCC
CTAAAGTTGCACTGGAGTAGATTGAGGATG
Found at i:128622718 original size:44 final size:44
Alignment explanation
Indices: 128622655--128622740 Score: 118
Period size: 44 Copynumber: 2.0 Consensus size: 44
128622645 AGTCACCGTG
*
128622655 ACAAATCTTACCTCCCTGAAGTTGCAGTGGAAAAGATTGAAGTC
1 ACAAATCTCACCTCCCTGAAGTTGCAGTGGAAAAGATTGAAGTC
* * * **
128622699 ACAAATCTCATCTCTCTGAAGTTGCAGTTGAGCAGATTGAAG
1 ACAAATCTCACCTCCCTGAAGTTGCAGTGGAAAAGATTGAAG
128622741 ATAGTGAATC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.27
Consensus pattern (44 bp):
ACAAATCTCACCTCCCTGAAGTTGCAGTGGAAAAGATTGAAGTC
Found at i:128622897 original size:44 final size:45
Alignment explanation
Indices: 128622804--128622902 Score: 112
Period size: 44 Copynumber: 2.2 Consensus size: 45
128622794 TCTTATTTCA
* * * * * *
128622804 CTGAAGTTGCAGTGGAGTAGATTGAAGCTACAAGTCTTATCTCCT
1 CTGAAGTTGTAATGGAGTAGATTGAAACAACAAATCTTATCACCT
* *
128622849 -TGAAGTTGTAATGGAGTAGATTTAAACAACAAATTTTAT-ACCT
1 CTGAAGTTGTAATGGAGTAGATTGAAACAACAAATCTTATCACCT
128622892 CTGAAGTTGTA
1 CTGAAGTTGTA
128622903 GAGAAGCACC
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
43 3 0.07
44 42 0.93
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.33
Consensus pattern (45 bp):
CTGAAGTTGTAATGGAGTAGATTGAAACAACAAATCTTATCACCT
Found at i:128623282 original size:3 final size:3
Alignment explanation
Indices: 128623267--128623324 Score: 107
Period size: 3 Copynumber: 19.3 Consensus size: 3
128623257 AGATATTTAC
*
128623267 TTA TTA TTC TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
128623315 TTA TTA TTA T
1 TTA TTA TTA T
128623325 ATTTTTTCTA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:128630306 original size:26 final size:24
Alignment explanation
Indices: 128630259--128630306 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
128630249 TTCAACTTTA
*
128630259 TTAACTCCTTATTTTTTCTCTCTC
1 TTAACTCCTGATTTTTTCTCTCTC
128630283 TTAACTCTCTGATTTTTTCT-TCTC
1 TTAACTC-CTGATTTTTTCTCTCTC
128630307 CCACAATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.12, C:0.27, G:0.02, T:0.58
Consensus pattern (24 bp):
TTAACTCCTGATTTTTTCTCTCTC
Found at i:128633573 original size:23 final size:23
Alignment explanation
Indices: 128633538--128633593 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 23
128633528 ATATGATTTA
128633538 AAAAAATATTCATATTTATATAATT
1 AAAAAATATTCATATTT-TAT-ATT
128633563 AAAAAA-A-TCATATTTTATATT
1 AAAAAATATTCATATTTTATATT
*
128633584 ATAAAATATT
1 AAAAAATATT
128633594 TATAAATTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
21 8 0.29
22 4 0.14
23 9 0.32
24 1 0.04
25 6 0.21
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.43
Consensus pattern (23 bp):
AAAAAATATTCATATTTTATATT
Found at i:128635955 original size:2 final size:2
Alignment explanation
Indices: 128635948--128635996 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
128635938 AACAACATAG
* *
128635948 AT AT AT AT AC AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
128635990 AT AT AT A
1 AT AT AT A
128635997 ATCTGAAAAC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:128644442 original size:28 final size:29
Alignment explanation
Indices: 128644392--128644456 Score: 80
Period size: 28 Copynumber: 2.2 Consensus size: 29
128644382 ATGTTATATT
* *
128644392 AAAAAGTATATCTTTTAATAAAAATAGAAA
1 AAAAATTATATCTTTCAATAAAAATA-AAA
128644422 AAAAATTA-ATCTTTCAA-AAAAATAAAA
1 AAAAATTATATCTTTCAATAAAAATAAAA
128644449 AATAAATT
1 AA-AAATT
128644457 TTTTTATTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 5 0.16
28 12 0.38
29 8 0.25
30 7 0.22
ACGTcount: A:0.63, C:0.05, G:0.03, T:0.29
Consensus pattern (29 bp):
AAAAATTATATCTTTCAATAAAAATAAAA
Found at i:128644803 original size:13 final size:13
Alignment explanation
Indices: 128644785--128644821 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
128644775 TAACCCGCCC
128644785 ATATTAATTTTTT
1 ATATTAATTTTTT
*
128644798 ATATTATTTTTTT
1 ATATTAATTTTTT
*
128644811 ATATAAATTTT
1 ATATTAATTTT
128644822 AAATATATAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
ATATTAATTTTTT
Found at i:128646815 original size:61 final size:61
Alignment explanation
Indices: 128646720--128646851 Score: 246
Period size: 61 Copynumber: 2.2 Consensus size: 61
128646710 ATCTCTGGCT
128646720 TTTCATGCTTCACATAACACTCAGCCTTATAAACAATTTTACTGTGCATGAAAGAAAAACA
1 TTTCATGCTTCACATAACACTCAGCCTTATAAACAATTTTACTGTGCATGAAAGAAAAACA
* *
128646781 TTTCATGCTTCACATAACACTCAGCCTTATAAACAATTTTATTGTGCATGAAAGAATAACA
1 TTTCATGCTTCACATAACACTCAGCCTTATAAACAATTTTACTGTGCATGAAAGAAAAACA
128646842 TTTCATGCTT
1 TTTCATGCTT
128646852 GAGCTCTAGG
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 69 1.00
ACGTcount: A:0.36, C:0.20, G:0.10, T:0.33
Consensus pattern (61 bp):
TTTCATGCTTCACATAACACTCAGCCTTATAAACAATTTTACTGTGCATGAAAGAAAAACA
Found at i:128651023 original size:6 final size:6
Alignment explanation
Indices: 128651012--128651038 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
128651002 CTTGAGATGG
128651012 CTGAGC CTGAGC CTGAGC CTGAGC CTG
1 CTGAGC CTGAGC CTGAGC CTGAGC CTG
128651039 GGCTAACATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.33, G:0.33, T:0.19
Consensus pattern (6 bp):
CTGAGC
Found at i:128656229 original size:12 final size:12
Alignment explanation
Indices: 128656212--128656239 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
128656202 TTTAAGATAA
128656212 AATAATGAGTAT
1 AATAATGAGTAT
128656224 AATAATGAGTAT
1 AATAATGAGTAT
128656236 AATA
1 AATA
128656240 CTGCAATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.14, T:0.32
Consensus pattern (12 bp):
AATAATGAGTAT
Found at i:128656979 original size:19 final size:18
Alignment explanation
Indices: 128656951--128656987 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
128656941 AAATATATAA
*
128656951 TAATATTTTATATTTCTT
1 TAATATTTTATAATTCTT
128656969 TAATGATTTTATAATTCTT
1 TAAT-ATTTTATAATTCTT
128656988 GTTATTCATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (18 bp):
TAATATTTTATAATTCTT
Found at i:128660727 original size:27 final size:27
Alignment explanation
Indices: 128660686--128660762 Score: 113
Period size: 27 Copynumber: 2.9 Consensus size: 27
128660676 AGTGAGTCAT
128660686 ATCGGGAAGCTCACAAAGAGCCAATTTA
1 ATCGGGAAGCTCACAAAGAGCC-ATTTA
128660714 AT-GGGAAGCTCACAAAGAGCC-TTTA
1 ATCGGGAAGCTCACAAAGAGCCATTTA
* *
128660739 ATCAGGAAGCTCACGAAGAGCCAT
1 ATCGGGAAGCTCACAAAGAGCCAT
128660763 ATAACAGAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
25 6 0.13
26 17 0.38
27 20 0.44
28 2 0.04
ACGTcount: A:0.38, C:0.22, G:0.23, T:0.17
Consensus pattern (27 bp):
