Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013055.1 Kokia drynarioides strain JFW-HI SEQ_128073, whole genome shotgun sequence
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: 217179
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 176 characters in sequence are not A, C, G, or T
Found at i:485 original size:3 final size:3
Alignment explanation
Indices: 416--471 Score: 96
Period size: 3 Copynumber: 19.0 Consensus size: 3
406 TTAAACCCAT
*
416 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTG
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
463 TTA TTA TTA
1 TTA TTA TTA
472 ATGAATTTAT
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
2 2 0.04
3 48 0.96
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1234 original size:18 final size:18
Alignment explanation
Indices: 1213--1264 Score: 65
Period size: 17 Copynumber: 3.0 Consensus size: 18
1203 TTTAAATTAG
1213 TTAAATTTTAAA-TTCAAA
1 TTAAATTTTAAACTT-AAA
*
1231 TT-AATTTTAAACTTAAT
1 TTAAATTTTAAACTTAAA
1248 TTAAA-TTTAAACTTAAA
1 TTAAATTTTAAACTTAAA
1265 AGAAAAGTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
17 24 0.80
18 6 0.20
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (18 bp):
TTAAATTTTAAACTTAAA
Found at i:1251 original size:17 final size:16
Alignment explanation
Indices: 1202--1263 Score: 61
Period size: 17 Copynumber: 3.7 Consensus size: 16
1192 ACTGAACTTT
* *
1202 TTTTAAATTAGTTAAA
1 TTTTAAATTAATTTAA
*
1218 TTTTAAATTCAAATTAA
1 TTTTAAATT-AATTTAA
1235 TTTTAAACTTAATTTAA
1 TTTTAAA-TTAATTTAA
*
1252 ATTTAAACTTAA
1 TTTTAAA-TTAA
1264 AAGAAAAGTT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
16 9 0.23
17 28 0.72
18 2 0.05
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (16 bp):
TTTTAAATTAATTTAA
Found at i:6408 original size:46 final size:43
Alignment explanation
Indices: 6188--6419 Score: 288
Period size: 43 Copynumber: 5.3 Consensus size: 43
6178 GTGAATTTCT
* * *
6188 ACAAACGCCGCTAAAGAACATGGTCTTTAGCGG-ACTTTTCCC
1 ACAAACCCCGCTAAAGAACATGGTCTTTAGCGGCGCTTATCCC
** *
6230 ACAAACCCCGCTAAA-AACCATGGTCTTTAGCAACGCTTCTCCC
1 ACAAACCCCGCTAAAGAA-CATGGTCTTTAGCGGCGCTTATCCC
* *
6273 ACAAACCCCGCTAAAGAACATGGTCTTTAGCAGCGCTTACCCC
1 ACAAACCCCGCTAAAGAACATGGTCTTTAGCGGCGCTTATCCC
* *
6316 CCAAACCCCGCTAAAGAACATGGTCTTTAGCGGCGCTTACCCC
1 ACAAACCCCGCTAAAGAACATGGTCTTTAGCGGCGCTTATCCC
* * *
6359 ACAAACCCCCCCACTAAAGAACATGGTCTTTAGCGGCGCTTTTCTC
1 ACAAA---CCCCGCTAAAGAACATGGTCTTTAGCGGCGCTTATCCC
*
6405 ACAAACGCCGCTAAA
1 ACAAACCCCGCTAAA
6420 ATTAACAGAT
Statistics
Matches: 167, Mismatches: 17, Indels: 11
0.86 0.09 0.06
Matches are distributed among these distances:
41 2 0.01
42 27 0.16
43 97 0.58
44 2 0.01
46 39 0.23
ACGTcount: A:0.29, C:0.34, G:0.16, T:0.20
Consensus pattern (43 bp):
ACAAACCCCGCTAAAGAACATGGTCTTTAGCGGCGCTTATCCC
Found at i:11688 original size:8 final size:8
Alignment explanation
Indices: 11664--11698 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
11654 ACATAGTTGC
*
11664 AAATAAAT
1 AAATAATT
*
11672 AACTAATT
1 AAATAATT
11680 AAATAATT
1 AAATAATT
11688 AAATAATT
1 AAATAATT
11696 AAA
1 AAA
11699 CATTTCAAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (8 bp):
AAATAATT
Found at i:11737 original size:14 final size:14
Alignment explanation
Indices: 11718--11744 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
11708 TTGTTTTTAA
11718 TAATTAAATATTTT
1 TAATTAAATATTTT
11732 TAATTAAATATTT
1 TAATTAAATATTT
11745 GAATCGTTTT
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TAATTAAATATTTT
Found at i:11791 original size:50 final size:48
Alignment explanation
Indices: 11732--11866 Score: 170
Period size: 50 Copynumber: 2.8 Consensus size: 48
11722 TAAATATTTT
*
11732 TAATTAAATATTTGAATCGTTTTTAATAAATAACTAATTATTAAACTAAA
1 TAATTAAATATTTGAATTGTTTTTAATAAATAACTAATTA-T-AACTAAA
* * *
11782 TAATTAAATATTTGGATTGTTTTTAAT-AAT---TAAATATAATTAAA
1 TAATTAAATATTTGAATTGTTTTTAATAAATAACTAATTATAACTAAA
*
11826 TAATTAAATATTTGAATTGCTTTTTATTAAATAACTAATTA
1 TAATTAAATATTTGAATTG-TTTTTAATAAATAACTAATTA
11867 AATAATTAAA
Statistics
Matches: 73, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
44 24 0.33
45 8 0.11
46 8 0.11
49 8 0.11
50 25 0.34
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (48 bp):
TAATTAAATATTTGAATTGTTTTTAATAAATAACTAATTATAACTAAA
Found at i:11876 original size:20 final size:20
Alignment explanation
Indices: 11851--11889 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
11841 ATTGCTTTTT
11851 ATTAAATAACTAATTAAATA
1 ATTAAATAACTAATTAAATA
**
11871 ATTAAATATTTAATTAAAT
1 ATTAAATAACTAATTAAAT
11890 GTTATTAGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (20 bp):
ATTAAATAACTAATTAAATA
Found at i:11877 original size:95 final size:91
Alignment explanation
Indices: 11665--11883 Score: 289
Period size: 91 Copynumber: 2.4 Consensus size: 91
11655 CATAGTTGCA
11665 AATAAATAACTAATTAAATAATTAAATAATTAAACATTTCAAGTTGTTTTTAATAATTAAATATT
1 AATAAATAACTAATTAAATAATTAAATAATTAAACATTTCAAGTTGTTTTTAATAATTAAATATT
*
11730 TTTAATTAAATATTTGAATCGTTTTT
66 TATAATTAAATATTTGAATCGTTTTT
* * * **
11756 AATAAATAACTAATT-ATTAAACTAAATAATTAAATATTTGGA-TTGTTTTTAATAATTAAATAT
1 AATAAATAACTAATTAAAT-AATTAAATAATTAAACATTTCAAGTTGTTTTTAATAATTAAATAT
*
11819 AATTAAATAATTAAATATTTGAATTGCTTTTT
65 --TT--ATAATTAAATATTTGAATCG-TTTTT
* *
11851 ATTAAATAACTAATTAAATAATTAAATATTTAA
1 AATAAATAACTAATTAAATAATTAAATAATTAA
11884 TTAAATGTTA
Statistics
Matches: 110, Mismatches: 11, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
90 23 0.21
91 34 0.31
92 2 0.02
94 18 0.16
95 31 0.28
96 2 0.02
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (91 bp):
AATAAATAACTAATTAAATAATTAAATAATTAAACATTTCAAGTTGTTTTTAATAATTAAATATT
TATAATTAAATATTTGAATCGTTTTT
Found at i:11878 original size:43 final size:43
Alignment explanation
Indices: 11778--11885 Score: 150
Period size: 44 Copynumber: 2.5 Consensus size: 43
11768 ATTATTAAAC
* *
11778 TAAATAATTAAATATTTGGATTGTTTTTAATAATTAAATATAAT
1 TAAATAATTAAATATTTGAATTGCTTTT-ATAATTAAATATAAT
11822 TAAATAATTAAATATTTGAATTGCTTTT-T-ATTAAATAACTAAT
1 TAAATAATTAAATATTTGAATTGCTTTTATAATTAAAT-A-TAAT
11865 TAAATAATTAAATATTT-AATT
1 TAAATAATTAAATATTTGAATT
11886 AAATGTTATT
Statistics
Matches: 60, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
41 7 0.12
42 6 0.10
43 21 0.35
44 26 0.43
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.47
Consensus pattern (43 bp):
TAAATAATTAAATATTTGAATTGCTTTTATAATTAAATATAAT
Found at i:16312 original size:41 final size:41
Alignment explanation
Indices: 16254--16522 Score: 256
Period size: 41 Copynumber: 6.6 Consensus size: 41
16244 ATAAATGCCA
* * *
16254 CTAATGCTTTGACCTTTAGCGGCGCTTTACCAGAAACGCCG
1 CTAATGCTCTGACCTTTAGCGGCGCTTTCCCACAAACGCCG
* * * * * *
16295 TTAATGCTCTGATCTTTAGCGGTGCTTTGCCAGAAACGTCG
1 CTAATGCTCTGACCTTTAGCGGCGCTTTCCCACAAACGCCG
* *
16336 TTAATGCTCTGACCTTTAACGGCGCTTTCCCA-AAA-GCATCG
1 CTAATGCTCTGACCTTTAGCGGCGCTTTCCCACAAACGC--CG
* * * ** * *
16377 GTAATACTCTAACCTTTAGCGGTACTTTCTCACAAGCGCCG
1 CTAATGCTCTGACCTTTAGCGGCGCTTTCCCACAAACGCCG
* * *
16418 CTAATGCTCTGACCTTTAGCGGCAC-TTCCCACAAGCGTCG
1 CTAATGCTCTGACCTTTAGCGGCGCTTTCCCACAAACGCCG
* * * * *
16458 CTAATGCTCTGACCTTTAGCTGCGTTTTTCCATAAGCGCCG
1 CTAATGCTCTGACCTTTAGCGGCGCTTTCCCACAAACGCCG
*
16499 CTAATGCTCTGACTTTTAGCGGCG
1 CTAATGCTCTGACCTTTAGCGGCG
16523 TTTTTTCTAT
Statistics
Matches: 190, Mismatches: 33, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
39 1 0.01
40 38 0.20
41 147 0.77
42 2 0.01
43 2 0.01
ACGTcount: A:0.21, C:0.29, G:0.20, T:0.30
Consensus pattern (41 bp):
CTAATGCTCTGACCTTTAGCGGCGCTTTCCCACAAACGCCG
Found at i:16394 original size:82 final size:80
Alignment explanation
Indices: 16254--16522 Score: 283
Period size: 82 Copynumber: 3.3 Consensus size: 80
16244 ATAAATGCCA
* * * *
16254 CTAATGCTTTGACCTTTAGCGGCGCTTTACCAGAAACGC-CGTTAATGCTCTGATCTTTAGCGGT
1 CTAATGCTCTGACCTTTAGCGGCGCTTTCCCA-AAA-GCTCGCTAATGCTCTGACCTTTAGCGGT
* * *
16318 GCTTTGCCAGAAACGTCG
64 GCTTT-CCACAAGCGCCG
* * * * * *
