Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032244.1 Gossypioides kirkii chromosome KI_01
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: 38174113
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1000 characters in sequence are not A, C, G, or T
File 88 of 126
Found at i:27215066 original size:71 final size:71
Alignment explanation
Indices: 27214934--27215070 Score: 211
Period size: 71 Copynumber: 1.9 Consensus size: 71
27214924 TAGGTATCAA
* *
27214934 TAGAAGTCCCAGGCCATAACTTCTATGCTCTGTAGAGTTTATTCTACTGATAGAACTCTTGGTTG
1 TAGAAGTCCCAGGCCACAACTTCTATACTCTGTAGAGTTTATTCTACTGATAGAACTCTTGGTTG
27214999 TATAGG
66 TATAGG
* * * * *
27215005 TAGAAGTCCCAGGCCACAACTTCTTTACTCTTTGGAGTTTGTTCTACTGATAGAAGTCTTGGTTG
1 TAGAAGTCCCAGGCCACAACTTCTATACTCTGTAGAGTTTATTCTACTGATAGAACTCTTGGTTG
27215070 T
66 T
27215071 TAATCGATGT
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
71 59 1.00
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.36
Consensus pattern (71 bp):
TAGAAGTCCCAGGCCACAACTTCTATACTCTGTAGAGTTTATTCTACTGATAGAACTCTTGGTTG
TATAGG
Found at i:27231068 original size:29 final size:28
Alignment explanation
Indices: 27231035--27231194 Score: 69
Period size: 29 Copynumber: 5.5 Consensus size: 28
27231025 TCTCGATGGC
27231035 AAAAATGTAATTTCGGAAAAATTT-GGGGTT
1 AAAAATGTAATTT-GG-AAAATTTAGGGG-T
* *
27231065 AAAAATGGAATCTTGGAAAGTTTAGGGGT
1 AAAAATGTAAT-TTGGAAAATTTAGGGGT
* *
27231094 -AAAATGGTAATTTTTGGTGAAA--TCGGGGTT
1 AAAAAT-GTAA--TTTGG-AAAATTTAGGGG-T
* * *
27231124 AAAAATGGGATTTTGGAAAGTTTAGGGGT
1 AAAAAT-GTAATTTGGAAAATTTAGGGGT
** * *
27231153 -AAAATGGTAATTTTTAAAGGTTTTGGGGT
1 AAAAAT-GTAATTTGGAAA-ATTTAGGGGT
*
27231182 CAAAATGTAATTT
1 AAAAATGTAATTT
27231195 TCTAAAGTTT
Statistics
Matches: 102, Mismatches: 16, Indels: 25
0.71 0.11 0.17
Matches are distributed among these distances:
28 21 0.21
29 37 0.36
30 31 0.30
31 13 0.13
ACGTcount: A:0.36, C:0.03, G:0.28, T:0.34
Consensus pattern (28 bp):
AAAAATGTAATTTGGAAAATTTAGGGGT
Found at i:27231083 original size:30 final size:30
Alignment explanation
Indices: 27231035--27231166 Score: 89
Period size: 30 Copynumber: 4.5 Consensus size: 30
27231025 TCTCGATGGC
* *
27231035 AAAAATGTAATTTCGGAAAAATTTGGGGTT
1 AAAAATGGAATTTTGGAAAAATTTGGGGTT
* *
27231065 AAAAATGGAATCTTGG-AAAGTTTAGGGG-T
1 AAAAATGGAATTTTGGAAAAATTT-GGGGTT
** *
27231094 -AAAATGGTAATTTTTGGTGAAA-TCGGGGTT
1 AAAAATGG-AA-TTTTGGAAAAATTTGGGGTT
* *
27231124 AAAAATGGGATTTTGG-AAAGTTTAGGGG-T
1 AAAAATGGAATTTTGGAAAAATTT-GGGGTT
27231153 -AAAATGGTAATTTT
1 AAAAATGG-AATTTT
27231167 TAAAGGTTTT
Statistics
Matches: 80, Mismatches: 13, Indels: 19
0.71 0.12 0.17
Matches are distributed among these distances:
28 16 0.20
29 26 0.32
30 29 0.36
31 9 0.11
ACGTcount: A:0.36, C:0.02, G:0.28, T:0.33
Consensus pattern (30 bp):
AAAAATGGAATTTTGGAAAAATTTGGGGTT
Found at i:27231104 original size:59 final size:58
Alignment explanation
Indices: 27231036--27231165 Score: 181
Period size: 59 Copynumber: 2.2 Consensus size: 58
27231026 CTCGATGGCA
*
27231036 AAAAT-GTAATTTCGGAAAAATTTGGGGTTAAAAATGGAATCTTGGAAAGTTTAGGGGT
1 AAAATGGTAATTTCGGAAAAA-TCGGGGTTAAAAATGGAATCTTGGAAAGTTTAGGGGT
* ** * *
27231094 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTTAGGGGT
1 AAAATGGTAA-TTTCGGAAAAATCGGGGTTAAAAATGGAATCTTGGAAAGTTTAGGGGT
27231153 AAAATGGTAATTT
1 AAAATGGTAATTT
27231166 TTAAAGGTTT
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
58 8 0.12
59 48 0.75
60 8 0.12
ACGTcount: A:0.36, C:0.02, G:0.28, T:0.33
Consensus pattern (58 bp):
AAAATGGTAATTTCGGAAAAATCGGGGTTAAAAATGGAATCTTGGAAAGTTTAGGGGT
Found at i:27231181 original size:59 final size:59
Alignment explanation
Indices: 27231054--27231186 Score: 176
Period size: 59 Copynumber: 2.3 Consensus size: 59
27231044 ATTTCGGAAA
***
27231054 AATTTGGGGTTAAAAATGGAATCTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGGTG
1 AATTTGGGGTTAAAAATGGAATCTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTAAAG
* * * *
27231113 AAATCGGGGTTAAAAATGGGATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTAAAG
1 AATTTGGGGTTAAAAATGGAATCTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTAAAG
** *
27231172 GTTTTGGGGTCAAAA
1 AATTTGGGGTTAAAA
27231187 TGTAATTTTC
Statistics
Matches: 62, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
59 62 1.00
ACGTcount: A:0.34, C:0.02, G:0.30, T:0.34
Consensus pattern (59 bp):
AATTTGGGGTTAAAAATGGAATCTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTAAAG
Found at i:27231195 original size:29 final size:28
Alignment explanation
Indices: 27231140--27231235 Score: 95
Period size: 29 Copynumber: 3.2 Consensus size: 28
27231130 GGGATTTTGG
*
27231140 AAAGTTTAGGGGT-AAAATGGTAATTTTT
1 AAAGTTTTGGGGTCAAAAT-GTAATTTTT
27231168 AAAGGTTTTGGGGTCAAAATGTAATTTTCT
1 AAA-GTTTTGGGGTCAAAATGTAATTTT-T
* * *
27231198 AAAGTTTTGGGATCACAAATATCATTTTT
1 AAAGTTTTGGGGTCA-AAATGTAATTTTT
27231227 GAACAGTTT
1 -AA-AGTTT
27231236 AGAGACTTAT
Statistics
Matches: 58, Mismatches: 4, Indels: 9
0.82 0.06 0.13
Matches are distributed among these distances:
28 3 0.05
29 29 0.50
30 21 0.36
31 5 0.09
ACGTcount: A:0.33, C:0.06, G:0.21, T:0.40
Consensus pattern (28 bp):
AAAGTTTTGGGGTCAAAATGTAATTTTT
Found at i:27231201 original size:30 final size:29
Alignment explanation
Indices: 27231140--27231217 Score: 97
Period size: 29 Copynumber: 2.7 Consensus size: 29
27231130 GGGATTTTGG
*
27231140 AAAGTTTAGGGGT-AAAATGGTAATTTTT
1 AAAGTTTTGGGGTCAAAATGGTAATTTTT
27231168 AAAGGTTTTGGGGTCAAAAT-GTAATTTTCT
1 AAA-GTTTTGGGGTCAAAATGGTAATTTT-T
*
27231198 AAAGTTTTGGGATCACAAAT
1 AAAGTTTTGGGGTCA-AAAT
27231218 ATCATTTTTG
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
28 3 0.07
29 28 0.64
30 13 0.30
ACGTcount: A:0.35, C:0.05, G:0.23, T:0.37
Consensus pattern (29 bp):
AAAGTTTTGGGGTCAAAATGGTAATTTTT
Found at i:27233136 original size:6 final size:6
Alignment explanation
Indices: 27233118--27233233 Score: 77
Period size: 6 Copynumber: 20.0 Consensus size: 6
27233108 AGTTTAGTTT
* * * *
27233118 TTTAAA TTTTAAA TTTAAA ATT--A TTTCATA TTTAAG CT-AAA TTTAAA
1 TTTAAA -TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA
* **
27233165 TTTAGAA --CAAA TTTAAA TTTAAA TTTAAA -TTAAGA -ACAAA TTTAAA
1 TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA-A TTTAAA TTTAAA
27233211 TTTAAA TTTAAA -TTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA
27233234 CTTAGAAATA
Statistics
Matches: 86, Mismatches: 13, Indels: 21
0.72 0.11 0.17
Matches are distributed among these distances:
4 5 0.06
5 14 0.16
6 55 0.64
7 12 0.14
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (6 bp):
TTTAAA
Found at i:27233167 original size:17 final size:16
Alignment explanation
Indices: 27233125--27233234 Score: 70
Period size: 17 Copynumber: 6.8 Consensus size: 16
27233115 TTTTTTAAAT
*
27233125 TTTAAATTTAAA-ATTA
1 TTTAAATTTAAACA-AA
* *
27233141 TTTCATATTTAAGCTAAA
1 TTT-AAATTTAAAC-AAA
27233159 TTTAAATTTAGAACAAA
1 TTTAAATTTA-AACAAA
27233176 TTTAAATTT----AAA
1 TTTAAATTTAAACAAA
*
27233188 TTTAAATTAAGAACAAA
1 TTTAAATTTA-AACAAA
*
27233205 TTTAAATTTAAATTTAAA
1 TTTAAATTTAAA--CAAA
27233223 -TTAAATTTAAAC
1 TTTAAATTTAAAC
27233235 TTAGAAATAA
Statistics
Matches: 74, Mismatches: 9, Indels: 23
0.70 0.08 0.22
Matches are distributed among these distances:
12 11 0.15
16 5 0.07
17 48 0.65
18 9 0.12
19 1 0.01
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.43
Consensus pattern (16 bp):
TTTAAATTTAAACAAA
Found at i:27233181 original size:23 final size:23
Alignment explanation
Indices: 27233155--27233233 Score: 79
Period size: 23 Copynumber: 3.2 Consensus size: 23
27233145 ATATTTAAGC
27233155 TAAATTTAAATTTAGAACAAATT
1 TAAATTTAAATTTAGAACAAATT
27233178 TAAATTTAAATTTAAATTAAGAACAAATT
1 TAAATTTAAA--T---TT-AGAACAAATT
*
27233207 TAAATTTAAATTTA-AATTAAATT
1 TAAATTTAAATTTAGAA-CAAATT
27233230 TAAA
1 TAAA
27233234 CTTAGAAATA
Statistics
Matches: 48, Mismatches: 1, Indels: 14
0.76 0.02 0.22
Matches are distributed among these distances:
22 2 0.04
23 20 0.42
24 2 0.04
25 1 0.02
27 1 0.02
28 2 0.04
29 20 0.42
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (23 bp):
TAAATTTAAATTTAGAACAAATT
Found at i:27233192 original size:29 final size:29
Alignment explanation
Indices: 27233155--27233226 Score: 135
Period size: 29 Copynumber: 2.5 Consensus size: 29
27233145 ATATTTAAGC
*
27233155 TAAATTTAAATTTAGAACAAATTTAAATT
1 TAAATTTAAATTAAGAACAAATTTAAATT
27233184 TAAATTTAAATTAAGAACAAATTTAAATT
1 TAAATTTAAATTAAGAACAAATTTAAATT
27233213 TAAATTTAAATTAA
1 TAAATTTAAATTAA
27233227 ATTTAAACTT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (29 bp):
TAAATTTAAATTAAGAACAAATTTAAATT
Found at i:27233245 original size:23 final size:23
Alignment explanation
Indices: 27233155--27233247 Score: 75
Period size: 23 Copynumber: 4.0 Consensus size: 23
27233145 ATATTTAAGC
*
27233155 TAAATTTAAATTTAGAACA-AATT
1 TAAATTTAAATTTA-AACATAAAT
* *
27233178 TAAATTTAAATTTAAA-TTAAGAA
1 TAAATTTAAATTTAAACATAA-AT
* **
27233201 CAAATTTAAATTTAAATTTAAAT
1 TAAATTTAAATTTAAACATAAAT
*
27233224 TAAATTTAAACTTAGAA-ATAAAT
1 TAAATTTAAATTTA-AACATAAAT
27233247 T
1 T
27233248 TGAAACCAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
22 4 0.07
23 48 0.83
24 6 0.10
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (23 bp):
TAAATTTAAATTTAAACATAAAT
Found at i:27233974 original size:200 final size:200
Alignment explanation
Indices: 27233616--27234656 Score: 1387
Period size: 200 Copynumber: 5.2 Consensus size: 200
27233606 TTCATTGACC
* * * * * * *
27233616 TGGTCTTCTTCTCTATGTCTCATCAGGAAGAAGATCGCAATCAT-CTGTTTTAATTCGCTTCTCA
1 TGGTATTCTTCTCTATATCTCATCAGGAAGATGACCGC-CTC-TGTTGTTTTAATTCGCTTCTCT
* * * * *
27233680 GGATCTCCTCAGGAAGGCGAATTTGGTCCACTTCTTTGTGTCTCATCAGGAACCTAACCTTTTTA
64 GGATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTA
* * * * * *
27233745 TTGCTTCGACCTGCTTCTTAGTATCTCATCAGGGAGCTGGGTTCGAAGATTTGCTCGTGTTGAAC
129 TTGTTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTACGAAGATTTGCTCGTGTTGAGC
27233810 GTTGAGT
194 GTTGAGT
* *
27233817 TGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTCTGTTGTTTTAATTTGCTTCTCTGG
1 TGGTATTCTTCTCTATATCTCATCAGGAAGATGACCGCCTCTGTTGTTTTAATTCGCTTCTCTGG
* *
27233882 ATCTCCTCAGGAAGACAAATTTGGTCCACTCCTCTGTATCTCATCAGGAAGCTAACCATTTTATT
66 ATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATT
* *
27233947 GTTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTAGGTACGAAGATTTACTCGCT-TTGAGCG
131 GTTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTACGAAGATTTGCTCG-TGTTGAGCG
*
27234011 TTGATT
195 TTGAGT
** * * * *
27234017 TGGTATTCTTCTCTACGTCGCATTAGGAAGATGACCGCCTCTATTGTTTTAATTCGTTTCTCTGG