ATCGGGAAGCTCACAAAGAGCCATTTA
Found at i:128661224 original size:21 final size:21
Alignment explanation
Indices: 128661198--128661239 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
128661188 TAAAATTACC
*
128661198 TCAATTTAATACAATTCACAT
1 TCAATTCAATACAATTCACAT
* *
128661219 TCAATTCCATCCAATTCACAT
1 TCAATTCAATACAATTCACAT
128661240 CCTAGGAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.26, G:0.00, T:0.36
Consensus pattern (21 bp):
TCAATTCAATACAATTCACAT
Found at i:128661225 original size:11 final size:11
Alignment explanation
Indices: 128661209--128661241 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
128661199 CAATTTAATA
*
128661209 CAATTCACATT
1 CAATTCACATC
128661220 CAATTC-CATC
1 CAATTCACATC
128661230 CAATTCACATC
1 CAATTCACATC
128661241 C
1 C
128661242 TAGGAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.33, C:0.36, G:0.00, T:0.30
Consensus pattern (11 bp):
CAATTCACATC
Found at i:128664889 original size:29 final size:29
Alignment explanation
Indices: 128664840--128664904 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
128664830 GTGACGAGAT
** * *
128664840 CGGCACTAAGTGTGCGTGCTGGAAATATA
1 CGGCACTAAGTGTGCAAGCTGAAAAAATA
*
128664869 TGGCACTAAGTGTGCAAGCTGAAAAAATA
1 CGGCACTAAGTGTGCAAGCTGAAAAAATA
128664898 CGGCACT
1 CGGCACT
128664905 GGGTGTGCGA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.32, C:0.18, G:0.28, T:0.22
Consensus pattern (29 bp):
CGGCACTAAGTGTGCAAGCTGAAAAAATA
Found at i:128671520 original size:13 final size:13
Alignment explanation
Indices: 128671502--128671527 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
128671492 GAAATACTCG
128671502 GTCCTATTCCACA
1 GTCCTATTCCACA
128671515 GTCCTATTCCACA
1 GTCCTATTCCACA
128671528 TAATAAGATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.38, G:0.08, T:0.31
Consensus pattern (13 bp):
GTCCTATTCCACA
Found at i:128683050 original size:58 final size:57
Alignment explanation
Indices: 128682962--128683077 Score: 144
Period size: 58 Copynumber: 2.0 Consensus size: 57
128682952 GTTTGAATGC
* *
128682962 TTTTTTGTTTAAATTAATCCTTGAACTTGGTAATTGTTCTCACATTGGAGCTTGAACT
1 TTTTTTGTCTAAATTAATCCTAGAACTTGGTAATTGTTCTCA-ATTGGAGCTTGAACT
* * * * *
128683020 TTTTTTGTCTAAGTTAATCCCTAG-ATTTGGTCATTGTTCTCAATTGGGGCTTGGACT
1 TTTTTTGTCTAAATTAAT-CCTAGAACTTGGTAATTGTTCTCAATTGGAGCTTGAACT
128683077 T
1 T
128683078 GGCAATTATT
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
57 14 0.28
58 32 0.64
59 4 0.08
ACGTcount: A:0.21, C:0.15, G:0.18, T:0.47
Consensus pattern (57 bp):
TTTTTTGTCTAAATTAATCCTAGAACTTGGTAATTGTTCTCAATTGGAGCTTGAACT
Found at i:128684722 original size:30 final size:30
Alignment explanation
Indices: 128684677--128684733 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
128684667 GTAACCTTAA
*
128684677 TATAATGTCAACTTGTGTGAGCAACTTTAT
1 TATAATATCAACTTGTGTGAGCAACTTTAT
*
128684707 TATAATATCAGCTTGTGTGAGCAACTT
1 TATAATATCAACTTGTGTGAGCAACTT
128684734 ATTCCCGTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.39
Consensus pattern (30 bp):
TATAATATCAACTTGTGTGAGCAACTTTAT
Found at i:128691537 original size:40 final size:39
Alignment explanation
Indices: 128691452--128691565 Score: 106
Period size: 40 Copynumber: 2.9 Consensus size: 39
128691442 CGTCAGATAG
* *
128691452 ACCG-AACACACCATACAGAAGCTCATAAGAGCTTATCCA
1 ACCGAAACACGCCA-ACAAAAGCTCATAAGAGCTTATCCA
* * *
128691491 ATCGAAATACGCCAAACAAAAGCTCATAAGAG-TTGGTCCA
1 ACCGAAACACGCC-AACAAAAGCTCATAAGAGCTT-ATCCA
* * * *
128691531 CCCGAAACACGTCAACAGAAGCTCATAAAAGCTTA
1 ACCGAAACACGCCAACAAAAGCTCATAAGAGCTTA
128691566 ATAGAAGCTC
Statistics
Matches: 59, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
39 21 0.36
40 37 0.63
41 1 0.02
ACGTcount: A:0.42, C:0.27, G:0.15, T:0.16
Consensus pattern (39 bp):
ACCGAAACACGCCAACAAAAGCTCATAAGAGCTTATCCA
Found at i:128696575 original size:17 final size:17
Alignment explanation
Indices: 128696555--128696588 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
128696545 AGGCTTAGGT
128696555 TTAAAAATTTTAATTAA
1 TTAAAAATTTTAATTAA
**
128696572 TTAAATTTTTTAATTAA
1 TTAAAAATTTTAATTAA
128696589 AAATCTATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTAAAAATTTTAATTAA
Found at i:128704869 original size:21 final size:21
Alignment explanation
Indices: 128704839--128704883 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
128704829 GAAGGATCAA
128704839 ATGCTAGAGTC-CTAGAAAAAC
1 ATGCTAGAGTCAC-AGAAAAAC
* *
128704860 ATGCTGGAGTCACAGAACAAC
1 ATGCTAGAGTCACAGAAAAAC
128704881 ATG
1 ATG
128704884 ATGAGCCAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.40, C:0.20, G:0.22, T:0.18
Consensus pattern (21 bp):
ATGCTAGAGTCACAGAAAAAC
Found at i:128712880 original size:135 final size:135
Alignment explanation
Indices: 128712638--128713350 Score: 1032
Period size: 135 Copynumber: 5.3 Consensus size: 135
128712628 AAAGACAGAT
* * * * * *
128712638 ATCATCAGCCTTATCTTTACTGAGCAGGAGTGGAGCAGGTTAAACATACCCGATCTTATCTTCAC
1 ATCATCAACCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAATATACCAGATCTTATCTTCAT
*
128712703 TGAGCAGGAGTGAAGCAGATCGAGTTTTGGAGAATCTTATCTCCACGTACCGGCGATGGAGCAGA
66 TGAGCAGGAGTGAAGCAGATCGAATTTTGGAGAATCTTATCTCCACGTACCGGCGATGGAGCAGA
128712768 TTCCA
131 TTCCA
* *
128712773 ATCATCAACCTTATCTTCACTGAGTAGGAGTGGAGCAGGCTAAATATACCAGATATTATCTTCAT
1 ATCATCAACCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAATATACCAGATCTTATCTTCAT
* *
128712838 TGAGCAAGAGTGAAGCAGATCGAATTTTGGAGAATCTTATCTCCACGTACCGGCGATAGAGCAGA
66 TGAGCAGGAGTGAAGCAGATCGAATTTTGGAGAATCTTATCTCCACGTACCGGCGATGGAGCAGA
128712903 TTCCA
131 TTCCA
128712908 ATCATCAACCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAATATACCAGATCTTATCTTCAT
1 ATCATCAACCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAATATACCAGATCTTATCTTCAT
* * *
128712973 TGAGCAGGAGTGAAGTAGATCGAATTTTGGATAATCTTATCTCTACGTACCGGCGATGGAGCAGA
66 TGAGCAGGAGTGAAGCAGATCGAATTTTGGAGAATCTTATCTCCACGTACCGGCGATGGAGCAGA
128713038 TTCCA
131 TTCCA
* *
128713043 ATCATCAACCTTATCTTCACTGAGCAGGAATGGAGCAGGCTAAATATACCAGATCTTATCTTTAT
1 ATCATCAACCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAATATACCAGATCTTATCTTCAT
* * ** *
128713108 TGAGCAAGAGTGAAGCAGATCGAATTTTGGAGAATCTTATCTCCACGTAACGGCGATTAAACAGA
66 TGAGCAGGAGTGAAGCAGATCGAATTTTGGAGAATCTTATCTCCACGTACCGGCGATGGAGCAGA
128713173 TTCCA
131 TTCCA
* * * **
128713178 ATCATCAGCTTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAATATACCAGGTCTTATCTTCGC
1 ATCATCAACCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAATATACCAGATCTTATCTTCAT
* * * * * * * * * * *
128713243 TGAGCAGGAGCGGAGCAAACCAAATTTCGGTGAATCTTATCTCCA-TTGATCGACAATGGAGCAG