16336 TTAATGCTCTGACCTTTAACGGCGCTTTCCCAAAAGCATCGGTAATACTCTAACCTTTAGCGGTA
1 CTAATGCTCTGACCTTTAGCGGCGCTTTCCCAAAAGC-TCGCTAATGCTCTGACCTTTAGCGGTG
16401 CTTTCTCACAAGCGCCG
65 CTTTC-CACAAGCGCCG
* *
16418 CTAATGCTCTGACCTTTAGCGGCAC-TTCCCACAAGCGTCGCTAATGCTCTGACCTTTAGCTGCG
1 CTAATGCTCTGACCTTTAGCGGCGCTTTCCCAAAAGC-TCGCTAATGCTCTGACCTTTAGC-G-G
* *
16482 T-TTTTCCATAAGCGCCG
63 TGCTTTCCACAAGCGCCG
*
16499 CTAATGCTCTGACTTTTAGCGGCG
1 CTAATGCTCTGACCTTTAGCGGCG
16523 TTTTTTCTAT
Statistics
Matches: 158, Mismatches: 24, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
80 2 0.01
81 66 0.42
82 88 0.56
83 2 0.01
ACGTcount: A:0.21, C:0.29, G:0.20, T:0.30
Consensus pattern (80 bp):
CTAATGCTCTGACCTTTAGCGGCGCTTTCCCAAAAGCTCGCTAATGCTCTGACCTTTAGCGGTGC
TTTCCACAAGCGCCG
Found at i:16565 original size:41 final size:40
Alignment explanation
Indices: 16469--16607 Score: 138
Period size: 40 Copynumber: 3.4 Consensus size: 40
16459 TAATGCTCTG
* * * * *
16469 ACCTTTAGCTGCGTTTTTCCATAAGCGCCGCTAATGCTCTG
1 ACCTTTTGCTGCGTTTTTCTATAAACGCCGCTATTGCT-TT
*
16510 A-CTTTTAGCGGCGTTTTTTCTATAAACGCCGCTATTGCTTT
1 ACCTTTT-GCTGCG-TTTTTCTATAAACGCCGCTATTGCTTT
* * *
16551 ACCTTTTGCCGCG-TTTACGTAAAAACGCCGCTATTGCTTT
1 ACCTTTTGCTGCGTTTTTC-TATAAACGCCGCTATTGCTTT
*
16591 ATCTTTTGCTGCGTTTT
1 ACCTTTTGCTGCGTTTT
16608 CTGTCCAAAC
Statistics
Matches: 82, Mismatches: 11, Indels: 10
0.80 0.11 0.10
Matches are distributed among these distances:
39 4 0.05
40 35 0.43
41 16 0.20
42 27 0.33
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (40 bp):
ACCTTTTGCTGCGTTTTTCTATAAACGCCGCTATTGCTTT
Found at i:18031 original size:6 final size:6
Alignment explanation
Indices: 18017--18057 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
18007 CTTGATCCCA
* * *
18017 AACCCG AACCTG AACCTG AACCTG AACTTG AACTTG AACCT
1 AACCTG AACCTG AACCTG AACCTG AACCTG AACCTG AACCT
18058 AAACTCGAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.34, C:0.32, G:0.15, T:0.20
Consensus pattern (6 bp):
AACCTG
Found at i:18062 original size:18 final size:18
Alignment explanation
Indices: 18027--18062 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
18017 AACCCGAACC
*
18027 TGAACCTGAACCTGAACT
1 TGAACCTGAACCTAAACT
*
18045 TGAACTTGAACCTAAACT
1 TGAACCTGAACCTAAACT
18063 CGAATCCGAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.25
Consensus pattern (18 bp):
TGAACCTGAACCTAAACT
Found at i:18137 original size:7 final size:7
Alignment explanation
Indices: 18125--18175 Score: 52
Period size: 7 Copynumber: 7.6 Consensus size: 7
18115 GCTCAAACCA
18125 TTGACCG
1 TTGACCG
18132 TTGACC-
1 TTGACCG
*
18138 TTGATCG
1 TTGACCG
*
18145 TTGATCG
1 TTGACCG
18152 TTGACC-
1 TTGACCG
*
18158 TTGATCG
1 TTGACCG
*
18165 TTAACCG
1 TTGACCG
18172 TTGA
1 TTGA
18176 TCATTGAGTT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
6 10 0.28
7 26 0.72
ACGTcount: A:0.18, C:0.22, G:0.24, T:0.37
Consensus pattern (7 bp):
TTGACCG
Found at i:18141 original size:13 final size:14
Alignment explanation
Indices: 18125--18182 Score: 66
Period size: 13 Copynumber: 4.3 Consensus size: 14
18115 GCTCAAACCA
*
18125 TTGACCGTTGA-CC
1 TTGACCGTTGATCG
*
18138 TTGATCGTTGATCG
1 TTGACCGTTGATCG
18152 TTGACC-TTGATCG
1 TTGACCGTTGATCG
* *
18165 TTAACCGTTGATCA
1 TTGACCGTTGATCG
18179 TTGA
1 TTGA
18183 GTTGTTTGAA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
13 22 0.59
14 15 0.41
ACGTcount: A:0.19, C:0.21, G:0.22, T:0.38
Consensus pattern (14 bp):
TTGACCGTTGATCG
Found at i:18153 original size:20 final size:20
Alignment explanation
Indices: 18125--18175 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
18115 GCTCAAACCA
18125 TTGACCGTTGACCTTGATCG
1 TTGACCGTTGACCTTGATCG
*
18145 TTGATCGTTGACCTTGATCG
1 TTGACCGTTGACCTTGATCG
*
18165 TTAACCGTTGA
1 TTGACCGTTGA
18176 TCATTGAGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.18, C:0.22, G:0.24, T:0.37
Consensus pattern (20 bp):
TTGACCGTTGACCTTGATCG
Found at i:20749 original size:22 final size:22
Alignment explanation
Indices: 20724--20765 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
20714 AATATATTTT
*
20724 ATTTTTAAAACAATTGTAAAGC
1 ATTTATAAAACAATTGTAAAGC
*
20746 ATTTATAAAACAATTTTAAA
1 ATTTATAAAACAATTGTAAA
20766 TTTTATATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.50, C:0.07, G:0.05, T:0.38
Consensus pattern (22 bp):
ATTTATAAAACAATTGTAAAGC
Found at i:23080 original size:72 final size:72
Alignment explanation
Indices: 22991--23128 Score: 213
Period size: 72 Copynumber: 1.9 Consensus size: 72
22981 AATACTGCTA
* * *
22991 ACACGAGCTTCAAAGAATTCACAACATGTGTTGAATCTCAAGCCATCGATAAAGAATAATTTGAT
1 ACACAAGCTTCAAAGAATCCACAACATGCGTTGAATCTCAAGCCATCGATAAAGAATAATTTGAT
23056 GCTACTT
66 GCTACTT
* * * *
23063 ACACAAGCTTCAGAGAATCCACAACATGCGTTGGATCTCAAGCCATCGATAATGAATGATTTGAT
1 ACACAAGCTTCAAAGAATCCACAACATGCGTTGAATCTCAAGCCATCGATAAAGAATAATTTGAT
23128 G
66 G
23129 TATGCGTTGG
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
72 59 1.00
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.26
Consensus pattern (72 bp):
ACACAAGCTTCAAAGAATCCACAACATGCGTTGAATCTCAAGCCATCGATAAAGAATAATTTGAT
GCTACTT
Found at i:23151 original size:42 final size:42
Alignment explanation
Indices: 23088--23172 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
23078 AATCCACAAC
*
23088 ATGCGTTGGATCTCAAGCCATCGATAATGAATGATTTGATGT
1 ATGCGTTGGATCTCAAACCATCGATAATGAATGATTTGATGT
23130 ATGCGTTGGATCTCAAACCATCGATAATGAATGATTTGATGT
1 ATGCGTTGGATCTCAAACCATCGATAATGAATGATTTGATGT
23172 A
1 A
23173 ACCTCCCCGA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.33
Consensus pattern (42 bp):
ATGCGTTGGATCTCAAACCATCGATAATGAATGATTTGATGT
Found at i:24199 original size:3 final size:3
Alignment explanation
Indices: 24191--24272 Score: 53
Period size: 3 Copynumber: 27.7 Consensus size: 3
24181 CAGCTTTTTA
* * * *
24191 TTC TTC TTC TTT TTC TTT TTC TTT TTC TTC TTC ATT- TTC TTG TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC -TTC TTC TTC TTC
* * * *
24236 TTG TTC TTG TTA TTC TTC TT- TGT- TTC TTC TTT TTC TT
1 TTC TTC TTC TTC TTC TTC TTC T-TC TTC TTC TTC TTC TT
24273 TTATTGCCCT
Statistics
Matches: 60, Mismatches: 15, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
2 4 0.07
3 54 0.90
4 2 0.03
ACGTcount: A:0.02, C:0.20, G:0.05, T:0.73
Consensus pattern (3 bp):
TTC
Found at i:24206 original size:6 final size:6
Alignment explanation
Indices: 24191--24274 Score: 71
Period size: 6 Copynumber: 14.2 Consensus size: 6
24181 CAGCTTTTTA
* * * * *
24191 TTCTTC TTCTTT TTCTTT TTCTTT TTCTTC TTCATT TTCTTG TTCTTG
1 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT
* * * * *
24239 TTCTTG TTATTC TTCTTT GT-TTC TTCTTT TTCTTT T
1 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT T
24275 ATTGCCCTAA
Statistics
Matches: 63, Mismatches: 14, Indels: 2
0.80 0.18 0.03
Matches are distributed among these distances:
5 3 0.05
6 60 0.95
ACGTcount: A:0.02, C:0.19, G:0.05, T:0.74
Consensus pattern (6 bp):
TTCTTT
Found at i:26819 original size:23 final size:22
Alignment explanation
Indices: 26769--26821 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
26759 TATTTTTATT
* *
26769 TTTATTAAATTATATTTAATAA
1 TTTATTAAAATATATTAAATAA
*
26791 TATTATTAAAATATGATTAAATTA
1 T-TTATTAAAATAT-ATTAAATAA
26815 TTTATTA
1 TTTATTA
26822 TCATTTTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 1 0.04
23 17 0.65
24 8 0.31
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
TTTATTAAAATATATTAAATAA
Found at i:27321 original size:2 final size:2
Alignment explanation
Indices: 27314--27342 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
27304 TCTTAGACTT
27314 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
27343 GGGGAGTGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:29574 original size:18 final size:17
Alignment explanation
Indices: 29551--29585 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
29541 TATTTTAAAA
29551 TTTTTAATATATGTATTT
1 TTTTTAATATA-GTATTT
*
29569 TTTTTAATTTAGTATTT
1 TTTTTAATATAGTATTT
29586 AATCATTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.69