1 TGGTATTCTTCTCTATATCTCATCAGGAAGATGACCGCCTCTGTTGTTTTAATTCGCTTCTCTGG
* * *
27234082 ATCTCCTTAGGAAGACAAATTTGGTCCACTTCTCTGTATCTCATCAGGCAGCTAACCATTTTATT
66 ATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATT
* * *
27234147 ATTTTGACCTGCTTCTCAATGTCTCATCAGGAAGCTGGGTACGAAGATTTGCTCGCT-TTGAGCG
131 GTTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTACGAAGATTTGCTCG-TGTTGAGCG
*
27234211 TTGATT
195 TTGAGT
** ** * *
27234217 TGGTATTCTTCTCTACGTCTCATCAGGAAGATGATTGCCTCTGTTGTTTTAATTCGTTTCTCTAG
1 TGGTATTCTTCTCTATATCTCATCAGGAAGATGACCGCCTCTGTTGTTTTAATTCGCTTCTCTGG
* * *
27234282 ATCTCCTCAAGAAGACGAATTTGGTCCACTTCTCTGTGTCTCATCAGGAAGCTAACCTTTTTATT
66 ATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATT
* * * * *
27234347 GCTTCGACTTGCTTCTTAGTGTCTCATCAGGAAGCT--G-ACCGCAA-CTTGGCTCGTGTTGAGC
131 GTTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTA-CG-AAGATTTGCTCGTGTTGAGC
27234408 GTTGAGT
194 GTTGAGT
* *
27234415 TGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCT-TGCTTGTTTTAATTCGCTTCTCTA
1 TGGTATTCTTCTCTATATCTCATCAGGAAGATGACCGCCTCTG-TTGTTTTAATTCGCTTCTCTG
* *
27234479 GATCTCCTCAAGAAGACGAATTTGGTCCACTTCTTTGTATCTCATCAGGAAGCTAACCATTTTAT
65 GATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTAT
* * * * * *
27234544 TGTTTCGACTTGCTTCTCGGGGTCTCATCAGGAAGTTGGGTACGAAGATTGGCTCGTGTTGAACG
130 TGTTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTACGAAGATTTGCTCGTGTTGAGCG
27234609 TTGAGT
195 TTGAGT
*
27234615 TGGTATTCTTTCTCTGTATCTCATCAGGAAGATGACCGCCTC
1 TGGTATTC-TTCTCTATATCTCATCAGGAAGATGACCGCCTC
27234657 GCTGTCCTGT
Statistics
Matches: 750, Mismatches: 78, Indels: 23
0.88 0.09 0.03
Matches are distributed among these distances:
197 4 0.01
198 171 0.23
199 5 0.01
200 503 0.67
201 67 0.09
ACGTcount: A:0.20, C:0.22, G:0.21, T:0.37
Consensus pattern (200 bp):
TGGTATTCTTCTCTATATCTCATCAGGAAGATGACCGCCTCTGTTGTTTTAATTCGCTTCTCTGG
ATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATT
GTTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTACGAAGATTTGCTCGTGTTGAGCGT
TGAGT
Found at i:27246845 original size:29 final size:29
Alignment explanation
Indices: 27246812--27246884 Score: 69
Period size: 29 Copynumber: 2.5 Consensus size: 29
27246802 TCTCGATGGC
*
27246812 AAAAATGTAATTTTGAGAAAA-TTTAGGGTT
1 AAAAATGTAATTTT-A-AAAAGTTTAGGGGT
* **
27246842 AAAAATGGAATCGTAAAAAGTTTAGGGGT
1 AAAAATGTAATTTTAAAAAGTTTAGGGGT
27246871 -AAAATGGTAATTTT
1 AAAAAT-GTAATTTT
27246885 TGGTGAAATC
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
28 9 0.26
29 14 0.41
30 11 0.32
ACGTcount: A:0.44, C:0.01, G:0.22, T:0.33
Consensus pattern (29 bp):
AAAAATGTAATTTTAAAAAGTTTAGGGGT
Found at i:27246898 original size:29 final size:29
Alignment explanation
Indices: 27246866--27247062 Score: 89
Period size: 29 Copynumber: 6.7 Consensus size: 29
27246856 AAAAAGTTTA
27246866 GGGGTAAAATGGTAATTTTTGGTGAAA-TC
1 GGGGTAAAATGGTAATTTTT-GTGAAAGTC
27246895 GGGGTTAAAAATAGG--A-TTTTG-GAAAGTTC
1 GGGG-T-AAAAT-GGTAATTTTTGTGAAAG-TC
* *
27246924 GGGGGTAAAATAGTAATTTTAGGTGAAA-TC
1 -GGGGTAAAATGGTAATTTT-TGTGAAAGTC
* *
27246954 GGGGTTAAAAAT-G-AGA-TTTT-AGAAAGTTAA
1 GGGG-T-AAAATGGTA-ATTTTTGTGAAAG-T-C
27246984 GGGGTAAAATGGTAATTTTTGATGAAA-TC
1 GGGGTAAAATGGTAATTTTTG-TGAAAGTC
* *
27247013 GAGGTTAAAAATGG--ATTTTTG-GAAAGTTT
1 G-GGGT-AAAATGGTAATTTTTGTGAAAG-TC
27247042 GAGGGTAAAATGGTAATTTTT
1 G-GGGTAAAATGGTAATTTTT
27247063 AGAGGTTTTG
Statistics
Matches: 130, Mismatches: 10, Indels: 55
0.67 0.05 0.28
Matches are distributed among these distances:
27 13 0.10
28 18 0.14
29 38 0.29
30 33 0.25
31 18 0.14
32 10 0.08
ACGTcount: A:0.36, C:0.02, G:0.29, T:0.34
Consensus pattern (29 bp):
GGGGTAAAATGGTAATTTTTGTGAAAGTC
Found at i:27246900 original size:59 final size:59
Alignment explanation
Indices: 27246837--27247062 Score: 287
Period size: 59 Copynumber: 3.8 Consensus size: 59
27246827 AGAAAATTTA
** *
27246837 GGGTTAAAAATGGAATCGTAAAAAGTTTAGGGGTAAAATGGTAATTTTTGGTGAAATCG
1 GGGTTAAAAATGGAATTTTAGAAAGTTTAGGGGTAAAATGGTAATTTTTGGTGAAATCG
* ** * *
27246896 GGGTTAAAAATAGG-ATTTTGGAAAGTTCGGGGGTAAAATAGTAATTTTAGGTGAAATCG
1 GGGTTAAAAAT-GGAATTTTAGAAAGTTTAGGGGTAAAATGGTAATTTTTGGTGAAATCG
* *
27246955 GGGTTAAAAAT-GAGATTTTAGAAAGTTAAGGGGTAAAATGGTAATTTTTGATGAAATCG
1 GGGTTAAAAATGGA-ATTTTAGAAAGTTTAGGGGTAAAATGGTAATTTTTGGTGAAATCG
* * *
27247014 AGGTTAAAAATGGATTTTTGGAAAGTTT-GAGGGTAAAATGGTAATTTTT
1 GGGTTAAAAATGGAATTTTAGAAAGTTTAG-GGGTAAAATGGTAATTTTT
27247063 AGAGGTTTTG
Statistics
Matches: 144, Mismatches: 18, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
57 1 0.01
58 1 0.01
59 138 0.96
60 4 0.03
ACGTcount: A:0.37, C:0.02, G:0.28, T:0.33
Consensus pattern (59 bp):
GGGTTAAAAATGGAATTTTAGAAAGTTTAGGGGTAAAATGGTAATTTTTGGTGAAATCG
Found at i:27246914 original size:30 final size:31
Alignment explanation
Indices: 27246880--27246973 Score: 94
Period size: 30 Copynumber: 3.2 Consensus size: 31
27246870 TAAAATGGTA
27246880 ATTTTTGGTGAAATCGGGGTTAAAAATAG-G
1 ATTTTTGGTGAAATCGGGGTTAAAAATAGAG
*
27246910 A-TTTT-G-GAAAGTTCGGGGGT-AAAATAGTA-
1 ATTTTTGGTGAAA--TCGGGGTTAAAAATAG-AG
*
27246939 ATTTTAGGTGAAATCGGGGTTAAAAAT-GAG
1 ATTTTTGGTGAAATCGGGGTTAAAAATAGAG
27246969 ATTTT
1 ATTTT
27246974 AGAAAGTTAA
Statistics
Matches: 52, Mismatches: 3, Indels: 18
0.71 0.04 0.25
Matches are distributed among these distances:
27 4 0.08
28 8 0.15
29 13 0.25
30 17 0.33
31 6 0.12
32 4 0.08
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.34
Consensus pattern (31 bp):
ATTTTTGGTGAAATCGGGGTTAAAAATAGAG
Found at i:27247099 original size:29 final size:29
Alignment explanation
Indices: 27247039--27247103 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 29
27247029 TTTTGGAAAG
*
27247039 TTTGAGGGTAAAATGGTAATTTTTAGAGGT
1 TTTG-GGGTAAAATGGTAATTTTTAGAAGT
27247069 TTTGGGGTCAAAAT-GTAATTTTCT-GAAGT
1 TTTGGGGT-AAAATGGTAATTTT-TAGAAGT
27247098 TTTGGG
1 TTTGGG
27247104 ATCACAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
29 22 0.69
30 10 0.31
ACGTcount: A:0.26, C:0.03, G:0.29, T:0.42
Consensus pattern (29 bp):
TTTGGGGTAAAATGGTAATTTTTAGAAGT
Found at i:27249118 original size:42 final size:42
Alignment explanation
Indices: 27249068--27249151 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 42
27249058 ATATTTAAGC
* *
27249068 TAAATTTAAATTTAGAA-TAAATTTAAATTTAAAAATGAATTT
1 TAAATTTAAATTTA-AATTAAATTTAAACTTAAAAATAAATTT
*
27249110 TAAATTTAAATTTAAATTAAATTTAAACTTAGAAATAAATTT
1 TAAATTTAAATTTAAATTAAATTTAAACTTAAAAATAAATTT
27249152 GAAACCAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
41 2 0.05
42 36 0.95
ACGTcount: A:0.52, C:0.01, G:0.04, T:0.43
Consensus pattern (42 bp):
TAAATTTAAATTTAAATTAAATTTAAACTTAAAAATAAATTT
Found at i:27249131 original size:5 final size:6
Alignment explanation
Indices: 27249068--27249136 Score: 72
Period size: 6 Copynumber: 11.7 Consensus size: 6
27249058 ATATTTAAGC
* * *
27249068 TAAATT TAAATT TAGAA-- TAAATT TAAATT TAAAAAT GAATTT TAAATT
1 TAAATT TAAATT TA-AATT TAAATT TAAATT T-AAATT TAAATT TAAATT
27249116 TAAATT TAAA-T TAAATT TAAA
1 TAAATT TAAATT TAAATT TAAA
27249137 CTTAGAAATA
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
4 2 0.04
5 7 0.13
6 37 0.71
7 6 0.12
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (6 bp):
TAAATT
Found at i:27249136 original size:17 final size:17
Alignment explanation
Indices: 27249032--27249136 Score: 74
Period size: 17 Copynumber: 6.0 Consensus size: 17
27249022 GTTTAGTTTT
27249032 TTAAATTTTAAATTTTAAA
1 TTAAA-TTTAAA-TTTAAA
* *
27249051 TT--ATTTCATATTTAAG
1 TTAAATTT-AAATTTAAA
*
27249067 CTAAATTTAAATTTAGAA
1 TTAAATTTAAATTTA-AA
27249085 -TAAATTTAAATTTAAAAA
1 TTAAATTTAAATTT--AAA
* *
27249103 TGAATTTTAAATTTAAA
1 TTAAATTTAAATTTAAA
27249120 TTTAAA-TTAAATTTAAA
1 -TTAAATTTAAATTTAAA
27249137 CTTAGAAATA
Statistics
Matches: 69, Mismatches: 9, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
16 9 0.13
17 36 0.52
18 10 0.14
19 14 0.20
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.47
Consensus pattern (17 bp):
TTAAATTTAAATTTAAA
Found at i:27252521 original size:29 final size:29
Alignment explanation
Indices: 27252431--27252521 Score: 67
Period size: 29 Copynumber: 3.1 Consensus size: 29
27252421 AATCGGGATC
* **
27252431 AAAAATAGAGTTTTTGGACATTTTGGGGT
1 AAAAATGGAGTTTTTGGACATTCGGGGGT
* ** ** * **
27252460 -AAAATGGTAATTTTTAAAGTTTCGAGGAC
1 AAAAATGG-AGTTTTTGGACATTCGGGGGT
27252489 AAAAATGGAGTTTTTGGACATTCGGGGGT
1 AAAAATGGAGTTTTTGGACATTCGGGGGT
27252518 AAAA
1 AAAA
27252522 TGGTAAGTTT
Statistics
Matches: 41, Mismatches: 19, Indels: 4
0.64 0.30 0.06
Matches are distributed among these distances:
28 6 0.15
29 28 0.68
30 7 0.17
ACGTcount: A:0.35, C:0.05, G:0.26, T:0.33
Consensus pattern (29 bp):
AAAAATGGAGTTTTTGGACATTCGGGGGT
Found at i:27252596 original size:58 final size:58
Alignment explanation
Indices: 27252401--27252619 Score: 242
Period size: 58 Copynumber: 3.8 Consensus size: 58
27252391 TATCCGAGGA
*** * * **
27252401 TAAAATGGTAATTTTTAAAAAATCGGGATCAAAAATAGAGTTTTTGGACATTTTGGGG
1 TAAAATGGTAATTTTTAAAGTTTCGGGGTCAAAAATGGAGTTTTTGGACATTCAGGGG
* * *
27252459 TAAAATGGTAATTTTTAAAGTTTCGAGGACAAAAATGGAGTTTTTGGACATTCGGGGG
1 TAAAATGGTAATTTTTAAAGTTTCGGGGTCAAAAATGGAGTTTTTGGACATTCAGGGG
** * * *
27252517 TAAAATGGTAAGTTTGAAAAGTTTCGGGGTTAAAAATGGAG-TTTTGGATATTCAGGGT
1 TAAAATGGTAA-TTTTTAAAGTTTCGGGGTCAAAAATGGAGTTTTTGGACATTCAGGGG
** * *
27252575 TAAAATGGTAATTTTTGAAAGTTTTAGGGTCAAAATTGGAATTTT
1 TAAAATGGTAATTTTT-AAAGTTTCGGGGTCAAAAATGGAGTTTT
27252620 AAAAAGTTTA
Statistics
Matches: 134, Mismatches: 24, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
57 3 0.02
58 104 0.78
59 27 0.20
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.36
Consensus pattern (58 bp):
TAAAATGGTAATTTTTAAAGTTTCGGGGTCAAAAATGGAGTTTTTGGACATTCAGGGG
Found at i:27252610 original size:30 final size:29
Alignment explanation
Indices: 27252570--27252737 Score: 99
Period size: 29 Copynumber: 5.7 Consensus size: 29
27252560 TTGGATATTC
*
27252570 AGGGTTAAAATGGTAATTTTTGAAAGTTTT
1 AGGGTCAAAATGG-AATTTTTGAAAGTTTT
**
27252600 AGGGTCAAAATTGGAATTTTAAAAAG-TTT
1 AGGGTCAAAA-TGGAATTTTTGAAAGTTTT
* *** *
27252629 AGGGGTAAAAATGTCTTTTTTGGAAGTTTT
1 A-GGGTCAAAATGGAATTTTTGAAAGTTTT
* * * *
27252659 GGGGTCAAAAAAGGAA-TTTTGGAAGTTTG
1 AGGGTC-AAAATGGAATTTTTGAAAGTTTT
* * ** *
27252688 GGGGTAAAAATATAATTCTTGAAAG-TTT
1 AGGGTCAAAATGGAATTTTTGAAAGTTTT
*
27252716 CGAGGTCAAAACTGGAATTTTT
1 AG-GGTCAAAA-TGGAATTTTT
27252738 AGAAGTTCGA
Statistics
Matches: 102, Mismatches: 29, Indels: 14
0.70 0.20 0.10
Matches are distributed among these distances:
28 9 0.09
29 48 0.47
30 42 0.41
31 3 0.03
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.36
Consensus pattern (29 bp):
AGGGTCAAAATGGAATTTTTGAAAGTTTT