66 TGAGCAGGAGTGAAGCAGATCGAATTTTGGAGAATCTTATCTCCACGT-ACCGGCGATGGAGCAG
*
128713307 ATTTCA
130 ATTCCA
* * * *
128713313 ACCACCAATCTTATCTTCACTAAGCAGGAGTGGAGCAG
1 ATCATCAACCTTATCTTCACTGAGCAGGAGTGGAGCAG
128713351 ACCAGATTTC
Statistics
Matches: 520, Mismatches: 57, Indels: 2
0.90 0.10 0.00
Matches are distributed among these distances:
134 1 0.00
135 519 1.00
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (135 bp):
ATCATCAACCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAATATACCAGATCTTATCTTCAT
TGAGCAGGAGTGAAGCAGATCGAATTTTGGAGAATCTTATCTCCACGTACCGGCGATGGAGCAGA
TTCCA
Found at i:128712967 original size:45 final size:46
Alignment explanation
Indices: 128712647--128713259 Score: 170
Period size: 45 Copynumber: 13.6 Consensus size: 46
128712637 TATCATCAGC
* * *
128712647 CTTATCTTTACTGAGCAGGAGTGGAGCAGGTT-AAACATACCCGAT
1 CTTATCTTCACTGAGCAGGAGTGGAGCAGGTTCAAATATACCAGAT
* * * * * ***
128712692 CTTATCTTCACTGAGCAGGAGTGAAGCA-GATCGAGTTTTGGAGAAT
1 CTTATCTTCACTGAGCAGGAGTGGAGCAGGTTCAAATATACCAG-AT
* * * * * *
128712738 CTTATCTCCAC-GTA-CCGGCGATGGAGCAGATTCCAATCAT--CA-AC
1 CTTATCTTCACTG-AGCAGGAG-TGGAGCAGGTTCAAAT-ATACCAGAT
* *
128712782 CTTATCTTCACTGAGTAGGAGTGGAGCAGGCT-AAATATACCAGAT
1 CTTATCTTCACTGAGCAGGAGTGGAGCAGGTTCAAATATACCAGAT
* * * * * * * ***
128712827 ATTATCTTCATTGAGCAAGAGTGAAGCA-GATCGAATTTTGGAGAAT
1 CTTATCTTCACTGAGCAGGAGTGGAGCAGGTTCAAATATACCAG-AT
* * * * * * *
128712873 CTTATCTCCAC-GTA-CCGGCGATAGAGCAGATTCCAATCAT--CA-AC
1 CTTATCTTCACTG-AGCAGGAG-TGGAGCAGGTTCAAAT-ATACCAGAT
*
128712917 CTTATCTTCACTGAGCAGGAGTGGAGCAGGCT-AAATATACCAGAT
1 CTTATCTTCACTGAGCAGGAGTGGAGCAGGTTCAAATATACCAGAT
* * * * * * *** *
128712962 CTTATCTTCATTGAGCAGGAGTGAAGTA-GATCGAATTTTGGATAAT
1 CTTATCTTCACTGAGCAGGAGTGGAGCAGGTTCAAATATACCA-GAT
* * * * *
128713008 CTTATC-TCTAC-GTA-CCGGCGATGGAGCAGATTCCAATCAT--CA-AC
1 CTTATCTTC-ACTG-AGCAGGAG-TGGAGCAGGTTCAAAT-ATACCAGAT
* *
128713052 CTTATCTTCACTGAGCAGGAATGGAGCAGGCT-AAATATACCAGAT
1 CTTATCTTCACTGAGCAGGAGTGGAGCAGGTTCAAATATACCAGAT
* * * * * * * ***
128713097 CTTATCTTTATTGAGCAAGAGTGAAGCA-GATCGAATTTTGGAGAAT
1 CTTATCTTCACTGAGCAGGAGTGGAGCAGGTTCAAATATACCAG-AT
* * * ** * * * *
128713143 CTTATCTCCAC-GTAAC-GGCGATTAAACAGATTCCAATCAT--CAGCT
1 CTTATCTTCACTG-AGCAGGAG-TGGAGCAGGTTCAAAT-ATACCAGAT
* *
128713188 -TTATCTTCACTGAGCAGGAGTGGAGCAGGCT-AAATATACCAGGT
1 CTTATCTTCACTGAGCAGGAGTGGAGCAGGTTCAAATATACCAGAT
* *
128713232 CTTATCTTCGCTGAGCAGGAGCGGAGCA
1 CTTATCTTCACTGAGCAGGAGTGGAGCA
128713260 AACCAAATTT
Statistics
Matches: 394, Mismatches: 128, Indels: 92
0.64 0.21 0.15
Matches are distributed among these distances:
42 8 0.02
43 12 0.03
44 95 0.24
45 184 0.47
46 72 0.18
47 19 0.05
48 4 0.01
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.27
Consensus pattern (46 bp):
CTTATCTTCACTGAGCAGGAGTGGAGCAGGTTCAAATATACCAGAT
Found at i:128715760 original size:44 final size:45
Alignment explanation
Indices: 128715665--128715779 Score: 142
Period size: 44 Copynumber: 2.6 Consensus size: 45
128715655 ACAGGACAGA
* *
128715665 ACAGAAATAAGCCATGTAAGTCCATATTAGAAATATGGCTTTAGAG
1 ACAGGAATAAGCCATGTAAGTCCATATTA-AAATATGGCATTAGAG
* * * *
128715711 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATAAGCCATGTAAGTCCATATTAAAATATGGCATTAGAG
**
128715755 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATAAGCCATGTAAGTCCAT
128715780 GTCAAAGACA
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
44 34 0.58
46 25 0.42
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (45 bp):
ACAGGAATAAGCCATGTAAGTCCATATTAAAATATGGCATTAGAG
Found at i:128717211 original size:23 final size:23
Alignment explanation
Indices: 128717185--128717234 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
128717175 TATTACTTTT
128717185 TTTTACTATCATTTATTAAATTA
1 TTTTACTATCATTTATTAAATTA
* * **
128717208 TTTTCCTATTATTTATTGTATTA
1 TTTTACTATCATTTATTAAATTA
128717231 TTTT
1 TTTT
128717235 TTTACACTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.08, G:0.02, T:0.64
Consensus pattern (23 bp):
TTTTACTATCATTTATTAAATTA
Found at i:128719479 original size:18 final size:17
Alignment explanation
Indices: 128719448--128719491 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
128719438 ATCATAGGGT
**
128719448 TTTAAAATTTTATAAATA
1 TTTAAAATAATATAAA-A
*
128719466 TTTTAAATAATATAAAA
1 TTTAAAATAATATAAAA
128719483 TTTAAAATA
1 TTTAAAATA
128719492 TATTAGAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TTTAAAATAATATAAAA
Found at i:128719486 original size:27 final size:28
Alignment explanation
Indices: 128719450--128719509 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 28
128719440 CATAGGGTTT
*
128719450 TAAAATTTTATAAATAT-TT-TAAATAATA
1 TAAAATTTTA-AAATATATTAGAAATAA-A
128719478 TAAAA-TTTAAAATATATTAGAAATAAA
1 TAAAATTTTAAAATATATTAGAAATAAA
128719505 TAAAA
1 TAAAA
128719510 AATATATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 6 0.21
27 12 0.41
28 11 0.38
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (28 bp):
TAAAATTTTAAAATATATTAGAAATAAA
Found at i:128723408 original size:46 final size:46
Alignment explanation
Indices: 128723358--128723449 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
128723348 TCGAAGGCTC
128723358 TTTTTCTCTTTTACAGTTTAATTTTTGTTATGAAATAATTTTGGAT
1 TTTTTCTCTTTTACAGTTTAATTTTTGTTATGAAATAATTTTGGAT
128723404 TTTTTCTCTTTTACAGTTTAATTTTTGTTATGAAATAATTTTGGAT
1 TTTTTCTCTTTTACAGTTTAATTTTTGTTATGAAATAATTTTGGAT
128723450 ATCATGGATC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.24, C:0.07, G:0.11, T:0.59
Consensus pattern (46 bp):
TTTTTCTCTTTTACAGTTTAATTTTTGTTATGAAATAATTTTGGAT
Found at i:128726045 original size:16 final size:16
Alignment explanation
Indices: 128726021--128726054 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
128726011 AAGCGATAAG
*
128726021 TAATATTACATTTCAA
1 TAATATTACATTCCAA
*
128726037 TAATTTTACATTCCAA
1 TAATATTACATTCCAA
128726053 TA
1 TA
128726055 GTCAAATGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.41, C:0.15, G:0.00, T:0.44
Consensus pattern (16 bp):
TAATATTACATTCCAA
Found at i:128729618 original size:37 final size:37
Alignment explanation
Indices: 128729533--128729618 Score: 95
Period size: 37 Copynumber: 2.3 Consensus size: 37
128729523 ACATGTCACT
* *
128729533 TTTTAATATATATTAAGTAAATACCATTTCCATGTCA
1 TTTTAATATATATCAAGTAAATACCATTTCCAAGTCA
* * *
128729570 TGTTTCA-ATATATCATGTAAATATCATTTCCAAGT-A
1 T-TTTAATATATATCAAGTAAATACCATTTCCAAGTCA
128729606 TTTTAAGTATATA
1 TTTTAA-TATATA
128729619 CCGATAATAA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
35 4 0.10
36 2 0.05
37 30 0.75
38 4 0.10
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.44