Consensus pattern (17 bp):
TTTTTAATATAGTATTT
Found at i:33534 original size:13 final size:13
Alignment explanation
Indices: 33516--33543 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
33506 TTATTGAAAA
33516 ACACACTATATTT
1 ACACACTATATTT
33529 ACACACTATATTT
1 ACACACTATATTT
33542 AC
1 AC
33544 TATCTTCTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.25, G:0.00, T:0.36
Consensus pattern (13 bp):
ACACACTATATTT
Found at i:37787 original size:29 final size:28
Alignment explanation
Indices: 37738--38108 Score: 303
Period size: 29 Copynumber: 12.6 Consensus size: 28
37728 ATTTTATTTA
* * **
37738 AAAATAACATTTTGACCCCTAAATCTTTAT
1 AAAATCACATTTT-AACCCTAAA-CTTTCC
*
37768 AAAATTACATTTTAACCCTAAACTTTTCC
1 AAAATCACATTTTAACCCTAAAC-TTTCC
* *
37797 AAAATTACATTTTGACCACTAAACTTTTCC
1 AAAATCACATTTTAACC-CTAAAC-TTTCC
** * **
37827 AAAATCATTTTCTTTACCCTAAACTTTTTA
1 AAAATCACATT-TTAACCCTAAAC-TTTCC
* * * *
37857 AAAATAACA-TTTGACACTTAAACTTCCC
1 AAAATCACATTTTAAC-CCTAAACTTTCC
* * * *
37885 CAAATTACATTTTGACCCCTAAACTTTCTT
1 AAAATCACATTTT-AACCCTAAACTTTC-C
* *
37915 AAAATCACATTTTAACCCCAAAAATTTTCC
1 AAAATCACATTTTAA-CCC-TAAACTTTCC
* *
37945 AAAATTACATTTTAACCCTTAAACCTCTCC
1 AAAATCACATTTTAACCC-TAAA-CTTTCC
* * *
37975 AAAATCACATTTTGACCCCAAACCTTCCC
1 AAAATCACATTTTAACCCTAAA-CTTTCC
*
38004 AAAATCACATTTTAACCCTAAAATTCTCC
1 AAAATCACATTTTAACCCTAAACTT-TCC
*
38033 AAAATCACATTTTAACCCTAAAATTCTCC
1 AAAATCACATTTTAACCCTAAACTT-TCC
38062 AAAATCACATTTTAACCCTAAACTTTTCC
1 AAAATCACATTTTAACCCTAAAC-TTTCC
*
38091 AAAATTACATTTTAACCC
1 AAAATCACATTTTAACCC
38109 CGAATTCTCT
Statistics
Matches: 281, Mismatches: 48, Indels: 25
0.79 0.14 0.07
Matches are distributed among these distances:
28 16 0.06
29 154 0.55
30 99 0.35
31 12 0.04
ACGTcount: A:0.38, C:0.26, G:0.01, T:0.34
Consensus pattern (28 bp):
AAAATCACATTTTAACCCTAAACTTTCC
Found at i:42885 original size:8 final size:7
Alignment explanation
Indices: 42872--42950 Score: 61
Period size: 7 Copynumber: 10.7 Consensus size: 7
42862 TCGATGAAGA
42872 AAAAAAGG
1 AAAAAA-G
42880 AAAAAAG
1 AAAAAAG
*
42887 AAAAAAA
1 AAAAAAG
42894 AAAGAAAG
1 AAA-AAAG
*
42902 AAAGAAG
1 AAAAAAG
42909 AAGAAAAAG
1 -A-AAAAAG
42918 AAAAAA-
1 AAAAAAG
* *
42924 AAGAGAG
1 AAAAAAG
42931 AAAAAGAG
1 AAAAA-AG
*
42939 GAAAAAG
1 AAAAAAG
42946 AAAAA
1 AAAAA
42951 GATAGGTCAT
Statistics
Matches: 56, Mismatches: 10, Indels: 11
0.73 0.13 0.14
Matches are distributed among these distances:
6 4 0.07
7 27 0.48
8 20 0.36
9 5 0.09
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:42895 original size:19 final size:19
Alignment explanation
Indices: 42871--42950 Score: 74
Period size: 19 Copynumber: 4.1 Consensus size: 19
42861 TTCGATGAAG
42871 AAAAAAAGGAAAAAAGAAA
1 AAAAAAAGGAAAAAAGAAA
42890 AAAAAAA-GAAAGAAAGAAGA
1 AAAAAAAGGAAA-AAAGAA-A
* * *
42910 AGAAAAAGAAAAAAAAGAGAG
1 AAAAAAAG-GAAAAAAGA-AA
*
42931 AAAAAGAGG-AAAAAGAAA
1 AAAAAAAGGAAAAAAGAAA
42949 AA
1 AA
42951 GATAGGTCAT
Statistics
Matches: 49, Mismatches: 7, Indels: 11
0.73 0.10 0.16
Matches are distributed among these distances:
18 7 0.14
19 20 0.41
20 7 0.14
21 11 0.22
22 4 0.08
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (19 bp):
AAAAAAAGGAAAAAAGAAA
Found at i:42904 original size:22 final size:21
Alignment explanation
Indices: 42871--42950 Score: 63
Period size: 22 Copynumber: 3.7 Consensus size: 21
42861 TTCGATGAAG
*
42871 AAAAAAAGGAAAAAAGAAAAA
1 AAAAAAAAGAAAAAAGAAAAA
*
42892 AAAAAGAAAGAAAGAAGAAGAAA
1 AAAAA-AAAGAAAAAAGAA-AAA
* *
42915 AAGAAAAAA-AAGAGAGAAAAA
1 AA-AAAAAAGAAAAAAGAAAAA
**
42936 GAGGAAAAAGAAAAA
1 -AAAAAAAAGAAAAA
42951 GATAGGTCAT
Statistics
Matches: 45, Mismatches: 9, Indels: 9
0.71 0.14 0.14
Matches are distributed among these distances:
21 13 0.29
22 21 0.47
23 8 0.18
24 3 0.07
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (21 bp):
AAAAAAAAGAAAAAAGAAAAA
Found at i:42904 original size:31 final size:30
Alignment explanation
Indices: 42868--42950 Score: 100
Period size: 29 Copynumber: 2.8 Consensus size: 30
42858 AGATTCGATG
42868 AAGAAAAAAAGGAAAAAAGAAAAAAAAAAGA
1 AAGAAAAAAAGG-AAAAAGAAAAAAAAAAGA
42899 AAGAAAGAAGAA-GAAAAAG--AAAAAAAAGA
1 AAGAAA-AA-AAGGAAAAAGAAAAAAAAAAGA
* *
42928 GAGAAAAAGAGGAAAAAGAAAAA
1 AAGAAAAAAAGGAAAAAGAAAAA
42951 GATAGGTCAT
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
27 1 0.02
28 9 0.20
29 15 0.33
30 3 0.07
31 12 0.27
32 3 0.07
33 2 0.04
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (30 bp):
AAGAAAAAAAGGAAAAAGAAAAAAAAAAGA
Found at i:42937 original size:28 final size:29
Alignment explanation
Indices: 42889--42950 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 29
42879 GAAAAAAGAA
42889 AAAAAAAAGAAAGAAAGAAGAAGAAAAAG
1 AAAAAAAAGAAAGAAAGAAGAAGAAAAAG
* *
42918 AAAAAAAAGAGAGAAA-AAGAGGAAAAAG
1 AAAAAAAAGAAAGAAAGAAGAAGAAAAAG
42946 AAAAA
1 AAAAA
42951 GATAGGTCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 16 0.52
29 15 0.48
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (29 bp):
AAAAAAAAGAAAGAAAGAAGAAGAAAAAG
Found at i:42945 original size:9 final size:9
Alignment explanation
Indices: 42867--42947 Score: 73
Period size: 9 Copynumber: 9.3 Consensus size: 9
42857 CAGATTCGAT
42867 GAAGAAAAA
1 GAAGAAAAA
*
42876 -AAGGAAAA
1 GAAGAAAAA
42884 -AAGAAAAA
1 GAAGAAAAA
*
42892 -AA-AAAGA
1 GAAGAAAAA
42899 -AAGAAAGAA
1 GAAGAAA-AA
42908 GAAGAAAAA
1 GAAGAAAAA
*
42917 GAAAAAAAA
1 GAAGAAAAA
42926 GAGAGAAAAA
1 GA-AGAAAAA
*
42936 GAGGAAAAA
1 GAAGAAAAA
42945 GAA
1 GAA
42948 AAAGATAGGT
Statistics
Matches: 60, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
7 6 0.10
8 19 0.32
9 21 0.35
10 14 0.23
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (9 bp):
GAAGAAAAA
Found at i:42949 original size:25 final size:24
Alignment explanation
Indices: 42868--42952 Score: 77
Period size: 25 Copynumber: 3.4 Consensus size: 24
42858 AGATTCGATG
*
42868 AAGAAAAAAAG-GAAAAA-AGAAA
1 AAGAAAAAGAGAGAAAAAGAGAAA
*
42890 AA-AAAAAGAAAGAAAGAAGAAGAAA
1 AAGAAAAAGAGAGAAA-AAG-AGAAA
42915 AAGAAAAAAAAGAGAGAAAAAGAGGAAA
1 AAG---AAAAAGAGAGAAAAAGA-GAAA
42943 AAGAAAAAGA
1 AAGAAAAAGA
42953 TAGGTCATTT
Statistics
Matches: 51, Mismatches: 3, Indels: 15
0.74 0.04 0.22
Matches are distributed among these distances:
21 6 0.12
22 6 0.12
23 2 0.04
25 14 0.27
27 1 0.02
28 10 0.20
29 12 0.24
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (24 bp):
AAGAAAAAGAGAGAAAAAGAGAAA
Found at i:44055 original size:99 final size:98
Alignment explanation
Indices: 43894--44255 Score: 252
Period size: 99 Copynumber: 3.7 Consensus size: 98
43884 AAGGGAGAGG
* * * ** * * * * *
43894 TTGAGGTCGCAACGGCGAACCCGATACCTCTGAAGATATGAAGGGAAAGGTTAAGGCTGCAAC-A
1 TTGAGGCCACAACGGTGAACCCGATACCTCAAAAGATGTGATGGGAAAGATTGAGGCAGCAACGA
*
43958 GTGAACCCGGTACCATGAAGATGCGAAT-AGAAAGA
66 -CGAACCCGGTACCATGAA-ATGCG-ATGAGAAAGA
* * *
43993 TTGAGGCTACAACGGTGAACTCGATACCTCAAAAGATGTGATGGGAAAGATTGAGGCCGCAACGA
1 TTGAGGCCACAACGGTGAACCCGATACCTCAAAAGATGTGATGGGAAAGATTGAGGCAGCAACGA
* * * *
44058 CGAATCCGGTACCATGAAATGTGATGGGAAAGG
66 CGAACCCGGTACCATGAAATGCGATGAGAAAGA
* * * * * * * * *
44091 TTGAGGCCGCAATGGTGAACCCGATACCTTATAAGATGCGATAGGAAGGATTGAGGCAGCAATGG
1 TTGAGGCCACAACGGTGAACCCGATACCTCAAAAGATGTGATGGGAAAGATTGAGGCAGCAACGA
* * * *
44156 CAAATCTGGTACCATGAAGATGTGATTG-GAAA-A
66 CGAACCCGGTACCATGAA-ATGCGA-TGAGAAAGA
* * * ** * * * *
44189 GTTAAGGTCGCAACGGTGAATTCGATA-C-CATGAA-ATATGATGGGAAAGGTTGAGGCCGCAAC
1 -TTGAGGCCACAACGGTGAACCCGATACCTCA-AAAGATGTGATGGGAAAGATTGAGGCAGCAAC
44251 GACGA
64 GACGA
44256 GTCTTATACC
Statistics
Matches: 209, Mismatches: 48, Indels: 14
0.77 0.18 0.05
Matches are distributed among these distances:
97 27 0.13
98 81 0.39
99 98 0.47
100 3 0.01
ACGTcount: A:0.34, C:0.17, G:0.30, T:0.19
Consensus pattern (98 bp):
TTGAGGCCACAACGGTGAACCCGATACCTCAAAAGATGTGATGGGAAAGATTGAGGCAGCAACGA
CGAACCCGGTACCATGAAATGCGATGAGAAAGA
Found at i:44095 original size:48 final size:49
Alignment explanation
Indices: 43886--44251 Score: 260
Period size: 50 Copynumber: 7.4 Consensus size: 49
