Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008298.1 Hibiscus syriacus cultivar Beakdansim tig00110984_pilon, 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: 1334650
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 7
Found at i:183331 original size:2 final size:2
Alignment explanation
Indices: 183324--183349 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
183314 GGACAACAAG
183324 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
183350 GGATAAATGA
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):
AT
Found at i:193170 original size:108 final size:107
Alignment explanation
Indices: 192982--193196 Score: 308
Period size: 108 Copynumber: 2.0 Consensus size: 107
192972 GAATATGTTA
* * *
192982 AAATTTTAGTGTAGGGTAAATTATGTTGAGTGAGTTTCTCTTGTTCAACTTATGTTTAAAAAGTA
1 AAATTTTAGTGTAGGGTAAAATATGTTGAGTGAGTTTCTCTTGTTCAACTGATGTTTAAAAACTA
* * * *
193047 ATGATTTGACTATTAATATTATTATTGTATAATAATTCGGTTG
66 ATAATTTCACTATTAATATTATCATT-TATAACAATTCGGTTG
* *
193090 AAATTTTAGTGTAGGGTAAAATATGTTTGAGTGAGTTTCTCTTTTTCTACTGATGTTTAAAAACT
1 AAATTTTAGTGTAGGGTAAAATATG-TTGAGTGAGTTTCTCTTGTTCAACTGATGTTTAAAAACT
193155 -ATAATTTCA-TCATTAATATTATCATTTATAACAATTCGGTTG
65 AATAATTTCACT-ATTAATATTATCATTTATAACAATTCGGTTG
193197 TTGGACTGTT
Statistics
Matches: 96, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
107 16 0.17
108 45 0.47
109 35 0.36
ACGTcount: A:0.32, C:0.07, G:0.16, T:0.45
Consensus pattern (107 bp):
AAATTTTAGTGTAGGGTAAAATATGTTGAGTGAGTTTCTCTTGTTCAACTGATGTTTAAAAACTA
ATAATTTCACTATTAATATTATCATTTATAACAATTCGGTTG
Found at i:214424 original size:25 final size:26
Alignment explanation
Indices: 214385--214435 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
214375 AATGTTATAT
** *
214385 TTTTTAATATTTAA-TAATATTATTA
1 TTTTTAATAACTAATTAATATAATTA
214410 TTTTTAATAACTAATTAATATAATTA
1 TTTTTAATAACTAATTAATATAATTA
214436 ATAATATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 12 0.55
26 10 0.45
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (26 bp):
TTTTTAATAACTAATTAATATAATTA
Found at i:214470 original size:42 final size:41
Alignment explanation
Indices: 214396--214491 Score: 140
Period size: 42 Copynumber: 2.3 Consensus size: 41
214386 TTTTAATATT
214396 TAATAATATTATTATTTTTAATAACTAATTAATATAATTAA
1 TAATAATATTATTATTTTTAATAACTAATTAATATAATTAA
* *
214437 TAATATATAGTTATTA-TTTTAATAATTAATTAATATAATTTA
1 TAATA-ATA-TTATTATTTTTAATAACTAATTAATATAATTAA
*
214479 TAATAATTTTATT
1 TAATAATATTATT
214492 TTAATAAAAT
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
40 5 0.10
41 7 0.14
42 32 0.64
43 6 0.12
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (41 bp):
TAATAATATTATTATTTTTAATAACTAATTAATATAATTAA
Found at i:214486 original size:23 final size:23
Alignment explanation
Indices: 214409--214486 Score: 76
Period size: 23 Copynumber: 3.6 Consensus size: 23
214399 TAATATTATT
* *
214409 ATTTTTAATAACTAATTAATATA
1 ATTTATAATAATTAATTAATATA
* *
214432 ATTAATAAT-ATATAGTT-AT-T-
1 ATTTATAATAAT-TAATTAATATA
214452 ATTT-TAATAATTAATTAATATA
1 ATTTATAATAATTAATTAATATA
214474 ATTTATAATAATT
1 ATTTATAATAATT
214487 TTATTTTAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
19 8 0.19
20 7 0.16
21 2 0.05
22 7 0.16
23 19 0.44
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (23 bp):
ATTTATAATAATTAATTAATATA
Found at i:218921 original size:26 final size:27
Alignment explanation
Indices: 218879--218936 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 27
218869 TTTATAATAT
*
218879 TTTCCCGGAAATTATCGAATCAACAAA
1 TTTCCCGGAAATTATCGAAGCAACAAA
* *
218906 TTTCCC-GAGATTATCGAAGGAACAAA
1 TTTCCCGGAAATTATCGAAGCAACAAA
218932 TTTCC
1 TTTCC
218937 TCTGACTAGG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 22 0.79
27 6 0.21
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (27 bp):
TTTCCCGGAAATTATCGAAGCAACAAA
Found at i:219642 original size:2 final size:2
Alignment explanation
Indices: 219635--219677 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
219625 TAATTTTTAT