Consensus pattern (37 bp):
TTTTAATATATATCAAGTAAATACCATTTCCAAGTCA
Found at i:128730610 original size:33 final size:33
Alignment explanation
Indices: 128730493--128730610 Score: 85
Period size: 33 Copynumber: 3.6 Consensus size: 33
128730483 CATGGTTCAA
** * * * *
128730493 CTATGGTCTTACACATACATTGCCATGGCCTTG
1 CTATGGTCTTACATTTAAAATGCCATAGCCTAG
* ** * * *
128730526 CCATGGTCTTACATTTGTAGTGCCATAACCCAG
1 CTATGGTCTTACATTTAAAATGCCATAGCCTAG
* **
128730559 TTATGGTCTT-TTTATTAAAATGCCATAGCCTAG
1 CTATGGTCTTACAT-TTAAAATGCCATAGCCTAG
128730592 CTATGGTCTTACATTTAAA
1 CTATGGTCTTACATTTAAA
128730611 CATTTCCATG
Statistics
Matches: 61, Mismatches: 22, Indels: 4
0.70 0.25 0.05
Matches are distributed among these distances:
32 1 0.02
33 59 0.97
34 1 0.02
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.36
Consensus pattern (33 bp):
CTATGGTCTTACATTTAAAATGCCATAGCCTAG
Found at i:128731456 original size:10 final size:10
Alignment explanation
Indices: 128731441--128731489 Score: 53
Period size: 10 Copynumber: 4.7 Consensus size: 10
128731431 TCTTTCTCTT
128731441 TTTCTTTTTC
1 TTTCTTTTTC
128731451 TTTCTTTTTC
1 TTTCTTTTTC
**
128731461 GTTTGGTTTTC
1 -TTTCTTTTTC
*
128731472 TATTCTGTTTC
1 T-TTCTTTTTC
128731483 TTTCTTT
1 TTTCTTT
128731490 ATTTGTTTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
10 16 0.52
11 15 0.48
ACGTcount: A:0.02, C:0.16, G:0.08, T:0.73
Consensus pattern (10 bp):
TTTCTTTTTC
Found at i:128731509 original size:5 final size:5
Alignment explanation
Indices: 128731499--128731595 Score: 78
Period size: 5 Copynumber: 19.4 Consensus size: 5
128731489 TATTTGTTTT
* *
128731499 TATAA TATAA TATAA TATAG TATAA TATAA TATAA TAT-A TATAC T-TAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
* *
128731547 -ACATT TATAA TAT-A TATAA TA-ATA TATATA TAATAA TATATA TATAA
1 TATA-A TATAA TATAA TATAA TATA-A TATA-A T-ATAA TATA-A TATAA
128731594 TA
1 TA
128731596 AACTTATAAA
Statistics
Matches: 75, Mismatches: 8, Indels: 18
0.74 0.08 0.18
Matches are distributed among these distances:
4 12 0.16
5 47 0.63
6 13 0.17
7 3 0.04
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (5 bp):
TATAA
Found at i:128731540 original size:2 final size:2
Alignment explanation
Indices: 128731499--128731592 Score: 59
Period size: 2 Copynumber: 52.0 Consensus size: 2
128731489 TATTTGTTTT
128731499 TA TA -A TA TA -A TA TA -A TA TA GTA TA -A TA TA -A TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
* * *
128731536 TA TA TA CT- TA AA CA TT TA TA -A TA TA TA TA -A TA -A TA TA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
128731575 TA TA -A TA -A TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
128731593 ATAAACTTAT
Statistics
Matches: 73, Mismatches: 5, Indels: 28
0.69 0.05 0.26
Matches are distributed among these distances:
1 12 0.16
2 58 0.79
3 3 0.04
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (2 bp):
TA
Found at i:128731573 original size:14 final size:14
Alignment explanation
Indices: 128731556--128731596 Score: 82
Period size: 14 Copynumber: 2.9 Consensus size: 14
128731546 AACATTTATA
128731556 ATATATATAATAAT
1 ATATATATAATAAT
128731570 ATATATATAATAAT
1 ATATATATAATAAT
128731584 ATATATATAATAA
1 ATATATATAATAA
128731597 ACTTATAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATATATATAATAAT
Found at i:128733008 original size:23 final size:22
Alignment explanation
Indices: 128732982--128733042 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
128732972 GCCTTCTATT
*
128732982 CGTCCCATAAAAGGGCTCTCATA
1 CGTCCCAT-AAAGGGCTCTCAAA
** * *
128733005 CGTCCCACGAGGGGCACTCAAA
1 CGTCCCATAAAGGGCTCTCAAA
128733027 CGTCCCATAAAGGGCT
1 CGTCCCATAAAGGGCT
128733043 TTTATATACT
Statistics
Matches: 29, Mismatches: 9, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
22 22 0.76
23 7 0.24
ACGTcount: A:0.28, C:0.33, G:0.23, T:0.16
Consensus pattern (22 bp):
CGTCCCATAAAGGGCTCTCAAA
Found at i:128737595 original size:31 final size:31
Alignment explanation
Indices: 128737536--128737599 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
128737526 AAACCTAGAG
* * *
128737536 TTGACAATTTTTCTCACATTAGGACTTGAAT
1 TTGACAATTATTCCCACATTAAGACTTGAAT
128737567 TTGACAATTATTCCCACATTAA-AGCTTGAAT
1 TTGACAATTATTCCCACATTAAGA-CTTGAAT
128737598 TT
1 TT
128737600 TAGGGTTTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 1 0.03
31 28 0.97
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.41
Consensus pattern (31 bp):
TTGACAATTATTCCCACATTAAGACTTGAAT
Found at i:128738838 original size:20 final size:20
Alignment explanation
Indices: 128738815--128738853 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
128738805 TTTAATATCT
128738815 ATATT-TTTATAATTTTTAAA
1 ATATTATTTA-AATTTTTAAA
128738835 ATATTAATTTAAATTTTTA
1 ATATT-ATTTAAATTTTTA
128738854 TTATTTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 5 0.29
21 8 0.47
22 4 0.24
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
ATATTATTTAAATTTTTAAA
Found at i:128738896 original size:15 final size:16
Alignment explanation
Indices: 128738876--128738905 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
128738866 GGTCAAAATG
128738876 TAATTT-AATTTTTAC
1 TAATTTAAATTTTTAC
128738891 TAATTTAAATTTTTA
1 TAATTTAAATTTTTA
128738906 TAAATTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (16 bp):
TAATTTAAATTTTTAC
Found at i:128743054 original size:61 final size:61
Alignment explanation
Indices: 128742988--128743108 Score: 224
Period size: 61 Copynumber: 2.0 Consensus size: 61
128742978 TATTTAATAA
*
128742988 AATTTATATTCAAACTCCTTACCACTCACTTATTTTACTTACTTTTACAAGTGATTTTTTT
1 AATTTATATTCAAACTCCTTACCACCCACTTATTTTACTTACTTTTACAAGTGATTTTTTT
*
128743049 AATTTATATTCAAATTCCTTACCACCCACTTATTTTACTTACTTTTACAAGTGATTTTTT
1 AATTTATATTCAAACTCCTTACCACCCACTTATTTTACTTACTTTTACAAGTGATTTTTT
128743109 ATTTATTTAT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 58 1.00
ACGTcount: A:0.28, C:0.20, G:0.03, T:0.49
Consensus pattern (61 bp):
AATTTATATTCAAACTCCTTACCACCCACTTATTTTACTTACTTTTACAAGTGATTTTTTT
Found at i:128743917 original size:3 final size:3
Alignment explanation
Indices: 128743909--128743938 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
128743899 ATGCAGGTAT
128743909 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
128743939 GAGATGAGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:128746025 original size:19 final size:20
Alignment explanation
Indices: 128745988--128746025 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
128745978 AAGTTAATAA
*
128745988 AAATTTTGATTAAGGTGGAC
1 AAATTTTGATTAAGATGGAC
*
128746008 AAATTTT-ATTACGATGGA