43876 AAAATATGAA
* * * * * *
43886 GGGAGAGGTTGAGGTCGCAACGGCGAACCCGATACCTCTGAAGATATGAA
1 GGGAAAGGTTGAGGCCGCAACGGCGAATCCGATACC-ATGAAGATGTGAT
* * * * * * *
43936 GGGAAAGGTTAAGGCTGCAACAGTGAACCCGGTACCATGAAGATGCGAAT
1 GGGAAAGGTTGAGGCCGCAACGGCGAATCCGATACCATGAAGATGTG-AT
* * ** * *
43986 -AGAAAGATTGAGGCTACAACGGTGAA-CTCGATACC-TCAAAAGATGTGAT
1 GGGAAAGGTTGAGGCCGCAACGGCGAATC-CGATACCAT--GAAGATGTGAT
* * *
44035 GGGAAAGATTGAGGCCGCAACGACGAATCCGGTACCATGAA-ATGTGAT
1 GGGAAAGGTTGAGGCCGCAACGGCGAATCCGATACCATGAAGATGTGAT
* * * *
44083 GGGAAAGGTTGAGGCCGCAATGGTGAACCCGATACCTTAT-AAGATGCGAT
1 GGGAAAGGTTGAGGCCGCAACGGCGAATCCGATACC--ATGAAGATGTGAT
* * * * * *
44133 AGG-AAGGATTGAGGCAGCAATGGCAAATCTGGTACCATGAAGATGTGAT
1 GGGAAAGG-TTGAGGCCGCAACGGCGAATCCGATACCATGAAGATGTGAT
* * * * * * *
44182 TGGAAAAGTTAAGGTCGCAACGGTGAATTCGATACCATGAA-ATATGAT
1 GGGAAAGGTTGAGGCCGCAACGGCGAATCCGATACCATGAAGATGTGAT
44230 GGGAAAGGTTGAGGCCGCAACG
1 GGGAAAGGTTGAGGCCGCAACG
44252 ACGAGTCTTA
Statistics
Matches: 246, Mismatches: 57, Indels: 28
0.74 0.17 0.08
Matches are distributed among these distances:
48 65 0.26
49 80 0.33
50 99 0.40
51 2 0.01
ACGTcount: A:0.34, C:0.17, G:0.31, T:0.19
Consensus pattern (49 bp):
GGGAAAGGTTGAGGCCGCAACGGCGAATCCGATACCATGAAGATGTGAT
Found at i:44620 original size:78 final size:78
Alignment explanation
Indices: 44497--45107 Score: 692
Period size: 78 Copynumber: 7.9 Consensus size: 78
44487 TGAATATTCT
* * * ** ** * * *
44497 AATCTCTTACCCCGATCATGGGGCATATCACAATCATCTGATCTTTTACCCCGAGCCTAAGATAG
1 AATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCCTAGGGTAG
44562 ATCACCATCAGCC
66 ATCACCATCAGCC
* * * * *
44575 AATCTCTTACCCCAAGCTTGAGGCAGATTGCAACCATTCGATCTTTTACCCCGAG-CTTGGAGTA
1 AATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCCTAGG-GTA
44639 GATCACCATCAGCC
65 GATCACCATCAGCC
* * * * *
44653 AATCTCTTACCCCGAGCTTGGGGTAGATTACAACCATCCAATCTTTTACCCCGAG-CTTGAGGTA
1 AATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCCTAG-GGTA
44717 GATCACCATCAGCC
65 GATCACCATCAGCC
* * * * *
44731 AATCTCTTACCCCGAGCTTGGGGCAGATTGCATCCATCCAATCTTTTACCCCGAG-CTTGAAGAA
1 AATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCCTAG-GGTA
* *
44795 GATCACCAGCAACC
65 GATCACCATCAGCC
* * * * * * * *
44809 AATCTCTTA-CCCGAGCTCGGGGCAGATTACAGTCATTCGATCTTTTACCCCAAGCTTGGGGCAG
1 AATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCCTAGGGTAG
44873 ATCACCATCAGCC
66 ATCACCATCAGCC
* * * * *
44886 AATCTCTTACCCCAAGCTTGGGGCAGATTGTAGCTATCCGATCTTTTACCCTGAGCCTAGGGCAG
1 AATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCCTAGGGTAG
* *
44951 ATTACCATTAGCC
66 ATCACCATCAGCC
* * * *
44964 AATCTATTACCCCAAGC-TGGGGCAGATTGCAGCCATTCGATCTTTTACCCCGAGCCTGGGGTAG
1 AATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCCTAGGGTAG
*
45028 ATCACCATCAACC
66 ATCACCATCAGCC
* * * * *
45041 AATCTCTTACCCCGAGCTTAGGGCAGATTGTAGTCATCCGATCTTTTACCCCGAGCCTGGGGCAG
1 AATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCCTAGGGTAG
45106 AT
66 AT
45108 TGTAACCATT
Statistics
Matches: 459, Mismatches: 69, Indels: 10
0.85 0.13 0.02
Matches are distributed among these distances:
77 130 0.28
78 328 0.71
79 1 0.00
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (78 bp):
AATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCCTAGGGTAG
ATCACCATCAGCC
Found at i:45108 original size:155 final size:155
Alignment explanation
Indices: 44497--45107 Score: 737
Period size: 155 Copynumber: 3.9 Consensus size: 155
44487 TGAATATTCT
* * * ** * *
44497 AATCTCTTACCCCGATCATGGGGCATATCACAATCA-TCTGATCTTTTACCCCGAGCCTAAGATA
1 AATCTCTTACCCCGAGC-TGGGGCAGATTACAGCCATTC-GATCTTTTACCCCGAGCCTGAGGTA
* ** *
44561 GATCACCATCAGCCAATCTCTTACCCCAAGCTTGAGGCAGATTGCAACCATTCGATCTTTTACCC
64 GATCACCATCAGCCAATCTCTTACCCCAAGCTTGGGGCAGATTGCAGTCATCCGATCTTTTACCC
* *
44626 CGAGCTTGGAGTAGATCACCATCAGCC
129 CGAGCCTGGAGCAGATCACCATCAGCC
* * * * *
44653 AATCTCTTACCCCGAGCTTGGGGTAGATTACAACCATCCAATCTTTTACCCCGAGCTTGAGGTAG
1 AATCTCTTACCCCGAGC-TGGGGCAGATTACAGCCATTCGATCTTTTACCCCGAGCCTGAGGTAG
* *
44718 ATCACCATCAGCCAATCTCTTACCCCGAGCTTGGGGCAGATTGCA-TCCATCCAATCTTTTACCC
65 ATCACCATCAGCCAATCTCTTACCCCAAGCTTGGGGCAGATTGCAGT-CATCCGATCTTTTACCC
* * * * *
44782 CGAGCTTGAAGAAGATCACCAGCAACC
129 CGAGCCTGGAGCAGATCACCATCAGCC
* * * * *
44809 AATCTCTTA-CCCGAGCTCGGGGCAGATTACAGTCATTCGATCTTTTACCCCAAGCTTGGGGCAG
1 AATCTCTTACCCCGAGCT-GGGGCAGATTACAGCCATTCGATCTTTTACCCCGAGCCTGAGGTAG
*
44873 ATCACCATCAGCCAATCTCTTACCCCAAGCTTGGGGCAGATTGTAG-CTATCCGATCTTTTACCC
65 ATCACCATCAGCCAATCTCTTACCCCAAGCTTGGGGCAGATTGCAGTC-ATCCGATCTTTTACCC
* * *
44937 TGAGCCTAGG-GCAGATTACCATTAGCC
129 CGAGCCT-GGAGCAGATCACCATCAGCC
* * * *
44964 AATCTATTACCCCAAGCTGGGGCAGATTGCAGCCATTCGATCTTTTACCCCGAGCCTGGGGTAGA
1 AATCTCTTACCCCGAGCTGGGGCAGATTACAGCCATTCGATCTTTTACCCCGAGCCTGAGGTAGA
* * * *
45029 TCACCATCAACCAATCTCTTACCCCGAGCTTAGGGCAGATTGTAGTCATCCGATCTTTTACCCCG
66 TCACCATCAGCCAATCTCTTACCCCAAGCTTGGGGCAGATTGCAGTCATCCGATCTTTTACCCCG
*
45094 AGCCTGGGGCAGAT
131 AGCCTGGAGCAGAT
45108 TGTAACCATT
Statistics
Matches: 396, Mismatches: 50, Indels: 19
0.85 0.11 0.04
Matches are distributed among these distances:
154 4 0.01
155 240 0.61
156 151 0.38
157 1 0.00
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (155 bp):
AATCTCTTACCCCGAGCTGGGGCAGATTACAGCCATTCGATCTTTTACCCCGAGCCTGAGGTAGA
TCACCATCAGCCAATCTCTTACCCCAAGCTTGGGGCAGATTGCAGTCATCCGATCTTTTACCCCG
AGCCTGGAGCAGATCACCATCAGCC
Found at i:45280 original size:154 final size:156
Alignment explanation
Indices: 45099--45400 Score: 432
Period size: 154 Copynumber: 1.9 Consensus size: 156
45089 CCCCGAGCCT
** * * * * *
45099 GGGGCAGATTGTAACCATTCGATCTTTTACCCCGAGCCTAGGGCAAATCACCATCAGCTAATTTT
1 GGGGCAGATTACAACCATTCGATCTTTTACCCCAAGCATAGGGCAAATCACCATCAGCCAATCTC
*
45164 TTACCCCGAGCCT-GGGCCAGATTGCAACCATTCGATCTTTTACCCCG-TTAT-GAGGCAGATCA
66 TTACCCCGAGCCTAGGG-CAGATTGCAACCATCCGATCTTTTACCCCGATTATAG-GGCAGATCA
* *
45226 CCGTCAGCCAATC-CTTACCTCGTAATA
129 CAGTCACCCAATCTCTTACCTCGTAATA
* *
45253 GGGGCAGATTACAACCATTCGATCTTTTACCCCAATCATAGGGCAGATCACCATCAGCCAATCTC
1 GGGGCAGATTACAACCATTCGATCTTTTACCCCAAGCATAGGGCAAATCACCATCAGCCAATCTC
*
45318 TTATCCCGAGCCTAGGGCAGATTGCAACCATCCGATCTTTTACCCCGATTATAGGGCAGATCACA
66 TTACCCCGAGCCTAGGGCAGATTGCAACCATCCGATCTTTTACCCCGATTATAGGGCAGATCACA
*
45383 GTCACCCGATCTCTTACC
131 GTCACCCAATCTCTTACC
45401 CCGACCATGA
Statistics
Matches: 130, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
154 97 0.75
155 26 0.20
156 7 0.05
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.25
Consensus pattern (156 bp):
GGGGCAGATTACAACCATTCGATCTTTTACCCCAAGCATAGGGCAAATCACCATCAGCCAATCTC
TTACCCCGAGCCTAGGGCAGATTGCAACCATCCGATCTTTTACCCCGATTATAGGGCAGATCACA
GTCACCCAATCTCTTACCTCGTAATA
Found at i:45365 original size:39 final size:39
Alignment explanation
Indices: 44497--45365 Score: 411
Period size: 39 Copynumber: 22.4 Consensus size: 39
44487 TGAATATTCT
* * * * * * *
44497 AATCTCTTACCCCGATCATGGGGCATATCACAATCATCT
1 AATCTTTTACCCCGAGCCTGGGGCAGATTACAACCATCC
* ** ** * * * *
44536 GATCTTTTACCCCGAGCCTAAGATAGATCACCATCAGCC
1 AATCTTTTACCCCGAGCCTGGGGCAGATTACAACCATCC
* * * * * *
44575 AATCTCTTACCCCAAGCTTGAGGCAGATTGCAACCATTC
1 AATCTTTTACCCCGAGCCTGGGGCAGATTACAACCATCC
* * * * * * * *
44614 GATCTTTTACCCCGAGCTTGGAGTAGATCACCATCAGCC
1 AATCTTTTACCCCGAGCCTGGGGCAGATTACAACCATCC
* * *
44653 AATCTCTTACCCCGAGCTTGGGGTAGATTACAACCATCC
1 AATCTTTTACCCCGAGCCTGGGGCAGATTACAACCATCC
* * * * * * *
44692 AATCTTTTACCCCGAGCTTGAGGTAGATCACCATCAGCC
1 AATCTTTTACCCCGAGCCTGGGGCAGATTACAACCATCC
* * * *
44731 AATCTCTTACCCCGAGCTTGGGGCAGATTGCATCCATCC
1 AATCTTTTACCCCGAGCCTGGGGCAGATTACAACCATCC
* ** * * * * *
44770 AATCTTTTACCCCGAGCTTGAAGAAGATCACCAGCAACC
1 AATCTTTTACCCCGAGCCTGGGGCAGATTACAACCATCC
* ** *
44809 AATCTCTTA-CCCGAG-CTCGGGGCAGATTACAGTCATTC
1 AATCTTTTACCCCGAGCCT-GGGGCAGATTACAACCATCC
* * * * * * *
44847 GATCTTTTACCCCAAGCTTGGGGCAGATCACCATCAGCC
1 AATCTTTTACCCCGAGCCTGGGGCAGATTACAACCATCC
* * * ** * *
44886 AATCTCTTACCCCAAGCTTGGGGCAGATTGTAGCTATCC
1 AATCTTTTACCCCGAGCCTGGGGCAGATTACAACCATCC