Found at i:27252648 original size:58 final size:59
Alignment explanation
Indices: 27252586--27252765 Score: 170
Period size: 59 Copynumber: 3.1 Consensus size: 59
27252576 AAAATGGTAA
* * *
27252586 TTTTTGAAAGTTTTAGGGTCAAAATTGGAATTTTAAAAAGTTTAGGGGTAAAAATGT-CT
1 TTTTTGAAAGTTTTAGGGTCAAAAATGGAATTTT-AAAAGTTTAGGGGTAAAAATATAAT
* * * ** *
27252645 TTTTTGGAAGTTTTGGGGTCAAAAAAGGAATTTTGGAAGTTTGGGGGTAAAAATATAA-
1 TTTTTGAAAGTTTTAGGGTCAAAAATGGAATTTTAAAAGTTTAGGGGTAAAAATATAAT
* * * * *
27252703 TTCTTGAAAG-TTTCGAGGTCAAAACTGGAATTTTTAGAAG-TTCGAGGGTAAAAATATAAT
1 TTTTTGAAAGTTTTAG-GGTCAAAAATGGAA-TTTTAAAAGTTTAG-GGGTAAAAATATAAT
27252763 TTT
1 TTT
27252766 CGGATAGTTT
Statistics
Matches: 99, Mismatches: 17, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
57 4 0.04
58 41 0.41
59 52 0.53
60 2 0.02
ACGTcount: A:0.35, C:0.04, G:0.24, T:0.37
Consensus pattern (59 bp):
TTTTTGAAAGTTTTAGGGTCAAAAATGGAATTTTAAAAGTTTAGGGGTAAAAATATAAT
Found at i:27252763 original size:29 final size:28
Alignment explanation
Indices: 27252673--27252765 Score: 80
Period size: 29 Copynumber: 3.2 Consensus size: 28
27252663 TCAAAAAAGG
* * *
27252673 AATTTTGGAAGTTTGGGGGTAAAAATAT
1 AATTTTTGAAGTTCGAGGGTAAAAATAT
* * **
27252701 AATTCTTGAAAGTTTCGA-GGTCAAAACTGG
1 AATTTTTG-AAG-TTCGAGGGT-AAAAATAT
27252731 AATTTTTAGAAGTTCGAGGGTAAAAATAT
1 AATTTTT-GAAGTTCGAGGGTAAAAATAT
27252760 AATTTT
1 AATTTT
27252766 CGGATAGTTT
Statistics
Matches: 49, Mismatches: 11, Indels: 9
0.71 0.16 0.13
Matches are distributed among these distances:
28 6 0.12
29 22 0.45
30 20 0.41
31 1 0.02
ACGTcount: A:0.37, C:0.05, G:0.23, T:0.35
Consensus pattern (28 bp):
AATTTTTGAAGTTCGAGGGTAAAAATAT
Found at i:27252763 original size:59 final size:58
Alignment explanation
Indices: 27252429--27252765 Score: 217
Period size: 58 Copynumber: 5.8 Consensus size: 58
27252419 AAAATCGGGA
* * * * *
27252429 TCAAAAATAGAGTTTTTGGACATTTTG-GGGT-AAAATGGTAATTTTTAAAGTTTCGAGG
1 TCAAAAATGGAATTTTTGGA-AGTTCGAGGGTAAAAAT-GTAATTTTGAAAGTTTCGAGG
* * * * *
27252487 ACAAAAATGGAGTTTTTGGACA-TTCGGGGGT-AAAATGGTAAGTTTGAAAAGTTTCGGGG
1 TCAAAAATGGAATTTTTGGA-AGTTCGAGGGTAAAAAT-GTAATTTTG-AAAGTTTCGAGG
* * * *
27252546 TTAAAAATGG-AGTTTTGGATA-TTC-AGGGTTAAAATGGTAATTTTTGAAAGTTT-TAGGG
1 TCAAAAATGGAATTTTTGGA-AGTTCGAGGGTAAAAAT-GTAA-TTTTGAAAGTTTCGA-GG
* *** * ** * * *
27252604 TCAAAATTGGAATTTTAAAAAGTT-TAGGGGTAAAAATGTCTTTTTTGGAAGTTTTGGGG
1 TCAAAAATGGAATTTTTGGAAGTTCGA-GGGTAAAAATGT-AATTTTGAAAGTTTCGAGG
* * * *
27252663 TCAAAAAAGGAA-TTTTGGAAGTTTGGGGGTAAAAATATAATTCTTGAAAGTTTCGAGG
1 TCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGTAATT-TTGAAAGTTTCGAGG
* * *
27252721 TCAAAACTGGAATTTTTAGAAGTTCGAGGGTAAAAATATAATTTT
1 TCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTT
27252766 CGGATAGTTT
Statistics
Matches: 220, Mismatches: 45, Indels: 28
0.75 0.15 0.10
Matches are distributed among these distances:
57 9 0.04
58 119 0.54
59 83 0.38
60 9 0.04
ACGTcount: A:0.34, C:0.05, G:0.26, T:0.35
Consensus pattern (58 bp):
TCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTGAAAGTTTCGAGG
Found at i:27254674 original size:17 final size:17
Alignment explanation
Indices: 27254634--27254709 Score: 71
Period size: 17 Copynumber: 4.2 Consensus size: 17
27254624 TATAATAAGT
*
27254634 TTTAAATTTATATATAAA
1 TTTAAATTTA-AAATAAA
* *
27254652 TCTAAATTTAAAACAAA
1 TTTAAATTTAAAATAAA
*
27254669 TTTAAATTTAAGATAAA
1 TTTAAATTTAAAATAAA
27254686 TTTATATTATCTTAAAATAAA
1 TTTA-A--AT-TTAAAATAAA
27254707 TTT
1 TTT
27254710 TAAAATGGGT
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
17 23 0.49
18 10 0.21
20 2 0.04
21 12 0.26
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.45
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:27255432 original size:16 final size:16
Alignment explanation
Indices: 27255411--27255465 Score: 55
Period size: 16 Copynumber: 3.7 Consensus size: 16
27255401 TATATTTTAA
27255411 AATATAATAAATTATT
1 AATATAATAAATTATT
27255427 AATATAAT---TTATT
1 AATATAATAAATTATT
* *
27255440 ATTTTAATAAATTATT
1 AATATAATAAATTATT
*
27255456 TA-ATAATAAA
1 AATATAATAAA
27255466 CTTTAACATT
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
13 11 0.35
15 7 0.23
16 13 0.42
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AATATAATAAATTATT
Found at i:27255617 original size:23 final size:23
Alignment explanation
Indices: 27255586--27255639 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
27255576 ATTCAATCAT
* *
27255586 AAATGTTTT-ATACTATAAAATAC
1 AAATATTTTAATAATAT-AAATAC
*
27255609 AAATATTTTAATAATATAAATAT
1 AAATATTTTAATAATATAAATAC
27255632 AAATATTT
1 AAATATTT
27255640 GTTTAAATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 21 0.78
24 6 0.22
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.43
Consensus pattern (23 bp):
AAATATTTTAATAATATAAATAC
Found at i:27256602 original size:27 final size:31
Alignment explanation
Indices: 27256549--27256604 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 31
27256539 GGTTAAAAGA
*
27256549 GGTCCAAAATATTGTTTTTCAATTTTTAAGG
1 GGTCCAAAATATTGTTTTTCAACTTTTAAGG
27256580 GGTCC-AAAT-TT-TTTTT-AACTTTTAA
1 GGTCCAAAATATTGTTTTTCAACTTTTAA
27256605 AGGTCAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 8 0.33
28 5 0.21
29 2 0.08
30 4 0.17
31 5 0.21
ACGTcount: A:0.29, C:0.11, G:0.12, T:0.48
Consensus pattern (31 bp):
GGTCCAAAATATTGTTTTTCAACTTTTAAGG
Found at i:27256602 original size:28 final size:31
Alignment explanation
Indices: 27256544--27256607 Score: 73
Period size: 28 Copynumber: 2.2 Consensus size: 31
27256534 CTTAAGGTTA
*
27256544 AAAGAGGTCCAAAATATTGTTTTTCAATTTT
1 AAAGGGGTCCAAAATATTGTTTTTCAATTTT
*
27256575 TAAGGGGTCC-AAAT-TT-TTTTT-AACTTTT
1 AAAGGGGTCCAAAATATTGTTTTTCAA-TTTT
27256603 AAAGG
1 AAAGG
27256608 TCAAAAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
27 2 0.07
28 13 0.45
29 2 0.07
30 4 0.14
31 8 0.28
ACGTcount: A:0.33, C:0.09, G:0.16, T:0.42
Consensus pattern (31 bp):
AAAGGGGTCCAAAATATTGTTTTTCAATTTT
Found at i:27256690 original size:30 final size:29
Alignment explanation
Indices: 27256638--27256725 Score: 83
Period size: 30 Copynumber: 3.0 Consensus size: 29
27256628 TTTTAGGGGC
*
27256638 CCCAA-AATTTTTCTTT-AGCTTTTAAAGA
1 CCCAAGAATTTTT-TTTCAACTTTTAAAGA
*
27256666 CCCCA-AATTTTTTTTACCAACTTTTAAGAGA
1 CCCAAGAATTTTTTTT--CAACTTTTAA-AGA
* *
27256697 TCTAAGAATTTTTTTTCAACTTTTAAAGA
1 CCCAAGAATTTTTTTTCAACTTTTAAAGA
27256726 ATCTAAAACT
Statistics
Matches: 50, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
27 3 0.06
28 11 0.22
29 3 0.06
30 18 0.36
31 5 0.10
32 10 0.20
ACGTcount: A:0.33, C:0.17, G:0.07, T:0.43
Consensus pattern (29 bp):
CCCAAGAATTTTTTTTCAACTTTTAAAGA
Found at i:27256730 original size:30 final size:31
Alignment explanation
Indices: 27256671--27256731 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 31
27256661 AAAGACCCCA
27256671 AATTTTTTTTACCAACTTTTAAGAGATCTAAG
1 AATTTTTTTTA-CAACTTTTAAGAGATCTAAG
27256703 AATTTTTTTT-CAACTTTTAA-AGAATCTAA
1 AATTTTTTTTACAACTTTTAAGAG-ATCTAA
27256732 AACTCCATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
29 2 0.07
30 16 0.57
32 10 0.36
ACGTcount: A:0.36, C:0.11, G:0.07, T:0.46
Consensus pattern (31 bp):
AATTTTTTTTACAACTTTTAAGAGATCTAAG
Found at i:27257438 original size:14 final size:14
Alignment explanation
Indices: 27257419--27257465 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
27257409 GTTTATAAAT
27257419 TTTTAAAATTTATA
1 TTTTAAAATTTATA
** *
27257433 TTTTAATGTGTA-A
1 TTTTAAAATTTATA
*
27257446 TTTTAAAATTTATG
1 TTTTAAAATTTATA
27257460 TTTTAA
1 TTTTAA
27257466 TGTGTAATGA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.57
Consensus pattern (14 bp):
TTTTAAAATTTATA
Found at i:27257451 original size:27 final size:27
Alignment explanation
Indices: 27257419--27257473 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
27257409 GTTTATAAAT
27257419 TTTTAAAATTTATATTTTAATGTGTAA
1 TTTTAAAATTTATATTTTAATGTGTAA
*
27257446 TTTTAAAATTTATGTTTTAATGTGTAA
1 TTTTAAAATTTATATTTTAATGTGTAA
27257473 T
1 T
27257474 GATTGAATGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.56
Consensus pattern (27 bp):
TTTTAAAATTTATATTTTAATGTGTAA
Found at i:27258931 original size:14 final size:13
Alignment explanation
Indices: 27258909--27258946 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
27258899 CTTAACTTAT
27258909 AATTCAATAATTTA
1 AATTCAATAA-TTA
*
27258923 AATTTAATAATTA
1 AATTCAATAATTA
27258936 AATTC-ATAATT
1 AATTCAATAATT
27258947 TTAGTACGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 6 0.27
13 7 0.32
14 9 0.41
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (13 bp):
AATTCAATAATTA
Found at i:27261162 original size:17 final size:17
Alignment explanation
Indices: 27261140--27261172 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
27261130 TCAATCAAAT
27261140 ATTTTTTTTCATTTTTC
1 ATTTTTTTTCATTTTTC
*
27261157 ATTTTTTTTTATTTTT
1 ATTTTTTTTCATTTTT
27261173 TTGATTAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.82
Consensus pattern (17 bp):
ATTTTTTTTCATTTTTC
Found at i:27263348 original size:43 final size:43
Alignment explanation
Indices: 27263299--27263456 Score: 158
Period size: 43 Copynumber: 3.7 Consensus size: 43
27263289 TATTGAAAGG
* *
27263299 AAGACTTATGTGTCGGATAGAGCATGAGATTATTTATAAATGA
1 AAGACTTATGTCTCGGATAGAGCATAAGATTATTTATAAATGA
* * * ** * *
27263342 AAGACTTATGTCTAGGTTAAAGCATAAGATTGCTTATAAAAGG
1 AAGACTTATGTCTCGGATAGAGCATAAGATTATTTATAAATGA
** *
27263385 AAGACTTATGTCTCGGCA-AGAGCATAAGGGTATTTGTAAATGA
1 AAGACTTATGTCTCGG-ATAGAGCATAAGATTATTTATAAATGA
*
27263428 AAGAACTTATGACTC-GATTAGAGCATAAG
1 AAG-ACTTATGTCTCGGA-TAGAGCATAAG
27263457 GTTAATACAG
Statistics
Matches: 91, Mismatches: 20, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
42 1 0.01
43 70 0.77
44 20 0.22
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.29
Consensus pattern (43 bp):
AAGACTTATGTCTCGGATAGAGCATAAGATTATTTATAAATGA
Found at i:27286581 original size:25 final size:26
Alignment explanation
Indices: 27286536--27286584 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
27286526 TCTTGCTATA
*
27286536 TGGATTTTAATTTTGGGACTTTGGTT
1 TGGATTTTAATTTTGGAACTTTGGTT
*
27286562 TGGATTTTGA-TTTGGAACTTTGG
1 TGGATTTTAATTTTGGAACTTTGG
27286585 ATATTGTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.16, C:0.04, G:0.29, T:0.51
Consensus pattern (26 bp):
TGGATTTTAATTTTGGAACTTTGGTT
Found at i:27307577 original size:108 final size:108
Alignment explanation
Indices: 27307421--27307639 Score: 368
Period size: 108 Copynumber: 2.0 Consensus size: 108
27307411 TTACCTACTC
* *
27307421 CAAACTATCCACTGGACATGTTTGGAAATAAAGGAGTTGAAGATGAAATTGAGTTGGAAGGGACC
1 CAAACTATCCACTGGACATGTCTGGAAATAAAGGAGTTGAAGATGAAATCGAGTTGGAAGGGACC