1 AAATTTTGATTAAGATGGA
128746026 TGACACTGGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 9 0.56
20 7 0.44
ACGTcount: A:0.37, C:0.05, G:0.21, T:0.37
Consensus pattern (20 bp):
AAATTTTGATTAAGATGGAC
Found at i:128750084 original size:10 final size:9
Alignment explanation
Indices: 128750046--128750095 Score: 57
Period size: 10 Copynumber: 5.4 Consensus size: 9
128750036 TAAACACTAT
128750046 AAAATT-TA
1 AAAATTATA
128750054 AAAATTATTA
1 AAAATTA-TA
*
128750064 GAAATTATA
1 AAAATTATA
*
128750073 AAATATTGTA
1 AAA-ATTATA
128750083 AAAATTATA
1 AAAATTATA
128750092 AAAA
1 AAAA
128750096 AATTATTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
8 6 0.17
9 13 0.37
10 16 0.46
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (9 bp):
AAAATTATA
Found at i:128750087 original size:37 final size:34
Alignment explanation
Indices: 128750046--128750138 Score: 87
Period size: 37 Copynumber: 2.5 Consensus size: 34
128750036 TAAACACTAT
128750046 AAAATTTAAAAATTATTAGAAATTATAAAATATTGTA
1 AAAATTTAAAAATTATTAGAAA-TATAAAAT-TT-TA
** *
128750083 AAAATTATAAAAAAATTATTTTAAATATTAAATTTTA
1 AAAATT-T--AAAAATTATTAGAAATATAAAATTTTA
*
128750120 AAAATAGTAAAAATTATTA
1 AAAAT-TTAAAAATTATTA
128750139 TATTTTGAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
35 10 0.21
37 14 0.30
38 3 0.06
39 7 0.15
40 13 0.28
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (34 bp):
AAAATTTAAAAATTATTAGAAATATAAAATTTTA
Found at i:128750546 original size:19 final size:20
Alignment explanation
Indices: 128750507--128750546 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
128750497 TAAGATAGTA
*
128750507 AAAAATTATTTGGAATAATT
1 AAAAATTATTTGAAATAATT
*
128750527 AAAAATTATTT-AAATTATT
1 AAAAATTATTTGAAATAATT
128750546 A
1 A
128750547 TTTAATTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (20 bp):
AAAAATTATTTGAAATAATT
Found at i:128750788 original size:20 final size:21
Alignment explanation
Indices: 128750759--128750803 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
128750749 TAAAATTTCT
*
128750759 ATTTTTTAAA-TTTTTAGTAA
1 ATTTTATAAATTTTTTAGTAA
*
128750779 ATTTTATAAATTTTTTTGTAA
1 ATTTTATAAATTTTTTAGTAA
128750800 ATTT
1 ATTT
128750804 ACATTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (21 bp):
ATTTTATAAATTTTTTAGTAA
Found at i:128750810 original size:47 final size:47
Alignment explanation
Indices: 128750751--128750857 Score: 123
Period size: 48 Copynumber: 2.3 Consensus size: 47
128750741 TAAAATATTA
*
128750751 AAATTTCTA-TTTTTTAAATTTTTAGTAAATTTTATAAATTTTTTTGT
1 AAATTTCTATTTTTTTAAATTTTTAATAAATTTTAT-AATTTTTTTGT
* * *
128750798 AAATTTAC-ATTTTTTTATATTTTTAATAAGTTTTATAA-TTTTTTAT
1 AAATTT-CTATTTTTTTAAATTTTTAATAAATTTTATAATTTTTTTGT
128750844 AAATATT-TATTTTT
1 AAAT-TTCTATTTTT
128750858 AAAGATTTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
46 17 0.33
47 11 0.21
48 24 0.46
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.63
Consensus pattern (47 bp):
AAATTTCTATTTTTTTAAATTTTTAATAAATTTTATAATTTTTTTGT
Found at i:128750852 original size:20 final size:18
Alignment explanation
Indices: 128750810--128750859 Score: 57
Period size: 19 Copynumber: 2.8 Consensus size: 18
128750800 ATTTACATTT
*
128750810 TTTTATATTTTTAATAAG
1 TTTTATATTTTTAATAAA
*
128750828 TTTTATAATTTTTTATAAA
1 TTTTAT-ATTTTTAATAAA
*
128750847 TATT-TATTTTTAA
1 TTTTATATTTTTAA
128750860 AGATTTTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (18 bp):
TTTTATATTTTTAATAAA
Found at i:128753560 original size:37 final size:37
Alignment explanation
Indices: 128753510--128753583 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
128753500 GTTTGGGAGT
128753510 TAGTTACGTGCGAGGAAGGATTAGCACCCTCGACACG
1 TAGTTACGTGCGAGGAAGGATTAGCACCCTCGACACG
128753547 TAGTTACGTGCGAGGAAGGATTAGCACCCTCGACACG
1 TAGTTACGTGCGAGGAAGGATTAGCACCCTCGACACG
128753584 CCCAAAAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.27, C:0.24, G:0.30, T:0.19
Consensus pattern (37 bp):
TAGTTACGTGCGAGGAAGGATTAGCACCCTCGACACG
Found at i:128754185 original size:2 final size:2
Alignment explanation
Indices: 128754178--128754218 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
128754168 TGTACGTAAA
128754178 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
128754219 AATAGTAATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:128754655 original size:3 final size:3
Alignment explanation
Indices: 128754631--128755215 Score: 220
Period size: 3 Copynumber: 189.7 Consensus size: 3
128754621 AAGTACCTAT
*
128754631 TAA TAA TAT TATA TAA -ATA TAA TAAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TA-A TAA TA-A TAA T-AA TAA TAA TAA TAA TAA TAA TAA
* * *
128754678 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA CAA TAA TAG CAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * *
128754726 TAA TAG TAA AAA TACA -AA -AGA TAG T-A TGACG TAA TAA TGAGG TAA
1 TAA TAA TAA TAA TA-A TAA TA-A TAA TAA T-A-A TAA TAA T-A-A TAA
* * *
128754771 GGAA -AA TAA -AA T-A TAA T-A TAT TAGA TATA TAA -ATA TAA TAG TAA
1 -TAA TAA TAA TAA TAA TAA TAA TAA TA-A TA-A TAA TA-A TAA TAA TAA
** * *
128754815 -ATA TAA TAA TGT TAA AAA CACCA TACA TAA -AGA GT-A TATA TAA -ACA
1 TA-A TAA TAA TAA TAA TAA TA--A TA-A TAA TA-A -TAA TA-A TAA TA-A
* * * * *
128754861 TATA TAA TAA AAA T-A TACA CTAA TAT TTA TAAA TAA TAA TAG TAA -ATG
1 TA-A TAA TAA TAA TAA TA-A -TAA TAA TAA T-AA TAA TAA TAA TAA TA-A
* * * * *
128754909 TAA TAA TAA TAA TAT TAA GT-A TAG T-A TAAA TAA TATG TACA TAA CAG
1 TAA TAA TAA TAA TAA TAA -TAA TAA TAA T-AA TAA TA-A TA-A TAA TAA
*
128754956 TAA TAA TAA TAA GTAA CAA TAA TAA TAA TAA TAA T-A TAGA -AA TTCAA
1 TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA -T-AA
* *
128755003 -AA -AA GTAA -ACA TAA T-A TAA TGA TAT TAA -AA TAA -AA T-A TACA
1 TAA TAA -TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A
* * *
128755044 CTAA TAT TTA TAAA TAA TAA TAG TAA -ATA TAA TAA TAA TAA TAA TAA
1 -TAA TAA TAA T-AA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA
128755091 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * *
128755139 TAA TAA TAT TAA GT-A TAG T-A TAAA TAA TATG TACA TAA CAG TAA TAA
1 TAA TAA TAA TAA -TAA TAA TAA T-AA TAA TA-A TA-A TAA TAA TAA TAA
*
128755186 TAA TAA GTAA CAA TAA TAA TAA TAA TAA TA
1 TAA TAA -TAA TAA TAA TAA TAA TAA TAA TA
128755216 TAGAAATTCA
Statistics
Matches: 437, Mismatches: 78, Indels: 134
0.67 0.12 0.21
Matches are distributed among these distances:
2 41 0.09
3 321 0.73
4 65 0.15
5 10 0.02
ACGTcount: A:0.59, C:0.04, G:0.05, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:128755274 original size:16 final size:16
Alignment explanation