* * * * ** *
44925 GATCTTTTACCCTGAGCCTAGGGCAGATTACCATTAGCC
1 AATCTTTTACCCCGAGCCTGGGGCAGATTACAACCATCC
* * * * *
44964 AATCTATTACCCCAAG-CTGGGGCAGATTGCAGCCATTC
1 AATCTTTTACCCCGAGCCTGGGGCAGATTACAACCATCC
* * * * * *
45002 GATCTTTTACCCCGAGCCTGGGGTAGATCACCATCAACC
1 AATCTTTTACCCCGAGCCTGGGGCAGATTACAACCATCC
* * * ** **
45041 AATCTCTTACCCCGAGCTTAGGGCAGATTGTAGTCATCC
1 AATCTTTTACCCCGAGCCTGGGGCAGATTACAACCATCC
* ** *
45080 GATCTTTTACCCCGAGCCTGGGGCAGATTGTAACCATTC
1 AATCTTTTACCCCGAGCCTGGGGCAGATTACAACCATCC
* * * * * * * *
45119 GATCTTTTACCCCGAGCCTAGGGCAAATCACCATCAGCT
1 AATCTTTTACCCCGAGCCTGGGGCAGATTACAACCATCC
* * * *
45158 AATTTTTTACCCCGAGCCTGGGCCAGATTGCAACCATTC
1 AATCTTTTACCCCGAGCCTGGGGCAGATTACAACCATCC
* *** * * *** *
45197 GATCTTTTACCCCG-TTATGAGGCAGATCACCGTCAGCC
1 AATCTTTTACCCCGAGCCTGGGGCAGATTACAACCATCC
* * * *
45235 AATC-CTTACCTCGTA--ATAGGGGCAGATTACAACCATTC
1 AATCTTTTACCCCG-AGCCT-GGGGCAGATTACAACCATCC
* * * * * * * * *
45273 GATCTTTTACCCCAATCATAGGGCAGATCACCATCAGCC
1 AATCTTTTACCCCGAGCCTGGGGCAGATTACAACCATCC
* * * *
45312 AATCTCTTATCCCGAGCCTAGGGCAGATTGCAACCATCC
1 AATCTTTTACCCCGAGCCTGGGGCAGATTACAACCATCC
*
45351 GATCTTTTACCCCGA
1 AATCTTTTACCCCGA
45366 TTATAGGGCA
Statistics
Matches: 598, Mismatches: 222, Indels: 20
0.71 0.26 0.02
Matches are distributed among these distances:
37 10 0.02
38 83 0.14
39 502 0.84
40 3 0.01
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.26
Consensus pattern (39 bp):
AATCTTTTACCCCGAGCCTGGGGCAGATTACAACCATCC
Found at i:45417 original size:78 final size:78
Alignment explanation
Indices: 45042--45456 Score: 296
Period size: 78 Copynumber: 5.3 Consensus size: 78
45032 CCATCAACCA
* * * *** * * * *
45042 ATCTCTTACCCCGAGCTTAGGGCAGATTGTAGTCATCCGATCTTTTACCCCGAGCC-TGGGGCAG
1 ATCTTTTACCCCGATCATAGGGCAGATCACAGTCAGCCAATCTCTTACCCCGA-CCATGAGGCAG
** *
45106 ATTGTAACCATTCG
65 ATTACAACCATCCG
* * * * * *
45120 ATCTTTTACCCCGAGCCTAGGGCAAATCACCA-TCAGCTAATTTTTTACCCCGAGCC-TG-GGCC
1 ATCTTTTACCCCGATCATAGGGCAGATCA-CAGTCAGCCAATCTCTTACCCCGA-CCATGAGG-C
* *
45182 AGATTGCAACCATTCG
63 AGATTACAACCATCCG
* * * *
45198 ATCTTTTACCCCG-TTAT-GAGGCAGATCACCGTCAGCCAATC-CTTACCTCGTA--ATAGGGGC
1 ATCTTTTACCCCGATCATAG-GGCAGATCACAGTCAGCCAATCTCTTACCCCG-ACCAT-GAGGC
*
45258 AGATTACAACCATTCG
63 AGATTACAACCATCCG
* *
45274 ATCTTTTACCCCAATCATAGGGCAGATCACCA-TCAGCCAATCTCTTATCCCGAGCC-T-AGGGC
1 ATCTTTTACCCCGATCATAGGGCAGATCA-CAGTCAGCCAATCTCTTACCCCGA-CCATGA-GGC
*
45336 AGATTGCAACCATCCG
63 AGATTACAACCATCCG
* * * **
45352 ATCTTTTACCCCGATTATAGGGCAGATCACAGTCACCCGATCTCTTACCCCGACCATGATACAGA
1 ATCTTTTACCCCGATCATAGGGCAGATCACAGTCAGCCAATCTCTTACCCCGACCATGAGGCAGA
* * **
45417 TCACAGCCATCTA
66 TTACAACCATCCG
* *
45430 ATCTCTTACCCCGATCATGGGGCAGAT
1 ATCTTTTACCCCGATCATAGGGCAGAT
45457 TGCAGTTATC
Statistics
Matches: 274, Mismatches: 44, Indels: 38
0.77 0.12 0.11
Matches are distributed among these distances:
75 1 0.00
76 38 0.14
77 49 0.18
78 183 0.67
79 3 0.01
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.26
Consensus pattern (78 bp):
ATCTTTTACCCCGATCATAGGGCAGATCACAGTCAGCCAATCTCTTACCCCGACCATGAGGCAGA
TTACAACCATCCG
Found at i:46967 original size:33 final size:34
Alignment explanation
Indices: 46925--47007 Score: 109
Period size: 33 Copynumber: 2.5 Consensus size: 34
46915 AATGCAAACT
46925 ATTTAATTAATAAATTAAATAGTA-CATTAAACAA
1 ATTTAATTAATAAATTAAAT-GTAGCATTAAACAA
* *
46959 A-TTAATTAATAAATT-AATTTAGCATTAAATAA
1 ATTTAATTAATAAATTAAATGTAGCATTAAACAA
*
46991 ATTTAATTAAAAAATTA
1 ATTTAATTAATAAATTA
47008 TAATTATAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
31 2 0.05
32 13 0.30
33 27 0.63
34 1 0.02
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (34 bp):
ATTTAATTAATAAATTAAATGTAGCATTAAACAA
Found at i:46974 original size:21 final size:21
Alignment explanation
Indices: 46936--46975 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
46926 TTTAATTAAT
* *
46936 AAATTAAATAGTACATTAAAC
1 AAATTAAATAATAAATTAAAC
*
46957 AAATTAATTAATAAATTAA
1 AAATTAAATAATAAATTAA
46976 TTTAGCATTA
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:0.60, C:0.05, G:0.03, T:0.33
Consensus pattern (21 bp):
AAATTAAATAATAAATTAAAC
Found at i:48440 original size:17 final size:18
Alignment explanation
Indices: 48416--48458 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
48406 TTTTAGTTGA
*
48416 TGTTTTTTGCTATTTTGG
1 TGTTTTTTACTATTTTGG
*
48434 T-TTTTTTACTGTTTTGG
1 TGTTTTTTACTATTTTGG
48451 TGTTTTTT
1 TGTTTTTT
48459 TACTGTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.05, C:0.05, G:0.19, T:0.72
Consensus pattern (18 bp):
TGTTTTTTACTATTTTGG
Found at i:48505 original size:12 final size:12
Alignment explanation
Indices: 48476--48568 Score: 77
Period size: 12 Copynumber: 8.1 Consensus size: 12
48466 TTAGTGATGA
*
48476 TATTTTTATTGT
1 TATTTTTGTTGT
* *
48488 TGTTTTTGTTGC
1 TATTTTTGTTGT
48500 TATTTTTGTTGT
1 TATTTTTGTTGT
48512 TATTTTTGTTG-
1 TATTTTTGTTGT
48523 ---TTTTGTTGT
1 TATTTTTGTTGT
* * *
48532 TACTTTTGCTGC
1 TATTTTTGTTGT
* *
48544 TGTTTTGGTTGT
1 TATTTTTGTTGT
*
48556 TATTTTGGTTGT
1 TATTTTTGTTGT
48568 T
1 T
48569 TGAATGCTAT
Statistics
Matches: 64, Mismatches: 13, Indels: 8
0.75 0.15 0.09
Matches are distributed among these distances:
8 8 0.12
12 56 0.88
ACGTcount: A:0.06, C:0.04, G:0.20, T:0.69
Consensus pattern (12 bp):
TATTTTTGTTGT
Found at i:48507 original size:58 final size:57
Alignment explanation
Indices: 48383--48494 Score: 149
Period size: 58 Copynumber: 1.9 Consensus size: 57
48373 ATTATATTGT
*
48383 TGTTTTGGTGCTTTTTTTTACTGTTTTAGTTGATGTTTTTTGCTATTTTGGTTTTTTTAC
1 TGTTTTGGTG--TTTTTTTACTGTTTTAGTTGATGTATTTT-CTATTTTGGTTTTTTTAC
48443 TGTTTTGGTGTTTTTTTACTGTTTTAG-TGATGATATTTT-TATTGTT-GTTTTT
1 TGTTTTGGTGTTTTTTTACTGTTTTAGTTGATG-TATTTTCTATT-TTGGTTTTT
48495 GTTGCTATTT
Statistics
Matches: 49, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
56 10 0.20
57 7 0.14
58 22 0.45
60 10 0.20
ACGTcount: A:0.10, C:0.04, G:0.19, T:0.67
Consensus pattern (57 bp):
TGTTTTGGTGTTTTTTTACTGTTTTAGTTGATGTATTTTCTATTTTGGTTTTTTTAC
Found at i:48528 original size:20 final size:20
Alignment explanation
Indices: 48503--48569 Score: 80
Period size: 23 Copynumber: 3.1 Consensus size: 20
48493 TTGTTGCTAT
48503 TTTTGTTGTTATTTTTGTTG
1 TTTTGTTGTTATTTTTGTTG
*
48523 TTTTGTTGTTACTTTTGCTGCTG
1 TTTTGTTGTTA-TTTT--TGTTG
*
48546 TTTTGGTTGTTATTTTGGTTG
1 TTTT-GTTGTTATTTTTGTTG
48567 TTT
1 TTT
48570 GAATGCTATT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
20 11 0.28
21 10 0.25
23 12 0.30
24 7 0.17
ACGTcount: A:0.04, C:0.04, G:0.22, T:0.69
Consensus pattern (20 bp):
TTTTGTTGTTATTTTTGTTG
Found at i:48555 original size:32 final size:32
Alignment explanation
Indices: 48486--48556 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 32
48476 TATTTTTATT
* * * *
48486 GTTGTTTTTGTTGCTATTTTTGTTGTTATTTTT
1 GTTG-TTTTGTTGCTACTTTTGCTGCTATTTTG
* *
48519 GTTGTTTTGTTGTTACTTTTGCTGCTGTTTTG
1 GTTGTTTTGTTGCTACTTTTGCTGCTATTTTG
48551 GTTGTT
1 GTTGTT
48557 ATTTTGGTTG
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
32 28 0.88
33 4 0.12
ACGTcount: A:0.04, C:0.06, G:0.23, T:0.68
Consensus pattern (32 bp):
GTTGTTTTGTTGCTACTTTTGCTGCTATTTTG
Found at i:52139 original size:31 final size:31
Alignment explanation
Indices: 52104--52170 Score: 134
Period size: 31 Copynumber: 2.2 Consensus size: 31
52094 TACTAAATAA
52104 TGAAAGCTTGGACTCAAATCGAATCTAAGTC
1 TGAAAGCTTGGACTCAAATCGAATCTAAGTC
52135 TGAAAGCTTGGACTCAAATCGAATCTAAGTC
1 TGAAAGCTTGGACTCAAATCGAATCTAAGTC
52166 TGAAA
1 TGAAA
52171 ACAAGAAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.25
Consensus pattern (31 bp):
TGAAAGCTTGGACTCAAATCGAATCTAAGTC
Found at i:52819 original size:21 final size:21
Alignment explanation
Indices: 52780--52847 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 21
52770 GACTTCTATT
***
52780 GATACAAGTGACAGGTCTACC
1 GATACAAGTGACTCTTCTACC
52801 GATACAAGTGACTCTTCTACC
1 GATACAAGTGACTCTTCTACC
* *
52822 GAAACAAGT-ATTACTTCTACC
1 GATACAAGTGACT-CTTCTACC
52843 GATAC
1 GATAC