*
27307486 AACGTGGTGCAAGAAGACGCTTACATTAAAGATAAGTATGAGG
66 AACGTGGTGCAAGAAGACGCTAACATTAAAGATAAGTATGAGG
*
27307529 CAAACTATCCACTGGACATGTCTGGAAATGAAA-GAGTTGAAGATGAAATCGAGTTGGGAGGGAC
1 CAAACTATCCACTGGACATGTCTGGAAAT-AAAGGAGTTGAAGATGAAATCGAGTTGGAAGGGAC
* *
27307593 CAACGTGGTGCAAGAAGACGCTAACATTGAAGATGAGTATGAGG
65 CAACGTGGTGCAAGAAGACGCTAACATTAAAGATAAGTATGAGG
27307637 CAA
1 CAA
27307640 TGTTCCAGCC
Statistics
Matches: 104, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
108 101 0.97
109 3 0.03
ACGTcount: A:0.37, C:0.13, G:0.29, T:0.21
Consensus pattern (108 bp):
CAAACTATCCACTGGACATGTCTGGAAATAAAGGAGTTGAAGATGAAATCGAGTTGGAAGGGACC
AACGTGGTGCAAGAAGACGCTAACATTAAAGATAAGTATGAGG
Found at i:27309029 original size:269 final size:269
Alignment explanation
Indices: 27308550--27309087 Score: 1067
Period size: 269 Copynumber: 2.0 Consensus size: 269
27308540 CAAGCCCGAA
27308550 CCCGACTCGGCATGACCCAACCTGTTTTAAGTTTATAATACTTTGTATTATATTATTTTTATATA
1 CCCGACTCGGCATGACCCAACCTGTTTTAAGTTTATAATACTTTGTATTATATTATTTTTATATA
27308615 TTATATAATTTATAACACATTAAAAAATAAATATATATTAAATATATAGTACTACTTTAATATAA
66 TTATATAATTTATAACACATTAAAAAATAAATATATATTAAATATATAGTACTACTTTAATATAA
*
27308680 ATATTAAAATAATGTTAAAATGATTATAAAAAATTTCAATAAATAAAAATTGCATAAAAATATTA
131 ATATTAAAATAATATTAAAATGATTATAAAAAATTTCAATAAATAAAAATTGCATAAAAATATTA
27308745 AATATTAAAATAAAATAACTATTTTTAAAAAAATTAAAAAATAATATGAACGAACTTAAAATAGA
196 AATATTAAAATAAAATAACTATTTTTAAAAAAATTAAAAAATAATATGAACGAACTTAAAATAGA
27308810 CAAAATTTT
261 CAAAATTTT
27308819 CCCGACTCGGCATGACCCAACCTGTTTTAAGTTTATAATACTTTGTATTATATTATTTTTATATA
1 CCCGACTCGGCATGACCCAACCTGTTTTAAGTTTATAATACTTTGTATTATATTATTTTTATATA
27308884 TTATATAATTTATAACACATTAAAAAATAAATATATATTAAATATATAGTACTACTTTAATATAA
66 TTATATAATTTATAACACATTAAAAAATAAATATATATTAAATATATAGTACTACTTTAATATAA
27308949 ATATTAAAATAATATTAAAATGATTATAAAAAATTTCAATAAATAAAAATTGCATAAAAATATTA
131 ATATTAAAATAATATTAAAATGATTATAAAAAATTTCAATAAATAAAAATTGCATAAAAATATTA
27309014 AATATTAAAATAAAATAACTATTTTTAAAAAAATTAAAAAATAATATGAACGAACTTAAAATAGA
196 AATATTAAAATAAAATAACTATTTTTAAAAAAATTAAAAAATAATATGAACGAACTTAAAATAGA
27309079 CAAAATTTT
261 CAAAATTTT
27309088 ATGCCAAATT
Statistics
Matches: 268, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
269 268 1.00
ACGTcount: A:0.50, C:0.08, G:0.05, T:0.37
Consensus pattern (269 bp):
CCCGACTCGGCATGACCCAACCTGTTTTAAGTTTATAATACTTTGTATTATATTATTTTTATATA
TTATATAATTTATAACACATTAAAAAATAAATATATATTAAATATATAGTACTACTTTAATATAA
ATATTAAAATAATATTAAAATGATTATAAAAAATTTCAATAAATAAAAATTGCATAAAAATATTA
AATATTAAAATAAAATAACTATTTTTAAAAAAATTAAAAAATAATATGAACGAACTTAAAATAGA
CAAAATTTT
Found at i:27315608 original size:12 final size:12
Alignment explanation
Indices: 27315591--27315615 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
27315581 TGTTATTATG
27315591 ATGAATGCTATT
1 ATGAATGCTATT
27315603 ATGAATGCTATT
1 ATGAATGCTATT
27315615 A
1 A
27315616 ATTATTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (12 bp):
ATGAATGCTATT
Found at i:27317890 original size:112 final size:112
Alignment explanation
Indices: 27317744--27317980 Score: 420
Period size: 112 Copynumber: 2.1 Consensus size: 112
27317734 CCCACACTTT
* * *
27317744 TACCGATACAACAAGTTCTAGAGAGCTAGGAAAGATTTCCCTGCAAGTTCTATCGATACAGGTGA
1 TACCGATACAACAAGTTCTAAAGAGCTAGGAAAGATTTCCCTACAAGTTCTACCGATACAGGTGA
27317809 TTCAACTATCGATACTACTACGAACTATCGATACCTTGAAAAAATTA
66 TTCAACTATCGATACTACTACGAACTATCGATACCTTGAAAAAATTA
*
27317856 TACCGATACTACAAGTTCTAAAGAGCTAGGAAAGATTTCCCTACAAGTTCTACCGATACAGGTGA
1 TACCGATACAACAAGTTCTAAAGAGCTAGGAAAGATTTCCCTACAAGTTCTACCGATACAGGTGA
* *
27317921 TTCAACTATCGATACTATTAGGAACTATCGATACCTTGAAAAAATTA
66 TTCAACTATCGATACTACTACGAACTATCGATACCTTGAAAAAATTA
27317968 TACCGATACAACA
1 TACCGATACAACA
27317981 CAAGTCAGTA
Statistics
Matches: 118, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
112 118 1.00
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.27
Consensus pattern (112 bp):
TACCGATACAACAAGTTCTAAAGAGCTAGGAAAGATTTCCCTACAAGTTCTACCGATACAGGTGA
TTCAACTATCGATACTACTACGAACTATCGATACCTTGAAAAAATTA
Found at i:27321127 original size:82 final size:82
Alignment explanation
Indices: 27320990--27321151 Score: 272
Period size: 82 Copynumber: 2.0 Consensus size: 82
27320980 CTTCCTTCTC
*
27320990 TTCTTCCTTTCCTTCTTCTTTTTTTTCATACTTCTGTTGTTCACCTCCCTGATTGGCTTCCTCGT
1 TTCTTCCTTTCCTTCTTCTTTTTTTTCATACTTCTCTTGTTCACCTCCCTGATTGGCTTCCTCGT
27321055 CC-CTATGTTGCTCAAGT
66 CCGC-ATGTTGCTCAAGT
* *
27321072 TTCTTCCTTTCCTTCTTCTTTTTTTTCATACTTCTCTTGTTCACCTCCCTGATTGGTTTTCTCGT
1 TTCTTCCTTTCCTTCTTCTTTTTTTTCATACTTCTCTTGTTCACCTCCCTGATTGGCTTCCTCGT
*
27321137 CCGCGTGTTGCTCAA
66 CCGCATGTTGCTCAA
27321152 ATTTAGGTGG
Statistics
Matches: 75, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
82 74 0.99
83 1 0.01
ACGTcount: A:0.08, C:0.30, G:0.11, T:0.51
Consensus pattern (82 bp):
TTCTTCCTTTCCTTCTTCTTTTTTTTCATACTTCTCTTGTTCACCTCCCTGATTGGCTTCCTCGT
CCGCATGTTGCTCAAGT
Found at i:27341858 original size:24 final size:24
Alignment explanation
Indices: 27341817--27341864 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
27341807 AGTTGGTTCA
* ** *
27341817 AAGGATAAGAAACGGAAGAGGCAC
1 AAGGACAAGAAAAAGAAGAAGCAC
27341841 AAGGACAAGAAAAAGAAGAAGCAC
1 AAGGACAAGAAAAAGAAGAAGCAC
27341865 CATGACGAGG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.56, C:0.12, G:0.29, T:0.02
Consensus pattern (24 bp):
AAGGACAAGAAAAAGAAGAAGCAC
Found at i:27342617 original size:13 final size:13
Alignment explanation
Indices: 27342601--27342644 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
27342591 TGAAAAACAA
27342601 AAAAAAAAAAAAG
1 AAAAAAAAAAAAG
* *
27342614 AAAAAGAAGAAAG
1 AAAAAAAAAAAAG
*
27342627 -AAAAAGAAAAAG
1 AAAAAAAAAAAAG
27342639 AAAAAA
1 AAAAAA
27342645 TTACTGATAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
12 9 0.36
13 16 0.64
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAG
Found at i:27346197 original size:25 final size:24
Alignment explanation
Indices: 27346168--27346244 Score: 82
Period size: 26 Copynumber: 3.0 Consensus size: 24
27346158 AACACAGATT
27346168 TTAGCTTTTACGAGCCCAGACAGAG
1 TTAGCTTTT-CGAGCCCAGACAGAG
* * * *
27346193 TTAGCTCTTTCAAACCCAGATAGATT
1 TTAGCT-TTTCGAGCCCAGACAGA-G
27346219 TTAGCTTATTCGAGCCCAGACAGAG
1 TTAGCTT-TTCGAGCCCAGACAGAG
27346244 T
1 T
27346245 AACGCTCTTA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
25 19 0.46
26 22 0.54
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (24 bp):
TTAGCTTTTCGAGCCCAGACAGAG
Found at i:27347592 original size:98 final size:98
Alignment explanation
Indices: 27347420--27347613 Score: 361
Period size: 98 Copynumber: 2.0 Consensus size: 98
27347410 TGAAAAATGA
*
27347420 ACTGTTACACGCTTACTAAATGACTACACCCAAGGTTTTTCATGAGCACATTGCTCATATGGGTG
1 ACTGTTACACGCTTACTAAAGGACTACACCCAAGGTTTTTCATGAGCACATTGCTCATATGGGTG
*
27347485 TAATGTCATTAAAGGATATTTGGTTTTAGTGGG
66 TAATATCATTAAAGGATATTTGGTTTTAGTGGG
*
27347518 ACTGTTACACGCTTACTAAAGGACTACACCCAAGGTTTTTCATGAGCACATTGCTTATATGGGTG
1 ACTGTTACACGCTTACTAAAGGACTACACCCAAGGTTTTTCATGAGCACATTGCTCATATGGGTG
27347583 TAATATCATTAAAGGATATTTGGTTTTAGTG
66 TAATATCATTAAAGGATATTTGGTTTTAGTG
27347614 AGAGTTTCTA
Statistics
Matches: 93, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
98 93 1.00
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (98 bp):
ACTGTTACACGCTTACTAAAGGACTACACCCAAGGTTTTTCATGAGCACATTGCTCATATGGGTG
TAATATCATTAAAGGATATTTGGTTTTAGTGGG
Found at i:27349866 original size:15 final size:15
Alignment explanation
Indices: 27349843--27349885 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
27349833 ATTTTTAAAT
27349843 ATATATTTATATTATA
1 ATATATTTATATT-TA
*
27349859 TTAT-TTTAATATTTA
1 ATATATTT-ATATTTA
27349874 ATATATTTATAT
1 ATATATTTATAT
27349886 GTTTTTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
15 12 0.52
16 11 0.48
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
ATATATTTATATTTA
Found at i:27349882 original size:16 final size:17
Alignment explanation
Indices: 27349843--27349882 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
27349833 ATTTTTAAAT
27349843 ATATATTT-ATATTATA
1 ATATATTTAATATTATA
*
27349859 TTAT-TTTAATATT-TA
1 ATATATTTAATATTATA
27349874 ATATATTTA
1 ATATATTTA
27349883 TATGTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
ATATATTTAATATTATA
Found at i:27350118 original size:24 final size:24
Alignment explanation
Indices: 27350082--27350130 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
27350072 GTCTAAAAGC
27350082 TTAAATTTCTAATTGGCTCAATTT
1 TTAAATTTCTAATTGGCTCAATTT
*
27350106 TTAAATTTTTAATTGGCTCAATTT
1 TTAAATTTCTAATTGGCTCAATTT
27350130 T
1 T
27350131 ACCTCTCGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.10, G:0.08, T:0.53
Consensus pattern (24 bp):
TTAAATTTCTAATTGGCTCAATTT
Found at i:27360755 original size:24 final size:24
Alignment explanation
Indices: 27360693--27360831 Score: 118
Period size: 24 Copynumber: 5.8 Consensus size: 24
27360683 TATATATATG
* * *
27360693 AGTTGGCGAGCGT-AACATATGAA
1 AGTTGGCGAGCGTAAACGTGTGCA
* * * *
27360716 AGCTGACGAGCATAAATGTGTGCA
1 AGTTGGCGAGCGTAAACGTGTGCA
27360740 AGTTGGCGAGCGTAAACGTGTGCA
1 AGTTGGCGAGCGTAAACGTGTGCA
* *
27360764 AGTTGGCGAGCGTAAACGTATAGGAA
1 AGTTGGCGAGCGTAAACGTGT--GCA
* * * *
27360790 AGCTGACTAGTGTAAACGTGTGCA
1 AGTTGGCGAGCGTAAACGTGTGCA
* *
27360814 AGATGGCAAGCGTAAACG
1 AGTTGGCGAGCGTAAACG
27360832 CATACAAAAG
Statistics
Matches: 90, Mismatches: 23, Indels: 5
0.76 0.19 0.04
Matches are distributed among these distances:
23 10 0.11
24 62 0.69
26 18 0.20
ACGTcount: A:0.32, C:0.15, G:0.32, T:0.20
Consensus pattern (24 bp):
AGTTGGCGAGCGTAAACGTGTGCA
Found at i:27360811 original size:74 final size:71
Alignment explanation
Indices: 27360693--27360831 Score: 188
Period size: 74 Copynumber: 1.9 Consensus size: 71
27360683 TATATATATG
* * * *
27360693 AGTTGGCGAGCGTAACATATGAAAGCTGACGAGCATAAATGTGTGCAAGTTGGCGAGCGTAAACG
1 AGTTGGCGAGCGTAACATAGGAAAGCTGACGAGCATAAACGTGTGCAAGATGGCAAGCGTAAACG
27360758 TGTGCA
66 TGTGCA
* **
27360764 AGTTGGCGAGCGTAAACGTATAGGAAAGCTGACTAGTGTAAACGTGTGCAAGATGGCAAGCGTAA
1 AGTTGGCGAGCGT-AAC--ATAGGAAAGCTGACGAGCATAAACGTGTGCAAGATGGCAAGCGTAA
27360829 ACG
63 ACG
27360832 CATACAAAAG
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
71 13 0.22
72 3 0.05
74 42 0.72
ACGTcount: A:0.32, C:0.15, G:0.32, T:0.20
Consensus pattern (71 bp):
AGTTGGCGAGCGTAACATAGGAAAGCTGACGAGCATAAACGTGTGCAAGATGGCAAGCGTAAACG
TGTGCA
Found at i:27360866 original size:24 final size:24
Alignment explanation
Indices: 27360715--27360979 Score: 197
Period size: 24 Copynumber: 10.7 Consensus size: 24
27360705 TAACATATGA
* *
27360715 AAGCTGACGAGCATAAATGTGTGC
1 AAGCTGACGAGCGTAAACGTGTGC