Indices: 128755080--128755273 Score: 56
Period size: 18 Copynumber: 11.1 Consensus size: 16
128755070 ATATAATAAT
*
128755080 AATAATAATAATAATAA
1 AATAA-AATAATATTAA
*
128755097 TAATAATAATAATAATAA
1 -AATAA-AATAATATTAA
*
128755115 TAATAATAATAATAATAA
1 -AATAA-AATAATATTAA
128755133 TAATAATAATAATATTAA
1 -AATAA-AATAATATTAA
128755151 GTATAGTATAAATAATATGT-A
1 --A-A-TA-AAATAATAT-TAA
* * *
128755172 CATAACAGTAATAATAA
1 AATAA-AATAATATTAA
*
128755189 TAAGTAACAATAATAATAA
1 -AA-TAA-AATAATATTAA
* *
128755208 TAATAATATAGAAATTCAA
1 -AATAAAATA-ATATT-AA
* *
128755227 AA-AAAACTAA-A-CAT
1 AATAAAA-TAATATTAA
*
128755241 AATATAATAATATTAA
1 AATAAAATAATATTAA
128755257 AATAAAATAAT-TTAA
1 AATAAAATAATATTAA
128755272 AA
1 AA
128755274 AATACTATGT
Statistics
Matches: 145, Mismatches: 16, Indels: 33
0.75 0.08 0.17
Matches are distributed among these distances:
14 6 0.04
15 10 0.07
16 14 0.10
17 16 0.11
18 64 0.44
19 21 0.14
20 1 0.01
21 11 0.08
22 2 0.01
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (16 bp):
AATAAAATAATATTAA
Found at i:128766841 original size:3 final size:3
Alignment explanation
Indices: 128766817--128767372 Score: 191
Period size: 3 Copynumber: 180.7 Consensus size: 3
128766807 AAGTACCTAT
*
128766817 TAA TAA TAT TACA TAA -ATA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TA-A TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
128766863 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * * *
128766911 TAA TAG TAA AAA TACA AAA GAA -AG T-A TGACG TAA TAA TGAGG TAA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA T-A-A TAA TAA T-A-A TAA
* * *
128766956 GGAA -AA TAA -AA TAA -ATA TAT TAGA TATA TAA -ATA TAA TAG TAA
1 -TAA TAA TAA TAA TAA TA-A TAA TA-A TA-A TAA TA-A TAA TAA TAA
**
128766999 -ATA TAA TAA TGT TAA -AA -AA TACCA TACA TAA -AGA T-A TATA TAA
1 TA-A TAA TAA TAA TAA TAA TAA TA--A TA-A TAA TA-A TAA TA-A TAA
* * * *
128767042 -ACA TATA TAA TAA AAA T-A TACA CTAA TAT TTA TAAA TAA TAA TAG
1 TA-A TA-A TAA TAA TAA TAA TA-A -TAA TAA TAA T-AA TAA TAA TAA
* * *
128767087 TAA -ATG TAA TAA TAA TAA TAA TAA TAT TAA GT-A TAG T-A TAAA TAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA T-AA TAA
* * *
128767132 T-A TGCACA TAA CAG TAA TAA TAA TAA GTAA CAA TAA TAA TAA TAA TAA
1 TAA T--A-A TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA
* * *
128767180 T-A TAGA -AA TTCAA -AA AAA GTAA -ACA TAA T-A TAA TGA TAT TAA
1 TAA TA-A TAA -T-AA TAA TAA -TAA TA-A TAA TAA TAA TAA TAA TAA
* * *
128767222 -AA TAA -AA T-A TACA CTAA TAT TTA TAAA TAA TAA TAG TAA -ATA TAA
1 TAA TAA TAA TAA TA-A -TAA TAA TAA T-AA TAA TAA TAA TAA TA-A TAA
* *
128767267 TAA TAA TAA T-A TAA TAA TAA TGA TAA TAA TAA TAA TAT TAA GT-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA
* * * *
128767311 TAG T-A TAAA TAA TATG TACA TAA TAG TAA TAA TAA TAA GTAA CAA TAA
1 TAA TAA T-AA TAA TA-A TA-A TAA TAA TAA TAA TAA TAA -TAA TAA TAA
128767359 TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TA
128767373 TAGAAATTCA
Statistics
Matches: 415, Mismatches: 69, Indels: 138
0.67 0.11 0.22
Matches are distributed among these distances:
2 44 0.11
3 298 0.72
4 60 0.14
5 11 0.03
6 2 0.00
ACGTcount: A:0.60, C:0.03, G:0.06, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:128767168 original size:19 final size:19
Alignment explanation
Indices: 128767140--128767176 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
128767130 AATATGCACA
*
128767140 TAACAGTAATAATAATAAG
1 TAACAATAATAATAATAAG
128767159 TAACAATAATAATAATAA
1 TAACAATAATAATAATAA
128767177 TAATATAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.27
Consensus pattern (19 bp):
TAACAATAATAATAATAAG
Found at i:128767280 original size:26 final size:26
Alignment explanation
Indices: 128767263--128767372 Score: 87
Period size: 26 Copynumber: 3.9 Consensus size: 26
128767253 AATAGTAAAT
128767263 ATAATAATAATAATATAATAATAATG
1 ATAATAATAATAATATAATAATAATG
*
128767289 ATAATAATAATAATATTAAGT-ATAGTATAA
1 ATAATAATAATAATA-TAA-TAATA--AT-G
* *
128767319 ATAATATGTACATAATAGTAATAATAATA
1 ATAATA-ATA-ATAATA-TAATAATAATG
*
128767348 AGTAACAATAATAATAATAATAATA
1 A-TAATAATAATAAT-ATAATAATA
128767373 TAGAAATTCA
Statistics
Matches: 69, Mismatches: 5, Indels: 18
0.75 0.05 0.20
Matches are distributed among these distances:
26 15 0.22
27 6 0.09
28 14 0.20
29 7 0.10
30 12 0.17
31 3 0.04
32 12 0.17
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (26 bp):
ATAATAATAATAATATAATAATAATG
Found at i:128767430 original size:16 final size:16
Alignment explanation
Indices: 128767397--128767429 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
128767387 AACTAAACAT
*
128767397 AATATAATAATATTAA
1 AATAAAATAATATTAA
128767413 AATAAAATAAT-TTAA
1 AATAAAATAATATTAA
128767428 AA
1 AA
128767430 AATACTATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AATAAAATAATATTAA
Found at i:128773577 original size:3 final size:3
Alignment explanation
Indices: 128773564--128773603 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
128773554 TTTAAGTAAA
128773564 TAT TAT T-T TAT TAT TAT TAT TA- TAT TAT TA- TAT TA- TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
128773604 ATTAAATAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
2 8 0.24
3 25 0.76
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:128773577 original size:8 final size:8
Alignment explanation
Indices: 128773564--128773599 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
128773554 TTTAAGTAAA
*
128773564 TATTATTT
1 TATTATAT
128773572 TATTATTAT
1 TATTA-TAT
128773581 TATTATAT
1 TATTATAT
128773589 TATTATAT
1 TATTATAT
128773597 TAT
1 TAT
128773600 ATTAATTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
8 19 0.73
9 7 0.27
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (8 bp):
TATTATAT
Found at i:128773607 original size:22 final size:22
Alignment explanation
Indices: 128773563--128773603 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
128773553 ATTTAAGTAA
*
128773563 ATATTATTTTATTATTATTATT
1 ATATTATTATATTATTATTATT
128773585 ATATTATTATATTA-TATTA
1 ATATTATTATATTATTATTA
128773604 ATTAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
ATATTATTATATTATTATTATT
Found at i:128774889 original size:18 final size:18
Alignment explanation
Indices: 128774866--128774940 Score: 132
Period size: 18 Copynumber: 4.2 Consensus size: 18
128774856 AGATAAATGC
128774866 ACTGAATGACTGATTGTT
1 ACTGAATGACTGATTGTT
128774884 ACTGAATGACTGATTGTT
1 ACTGAATGACTGATTGTT
* *
128774902 ATTGAATGATTGATTGTT
1 ACTGAATGACTGATTGTT
128774920 ACTGAATGACTGATTGTT
1 ACTGAATGACTGATTGTT
128774938 ACT