52848 TAAAAACTCT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
20 2 0.05
21 38 0.95
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (21 bp):
GATACAAGTGACTCTTCTACC
Found at i:53688 original size:52 final size:52
Alignment explanation
Indices: 53583--53818 Score: 286
Period size: 52 Copynumber: 4.6 Consensus size: 52
53573 ATTTCAATTA
* * * *
53583 ATACTCACGT-TGACACATAGTCAT---TCCTCTTAATTCGTAAAGGAATT-TT
1 ATACTCAC-TATGACACATAGTCATCGGACCTCATAATCCGTAAA-GAATTCAT
* *
53632 ATACTCACTATGGCATATAGTCATCGGACCTCATAATCCGTAAAGAATTCAT
1 ATACTCACTATGACACATAGTCATCGGACCTCATAATCCGTAAAGAATTCAT
* *
53684 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCTTAAAGAATTCAT
1 ATACTCACTATGACACATAGTCATCGGACCTCATAATCCGTAAAGAATTCAT
* * *
53736 ATACTCACAATGACACATAGTCTTCGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACTATGACACATAGTCATCGGACCTCATAATCCGTAAAGAATTCAT
* *
53788 ATACTTA-TGATGACACATAATCATCGGACCT
1 ATACTCACT-ATGACACATAGTCATCGGACCT
53819 TTTTCATTTA
Statistics
Matches: 163, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
48 1 0.01
49 20 0.12
51 5 0.03
52 137 0.84
ACGTcount: A:0.34, C:0.23, G:0.13, T:0.30
Consensus pattern (52 bp):
ATACTCACTATGACACATAGTCATCGGACCTCATAATCCGTAAAGAATTCAT
Found at i:66618 original size:27 final size:26
Alignment explanation
Indices: 66579--66634 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 26
66569 CAGCATAAAC
*
66579 TATTAAACAAAATATAACCATCAAAAT
1 TATTAAACAAAATAGAACCATC-AAAT
* *
66606 TATTCAACGAAATAGAACCATCAAAT
1 TATTAAACAAAATAGAACCATCAAAT
66632 TAT
1 TAT
66635 CCATAGTATG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 7 0.27
27 19 0.73
ACGTcount: A:0.54, C:0.16, G:0.04, T:0.27
Consensus pattern (26 bp):
TATTAAACAAAATAGAACCATCAAAT
Found at i:69488 original size:15 final size:15
Alignment explanation
Indices: 69468--69497 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
69458 CTACTTAAAT
69468 TTTTTTTTATGATAA
1 TTTTTTTTATGATAA
69483 TTTTTTTTATGATAA
1 TTTTTTTTATGATAA
69498 AAAAAACAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (15 bp):
TTTTTTTTATGATAA
Found at i:70192 original size:14 final size:14
Alignment explanation
Indices: 70175--70203 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
70165 AAAAACTTTA
70175 AAACATAATTTCTT
1 AAACATAATTTCTT
70189 AAACATAATTTCTT
1 AAACATAATTTCTT
70203 A
1 A
70204 TGTTATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (14 bp):
AAACATAATTTCTT
Found at i:70539 original size:20 final size:22
Alignment explanation
Indices: 70496--70539 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
70486 TTAAGTTTTG
*
70496 AAAAAATATATAATTTTAATAA
1 AAAAAATATATAATATTAATAA
70518 AAAAAATATAT-ATATTAA-AA
1 AAAAAATATATAATATTAATAA
70538 AA
1 AA
70540 GGTTTTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.19
21 6 0.29
22 11 0.52
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (22 bp):
AAAAAATATATAATATTAATAA
Found at i:75641 original size:2 final size:2
Alignment explanation
Indices: 75598--75623 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
75588 TTGCTTTTAG
75598 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
75624 AAAGTATGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:80794 original size:15 final size:16
Alignment explanation
Indices: 80774--80803 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
80764 TTTCATGATC
80774 TCATTGT-TTTATTTG
1 TCATTGTATTTATTTG
80789 TCATTGTATTTATTT
1 TCATTGTATTTATTT
80804 ATTTTTGTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.17, C:0.07, G:0.10, T:0.67
Consensus pattern (16 bp):
TCATTGTATTTATTTG
Found at i:88809 original size:2 final size:2
Alignment explanation
Indices: 88804--88831 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
88794 TTAAAAAACC
88804 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
88832 TATTTAAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:95434 original size:2 final size:2
Alignment explanation
Indices: 95423--95473 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
95413 TCTTCTAATC
95423 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
95464 AT AT AT AT AT
1 AT AT AT AT AT
95474 TGCTTGATAA
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:102470 original size:2 final size:2
Alignment explanation
Indices: 102463--102496 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
102453 GTAAGGATGA
102463 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
102497 TAAACTTATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:107555 original size:30 final size:30
Alignment explanation
Indices: 107521--107579 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
107511 ATTTGCTTAA
107521 AAAATATTTAA-AAT-TTATATTTCATATATC
1 AAAATA-TTAATAATATTAT-TTTCATATATC
*
107551 AAAATATTAATAATATTATTTTCTTATAT
1 AAAATATTAATAATATTATTTTCATATAT
107580 TTTTTATTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 4 0.15
30 18 0.69
31 4 0.15
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (30 bp):
AAAATATTAATAATATTATTTTCATATATC
Found at i:110473 original size:15 final size:15
Alignment explanation
Indices: 110453--110484 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
110443 CTTGTAGAAT
*
110453 AAGAAACTATAATTA
1 AAGAAACTAAAATTA
110468 AAGAAACTAAAATTA
1 AAGAAACTAAAATTA
110483 AA
1 AA
110485 TACTTTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.66, C:0.06, G:0.06, T:0.22
Consensus pattern (15 bp):
AAGAAACTAAAATTA
Found at i:111802 original size:15 final size:15
Alignment explanation
Indices: 111782--111813 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
111772 CTTGTGGAAT
*
111782 AAGAAACTACAATTA
1 AAGAAACTAAAATTA
111797 AAGAAACTAAAATTA
1 AAGAAACTAAAATTA
111812 AA
1 AA
111814 TACTTTTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.66, C:0.09, G:0.06, T:0.19
Consensus pattern (15 bp):
AAGAAACTAAAATTA
Found at i:115097 original size:24 final size:25
Alignment explanation
Indices: 115070--115117 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
115060 AAGTATATTT
* *
115070 ATCTATTTT-TTTTATATTTAAATA
1 ATCTATTTTGATTTATATTAAAATA
*
115094 ATCTCTTTTGATTTATATTAAAAT
1 ATCTATTTTGATTTATATTAAAAT
115118 TGAATTTCGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.33, C:0.06, G:0.02, T:0.58
Consensus pattern (25 bp):
ATCTATTTTGATTTATATTAAAATA
Found at i:128859 original size:3 final size:3
Alignment explanation
Indices: 128851--128876 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
128841 ACTTCATCAA
128851 CAC CAC CAC CAC CAC CAC CAC CAC CA
1 CAC CAC CAC CAC CAC CAC CAC CAC CA
128877 GCTTTAAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.65, G:0.00, T:0.00
Consensus pattern (3 bp):
CAC
Found at i:129600 original size:48 final size:47
Alignment explanation
Indices: 129513--129609 Score: 185
Period size: 48 Copynumber: 2.0 Consensus size: 47
129503 AAAATCCAAA
129513 GAAAAAGAAGAAATATTCAGGACCAGTCCTTTGTCTCTTATTATATT
1 GAAAAAGAAGAAATATTCAGGACCAGTCCTTTGTCTCTTATTATATT
129560 GAAAAAGAAGAAATATTCAGAGACCAGTCCTTTGTCTCTTATTATATT
1 GAAAAAGAAGAAATATTCAG-GACCAGTCCTTTGTCTCTTATTATATT
129608 GA
1 GA
129610 TTCAAGATCA
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
47 20 0.41
48 29 0.59
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.33
Consensus pattern (47 bp):
GAAAAAGAAGAAATATTCAGGACCAGTCCTTTGTCTCTTATTATATT
Found at i:129697 original size:2 final size:2
Alignment explanation
Indices: 129692--129723 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
129682 TAATATATAT
129692 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
129724 TTTGGTCCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:142270 original size:25 final size:25
Alignment explanation
Indices: 142249--142305 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
142239 TGATTTTTCC
142249 TGTTAAAATT-TTATCAATTTTTAT
1 TGTTAAAATTATTATCAATTTTTAT
*
142273 TGTTAAATTTATTATCAATTTTTAT
1 TGTTAAAATTATTATCAATTTTTAT
142298 TGTTAAAA
1 TGTTAAAA
142306 ATTGGTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