219635 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
219677 T
1 T
219678 TAAGAGAGAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:219856 original size:2 final size:2
Alignment explanation
Indices: 219849--219873 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
219839 AGGCCTATCA
219849 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
219874 AATTCAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:223107 original size:3 final size:3
Alignment explanation
Indices: 223086--223151 Score: 68
Period size: 3 Copynumber: 23.0 Consensus size: 3
223076 TATTATATAG
* * *
223086 ATA ATA A-A ATA ATG A-A ATA ATA ATTA A-A ACA TTA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA
223129 ATA ATA ATA ATA ATA A-A ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA
223152 TTGCAAATAA
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
2 7 0.13
3 43 0.81
4 3 0.06
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:223171 original size:12 final size:11
Alignment explanation
Indices: 223116--223173 Score: 53
Period size: 12 Copynumber: 4.9 Consensus size: 11
223106 TAATTAAAAC
223116 ATTAATAATAAT
1 ATTAA-AATAAT
*
223128 AATAATAATAAT
1 ATTAA-AATAAT
*
223140 AATAAAATAAT
1 ATTAAAATAAT
*
223151 ATTGCAAATAAT
1 ATT-AAAATAAT
223163 GATTAAAATAA
1 -ATTAAAATAA
223174 AGGAAATAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
11 8 0.20
12 29 0.73
13 3 0.08
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (11 bp):
ATTAAAATAAT
Found at i:224503 original size:3 final size:3
Alignment explanation
Indices: 224495--224562 Score: 57
Period size: 3 Copynumber: 22.3 Consensus size: 3
224485 ATATATATAT
* * * *
224495 ATA ATA ATAA ATA AT- ATA TTA TTA TATA ATA ATA TTT ATA ATA ATA
1 ATA ATA AT-A ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA
* *
224541 ATA ATA ATT TTA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA A
224563 ACGAAAAATT
Statistics
Matches: 52, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
2 2 0.04
3 45 0.87
4 5 0.10
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (3 bp):
ATA
Found at i:224520 original size:25 final size:23
Alignment explanation
Indices: 224483--224528 Score: 74
Period size: 25 Copynumber: 1.9 Consensus size: 23
224473 ATGTAATTTG
224483 TAATATATATATATAATAATAAA
1 TAATATATATATATAATAATAAA
224506 TAATATATTATTATATAATAATA
1 TAATATA-TA-TATATAATAATA
224529 TTTATAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 7 0.33
24 2 0.10
25 12 0.57
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
TAATATATATATATAATAATAAA
Found at i:224527 original size:18 final size:18
Alignment explanation
Indices: 224483--224562 Score: 80
Period size: 18 Copynumber: 4.6 Consensus size: 18
224473 ATGTAATTTG
*
224483 TAATAT-AT-ATATATAA
1 TAATATAATAATATATTA
224499 TAATA-AATAATATATTA
1 TAATATAATAATATATTA
*
224516 TTATATAATAATAT-TTA
1 TAATATAATAATATATTA
*
224533 TAATAATAATAATA-ATTT
1 TAAT-ATAATAATATATTA
224551 TAATAATAATAA
1 TAAT-ATAATAA
224563 ACGAAAAATT
Statistics
Matches: 55, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
16 7 0.13
17 17 0.31
18 31 0.56
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TAATATAATAATATATTA
Found at i:225137 original size:76 final size:76
Alignment explanation
Indices: 224703--225110 Score: 741
Period size: 76 Copynumber: 5.4 Consensus size: 76
224693 GAGGTCTTAA
* * * *
224703 AAACATCATGCATTGAAGGGCTTACAGATGACCCTAAGTCTTTG-AAACATC-AAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
224766 AGGCGTTTTGG
66 AGGCTTTTTGG
224777 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
224842 AGGCTTTTTGG
66 AGGCTTTTTGG
224853 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATC-AAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
224917 AGGCTTTTTTGG
66 AGGC-TTTTTGG
224929 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
224994 AGGCTTTTTGG
66 AGGCTTTTTGG
225005 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
225070 AGGCTTTTTGG
66 AGGCTTTTTGG
225081 AAACATCATGCACTGTAGGACTTACAGATG
1 AAACATCATGCACTGTAGGACTTACAGATG