1 ACT
128774941 AAATAATGAT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 53 1.00
ACGTcount: A:0.28, C:0.09, G:0.21, T:0.41
Consensus pattern (18 bp):
ACTGAATGACTGATTGTT
Found at i:128775909 original size:9 final size:9
Alignment explanation
Indices: 128775895--128775920 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
128775885 CTTTAGAATG
128775895 CCTCAAAAC
1 CCTCAAAAC
128775904 CCTCAAAAC
1 CCTCAAAAC
128775913 CCTCAAAA
1 CCTCAAAA
128775921 ATGCCCTTTT
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:0.46, C:0.42, G:0.00, T:0.12
Consensus pattern (9 bp):
CCTCAAAAC
Found at i:128781585 original size:14 final size:14
Alignment explanation
Indices: 128781566--128781592 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
128781556 AACCCATTAC
128781566 AGAAACTCTATTTT
1 AGAAACTCTATTTT
128781580 AGAAACTCTATTT
1 AGAAACTCTATTT
128781593 CTGTCACCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.41
Consensus pattern (14 bp):
AGAAACTCTATTTT
Found at i:128783595 original size:26 final size:26
Alignment explanation
Indices: 128783558--128783745 Score: 295
Period size: 26 Copynumber: 7.2 Consensus size: 26
128783548 TGATACAAAT
*
128783558 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
128783584 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
128783610 TAATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
128783636 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
128783662 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
128783688 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
128783714 TGATAATGGTTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
128783740 TGATAA
1 TGATAA
128783746 GAAATTCATG
Statistics
Matches: 149, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 149 1.00
ACGTcount: A:0.34, C:0.06, G:0.23, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:128785775 original size:136 final size:137
Alignment explanation
Indices: 128785530--128785815 Score: 529
Period size: 136 Copynumber: 2.1 Consensus size: 137
128785520 GAATAGTCTC
128785530 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
*
128785595 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTAGCCCAGTACC
128785660 ACTGTTA
131 ACTGTTA
*
128785667 CCCAAATGGGCTTGCATATG-TTATTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
128785731 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTAGCCCAGTACC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTAGCCCAGTACC
128785796 ACTGTTA
131 ACTGTTA
**
128785803 CCTGAATGGGCTT
1 CCCAAATGGGCTT
128785816 AGGCCCAATA
Statistics
Matches: 145, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
136 125 0.86
137 20 0.14
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (137 bp):
CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTAGCCCAGTACC
ACTGTTA
Found at i:128786952 original size:17 final size:19
Alignment explanation
Indices: 128786932--128786969 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
128786922 CAGGGGAAGG
128786932 AAGAAAG-A-AAAAGAGAA
1 AAGAAAGAAGAAAAGAGAA
128786949 AAGAAAGAAGAAAAGAGAA
1 AAGAAAGAAGAAAAGAGAA
128786968 AA
1 AA
128786970 TTAAAGGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.37
18 1 0.05
19 11 0.58
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (19 bp):
AAGAAAGAAGAAAAGAGAA
Found at i:128791238 original size:50 final size:49
Alignment explanation
Indices: 128791163--128791339 Score: 237
Period size: 50 Copynumber: 3.5 Consensus size: 49
128791153 CCATGGCAAC
*
128791163 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGATAAATGA
1 AAGTGATAAGTGATAGATTCGGCTACACTTATCTGATCAAGGA-AAATGA
* * *
128791213 AAGTGATAAGTAATAGTTTAGGCTACACTTATCTGATCAAGGAAAAGTGA
1 AAGTGATAAGTGATAGATTCGGCTACACTTATCTGATCAAGGAAAA-TGA
*
128791263 AAGTGATAAGTGATAGATTCGGCTACACTTATCTGATCAATGACAAATGA
1 AAGTGATAAGTGATAGATTCGGCTACACTTATCTGATCAAGGA-AAATGA
* * * *
128791313 CAAGTGAAAAGTGGTAGCTTCAGCTAC
1 -AAGTGATAAGTGATAGATTCGGCTAC
128791340 CTGATCAGTG
Statistics
Matches: 113, Mismatches: 11, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
49 3 0.03
50 85 0.75
51 25 0.22
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.27
Consensus pattern (49 bp):
AAGTGATAAGTGATAGATTCGGCTACACTTATCTGATCAAGGAAAATGA
Found at i:128791353 original size:31 final size:31
Alignment explanation
Indices: 128791315--128791462 Score: 242
Period size: 31 Copynumber: 4.8 Consensus size: 31
128791305 ACAAATGACA
*
128791315 AGTGAAAAGTGGTAGCTTCAGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
128791346 AGTGAAAAGTGGTAGCTTCTGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
128791377 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* *
128791408 AGTGAAAAATGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
128791439 AGTGAATAGTGGTAGCTTCGGCTA
1 AGTGAAAAGTGGTAGCTTCGGCTA
128791463 AAGTGACAAG
Statistics
Matches: 110, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 110 1.00
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.26
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
Found at i:128791551 original size:47 final size:46
Alignment explanation
Indices: 128791482--128791603 Score: 154
Period size: 47 Copynumber: 2.6 Consensus size: 46
128791472 GTGATTTCCG
* *
128791482 TATAAGACCATATCTGGGATATGGCATCGGTGTGATATATGCTACTA
1 TATAAGACCATATCTGGGATATGGCATCGGTGAGATATATGATAC-A
* * * *
128791529 TATAAGACCATATCTGGGATATGACATCAGTGAGATATGTGATTCA
1 TATAAGACCATATCTGGGATATGGCATCGGTGAGATATATGATACA
* * *
128791575 TGTAAGACCATAGCTGGGCTATGGCATCG
1 TATAAGACCATATCTGGGATATGGCATCG
128791604 ATATATGAAT
Statistics
Matches: 64, Mismatches: 11, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
46 25 0.39
47 39 0.61
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.30
Consensus pattern (46 bp):
TATAAGACCATATCTGGGATATGGCATCGGTGAGATATATGATACA
Found at i:128791631 original size:42 final size:43
Alignment explanation
Indices: 128791575--128791688 Score: 178
Period size: 42 Copynumber: 2.7 Consensus size: 43
128791565 ATGTGATTCA
128791575 TGTAAGACCATAGCTGGGCTATGGCATCGA-TATATGAATATG
1 TGTAAGACCATAGCTGGGCTATGGCATCGATTATATGAATATG
*
128791617 TGTAAGACCATAGCTGGGCTATGGCATC-ATTATGTGAATATG
1 TGTAAGACCATAGCTGGGCTATGGCATCGATTATATGAATATG
* **
128791659 TGTAAGACCATAGTTGAACTATGGCATCGA
1 TGTAAGACCATAGCTGGGCTATGGCATCGA
128791689 GAAAACGAAG
Statistics
Matches: 66, Mismatches: 4, Indels: 3
0.90 0.05 0.04
Matches are distributed among these distances:
41 1 0.02
42 64 0.97
43 1 0.02
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (43 bp):
TGTAAGACCATAGCTGGGCTATGGCATCGATTATATGAATATG