24 9 0.30
25 21 0.70
ACGTcount: A:0.35, C:0.04, G:0.05, T:0.56
Consensus pattern (25 bp):
TGTTAAAATTATTATCAATTTTTAT
Found at i:150580 original size:6 final size:6
Alignment explanation
Indices: 150569--150618 Score: 55
Period size: 6 Copynumber: 8.2 Consensus size: 6
150559 TCATTAAGAT
* * * *
150569 ATAAAA ATAAAA ATAAAA ACTAAAA CTAAAA CTAAAA CTAAAA CTAAAA
1 ATAAAA ATAAAA ATAAAA A-TAAAA ATAAAA ATAAAA ATAAAA ATAAAA
150618 A
1 A
150619 AACATAAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
6 36 0.88
7 5 0.12
ACGTcount: A:0.74, C:0.10, G:0.00, T:0.16
Consensus pattern (6 bp):
ATAAAA
Found at i:150593 original size:18 final size:18
Alignment explanation
Indices: 150570--150618 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
150560 CATTAAGATA
*
150570 TAAAAATAAAAATAAAAAC
1 TAAAACTAAAAAT-AAAAC
*
150589 TAAAACTAAAACTAAAAC
1 TAAAACTAAAAATAAAAC
150607 TAAAACTAAAAA
1 TAAAACTAAAAA
150619 AACATAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 16 0.59
19 11 0.41
ACGTcount: A:0.73, C:0.10, G:0.00, T:0.16
Consensus pattern (18 bp):
TAAAACTAAAAATAAAAC
Found at i:150681 original size:30 final size:31
Alignment explanation
Indices: 150611--150716 Score: 99
Period size: 30 Copynumber: 3.4 Consensus size: 31
150601 TAAAACTAAA
* * *
150611 ACTAAAAAAACATAAAA-AAAAATGAATTATTC
1 ACTAAAATAATATAAAATAAAAA--AATAATTC
*
150643 ATTAAAATAATATAAAATAAAAAAATAATT-
1 ACTAAAATAATATAAAATAAAAAAATAATTC
* * *
150673 ACTAAAATAATATGAGATAAAAAAATTATTC
1 ACTAAAATAATATAAAATAAAAAAATAATTC
* *
150704 ACCAAAACAATAT
1 ACTAAAATAATAT
150717 GTTTTGAACG
Statistics
Matches: 62, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
30 26 0.42
31 17 0.27
32 14 0.23
33 5 0.08
ACGTcount: A:0.64, C:0.08, G:0.03, T:0.25
Consensus pattern (31 bp):
ACTAAAATAATATAAAATAAAAAAATAATTC
Found at i:157164 original size:13 final size:13
Alignment explanation
Indices: 157131--157155 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
157121 AACTATTAAA
157131 CCAACAATGCAAG
1 CCAACAATGCAAG
157144 CCAACAATGCAA
1 CCAACAATGCAA
157156 CCAGCCAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.32, G:0.12, T:0.08
Consensus pattern (13 bp):
CCAACAATGCAAG
Found at i:157643 original size:13 final size:14
Alignment explanation
Indices: 157599--157635 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
157589 ACCTATAATG
*
157599 AAAATT-TTCAACA
1 AAAATTATTCAAAA
157612 AAAATTATTCAAAA
1 AAAATTATTCAAAA
157626 AAAATTATTC
1 AAAATTATTC
157636 TTAAAAATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 6 0.27
14 16 0.73
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (14 bp):
AAAATTATTCAAAA
Found at i:160905 original size:12 final size:12
Alignment explanation
Indices: 160888--160913 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
160878 GATCTGATGT
160888 TTAAATTAACAA
1 TTAAATTAACAA
160900 TTAAATTAACAA
1 TTAAATTAACAA
160912 TT
1 TT
160914 TTAGCAATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (12 bp):
TTAAATTAACAA
Found at i:162089 original size:68 final size:68
Alignment explanation
Indices: 161928--162094 Score: 228
Period size: 68 Copynumber: 2.5 Consensus size: 68
161918 AGAGGTTTAA
* ** * *
161928 TGTATAAGACCATAGCTAGGTTATGGCAACATTTGGAGCCTGTCAGGATAGTAAACATGAGTTTA
1 TGTATAAGACCATAGCTAGGTTATGGCAACATATGGAGCCTACCAGGACAGTAAACACGAGTTTA
161993 TAT
66 TAT
* * * *
161996 TGTGTAAGACCATAGCCAGGCTATGGAAACATATGGAGTCC-ACCAGGACAGTAAACACGAGTTT
1 TGTATAAGACCATAGCTAGGTTATGGCAACATATGGAG-CCTACCAGGACAGTAAACACGAGTTT
162060 ATAT
65 ATAT
*
162064 TGTATAAGACCATAGCTGGGTTATGGCAACA
1 TGTATAAGACCATAGCTAGGTTATGGCAACA
162095 AATGAAGTTC
Statistics
Matches: 84, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
68 82 0.98
69 2 0.02
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (68 bp):
TGTATAAGACCATAGCTAGGTTATGGCAACATATGGAGCCTACCAGGACAGTAAACACGAGTTTA
TAT
Found at i:168433 original size:30 final size:29
Alignment explanation
Indices: 168399--168501 Score: 93
Period size: 30 Copynumber: 3.4 Consensus size: 29
168389 GCTTTATTTT
**
168399 AAAATTATTTTTTGACCCTCAAATTTTCTA
1 AAAATTATAATTTGACCCTCAAATTTTC-A
*
168429 AAAATTCA-AATTTGACCCTTAAACTTTTCA
1 AAAATT-ATAATTTGACCCTCAAA-TTTTCA
*
168459 AAAATT-TGAATTTGACCCTCAAACTTTCCA
1 AAAATTAT-AATTTGACCCTCAAA-TTTTCA
* *
168489 AATATTCTAATTT
1 AAAATTATAATTT
168502 AATCCTTGAA
Statistics
Matches: 62, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
30 55 0.89
31 7 0.11
ACGTcount: A:0.37, C:0.18, G:0.04, T:0.41
Consensus pattern (29 bp):
AAAATTATAATTTGACCCTCAAATTTTCA
Found at i:168501 original size:60 final size:60
Alignment explanation
Indices: 168409--168521 Score: 154
Period size: 60 Copynumber: 1.9 Consensus size: 60
168399 AAAATTATTT
* * *
168409 TTTGACCCTCAAATTTTCTAAAAATTCAAATTTGACCCTTAAACTTTTCAAAAATTTGAA
1 TTTGACCCTCAAACTTTCCAAAAATTCAAATTTAACCCTTAAACTTTTCAAAAATTTGAA
* * * * *
168469 TTTGACCCTCAAACTTTCCAAATATTCTAATTTAATCCTTGAAGTTTTCAAAA
1 TTTGACCCTCAAACTTTCCAAAAATTCAAATTTAACCCTTAAACTTTTCAAAA
168522 TTCAAATTTA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 45 1.00
ACGTcount: A:0.36, C:0.19, G:0.05, T:0.39
Consensus pattern (60 bp):
TTTGACCCTCAAACTTTCCAAAAATTCAAATTTAACCCTTAAACTTTTCAAAAATTTGAA
Found at i:180277 original size:50 final size:50
Alignment explanation
Indices: 180223--180416 Score: 219
Period size: 50 Copynumber: 3.9 Consensus size: 50
180213 AGGTGCAGAT
* *
180223 TGAAGCCGCAGTGACAAATCTCATACACCTAAAGCTGTAGAGGGGTAGAA
1 TGAAGCCGCAATGGCAAATCTCATACACCTAAAGCTGTAGAGGGGTAGAA
* * * * * * *
180273 TGAAGCTGGAATGGCGAATCTTATACACCTAAAGCTGT-GAAGGTGCAGAT
1 TGAAGCCGCAATGGCAAATCTCATACACCTAAAGCTGTAG-AGGGGTAGAA
* * *
180323 TGAAGTCGCAATGGCAAATCTCGTACACCTAAAGCTATAGAGGGGTAGAA
1 TGAAGCCGCAATGGCAAATCTCATACACCTAAAGCTGTAGAGGGGTAGAA
* * * * *
180373 TGAAGGCGTAATGGCGAATCTTATTCACCTAAAGCTGTAGAGGG
1 TGAAGCCGCAATGGCAAATCTCATACACCTAAAGCTGTAGAGGG
180417 CAAATTGAAG
Statistics
Matches: 116, Mismatches: 26, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
49 1 0.01
50 114 0.98
51 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.27, T:0.22
Consensus pattern (50 bp):
TGAAGCCGCAATGGCAAATCTCATACACCTAAAGCTGTAGAGGGGTAGAA
Found at i:180342 original size:100 final size:100
Alignment explanation
Indices: 180189--180427 Score: 340
Period size: 100 Copynumber: 2.4 Consensus size: 100
180179 TAGAACGACA
* * * * *
180189 AATCTTTTACCCCTAAAGCTTTGAAGGTGCAGATTGAAGCCGCAGTGACAAATCTCATACACCTA
1 AATCTTATACACCTAAAGCTGTGAAGGTGCAGATTGAAGTCGCAATGACAAATCTCATACACCTA
*
180254 AAGCTGTAGAGGGGTAGAATGAA-GCTGGAATGGCG
66 AAGCTATAGAGGGGTAGAATGAAGGC-GGAATGGCG
* *
180289 AATCTTATACACCTAAAGCTGTGAAGGTGCAGATTGAAGTCGCAATGGCAAATCTCGTACACCTA
1 AATCTTATACACCTAAAGCTGTGAAGGTGCAGATTGAAGTCGCAATGACAAATCTCATACACCTA
*
180354 AAGCTATAGAGGGGTAGAATGAAGGCGTAATGGCG
66 AAGCTATAGAGGGGTAGAATGAAGGCGGAATGGCG
* *
180389 AATCTTATTCACCTAAAGCTGT-AGAGG-GCAAATTGAAGT
1 AATCTTATACACCTAAAGCTGTGA-AGGTGCAGATTGAAGT
180428 TACAAGAACA
Statistics
Matches: 126, Mismatches: 11, Indels: 5
0.89 0.08 0.04
Matches are distributed among these distances:
99 12 0.10
100 112 0.89
101 2 0.02
ACGTcount: A:0.33, C:0.18, G:0.26, T:0.23
Consensus pattern (100 bp):
AATCTTATACACCTAAAGCTGTGAAGGTGCAGATTGAAGTCGCAATGACAAATCTCATACACCTA
AAGCTATAGAGGGGTAGAATGAAGGCGGAATGGCG
Found at i:180586 original size:20 final size:20
Alignment explanation
Indices: 180561--180601 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
180551 AGAGGGTAAA
180561 TTGAAGACCAT-CAGATCTTT
1 TTGAAGACCATCCA-ATCTTT
180581 TTGAAGACCATCCAATCTTT
1 TTGAAGACCATCCAATCTTT
180601 T
1 T
180602 ACCCTAACCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 18 0.90
21 2 0.10
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (20 bp):
TTGAAGACCATCCAATCTTT
Found at i:180719 original size:40 final size:39
Alignment explanation
Indices: 180581--180720 Score: 122
Period size: 40 Copynumber: 3.5 Consensus size: 39
180571 TCAGATCTTT
* * *
180581 TTGAAGACCATCCAATCTTTTACCCTAACCAAAGGGAAGA
1 TTGAAGACCATCAAATCTTTTACCCTAACCAGAGGCAA-A