* *
27360739 AAGTTGGCGAGCGTAAACGTGTGC
1 AAGCTGACGAGCGTAAACGTGTGC
* * * *
27360763 AAGTTGGCGAGCGTAAACGTATAGGA
1 AAGCTGACGAGCGTAAACGTGT--GC
* *
27360789 AAGCTGACTAGTGTAAACGTGTGC
1 AAGCTGACGAGCGTAAACGTGTGC
* * * ** *
27360813 AAGATGGCAAGCGTAAACGCATAC
1 AAGCTGACGAGCGTAAACGTGTGC
* *
27360837 AAAAGCTGACGAGCATAAATGTGTGC
1 --AAGCTGACGAGCGTAAACGTGTGC
* * * *
27360863 AAGCCGACGAGCGTAAACACATATGA
1 AAGCTGACGAGCGT-AA-ACGTGTGC
**
27360889 AAGCTGATAAGCGTAAACGTGTGC
1 AAGCTGACGAGCGTAAACGTGTGC
* * *
27360913 AAGCTGACGAGCGTAAATGCATATGG
1 AAGCTGACGAGCGTAAA--CGTGTGC
*
27360939 AAGCTGACGAGCGTAAACATGTGC
1 AAGCTGACGAGCGTAAACGTGTGC
*
27360963 AAGCTGACGAGTGTAAA
1 AAGCTGACGAGCGTAAA
27360980 TGTATGAAGG
Statistics
Matches: 186, Mismatches: 47, Indels: 16
0.75 0.19 0.06
Matches are distributed among these distances:
24 112 0.60
25 4 0.02
26 70 0.38
ACGTcount: A:0.35, C:0.17, G:0.29, T:0.18
Consensus pattern (24 bp):
AAGCTGACGAGCGTAAACGTGTGC
Found at i:27360981 original size:50 final size:50
Alignment explanation
Indices: 27360746--27360979 Score: 279
Period size: 50 Copynumber: 4.7 Consensus size: 50
27360736 TGCAAGTTGG
* * * *
27360746 CGAGCGTAAACGTGTGCAAGTTGGCGAGCGTAAACGTATAGGAAAGCTGA
1 CGAGCGTAAACGTGTGCAAGCTGACGAGCGTAAACGCATATGAAAGCTGA
* * * * * **
27360796 CTAGTGTAAACGTGTGCAAGATGGCAAGCGTAAACGCATACAAAAGCTGA
1 CGAGCGTAAACGTGTGCAAGCTGACGAGCGTAAACGCATATGAAAGCTGA
* * * *
27360846 CGAGCATAAATGTGTGCAAGCCGACGAGCGTAAACACATATGAAAGCTGA
1 CGAGCGTAAACGTGTGCAAGCTGACGAGCGTAAACGCATATGAAAGCTGA
** * *
27360896 TAAGCGTAAACGTGTGCAAGCTGACGAGCGTAAATGCATATGGAAGCTGA
1 CGAGCGTAAACGTGTGCAAGCTGACGAGCGTAAACGCATATGAAAGCTGA
* *
27360946 CGAGCGTAAACATGTGCAAGCTGACGAGTGTAAA
1 CGAGCGTAAACGTGTGCAAGCTGACGAGCGTAAA
27360980 TGTATGAAGG
Statistics
Matches: 154, Mismatches: 30, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 154 1.00
ACGTcount: A:0.35, C:0.18, G:0.29, T:0.18
Consensus pattern (50 bp):
CGAGCGTAAACGTGTGCAAGCTGACGAGCGTAAACGCATATGAAAGCTGA
Found at i:27364191 original size:57 final size:58
Alignment explanation
Indices: 27364060--27364194 Score: 148
Period size: 57 Copynumber: 2.3 Consensus size: 58
27364050 GTTTGGTAGC
* *
27364060 TAATGGTCGGCACCACTTTTTTTAGTACTCGAGGAATTTTTTTCACTAGTTTTGCCCTAT
1 TAATGGCCGGCACCACTTTTTTCAGTACTC--GGAATTTTTTTCACTAGTTTTGCCCTAT
* *** *
27364120 TAATGGCCGACACCACTTTTTTCAGTACTC-GAATTTTTTTTGTTGGTGTTTGCCCTA-
1 TAATGGCCGGCACCACTTTTTTCAGTACTCGGAATTTTTTTCACTAGT-TTTGCCCTAT
* *
27364177 TGATGGCTGGCACCACTT
1 TAATGGCCGGCACCACTT
27364195 ATCAAATTTA
Statistics
Matches: 64, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
57 28 0.44
58 9 0.14
60 27 0.42
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.41
Consensus pattern (58 bp):
TAATGGCCGGCACCACTTTTTTCAGTACTCGGAATTTTTTTCACTAGTTTTGCCCTAT
Found at i:27367271 original size:40 final size:40
Alignment explanation
Indices: 27367191--27367274 Score: 105
Period size: 40 Copynumber: 2.1 Consensus size: 40
27367181 CTTGTGTGTT
* * ***
27367191 AGGCCTTGATGGATAGCCGACCAATGGCAGGTCGGGCGTC
1 AGGCCGTGATGGATAGCCGACCAATGGCAGGCCACACGTC
* *
27367231 AGGCCGTGATGGATAGTCGCCCAATGGCAGGCCACACGTC
1 AGGCCGTGATGGATAGCCGACCAATGGCAGGCCACACGTC
27367271 AGGC
1 AGGC
27367275 TTGTTACATC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.21, C:0.27, G:0.36, T:0.15
Consensus pattern (40 bp):
AGGCCGTGATGGATAGCCGACCAATGGCAGGCCACACGTC
Found at i:27367483 original size:26 final size:26
Alignment explanation
Indices: 27367450--27367517 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 26
27367440 AACAATAAAA
27367450 AATA-TAATTTAAAAGTAAAAGTTTG
1 AATATTAATTTAAAAGTAAAAGTTTG
27367475 AATATTAA-TT-----TAAAAGTTTG
1 AATATTAATTTAAAAGTAAAAGTTTG
*
27367495 AATTTTAATTTAAAAGTAAAAGT
1 AATATTAATTTAAAAGTAAAAGT
27367518 AAAAAAAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 13
0.71 0.02 0.27
Matches are distributed among these distances:
20 17 0.49
21 2 0.06
25 6 0.17
26 10 0.29
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (26 bp):
AATATTAATTTAAAAGTAAAAGTTTG
Found at i:27367488 original size:20 final size:20
Alignment explanation
Indices: 27367465--27367511 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
27367455 AATTTAAAAG
27367465 TAAAAGTTTGAATATTAATT
1 TAAAAGTTTGAATATTAATT
*
27367485 TAAAAGTTTGAATTTTAATT
1 TAAAAGTTTGAATATTAATT
27367505 TAAAAGT
1 TAAAAGT
27367512 AAAAGTAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.45, C:0.00, G:0.11, T:0.45
Consensus pattern (20 bp):
TAAAAGTTTGAATATTAATT
Found at i:27367594 original size:37 final size:37
Alignment explanation
Indices: 27367556--27367634 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 37
27367546 TAAAACTTTG
*
27367556 AATTTAATAAAAATTAAATAATTATAATCGAAAATTGA
1 AATTTAA-AAAAATTAAATAATAATAATCGAAAATTGA
** * * *
27367594 AATTTAAAAAGTTTAAATAATAATAATTGAAATTTTA
1 AATTTAAAAAAATTAAATAATAATAATCGAAAATTGA
27367631 AATT
1 AATT
27367635 ACAAAATATA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
37 28 0.80
38 7 0.20
ACGTcount: A:0.56, C:0.01, G:0.05, T:0.38
Consensus pattern (37 bp):
AATTTAAAAAAATTAAATAATAATAATCGAAAATTGA
Found at i:27367669 original size:14 final size:14
Alignment explanation
Indices: 27367652--27367686 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
27367642 ATAAATTTAA
* *
27367652 TAAATTAAAGAAGT
1 TAAATTAAACAAAT
27367666 TAAATTAAACAAAT
1 TAAATTAAACAAAT
27367680 TAAATTA
1 TAAATTA
27367687 TAATTATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.60, C:0.03, G:0.06, T:0.31
Consensus pattern (14 bp):
TAAATTAAACAAAT
Found at i:27368094 original size:20 final size:20
Alignment explanation
Indices: 27368071--27368111 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
27368061 ACCGCCGACG
*
27368071 ACCTCCGATAACCGTCGATA
1 ACCTCCAATAACCGTCGATA
*
27368091 ACCTCCAATATCCGTCGATA
1 ACCTCCAATAACCGTCGATA
27368111 A
1 A
27368112 TCGTTGAGCA
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:0.32, C:0.34, G:0.12, T:0.22
Consensus pattern (20 bp):
ACCTCCAATAACCGTCGATA
Found at i:27379677 original size:21 final size:21
Alignment explanation
Indices: 27379653--27379696 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
27379643 TTACCCGTAG
*
27379653 AAGT-GAGTGTTCTACCGATAC
1 AAGTAGAG-GTTCTACCGACAC
*
27379674 AAGTATAGGTTCTACCGACAC
1 AAGTAGAGGTTCTACCGACAC
27379695 AA
1 AA
27379697 CCCATACTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.25
Consensus pattern (21 bp):
AAGTAGAGGTTCTACCGACAC
Found at i:27380428 original size:26 final size:26
Alignment explanation
Indices: 27380385--27380529 Score: 75
Period size: 26 Copynumber: 5.7 Consensus size: 26
27380375 AGCTTGCACA
* **
27380385 CGTTTACGCTCATTAGCTTTCATATG
1 CGTTTACACTCACCAGCTTTCATATG
* *
27380411 CGTTTACACTCACCAGCTTGCACA--
1 CGTTTACACTCACCAGCTTTCATATG
** *
27380435 CGTTTA-AGCTCGTCAACTTTCATATG
1 CGTTTACA-CTCACCAGCTTTCATATG
* * * * *
27380461 CATTTATACTCGCCAGCTTGCAGA--
1 CGTTTACACTCACCAGCTTTCATATG
** **
27380485 CGTTTATGCTCTTCAGCTTTCATATG
1 CGTTTACACTCACCAGCTTTCATATG
* *
27380511 TGCTTACACTCACCAGCTT
1 CGTTTACACTCACCAGCTT
27380530 GCACACATTT
Statistics
Matches: 86, Mismatches: 27, Indels: 12
0.69 0.22 0.10
Matches are distributed among these distances:
23 1 0.01
24 35 0.41
26 49 0.57
27 1 0.01
ACGTcount: A:0.21, C:0.28, G:0.14, T:0.36
Consensus pattern (26 bp):
CGTTTACACTCACCAGCTTTCATATG
Found at i:27380432 original size:50 final size:49
Alignment explanation
Indices: 27380374--27380535 Score: 207
Period size: 50 Copynumber: 3.2 Consensus size: 49
27380364 TTAAGCTTGT
*
27380374 CAGCTTGCACACGTTTACGCTCATTAGCTTTCATATGCGTTTACACTCAC
1 CAGCTTGCACACGTTTAAGCTC-TTAGCTTTCATATGCGTTTACACTCAC
* * * * *
27380424 CAGCTTGCACACGTTTAAGCTCGTCAACTTTCATATGCATTTATACTCGC
1 CAGCTTGCACACGTTTAAGCTC-TTAGCTTTCATATGCGTTTACACTCAC
* * * *
27380474 CAGCTTGCAGACGTTTATGCTCTTCAGCTTTCATATGTGCTTACACTCAC
1 CAGCTTGCACACGTTTAAGCTCTT-AGCTTTCATATGCGTTTACACTCAC
27380524 CAGCTTGCACAC
1 CAGCTTGCACAC
27380536 ATTTTGTAAC
Statistics
Matches: 94, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
49 1 0.01
50 93 0.99
ACGTcount: A:0.22, C:0.30, G:0.15, T:0.33
Consensus pattern (49 bp):
CAGCTTGCACACGTTTAAGCTCTTAGCTTTCATATGCGTTTACACTCAC
Found at i:27395255 original size:14 final size:15
Alignment explanation
Indices: 27395236--27395264 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
27395226 GCATGAAGTA
27395236 AAACTTA-GATGCTT
1 AAACTTATGATGCTT
27395250 AAACTTATGATGCTT
1 AAACTTATGATGCTT
27395265 GTAAATACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (15 bp):
AAACTTATGATGCTT
Found at i:27396062 original size:44 final size:43
Alignment explanation
Indices: 27395881--27396058 Score: 239
Period size: 43 Copynumber: 4.1 Consensus size: 43
27395871 GTGTTACAGT
* *
27395881 ATAACATTATTTATAAAAGGAAGACTTATGTCTCGATTAGAGC
1 ATAAGATTATTTATAAAAGGAAGACTTATGTCTCGGTTAGAGC
*
27395924 ATAAGATTGTTTATAAAAGGAAGACTTATGTCTCGGTTAGAGC
1 ATAAGATTATTTATAAAAGGAAGACTTATGTCTCGGTTAGAGC
* **
27395967 ATAAGATTGTTTATAAAAGGAAGACTTATGTCTCGGCAAGAGC
1 ATAAGATTATTTATAAAAGGAAGACTTATGTCTCGGTTAGAGC
* * * ** *
27396010 ATAAGGTTATTTGTAAATGGAAGAACTTATGAATCGGTTGGAGC
1 ATAAGATTATTTATAAAAGGAAG-ACTTATGTCTCGGTTAGAGC
27396054 ATAAG
1 ATAAG
27396059 GTTAATACAG
Statistics
Matches: 120, Mismatches: 14, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
43 100 0.83
44 20 0.17
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.31
Consensus pattern (43 bp):
ATAAGATTATTTATAAAAGGAAGACTTATGTCTCGGTTAGAGC
Found at i:27405846 original size:14 final size:13
Alignment explanation
Indices: 27405816--27405851 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
27405806 CACTTGAAGA
27405816 AAGAAAAAAAAAG
1 AAGAAAAAAAAAG
27405829 -AGAAAAGAAAAAG
1 AAGAAAA-AAAAAG
27405842 AAGAAAAAAA
1 AAGAAAAAAA
27405852 TTATATTTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 9 0.43
14 6 0.29
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (13 bp):
AAGAAAAAAAAAG
Found at i:27410659 original size:87 final size:85
Alignment explanation
Indices: 27410499--27410753 Score: 312
Period size: 87 Copynumber: 2.9 Consensus size: 85
27410489 GGTGATTACA
*
27410499 AAAAGGAAGACTTATGTCTCGATTAAAGCATAAGATTGTTTATAAAAGGAAGACTTATGTCTCGG
1 AAAAGGAAGACTTATGTCTCG-TTAGAGCATAAGATTGTTTATAAAAGGAAGACTTATGTCTCGG
* *
27410564 TAAGAGCATAAGGTTATTTGT
65 TTAGAGCATAAGGTTATTTAT
* *
27410585 AAATGGAAGAACTTATGTCTCAGTTAGAGCGTAAGATTGTTTATAAAAGGAAGACTTATGTCTCG
1 AAAAGGAAG-ACTTATGTCTC-GTTAGAGCATAAGATTGTTTATAAAAGGAAGACTTATGTCTCG
* * *
27410650 GTTACAGCATAAGATTGTTTAT
64 GTTAGAGCATAAGGTTATTTAT
** * * * * * *
27410672 AAAAGGAAGACTTATGTCTCGGCAAGAGCATAAGGTTATTTGTAAATGTAAGAACTTATGACTCG