Found at i:128796127 original size:22 final size:22
Alignment explanation
Indices: 128796099--128796140 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
128796089 CTCTCACAAC
128796099 AATTCTCTCTAAA-TTCTTTCCA
1 AATTCTCTC-AAATTTCTTTCCA
128796121 AATTCTCTCAAATTTCTTTC
1 AATTCTCTCAAATTTCTTTC
128796141 AATTTTTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.48
Consensus pattern (22 bp):
AATTCTCTCAAATTTCTTTCCA
Found at i:128797235 original size:7 final size:7
Alignment explanation
Indices: 128797223--128797248 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
128797213 TAATCGTTTT
128797223 GTATTTA
1 GTATTTA
128797230 GTATTTA
1 GTATTTA
128797237 GTATTTA
1 GTATTTA
128797244 GTATT
1 GTATT
128797249 ACCTATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:128801714 original size:126 final size:126
Alignment explanation
Indices: 128801489--128802168 Score: 913
Period size: 126 Copynumber: 5.4 Consensus size: 126
128801479 AGGCTTTTTC
* * * *
128801489 AGATACTACAGTAGCAAAAGAGCGTCCACGTGGGAGCTTTTTTCTGTAATTTTGCTGAAAGTGCA
1 AGATACCACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTTTTTCCGTAATTTTGCTAAAAGTGCA
* * *
128801554 TCATTCTTGAAGCATTTTTGACACTATTTGTTTAGAAACATCTTCTCAAAATTATCTTATT
66 TCCTTCTTGAAGCGTTTTTGACACTATTTGTTTAGAAACATCTTCTCAAAATTATTTTATT
* *
128801615 AGATACCACTGTAGCAAAATAGCGTCCACGTGGGAGCTTTTTTCCATAATTTTGCTAAAAGTGCA
1 AGATACCACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTTTTTCCGTAATTTTGCTAAAAGTGCA
* *
128801680 TCCTTCTTAAAGCGTTTTTGACACTATTTATTTAGAAACATCTTCTCAAAATTATTTTATT
66 TCCTTCTTGAAGCGTTTTTGACACTATTTGTTTAGAAACATCTTCTCAAAATTATTTTATT
* * *
128801741 AGATACCACTATAGCAAAAGAGCGTCCATGTGGGAGCTTTTTTCCGTAA-TTTG---AAAGTGTA
1 AGATACCACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTTTTTCCGTAATTTTGCTAAAAGTGCA
* * * * * *
128801802 TCATTCTTGAAGTGTTTTTGACACTATTTGTTCAGAAACATCTTTTAAAAATTATTTTATC
66 TCCTTCTTGAAGCGTTTTTGACACTATTTGTTTAGAAACATCTTCTCAAAATTATTTTATT
* * * * *
128801863 AGATACTACTGTAGTAAAAGAGCGTCCACGTGAGAGCTTTTTTCCGTTATTTTGCTGACAGAGTG
1 AGATACCACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTTTTTCCGTAATTTTGCT-A-AAAGTG
* *
128801928 CATCCTTCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTATC
64 CATCCTTCTTGAAGCGTTTTTGACACTATTTGTTTAGAAACATCTTCTCAAAATTATTTTATT
* * * * * * * *
128801991 AGATATCACTATAGCAAAAGAGCGTCCACGTGTGAGCTTTTTTTCATTATTTTGCTGACAGTGCA
1 AGATACCACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTTTTTCCGTAATTTTGCTAAAAGTGCA
* * *
128802056 TCCTTCTTGAAGAG-TTTTGTACACTATTTGTTTAGAAATATCTTCTCAAATTTATTTT-TT
66 TCCTTCTTGAAGCGTTTTTG-ACACTATTTGTTTAGAAACATCTTCTCAAAATTATTTTATT
* * *
128802116 CAGATACTACTGTAGTAAAAGAGCGTCCACGTGGGAGCTTTTTTCTGTAATTT
1 -AGATACCACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTTTTTCCGTAATTT
128802169 AATTAATAAA
Statistics
Matches: 487, Mismatches: 59, Indels: 16
0.87 0.10 0.03
Matches are distributed among these distances:
122 103 0.21
123 4 0.01
125 10 0.02
126 258 0.53
128 112 0.23
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.38
Consensus pattern (126 bp):
AGATACCACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTTTTTCCGTAATTTTGCTAAAAGTGCA
TCCTTCTTGAAGCGTTTTTGACACTATTTGTTTAGAAACATCTTCTCAAAATTATTTTATT
Found at i:128802303 original size:17 final size:17
Alignment explanation
Indices: 128802281--128802333 Score: 72
Period size: 17 Copynumber: 3.1 Consensus size: 17
128802271 TAAAAAACAT
*
128802281 TAAAAATCCTAAACCAC
1 TAAAAAACCTAAACCAC
*
128802298 TAAAAACCCTAAACCA-
1 TAAAAAACCTAAACCAC
128802314 TAAAAAACTCTAAACCAC
1 TAAAAAAC-CTAAACCAC
128802332 TA
1 TA
128802334 CACCCTAAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
16 7 0.22
17 23 0.72
18 2 0.06
ACGTcount: A:0.55, C:0.28, G:0.00, T:0.17
Consensus pattern (17 bp):
TAAAAAACCTAAACCAC
Found at i:128802457 original size:163 final size:161
Alignment explanation
Indices: 128802192--128802821 Score: 768
Period size: 163 Copynumber: 3.9 Consensus size: 161
128802182 TAAAAAACCC
*
128802192 TAAACCCTAATTTAATT-A-ATTTT-TTATTTTCATAGTTAATTTAATTAATTAACCCTCAA---
1 TAAACCCTAATTTAATTGATTTTTTCTTATTTTCATAGTTAATTTAATTAATTAACCCTCAACTC
** * *
128802251 -AA-T-TAAATTACTTTTTCCCTTAAAAAACATTAAAAATCCTAAACCACTAAAAACCCTAAACC
66 TAAGTGTTCATTAATTTTTCCCTTAAAAAACACTAAAAATCCTAAACCACTAAAAACCCTAAACC
*
128802313 ATAAAAAACTCTAAACCACTACACCCTAAACTA
131 ATAAAAAA-TCTAAACCACTA-ACCTTAAACTA
128802346 TTAAACCCTAATTTAATTGATTTTTTCTTATTTTCATAGTTAATTTAATTAATTAA-CCTCAACT
1 -TAAACCCTAATTTAATTGATTTTTTCTTATTTTCATAGTTAATTTAATTAATTAACCCTCAACT
* *
128802410 CTAAGTGTTCATTAATTTTTCCCCTAAAAAACACTAAAAATCCTAAACCACTAAAAATCCTAAAC
65 CTAAGTGTTCATTAATTTTTCCCTTAAAAAACACTAAAAATCCTAAACCACTAAAAACCCTAAAC
* *
128802475 CACTAAAAACTCTAAACTACTAAACCTTAAACTA
130 CA-TAAAAAATCTAAACCACT-AACCTTAAACTA
* *
128802509 CTAAACCCTAATTTAATTAATTTTTTCTTATTTTTATAGTTAATTTAATTAATTAACCCTCAACT
1 -TAAACCCTAATTTAATTGATTTTTTCTTATTTTCATAGTTAATTTAATTAATTAACCCTCAACT
* *
128802574 CT-AGATGTTCATTAATTTTTCCCTTAAAAAAACTCTAAAAACCCTAAACCACT-AAAACCCT-A
65 CTAAG-TGTTCATTAATTTTTCCCTT-AAAAAACACTAAAAATCCTAAACCACTAAAAACCCTAA
* * * *
128802636 ACCTTAAAACAATCAAAAACC-CTAACATTAAAAAACCA
128 ACCATAAAA-AATC-TAAACCACTAACCTT---AAACTA
* * * * *
128802674 TAAATCCTAATATAATTGATTTTTTTTTATTTTCATAGTTAATTTAATTAATTAACCTTCAAATC
1 TAAACCCTAATTTAATTGATTTTTTCTTATTTTCATAGTTAATTTAATTAATTAACCCTCAACTC
* **
128802739 TAAGTGTTCGTTAAATTTTT-CCTTAAAAAACACTAAAAATCCTAAACCACTAAAAATACTAAAC
66 TAAGTGTTCATT-AATTTTTCCCTTAAAAAACACTAAAAATCCTAAACCACTAAAAACCCTAAAC
**
128802803 CACCAAAAATCCTAAACCA
130 CATAAAAAAT-CTAAACCA
128802822 GTAAAACCTT
Statistics
Matches: 411, Mismatches: 39, Indels: 40
0.84 0.08 0.08
Matches are distributed among these distances:
155 17 0.04
156 1 0.00
157 10 0.02
158 29 0.07
161 2 0.00
162 11 0.03
163 163 0.40
164 131 0.32
165 47 0.11
ACGTcount: A:0.43, C:0.20, G:0.02, T:0.35
Consensus pattern (161 bp):
TAAACCCTAATTTAATTGATTTTTTCTTATTTTCATAGTTAATTTAATTAATTAACCCTCAACTC
TAAGTGTTCATTAATTTTTCCCTTAAAAAACACTAAAAATCCTAAACCACTAAAAACCCTAAACC
ATAAAAAATCTAAACCACTAACCTTAAACTA
Found at i:128802463 original size:17 final size:17
Alignment explanation
Indices: 128802441--128802498 Score: 91
Period size: 17 Copynumber: 3.4 Consensus size: 17
128802431 CCCTAAAAAA
128802441 CACTAAAAATCCTAAAC
1 CACTAAAAATCCTAAAC
128802458 CACTAAAAATCCTAAAC
1 CACTAAAAATCCTAAAC
128802475 CACTAAAAA-CTCTAAAC
1 CACTAAAAATC-CTAAAC
*
128802492 TACTAAA
1 CACTAAA
128802499 CCTTAAACTA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
16 1 0.03
17 38 0.97
ACGTcount: A:0.53, C:0.28, G:0.00, T:0.19
Consensus pattern (17 bp):
CACTAAAAATCCTAAAC
Done.