* * ** * *
180621 TTGAAGACCATTCAAA-CTCTCACCCCGACCATGAGGTAGA
1 TTGAAGACCA-TCAAATCTTTTACCCTAACCA-GAGGCAAA
* * *
180661 TTGAAG-CAATCCAATCTTTTACCCTAATCAGAGAGCAAA
1 TTGAAGACCATCAAATCTTTTACCCTAACCAGAG-GCAAA
180700 TTGAAGACCATCAAATCTTTT
1 TTGAAGACCATCAAATCTTTT
180721 TGAAGACCAT
Statistics
Matches: 76, Mismatches: 19, Indels: 10
0.72 0.18 0.10
Matches are distributed among these distances:
38 7 0.09
39 21 0.28
40 40 0.53
41 8 0.11
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.25
Consensus pattern (39 bp):
TTGAAGACCATCAAATCTTTTACCCTAACCAGAGGCAAA
Found at i:180740 original size:20 final size:20
Alignment explanation
Indices: 180700--180740 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
180690 AGAGAGCAAA
*
180700 TTGAAGACCATCAAATCTTT
1 TTGAAGACCATCAAATATTT
*
180720 TTGAAGACCATCCAATATTT
1 TTGAAGACCATCAAATATTT
180740 T
1 T
180741 ACCCTAACCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.34, C:0.20, G:0.10, T:0.37
Consensus pattern (20 bp):
TTGAAGACCATCAAATATTT
Found at i:180764 original size:40 final size:40
Alignment explanation
Indices: 180720--180823 Score: 131
Period size: 40 Copynumber: 2.6 Consensus size: 40
180710 TCAAATCTTT
*
180720 TTGAAGACCATCCAATATTTTACCCT-AACCATGGGACAGA
1 TTGAAG-CCATCCAATCTTTTACCCTCAACCATGGGACAGA
* * *
180760 TTGAAGCCTATCCAATCTCTTA-CCTCGACCATGGGGCAGA
1 TTGAAGCC-ATCCAATCTTTTACCCTCAACCATGGGACAGA
*
180800 TTGAAGCAATCCAATCTTTTACCC
1 TTGAAGCCATCCAATCTTTTACCC
180824 CTAAAGCTAT
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
39 17 0.31
40 38 0.69
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (40 bp):
TTGAAGCCATCCAATCTTTTACCCTCAACCATGGGACAGA
Found at i:180789 original size:139 final size:139
Alignment explanation
Indices: 180530--180823 Score: 457
Period size: 139 Copynumber: 2.1 Consensus size: 139
180520 AGTTACAATC
* * *
180530 ATCCAATCTTTTACCCTAATCAGAGGGTAAATTGAAGACCATCAGATCTTTTTGAAGACCATCCA
1 ATCCAATCTTTTACCCTAATCAGAGAGCAAATTGAAGACCATCAAATCTTTTTGAAGACCATCCA
* * *
180595 ATCTTTTACCCTAACCAAAGGGAAGATTGAAGACCATTCAAACTCTCACCCCGACCATGAGGTAG
66 ATATTTTACCCTAACCAAAGGGAAGATTGAAGACCATCCAAACTCTCACCCCGACCATGAGGCAG
180660 ATTGAAGCA
131 ATTGAAGCA
180669 ATCCAATCTTTTACCCTAATCAGAGAGCAAATTGAAGACCATCAAATCTTTTTGAAGACCATCCA
1 ATCCAATCTTTTACCCTAATCAGAGAGCAAATTGAAGACCATCAAATCTTTTTGAAGACCATCCA
* * * * *
180734 ATATTTTACCCTAACC-ATGGGACAGATTGAAG-CCTATCCAATCTCTTACCTCGACCATGGGGC
66 ATATTTTACCCTAACCAAAGGGA-AGATTGAAGACC-ATCCAAACTCTCACCCCGACCATGAGGC
180797 AGATTGAAGCA
129 AGATTGAAGCA
180808 ATCCAATCTTTTACCC
1 ATCCAATCTTTTACCC
180824 CTAAAGCTAT
Statistics
Matches: 142, Mismatches: 11, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
138 7 0.05
139 135 0.95
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.27
Consensus pattern (139 bp):
ATCCAATCTTTTACCCTAATCAGAGAGCAAATTGAAGACCATCAAATCTTTTTGAAGACCATCCA
ATATTTTACCCTAACCAAAGGGAAGATTGAAGACCATCCAAACTCTCACCCCGACCATGAGGCAG
ATTGAAGCA
Found at i:182442 original size:30 final size:30
Alignment explanation
Indices: 182393--182534 Score: 162
Period size: 30 Copynumber: 4.7 Consensus size: 30
182383 TTATTTTTTG
* * *
182393 ACCCCTAAAATTTCTAAAAATTT-AAGTTTA
1 ACCCTTAAACTTTCCAAAAATTTGAA-TTTA
* *
182423 ACCCTTAAACATTCCAAAAA-TTCAATTTTA
1 ACCCTTAAACTTTCCAAAAATTTGAA-TTTA
* * *
182453 ACCCTCAAACTATCCAAAAATTTGAATTTG
1 ACCCTTAAACTTTCCAAAAATTTGAATTTA
182483 ACCCTTAAACTTTCCAAAAATTTGAATTTA
1 ACCCTTAAACTTTCCAAAAATTTGAATTTA
* *
182513 ACCCCTAAACTTTTCAAAAATT
1 ACCCTTAAACTTTCCAAAAATT
182535 CCAATTTGAC
Statistics
Matches: 95, Mismatches: 15, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
29 2 0.02
30 89 0.94
31 4 0.04
ACGTcount: A:0.42, C:0.22, G:0.03, T:0.34
Consensus pattern (30 bp):
ACCCTTAAACTTTCCAAAAATTTGAATTTA
Found at i:182541 original size:30 final size:29
Alignment explanation
Indices: 182393--182553 Score: 146
Period size: 30 Copynumber: 5.4 Consensus size: 29
182383 TTATTTTTTG
* * *
182393 ACCCCTAAAATTTCTAAAAATTTAAGTTTA
1 ACCCCTAAACTTTCCAAAAATTCAA-TTTA
* *
182423 ACCCTTAAACATTCCAAAAATTCAATTTTA
1 ACCCCTAAACTTTCCAAAAATTCAA-TTTA
* * *
182453 A-CCCTCAAACTATCCAAAAATTTGAATTTG
1 ACCCCT-AAACTTTCCAAAAA-TTCAATTTA
* *
182483 ACCCTTAAACTTTCCAAAAATTTGAATTTA
1 ACCCCTAAACTTTCCAAAAA-TTCAATTTA
* *
182513 ACCCCTAAACTTTTCAAAAATTCCAATTTG
1 ACCCCTAAACTTTCCAAAAATT-CAATTTA
182543 ACCCC-AAACTT
1 ACCCCTAAACTT
182554 ATTCTGATTT
Statistics
Matches: 109, Mismatches: 18, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
29 11 0.10
30 91 0.83
31 7 0.06
ACGTcount: A:0.40, C:0.24, G:0.03, T:0.33
Consensus pattern (29 bp):
ACCCCTAAACTTTCCAAAAATTCAATTTA
Found at i:182541 original size:60 final size:59
Alignment explanation
Indices: 182388--182546 Score: 162
Period size: 60 Copynumber: 2.6 Consensus size: 59
182378 TAAAATTATT
* * * *
182388 TTTTGACCCCTAAA-ATTTCTAAAAATTTAAGTTTAACCCTTAAACATTCCAAAAATTCAA
1 TTTTAACCCCTAAACTTTTC-AAAAATTCAA-TTTGACCCTTAAACATTCCAAAAATTCAA
* * * * *
182448 TTTTAA-CCCTCAAACTATCCAAAAATTTGAATTTGACCCTTAAACTTTCCAAAAATTTGAA
1 TTTTAACCCCT-AAACTTTTCAAAAA-TTCAATTTGACCCTTAAACATTCCAAAAA-TTCAA
182509 -TTTAACCCCTAAACTTTTCAAAAATTCCAATTTGACCC
1 TTTTAACCCCTAAACTTTTCAAAAATT-CAATTTGACCC
182547 CAAACTTATT
Statistics
Matches: 82, Mismatches: 11, Indels: 12
0.78 0.10 0.11
Matches are distributed among these distances:
59 6 0.07
60 62 0.76
61 14 0.17
ACGTcount: A:0.39, C:0.23, G:0.04, T:0.35
Consensus pattern (59 bp):
TTTTAACCCCTAAACTTTTCAAAAATTCAATTTGACCCTTAAACATTCCAAAAATTCAA
Found at i:206701 original size:3 final size:3
Alignment explanation
Indices: 206693--206754 Score: 63
Period size: 3 Copynumber: 19.7 Consensus size: 3
206683 TATTTCCACT
*
206693 TTC TTC TTC GATTTC TTC TTC TTC TTC TTC TTC TTC TTC TT- TTT TTCC
1 TTC TTC TTC --TT-C TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT-C
*
206741 TTC ATC TTC TTC TT
1 TTC TTC TTC TTC TT
206755 TGGCTTCTCA
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
2 2 0.04
3 42 0.82
4 4 0.08
5 2 0.04
6 1 0.02
ACGTcount: A:0.03, C:0.29, G:0.02, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:207751 original size:2 final size:2
Alignment explanation
Indices: 207744--207791 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
207734 TCGAAGACAC
207744 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
*
207786 AA AG AG
1 AG AG AG
207792 CTTTCCATTT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:210653 original size:20 final size:20
Alignment explanation
Indices: 210628--210667 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
210618 AATTTTATAT
*
210628 TTTTAAAAAATTTATAAAAA
1 TTTTAAAAAATATATAAAAA
*
210648 TTTTAAAATATATATAAAAA
1 TTTTAAAAAATATATAAAAA
210668 AAAGTTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
TTTTAAAAAATATATAAAAA
Found at i:212756 original size:22 final size:22
Alignment explanation
Indices: 212728--212773 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
212718 ACTAAGTGAA
212728 GTTGACATGGCTACATAGATTG
1 GTTGACATGGCTACATAGATTG
212750 GTTGACATGGCTACATAGATTG
1 GTTGACATGGCTACATAGATTG
212772 GT
1 GT
212774 CGAGCATCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.26, C:0.13, G:0.28, T:0.33
Consensus pattern (22 bp):
GTTGACATGGCTACATAGATTG
Found at i:214619 original size:2 final size:2
Alignment explanation
Indices: 214612--214638 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
214602 ACAATAGATT
214612 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
214639 TCTATTTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:216630 original size:20 final size:20
Alignment explanation
Indices: 216607--216657 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
216597 TTTATTCCTT
*
216607 TTAATTTGTTTTGTA-TTTTA
1 TTAA-TTGTTTTATATTTTTA
*
216627 TTAATCGTTTTATATTTTTA
1 TTAATTGTTTTATATTTTTA
*
216647 TTTATTGTTTT
1 TTAATTGTTTT
216658 CTGTTTTGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 8 0.31
20 18 0.69
ACGTcount: A:0.20, C:0.02, G:0.08, T:0.71
Consensus pattern (20 bp):
TTAATTGTTTTATATTTTTA
Done.