1 AAAAGGAAGACTTATGTCTC-GTTAGAGCATAAGATTGTTTATAAAAGGAAG-ACTTATGTCTCG
*
27410737 GTTGGAGCATAAGGTTA
64 GTTAGAGCATAAGGTTA
27410754 ATATAATTTG
Statistics
Matches: 143, Mismatches: 23, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
86 42 0.29
87 100 0.70
88 1 0.01
ACGTcount: A:0.36, C:0.10, G:0.23, T:0.31
Consensus pattern (85 bp):
AAAAGGAAGACTTATGTCTCGTTAGAGCATAAGATTGTTTATAAAAGGAAGACTTATGTCTCGGT
TAGAGCATAAGGTTATTTAT
Found at i:27410693 original size:43 final size:43
Alignment explanation
Indices: 27410499--27410749 Score: 313
Period size: 43 Copynumber: 5.8 Consensus size: 43
27410489 GGTGATTACA
* *
27410499 AAAAGGAAGACTTATGTCTCGATTAAAGCATAAGATTGTTTAT
1 AAAAGGAAGACTTATGTCTCGGTTAGAGCATAAGATTGTTTAT
* * * *
27410542 AAAAGGAAGACTTATGTCTCGGTAAGAGCATAAGGTTATTTGT
1 AAAAGGAAGACTTATGTCTCGGTTAGAGCATAAGATTGTTTAT
* * *
27410585 AAATGGAAGAACTTATGTCTCAGTTAGAGCGTAAGATTGTTTAT
1 AAAAGGAAG-ACTTATGTCTCGGTTAGAGCATAAGATTGTTTAT
*
27410629 AAAAGGAAGACTTATGTCTCGGTTACAGCATAAGATTGTTTAT
1 AAAAGGAAGACTTATGTCTCGGTTAGAGCATAAGATTGTTTAT
** * * *
27410672 AAAAGGAAGACTTATGTCTCGGCAAGAGCATAAGGTTATTTGT
1 AAAAGGAAGACTTATGTCTCGGTTAGAGCATAAGATTGTTTAT
* * * *
27410715 AAATGTAAGAACTTATGACTCGGTTGGAGCATAAG
1 AAAAGGAAG-ACTTATGTCTCGGTTAGAGCATAAG
27410750 GTTAATATAA
Statistics
Matches: 177, Mismatches: 29, Indels: 3
0.85 0.14 0.01
Matches are distributed among these distances:
43 120 0.68
44 57 0.32
ACGTcount: A:0.36, C:0.10, G:0.23, T:0.31
Consensus pattern (43 bp):
AAAAGGAAGACTTATGTCTCGGTTAGAGCATAAGATTGTTTAT
Found at i:27410768 original size:130 final size:130
Alignment explanation
Indices: 27410499--27410759 Score: 416
Period size: 130 Copynumber: 2.0 Consensus size: 130
27410489 GGTGATTACA
27410499 AAAAGGAAGACTTATGTCTCGATTAAAGCATAAGATTGTTTATAAAAGGAAGACTTATGTCTCGG
1 AAAAGGAAGACTTATGTCTCGATTAAAGCATAAGATTGTTTATAAAAGGAAGACTTATGTCTCGG
* * * **
27410564 TAAGAGCATAAGGTTATTTGTAAATGGAAGAACTTATGTCTCAGTTAGAGCGTAAGATTGTTTAT
66 CAAGAGCATAAGGTTATTTGTAAATGGAAGAACTTATGACTCAGTTAGAGCATAAGATTGAATAT
* *
27410629 AAAAGGAAGACTTATGTCTCGGTTACAGCATAAGATTGTTTATAAAAGGAAGACTTATGTCTCGG
1 AAAAGGAAGACTTATGTCTCGATTAAAGCATAAGATTGTTTATAAAAGGAAGACTTATGTCTCGG
* * * *
27410694 CAAGAGCATAAGGTTATTTGTAAATGTAAGAACTTATGACTCGGTTGGAGCATAAGGTT-AATAT
66 CAAGAGCATAAGGTTATTTGTAAATGGAAGAACTTATGACTCAGTTAGAGCATAAGATTGAATAT
27410758 AA
1 AA
27410760 TTTGGAAGAA
Statistics
Matches: 120, Mismatches: 11, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
129 5 0.04
130 115 0.96
ACGTcount: A:0.36, C:0.10, G:0.23, T:0.31
Consensus pattern (130 bp):
AAAAGGAAGACTTATGTCTCGATTAAAGCATAAGATTGTTTATAAAAGGAAGACTTATGTCTCGG
CAAGAGCATAAGGTTATTTGTAAATGGAAGAACTTATGACTCAGTTAGAGCATAAGATTGAATAT
Found at i:27412569 original size:50 final size:50
Alignment explanation
Indices: 27412503--27412604 Score: 177
Period size: 50 Copynumber: 2.0 Consensus size: 50
27412493 AATTATCATC
* *
27412503 TAACTTAAGTGCCTAACCAATATGTCACATTTGTCACCACAATTCAAACA
1 TAACTTAAGTGCCTAACCAATATGCCACATTTGGCACCACAATTCAAACA
*
27412553 TAACTTAAGTGTCTAACCAATATGCCACATTTGGCACCACAATTCAAACA
1 TAACTTAAGTGCCTAACCAATATGCCACATTTGGCACCACAATTCAAACA
27412603 TA
1 TA
27412605 CTCATCTACC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.38, C:0.25, G:0.09, T:0.27
Consensus pattern (50 bp):
TAACTTAAGTGCCTAACCAATATGCCACATTTGGCACCACAATTCAAACA
Found at i:27413146 original size:20 final size:20
Alignment explanation
Indices: 27413104--27413146 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
27413094 AACTAAAATT
***
27413104 AAATATAAAAATTATAGGTA
1 AAATATAAAAATTATAAAAA
27413124 AAATATAAAAATTATAAAAA
1 AAATATAAAAATTATAAAAA
27413144 AAA
1 AAA
27413147 AATTATAGTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.26
Consensus pattern (20 bp):
AAATATAAAAATTATAAAAA
Found at i:27413234 original size:29 final size:27
Alignment explanation
Indices: 27413172--27413257 Score: 84
Period size: 29 Copynumber: 3.0 Consensus size: 27
27413162 GACACATGAA
*
27413172 AAAATGATAAAAAAATTATTATAATCAATA-
1 AAAATGATAAAAAAA--A-TATAA-AAATAT
27413202 AAAATGATAAAAAAAATATAGGAAAATAT
1 AAAATGATAAAAAAAATATA--AAAATAT
* *
27413231 AAAATTATAAAAAATATATAAAAATAT
1 AAAATGATAAAAAAAATATAAAAATAT
27413258 TTAAGATTTA
Statistics
Matches: 50, Mismatches: 3, Indels: 9
0.81 0.05 0.15
Matches are distributed among these distances:
27 11 0.22
28 5 0.10
29 19 0.38
30 15 0.30
ACGTcount: A:0.67, C:0.01, G:0.05, T:0.27
Consensus pattern (27 bp):
AAAATGATAAAAAAAATATAAAAATAT
Found at i:27413971 original size:21 final size:19
Alignment explanation
Indices: 27413928--27414022 Score: 84
Period size: 19 Copynumber: 4.7 Consensus size: 19
27413918 AAAATCTATC
* *
27413928 TTTTTTATATTTTATAGTAA
1 TTTTCTATATTTT-TAATAA
27413948 TTTCTCTATATTTTTAATACA
1 TTT-TCTATATTTTTAATA-A
*
27413969 TTTT-TATAATTTTAATAA
1 TTTTCTATATTTTTAATAA
* *
27413987 TTTTTATCTATATTTTAAATAT
1 --TTT-TCTATATTTTTAATAA
27414009 TTTTCTATATTTTT
1 TTTTCTATATTTTT
27414023 TTATAAATTT
Statistics
Matches: 62, Mismatches: 7, Indels: 13
0.76 0.09 0.16
Matches are distributed among these distances:
18 1 0.02
19 22 0.35
20 14 0.23
21 14 0.23
22 11 0.18
ACGTcount: A:0.29, C:0.05, G:0.01, T:0.64
Consensus pattern (19 bp):
TTTTCTATATTTTTAATAA
Found at i:27413991 original size:10 final size:10
Alignment explanation
Indices: 27413957--27414094 Score: 58
Period size: 10 Copynumber: 13.8 Consensus size: 10
27413947 ATTTCTCTAT
27413957 ATTTTTAATA
1 ATTTTTAATA
27413967 CATTTTT-ATA
1 -ATTTTTAATA
27413977 A-TTTTAATA
1 ATTTTTAATA
*
27413986 ATTTTTATCTA
1 ATTTTTA-ATA
*
27413997 TATTTTAAAT-
1 -ATTTTTAATA
*
27414007 ATTTTTCTATA
1 ATTTTT-AATA
* *
27414018 TTTTTTTATA
1 ATTTTTAATA
*
27414028 AATTTTAA-A
1 ATTTTTAATA
*
27414037 ATATTTCT-CTA
1 AT-TTT-TAATA
*
27414048 TATTTTTTATA
1 -ATTTTTAATA
27414059 ATATTTTAAT-
1 AT-TTTTAATA
27414069 ATTTTTAAT-
1 ATTTTTAATA
*
27414078 -TTTTTTATA
1 ATTTTTAATA
*
27414087 TTTTTTAA
1 ATTTTTAA
27414095 AATGTTTTTT
Statistics
Matches: 98, Mismatches: 15, Indels: 29
0.69 0.11 0.20
Matches are distributed among these distances:
8 11 0.11
9 19 0.19
10 33 0.34
11 27 0.28
12 8 0.08
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.64
Consensus pattern (10 bp):
ATTTTTAATA
Found at i:27414017 original size:19 final size:21
Alignment explanation
Indices: 27413927--27414021 Score: 69
Period size: 20 Copynumber: 4.7 Consensus size: 21
27413917 TAAAATCTAT
*
27413927 CTTTTT-TATATTTTATAGTAA
1 CTTTTTCTATATTTTA-AATAA
* *
27413948 -TTTCTCTATATTTTTAAT-A
1 CTTTTTCTATATTTTAAATAA
*
27413967 CATTTT-TATAATTTT-AATAA
1 CTTTTTCTAT-ATTTTAAATAA
*
27413987 TTTTTATCTATATTTTAAAT-A
1 CTTTT-TCTATATTTTAAATAA
27414008 -TTTTTCTATATTTT
1 CTTTTTCTATATTTT
27414022 TTTATAAATT
Statistics
Matches: 60, Mismatches: 7, Indels: 16
0.72 0.08 0.19
Matches are distributed among these distances:
19 17 0.28
20 22 0.37
21 15 0.25
22 6 0.10
ACGTcount: A:0.29, C:0.06, G:0.01, T:0.63
Consensus pattern (21 bp):
CTTTTTCTATATTTTAAATAA
Found at i:27414040 original size:22 final size:22
Alignment explanation
Indices: 27414015--27414065 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
27414005 ATATTTTTCT
*
27414015 ATATTTTTTTATAAATTTTAAA
1 ATATTTTTCTATAAATTTTAAA
* ** *
27414037 ATATTTCTCTATATTTTTTATA
1 ATATTTTTCTATAAATTTTAAA
27414059 ATATTTT
1 ATATTTT
27414066 AATATTTTTA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (22 bp):
ATATTTTTCTATAAATTTTAAA
Found at i:27414082 original size:17 final size:17
Alignment explanation
Indices: 27414052--27414091 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
27414042 TCTCTATATT
27414052 TTTTATAATATTTTAATA
1 TTTT-TAATATTTTAATA
* *
27414070 TTTTTAATTTTTTTATA
1 TTTTTAATATTTTAATA
27414087 TTTTT
1 TTTTT
27414092 TAAAATGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTTTAATATTTTAATA
Found at i:27414092 original size:9 final size:9
Alignment explanation
Indices: 27413928--27414093 Score: 64
Period size: 9 Copynumber: 16.8 Consensus size: 9
27413918 AAAATCTATC
27413928 TTTTTTATA
1 TTTTTTATA
*
27413937 TTTTATAGTAA
1 TTTTTTA-T-A
*
27413948 TTTCTCTATA
1 TTT-TTTATA
*
27413958 TTTTTAATA
1 TTTTTTATA
*
27413967 CATTTTTATA
1 -TTTTTTATA
* *
27413977 ATTTTAATAA
1 TTTTTTAT-A
27413987 TTTTTATCTATA
1 -TTTT-T-TATA
**
27413999 TTTTAAATA
1 TTTTTTATA
27414008 TTTTTCTATA
1 TTTTT-TATA
27414018 TTTTTTTATAAA
1 -TTTTTTAT--A
**
27414030 TTTTAAAATA
1 TTTT-TTATA
*
27414040 TTTCTCTATA
1 TTT-TTTATA
27414050 TTTTTTATAA
1 TTTTTTAT-A
*
27414060 TATTTTAATA
1 T-TTTTTATA
*
27414070 TTTTTAAT-
1 TTTTTTATA
27414078 TTTTTTATA
1 TTTTTTATA
27414087 TTTTTTA
1 TTTTTTA
27414094 AAATGTTTTT
Statistics
Matches: 120, Mismatches: 20, Indels: 34
0.69 0.11 0.20
Matches are distributed among these distances:
8 7 0.06
9 42 0.35
10 33 0.28
11 28 0.23
12 8 0.07
13 2 0.02
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.64
Consensus pattern (9 bp):
TTTTTTATA
Found at i:27414104 original size:92 final size:92
Alignment explanation
Indices: 27413947--27414115 Score: 211
Period size: 92 Copynumber: 1.8 Consensus size: 92
27413937 TTTTATAGTA
*
27413947 ATTTCTCTATATTTTTAATACATTTTTATAATTTTAATAATTTTTATCTATATTTTAAATATTTT
1 ATTTCTCTATATTTTTAATACATTTTTATAATTTT-ATAATTTTTATATATATTTTAAATATTTT
27414012 TCTAT-ATTTTTTTATAAATTTTAAAAT
65 TCTATCATTTTTTTATAAATTTTAAAAT
* * * *
27414039 ATTTCTCTATATTTTTTATA-ATATTTTA-ATATTTT-TAATTTTTTTATATTTTTTAAAATGTT
1 ATTTCTCTATATTTTTAATACAT-TTTTATA-ATTTTATAATTTTTATATATATTTT-AAAT-AT
*
27414101 TTTTTTATCATTTTT
62 TTTTCTATCATTTTT
27414116 ATGTCATGTG
Statistics
Matches: 66, Mismatches: 6, Indels: 9
0.81 0.07 0.11
Matches are distributed among these distances:
90 16 0.24
91 7 0.11
92 37 0.56
93 6 0.09
ACGTcount: A:0.30, C:0.05, G:0.01, T:0.64
Consensus pattern (92 bp):
ATTTCTCTATATTTTTAATACATTTTTATAATTTTATAATTTTTATATATATTTTAAATATTTTT
CTATCATTTTTTTATAAATTTTAAAAT
Found at i:27415456 original size:31 final size:32
Alignment explanation
Indices: 27415390--27415454 Score: 82
Period size: 30 Copynumber: 2.1 Consensus size: 32
27415380 TAGTGATAGT
*
27415390 AAATTTGTATTTTAATTTCTTCAAAAATAATA
1 AAATTTGTAATTTAATTTCTTCAAAAATAATA
*
27415422 AAATTT-TAATTTAATCTT-TT-AAAAATTATA
1 AAATTTGTAATTTAAT-TTCTTCAAAAATAATA
27415452 AAA
1 AAA
27415455 ATATAGACTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 12 0.40
31 10 0.33
32 8 0.27
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.46
Consensus pattern (32 bp):
AAATTTGTAATTTAATTTCTTCAAAAATAATA
Found at i:27416420 original size:12 final size:12
Alignment explanation
Indices: 27416403--27416515 Score: 80
Period size: 12 Copynumber: 9.8 Consensus size: 12
27416393 ATAACATCCA
27416403 AACAACAAAAAT
1 AACAACAAAAAT
* *
27416415 AACAACCAAAAC
1 AACAACAAAAAT
*
27416427 AGCAACAAAAAT
1 AACAACAAAAAT
*
27416439 AACAGC----A-
1 AACAACAAAAAT
*
27416446 AACAACATTAAA-
1 AACAACA-AAAAT
27416458 AACAACAAAAAT
1 AACAACAAAAAT
*
27416470 AGCAACAAAAAT
1 AACAACAAAAAT
27416482 AA-AAGCAAAAAT
1 AACAA-CAAAAAT
*
27416494 AAC-ACGAAAAT
1 AACAACAAAAAT
27416505 AACAACCAAAA
1 AACAA-CAAAA
27416516 CAGTAAAAAA
Statistics
Matches: 78, Mismatches: 13, Indels: 19
0.71 0.12 0.17
Matches are distributed among these distances:
7 5 0.06
8 1 0.01
11 14 0.18
12 54 0.69
13 4 0.05
ACGTcount: A:0.69, C:0.19, G:0.04, T:0.07
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:27416442 original size:15 final size:15
Alignment explanation
Indices: 27416427--27416489 Score: 60
Period size: 15 Copynumber: 4.3 Consensus size: 15
27416417 CAACCAAAAC
*
27416427 AGCAACAAAAATAAC
1 AGCAACAAAAATAAA
* *
27416442 AGCAAACAACATTAAA
1 AGC-AACAAAAATAAA
*
27416458 AACAACAAAAAT---
1 AGCAACAAAAATAAA
27416470 AGCAACAAAAATAAA
1 AGCAACAAAAATAAA
27416485 AGCAA
1 AGCAA
27416490 AAATAACACG
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
12 11 0.30
15 15 0.41
16 11 0.30
ACGTcount: A:0.68, C:0.17, G:0.06, T:0.08
Consensus pattern (15 bp):
AGCAACAAAAATAAA
Found at i:27416448 original size:43 final size:44
Alignment explanation
Indices: 27416389--27416526 Score: 147
Period size: 43 Copynumber: 3.1 Consensus size: 44
27416379 AAAACGCATA
*
27416389 AAAAATAACATCCAAACAACA-AAAATAACAACCAAAACAGCAAC
1 AAAAATAACA-GCAAACAACACAAAATAACAACCAAAACAGCAAC
** * *
27416433 AAAAATAACAGCAAACAACATTAAA-AACAACAAAAATAGCAAC
1 AAAAATAACAGCAAACAACACAAAATAACAACCAAAACAGCAAC
* * *
27416476 AAAAATAAAAGCAAAAATAACACGAAAATAACAACCAAAACAGTAA-
1 AAAAATAACAGC--AAACAACAC-AAAATAACAACCAAAACAGCAAC
27416522 AAAAA
1 AAAAA
27416527 GCACCAAAAC
Statistics
Matches: 78, Mismatches: 11, Indels: 8
0.80 0.11 0.08
Matches are distributed among these distances:
43 36 0.46
44 13 0.17
45 7 0.09
46 8 0.10
47 14 0.18
ACGTcount: A:0.69, C:0.19, G:0.04, T:0.08
Consensus pattern (44 bp):
AAAAATAACAGCAAACAACACAAAATAACAACCAAAACAGCAAC
Found at i:27416523 original size:20 final size:19
Alignment explanation
Indices: 27416509--27416597 Score: 79
Period size: 20 Copynumber: 4.4 Consensus size: 19
27416499 GAAAATAACA
27416509 ACCAAAACAGTAAAAAAAGC
1 ACCAAAACAGTAAAAAAA-C
*
27416529 ACCAAAACAATAAAAAAAC
1 ACCAAAACAGTAAAAAAAC
* * *
27416548 ACAAAAACAGCAAAAAACAGTA
1 ACCAAAACAGTAAAAAA-A--C
*
27416570 ACCAAATCAGTAAAAAAAAGC
1 ACCAAAACAGT-AAAAAAA-C
27416591 ACCAAAA
1 ACCAAAA
27416598 TAATAATATA
Statistics
Matches: 54, Mismatches: 11, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
19 15 0.28
20 18 0.33
21 6 0.11
22 9 0.17
23 6 0.11
ACGTcount: A:0.67, C:0.20, G:0.07, T:0.06
Consensus pattern (19 bp):
ACCAAAACAGTAAAAAAAC
Found at i:27416545 original size:19 final size:20
Alignment explanation
Indices: 27416509--27416603 Score: 68
Period size: 19 Copynumber: 4.7 Consensus size: 20
27416499 GAAAATAACA
* *
27416509 ACCAAAACAGTAAAAAAAGC
1 ACCAAAACAATAAAAAAAAC
27416529 ACCAAAACAAT-AAAAAAAC
1 ACCAAAACAATAAAAAAAAC
* **
27416548 ACAAAAACAGCAAAAAACAGTA-
1 ACCAAAACAATAAAAAA-A--AC
* *
27416570 ACCAAATCAGTAAAAAAAAGC
1 ACCAAAACAATAAAAAAAA-C
*
27416591 ACCAAAATAATAA
1 ACCAAAACAATAA
27416604 TATAATTTTT
Statistics
Matches: 58, Mismatches: 11, Indels: 11
0.73 0.14 0.14
Matches are distributed among these distances:
19 16 0.28
20 15 0.26
21 12 0.21
22 14 0.24
23 1 0.02
ACGTcount: A:0.67, C:0.19, G:0.06, T:0.07
Consensus pattern (20 bp):
ACCAAAACAATAAAAAAAAC
Found at i:27416982 original size:29 final size:31
Alignment explanation
Indices: 27416932--27416991 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 31
27416922 CATCTCAATC
27416932 ATATATGAAATATGTGATTAAT-TTTATTTTA
1 ATATATGAAATATGTGATTAATATTT-TTTTA
* *
27416963 ATATTTGATATAT-TGA-TAATATTTTTTTA
1 ATATATGAAATATGTGATTAATATTTTTTTA
27416992 TTTTATAAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
29 9 0.35
30 6 0.23
31 11 0.42
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.55
Consensus pattern (31 bp):
ATATATGAAATATGTGATTAATATTTTTTTA
Found at i:27417242 original size:19 final size:17
Alignment explanation
Indices: 27417207--27417264 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 17
27417197 AGTCAATTGA
*
27417207 AAATAATTTTTTAAAAAT
1 AAATTATTTTTT-AAAAT
27417225 AAATTATTCTTTTGAAAAACAT
1 AAATTATT-TTTT---AAA-AT
27417247 AAATTATTTTTTAAAAT
1 AAATTATTTTTTAAAAT
27417264 A
1 A
27417265 TTAAAATATT
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
17 3 0.09
18 10 0.29
19 4 0.11
21 8 0.23
22 10 0.29
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (17 bp):
AAATTATTTTTTAAAAT
Found at i:27417251 original size:22 final size:19
Alignment explanation
Indices: 27417207--27417262 Score: 69
Period size: 22 Copynumber: 2.8 Consensus size: 19
27417197 AGTCAATTGA
*
27417207 AAATAATTTTTT-AAAAAT
1 AAATTATTTTTTAAAAAAT
27417225 AAATTATTCTTTTGAAAAACAT
1 AAATTATT-TTTT-AAAAA-AT
27417247 AAATTATTTTTTAAAA
1 AAATTATTTTTTAAAA
27417263 TATTAAAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
18 7 0.21
19 4 0.12
20 4 0.12
21 8 0.24
22 10 0.30
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.45
Consensus pattern (19 bp):
AAATTATTTTTTAAAAAAT
Found at i:27417274 original size:20 final size:18
Alignment explanation
Indices: 27417206--27417274 Score: 57
Period size: 19 Copynumber: 3.4 Consensus size: 18
27417196 TAGTCAATTG
27417206 AAAATAATTTTTTAAAAAT
1 AAAAT-ATTTTTTAAAAAT
*
27417225 AAATTATTCTTTTGAAAAACAT
1 AAAATATT-TTTT--AAAA-AT
*
27417247 AAATTATTTTTTAAAATATT
1 AAAATATTTTTTAAAA-A-T
27417267 AAAATATT
1 AAAATATT
27417275 AAATAAAATA
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
18 3 0.07
19 13 0.31
20 8 0.19
21 8 0.19
22 10 0.24
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (18 bp):
AAAATATTTTTTAAAAAT
Found at i:27420845 original size:17 final size:16
Alignment explanation
Indices: 27420825--27420889 Score: 53
Period size: 17 Copynumber: 3.9 Consensus size: 16
27420815 ACTATATGTG
27420825 TAATAAATATATAAATT
1 TAATAAATATA-AAATT
* *
27420842 TAATAATTATAAAATC
1 TAATAAATATAAAATT
*
27420858 TAGA-AAAT-TTAAATT
1 TA-ATAAATATAAAATT
27420873 TAATGATAATATAAAAT
1 TAAT-A-AATATAAAAT
27420890 ATATAAAGAC
Statistics
Matches: 37, Mismatches: 6, Indels: 9
0.71 0.12 0.17
Matches are distributed among these distances:
14 1 0.03
15 7 0.19
16 10 0.27
17 14 0.38
18 5 0.14
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.38
Consensus pattern (16 bp):
TAATAAATATAAAATT
Found at i:27421619 original size:7 final size:7
Alignment explanation
Indices: 27421604--27421661 Score: 98
Period size: 7 Copynumber: 8.1 Consensus size: 7
27421594 TAATATAAAG
27421604 TATTAATA
1 TATT-ATA
27421612 TATTATA
1 TATTATA
27421619 TATTATA
1 TATTATA
27421626 TATTATA
1 TATTATA
27421633 TATTATA
1 TATTATA
27421640 TATTATA
1 TATTATA
27421647 TATTATA
1 TATTATA
*
27421654 TATGATA
1 TATTATA
27421661 T
1 T
27421662 GATATGATAT
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
7 45 0.92
8 4 0.08
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (7 bp):
TATTATA
Found at i:27424647 original size:40 final size:40
Alignment explanation
Indices: 27424592--27424671 Score: 126
Period size: 40 Copynumber: 2.0 Consensus size: 40
27424582 AGAAAATGTC
*
27424592 GCAAAAGGTAAAGCAAT-ACTAGCATTTTTCCATAAACGCT
1 GCAAAAGGTAAAGCAATAAC-AACATTTTTCCATAAACGCT
*
27424632 GCAAAAGGTAAAGCAATAACAACGTTTTTCCATAAACGCT
1 GCAAAAGGTAAAGCAATAACAACATTTTTCCATAAACGCT
27424672 CTAATGCTCT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
40 35 0.95
41 2 0.05
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (40 bp):
GCAAAAGGTAAAGCAATAACAACATTTTTCCATAAACGCT
Found at i:27424724 original size:41 final size:40
Alignment explanation
Indices: 27424672--27424798 Score: 137
Period size: 41 Copynumber: 3.1 Consensus size: 40
27424662 CATAAACGCT
* *
27424672 CTAATGCTCTGACTTTTAGCGGCGCTTTCTTATAAATACCG
1 CTAATGCTCTGAC-TTTAGCGGCGCTTTATCATAAATACCG
* * *
27424713 CTAATGTTCTGACCTTTAGCGGCGCTATATCATAAATGCCG
1 CTAATGCTCTGA-CTTTAGCGGCGCTTTATCATAAATACCG
* * * * *
27424754 CTAAAGGTCAGAGCATTAGCGGCGCTTTATCATAAACACCG
1 CTAATGCTCTGA-CTTTAGCGGCGCTTTATCATAAATACCG
27424795 CTAA
1 CTAA
27424799 AGGTCAGAGT
Statistics
Matches: 72, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
41 71 0.99
42 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (40 bp):
CTAATGCTCTGACTTTAGCGGCGCTTTATCATAAATACCG
Found at i:27424799 original size:41 final size:41
Alignment explanation
Indices: 27424687--27424857 Score: 166
Period size: 41 Copynumber: 4.2 Consensus size: 41
27424677 GCTCTGACTT
* * * * * * * *
27424687 TTAGCGGCGCTTTCTTATAAATACCGCTAATGTTCTGACCT
1 TTAGCGGCGCTTTATCATAAACACCGCTAAAGGTCAGAGCA
* **
27424728 TTAGCGGCGCTATATCATAAATGCCGCTAAAGGTCAGAGCA
1 TTAGCGGCGCTTTATCATAAACACCGCTAAAGGTCAGAGCA
*
27424769 TTAGCGGCGCTTTATCATAAACACCGCTAAAGGTCAGAGTA
1 TTAGCGGCGCTTTATCATAAACACCGCTAAAGGTCAGAGCA
* * * * *
27424810 TTAGC-G-ACTTTATTAGCAAACGCCGCTAAATGTCAGAGCA
1 TTAGCGGCGCTTTATCA-TAAACACCGCTAAAGGTCAGAGCA
27424850 TTAGCGGC
1 TTAGCGGC
27424858 TTAGCGACGT
Statistics
Matches: 108, Mismatches: 19, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
39 7 0.06
40 26 0.24
41 75 0.69
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.27
Consensus pattern (41 bp):
TTAGCGGCGCTTTATCATAAACACCGCTAAAGGTCAGAGCA
Found at i:27426611 original size:24 final size:23
Alignment explanation
Indices: 27426584--27426647 Score: 65
Period size: 26 Copynumber: 2.6 Consensus size: 23
27426574 ATCTAAACGC
*
27426584 AAATATATATAAAAAAATTATATT
1 AAATTTATATAAAAAAATT-TATT
*
27426608 AAATTTGGATATATAAAAAATTTGTT
1 AAATTT--ATATA-AAAAAATTTATT
*
27426634 ATATTTATATAAAA
1 AAATTTATATAAAA
27426648 TTTGAAAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
23 3 0.09
24 10 0.29
26 13 0.38
27 8 0.24
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.41
Consensus pattern (23 bp):
AAATTTATATAAAAAAATTTATT
Found at i:27426792 original size:20 final size:20
Alignment explanation
Indices: 27426767--27426805 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
27426757 CAAAAGGTAT
27426767 AGAGCAATAGCGGCGTTTTC
1 AGAGCAATAGCGGCGTTTTC
*
27426787 AGAGCATTAGCGGCGTTTT
1 AGAGCAATAGCGGCGTTTT
27426806 TTCCATAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.28
Consensus pattern (20 bp):
AGAGCAATAGCGGCGTTTTC
Found at i:27426995 original size:19 final size:19
Alignment explanation
Indices: 27426973--27427009 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
27426963 ATTTCTCATT
*
27426973 CATTTCTAAATTCCTAATC
1 CATTTCTAAATCCCTAATC
*
27426992 CATTTCTAGATCCCTAAT
1 CATTTCTAAATCCCTAAT
27427010 TTCCACCAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.30, C:0.27, G:0.03, T:0.41
Consensus pattern (19 bp):
CATTTCTAAATCCCTAATC
Found at i:27433222 original size:15 final size:15
Alignment explanation
Indices: 27433202--27433234 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
27433192 ATTTTAAGTT
*
27433202 ATTGGTTGGGTTTGA
1 ATTGGTTGGATTTGA
27433217 ATTGGTTGGATTTGA
1 ATTGGTTGGATTTGA
27433232 ATT
1 ATT
27433235 TACAGGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.00, G:0.33, T:0.48
Consensus pattern (15 bp):
ATTGGTTGGATTTGA
Found at i:27434318 original size:21 final size:21
Alignment explanation
Indices: 27434294--27434368 Score: 89
Period size: 21 Copynumber: 3.6 Consensus size: 21
27434284 ATTATTAAAT
27434294 ATAATTTAATAAAAATAATAA
1 ATAATTTAATAAAAATAATAA
* * **
27434315 ATAATTTAAT-CATATTTTAA
1 ATAATTTAATAAAAATAATAA
*
27434335 TATAATTTAATAAAAATAATAT
1 -ATAATTTAATAAAAATAATAA
27434357 ATAATTTAATAA
1 ATAATTTAATAA
27434369 CATTCTTAAT
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
20 6 0.14
21 32 0.74
22 5 0.12
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (21 bp):
ATAATTTAATAAAAATAATAA
Found at i:27434335 original size:11 final size:10
Alignment explanation
Indices: 27434291--27434367 Score: 57
Period size: 10 Copynumber: 7.4 Consensus size: 10
27434281 ATTATTATTA
27434291 AATATAATTT
1 AATATAATTT
**
27434301 AATA-AAAAT
1 AATATAATTT
27434310 AATAAATAATTT
1 AAT--ATAATTT
*
27434322 AATCATATTTT
1 AAT-ATAATTT
27434333 AATATAATTT
1 AATATAATTT
* * *
27434343 AATAAAAATA
1 AATATAATTT
27434353 ATATATAATTT
1 A-ATATAATTT
27434364 AATA
1 AATA
27434368 ACATTCTTAA
Statistics
Matches: 50, Mismatches: 13, Indels: 8
0.70 0.18 0.11
Matches are distributed among these distances:
9 6 0.12
10 21 0.42
11 17 0.34
12 6 0.12
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (10 bp):
AATATAATTT
Found at i:27434338 original size:42 final size:43
Alignment explanation
Indices: 27434291--27434384 Score: 154
Period size: 42 Copynumber: 2.2 Consensus size: 43
27434281 ATTATTATTA
* *
27434291 AATATAATTTAATAAAAATAATAAATAATTTAATCATATT-TT
1 AATATAATTTAATAAAAATAATAAATAATTTAATAACATTCTT
*
27434333 AATATAATTTAATAAAAATAATATATAATTTAATAACATTCTT
1 AATATAATTTAATAAAAATAATAAATAATTTAATAACATTCTT
27434376 AATATAATT
1 AATATAATT
27434385 ATTTTATATT
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
42 37 0.77
43 11 0.23
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (43 bp):
AATATAATTTAATAAAAATAATAAATAATTTAATAACATTCTT
Found at i:27434401 original size:15 final size:15
Alignment explanation
Indices: 27434381--27434425 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
27434371 TTCTTAATAT
*
27434381 AATTATTTTATATTA
1 AATTATTTTAAATTA
* *
27434396 AATTATATTAAAATA
1 AATTATTTTAAATTA
*
27434411 ATTTATTTTAAATTA
1 AATTATTTTAAATTA
27434426 TATTTTGAAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
AATTATTTTAAATTA
Found at i:27434406 original size:29 final size:26
Alignment explanation
Indices: 27434374--27434452 Score: 72
Period size: 30 Copynumber: 2.9 Consensus size: 26
27434364 AATAACATTC
27434374 TTAATATAATTATTTTATATTAAATTAT
1 TTAA-ATAATTATTTTATATTAAATT-T
* *
27434402 ATTAAAATAATTTATTTTAAATTATATTT
1 -TT-AAATAA-TTATTTTATATTAAATTT
*
27434431 TGAAA-AA-TATTTTATATTAAAT
1 TTAAATAATTATTTTATATTAAAT
27434453 ATTAAATTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
24 13 0.30
26 2 0.05
27 3 0.07
28 1 0.02
29 7 0.16
30 17 0.40
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (26 bp):
TTAAATAATTATTTTATATTAAATTT
Found at i:27434416 original size:25 final size:27
Alignment explanation
Indices: 27434387--27434452 Score: 82
Period size: 29 Copynumber: 2.4 Consensus size: 27
27434377 ATATAATTAT
27434387 TTTATATTAAATTATA-TT-AAAATAA
1 TTTATATTAAATTATATTTAAAAATAA
* *
27434412 TTTATTTTAAATTATATTTTGAAAAATAT
1 TTTATATTAAATTATA-TTT-AAAAATAA
27434441 TTTATATTAAAT
1 TTTATATTAAAT
27434453 ATTAAATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
25 15 0.44
27 2 0.06
29 17 0.50
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (27 bp):
TTTATATTAAATTATATTTAAAAATAA
Found at i:27434431 original size:12 final size:12
Alignment explanation
Indices: 27434410--27434465 Score: 53
Period size: 12 Copynumber: 4.8 Consensus size: 12
27434400 ATATTAAAAT
27434410 AATT-TATTTTA
1 AATTATATTTTA
27434421 AATTATATTTTGA
1 AATTATATTTT-A
*
27434434 AA-AATATTTTA
1 AATTATATTTTA
* * *
27434445 TATTAAATATTA
1 AATTATATTTTA
27434457 AATTATATT
1 AATTATATT
27434466 AAAATATTTC
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
11 6 0.18
12 25 0.74
13 3 0.09
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (12 bp):
AATTATATTTTA
Found at i:27435351 original size:2 final size:2
Alignment explanation
Indices: 27435344--27435376 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
27435334 GATATAAAAT
27435344 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
27435377 ATATATATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:27435381 original size:2 final size:2
Alignment explanation
Indices: 27435376--27435410 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
27435366 TCTCTCTCTC
27435376 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
27435411 TGAAGAAGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:27435739 original size:39 final size:39
Alignment explanation
Indices: 27435681--27435773 Score: 102
Period size: 39 Copynumber: 2.4 Consensus size: 39
27435671 GTATTAAACT
* *
27435681 TATA-AATTTAATAAAAAATATAA-A-ATTATTCAATTAT
1 TATATAATATAATAAAAAATA-AATATATTATTCAATTAA
* * *
27435718 TAATATAATATAATAATAAATAAATATCTTCTTCAATTAA
1 T-ATATAATATAATAAAAAATAAATATATTATTCAATTAA
27435758 TATATAATATAATAAA
1 TATATAATATAATAAA
27435774 TTTTACATAC
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
37 1 0.02
38 5 0.11
39 29 0.63
40 11 0.24
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (39 bp):
TATATAATATAATAAAAAATAAATATATTATTCAATTAA
Found at i:27436711 original size:18 final size:18
Alignment explanation
Indices: 27436690--27436759 Score: 61
Period size: 18 Copynumber: 3.9 Consensus size: 18
27436680 GAAAATTCAA
27436690 AAAAAATAAAAAAATATT
1 AAAAAATAAAAAAATATT
* * *
27436708 AAAATAT-AATAAATTTT
1 AAAAAATAAAAAAATATT
* *
27436725 AAAATATATAAAAATATT
1 AAAAAATAAAAAAATATT
* * *
27436743 ACAAATTCAAAAAATAT
1 AAAAAATAAAAAAATAT
27436760 ATAGAAGTTT
Statistics
Matches: 40, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
17 15 0.38
18 25 0.62
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (18 bp):
AAAAAATAAAAAAATATT
Found at i:27436728 original size:27 final size:26
Alignment explanation
Indices: 27436698--27436760 Score: 72
Period size: 27 Copynumber: 2.4 Consensus size: 26
27436688 AAAAAAAATA
* * *
27436698 AAAAAATATTAAAATATAATAAATTTT
1 AAAAAATATAAAAATATAACAAA-TTC
* *
27436725 AAAATATATAAAAATATTACAAATTC
1 AAAAAATATAAAAATATAACAAATTC
27436751 AAAAAATATA
1 AAAAAATATA
27436761 TAGAAGTTTC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 11 0.37
27 19 0.63
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (26 bp):
AAAAAATATAAAAATATAACAAATTC
Found at i:27436775 original size:20 final size:19
Alignment explanation
Indices: 27436734--27436798 Score: 71
Period size: 19 Copynumber: 3.4 Consensus size: 19
27436724 TAAAATATAT
27436734 AAAAATAT-TACAAA-TTCA
1 AAAAATATATA-AAATTTCA
* *
27436752 AAAAATATATAGAAGTTTCC
1 AAAAATATATA-AAATTTCA
*
27436772 AAAAATACATAAAATTTCA
1 AAAAATATATAAAATTTCA
27436791 AAAAATAT
1 AAAAATAT
27436799 GTAATTTTTA
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
18 8 0.21
19 17 0.45
20 13 0.34
ACGTcount: A:0.60, C:0.09, G:0.03, T:0.28
Consensus pattern (19 bp):
AAAAATATATAAAATTTCA
Found at i:27438799 original size:45 final size:45
Alignment explanation
Indices: 27438722--27438813 Score: 150
Period size: 45 Copynumber: 2.0 Consensus size: 45
27438712 CATCTTCTTC
*
27438722 ATCTATTCTCCATTGTCATCCAAAAAGAGGGAAGAAAACCTAAGA
1 ATCTATTCTCCATTGTAATCCAAAAAGAGGGAAGAAAACCTAAGA
*
27438767 ATCTATTCTCCATTGTAAATTCAAAAAG-GGGAAGAAAACCTAAGA
1 ATCTATTCTCCATTGT-AATCCAAAAAGAGGGAAGAAAACCTAAGA
27438812 AT
1 AT
27438814 TTCTAAAACA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
45 35 0.80
46 9 0.20
ACGTcount: A:0.43, C:0.17, G:0.15, T:0.24
Consensus pattern (45 bp):
ATCTATTCTCCATTGTAATCCAAAAAGAGGGAAGAAAACCTAAGA
Found at i:27441433 original size:10 final size:10
Alignment explanation
Indices: 27441418--27441442 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
27441408 AAACACTCCA
27441418 AAATAAATAT
1 AAATAAATAT
27441428 AAATAAATAT
1 AAATAAATAT
27441438 AAATA
1 AAATA
27441443 CAATTTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
AAATAAATAT
Found at i:27447334 original size:24 final size:24
Alignment explanation
Indices: 27447278--27447336 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
27447268 TTAAACTTTG
* *
27447278 TCTGGGCTCGTAAGAGCTAATTAT
1 TCTGAGCTCGTAAGAGCTAATCAT
*
27447302 T-TTAGGCTCGTAAGAGCTAATCAT
1 TCTGA-GCTCGTAAGAGCTAATCAT
27447326 TCTGAGCTCGT
1 TCTGAGCTCGT
27447337 GTTGGCTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
23 1 0.03
24 26 0.90
25 2 0.07
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.34
Consensus pattern (24 bp):
TCTGAGCTCGTAAGAGCTAATCAT
Found at i:27449237 original size:18 final size:18
Alignment explanation
Indices: 27449194--27449240 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
27449184 CAATATAAAA
27449194 TAAATTT-A-AATAAAATT
1 TAAATTTAATAAT-AAATT
27449211 TAAATTTAATAATAAATT
1 TAAATTTAATAATAAATT
27449229 GTAAA-TTAATAA
1 -TAAATTTAATAA
27449241 AAACAAATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 7 0.26
18 13 0.48
19 7 0.26
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (18 bp):
TAAATTTAATAATAAATT
Found at i:27454679 original size:23 final size:23
Alignment explanation
Indices: 27454627--27454679 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 23
27454617 TTAGAAAGCG
* **
27454627 AAATT-AAACTGTAATTTTTATG
1 AAATTAAAAATGTAATTTTTAAA
* *
27454649 ATAGTAAAAATGTAATTTTTAAA
1 AAATTAAAAATGTAATTTTTAAA
27454672 AAATTAAA
1 AAATTAAA
27454680 TTAAAGTTTT
Statistics
Matches: 23, Mismatches: 7, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
22 3 0.13
23 20 0.87
ACGTcount: A:0.51, C:0.02, G:0.08, T:0.40
Consensus pattern (23 bp):
AAATTAAAAATGTAATTTTTAAA
Found at i:27458952 original size:2 final size:2
Alignment explanation
Indices: 27458945--27458977 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
27458935 AAATTAACTT
27458945 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
27458978 AGCTGGCAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Done.