225111 TAGGAAATAG
Statistics
Matches: 325, Mismatches: 5, Indels: 6
0.97 0.01 0.02
Matches are distributed among these distances:
74 40 0.12
75 23 0.07
76 246 0.76
77 16 0.05
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (76 bp):
AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:225415 original size:18 final size:18
Alignment explanation
Indices: 225389--225430 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
225379 ATGAAAATCG
* *
225389 TTTTCTCATTCTGTTTGT
1 TTTTTTCATTCTATTTGT
225407 TTTTTTCATTCTATTTGT
1 TTTTTTCATTCTATTTGT
225425 TTTTTT
1 TTTTTT
225431 TTGTTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.07, C:0.12, G:0.07, T:0.74
Consensus pattern (18 bp):
TTTTTTCATTCTATTTGT
Found at i:226027 original size:22 final size:22
Alignment explanation
Indices: 226002--226056 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
225992 AATAAAGCTT
226002 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
226024 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
226046 TCATCTTTGAA
1 TCATCTTTGAA
226057 GAGTGTAGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:228731 original size:115 final size:114
Alignment explanation
Indices: 228522--228745 Score: 331
Period size: 115 Copynumber: 2.0 Consensus size: 114
228512 CATGCAGCTC
* * * * *
228522 ATCTTTTAATTCTAATGATTGGTTATGTGGTTCCTACCGAACCAGATCAGATAACTCAAAGAACA
1 ATCTTTCAAATCTAATGATTGGTTATGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACA
*
228587 CTTCAATAAGATGCTATTGGGCCTCCTTATTTCTACCATGAGCAAATTT
66 CTTCAAGAAGATGCTATTGGGCCTCCTTATTTCTACCATGAGCAAATTT
* *
228636 ATCTTTCAAATCTAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAATTCAAAGAAC
1 ATCTTTCAAATCTAATGATTGG-TTATGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAAC
* * * *
228701 ACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCA
65 ACTTCAAGAAGATGCTATTGGGCCTCCTTATTTCTACCATGAGCA
228746 CATGGCACTT
Statistics
Matches: 97, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
114 20 0.21
115 77 0.79
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (114 bp):
ATCTTTCAAATCTAATGATTGGTTATGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACA
CTTCAAGAAGATGCTATTGGGCCTCCTTATTTCTACCATGAGCAAATTT
Found at i:232918 original size:36 final size:36
Alignment explanation
Indices: 232855--232924 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
232845 CATAAATGCC
* * *
232855 AAAAATAAGAATGCAAACTGTGTAATGCAAAGATGT
1 AAAAATAAGAATACAAAATGTGAAATGCAAAGATGT
*
232891 AAAAAGTAAGAATACAAAATG-GAAATGCACAGAT
1 AAAAA-TAAGAATACAAAATGTGAAATGCAAAGAT
232925 ACAAAATGTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 16 0.55
37 13 0.45
ACGTcount: A:0.54, C:0.09, G:0.19, T:0.19
Consensus pattern (36 bp):
AAAAATAAGAATACAAAATGTGAAATGCAAAGATGT
Found at i:235295 original size:18 final size:17
Alignment explanation
Indices: 235240--235300 Score: 63
Period size: 18 Copynumber: 3.5 Consensus size: 17
235230 AACTTCTAAC
235240 ATATAAATAAAATAATTA
1 ATATAAA-AAAATAATTA
235258 ATATCTAAAAAAAT-ATTA
1 ATA--TAAAAAAATAATTA
*
235276 ATATAAAAATAATAAGTA
1 ATATAAAAA-AATAATTA
235294 ATA-AAAA
1 ATATAAAA
235301 TTTGAAAGAA
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
16 6 0.16
17 7 0.18
18 16 0.42
19 5 0.13
20 4 0.11
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (17 bp):
ATATAAAAAAATAATTA
Found at i:236113 original size:20 final size:20
Alignment explanation
Indices: 236084--236159 Score: 59
Period size: 20 Copynumber: 3.6 Consensus size: 20
236074 ATTTATATAG
*
236084 ATAATAAAAATAATGAAATA
1 ATAATTAAAATAATGAAATA
236104 ATAATTAAAACATAAT--AATA
1 ATAATT-AAA-ATAATGAAATA
236124 ATAA-TAAAATAATATTGCAAATA
1 ATAATTAAAAT-A-A-TG-AAATA
*
236147 ATGATTAAAATAA
1 ATAATTAAAATAA
236160 AAGGAAATAA
Statistics
Matches: 45, Mismatches: 2, Indels: 16
0.71 0.03 0.25
Matches are distributed among these distances:
17 2 0.04
18 4 0.09
19 2 0.04
20 14 0.31
21 3 0.07
22 6 0.13
23 8 0.18
24 6 0.13
ACGTcount: A:0.64, C:0.03, G:0.04, T:0.29
Consensus pattern (20 bp):
ATAATTAAAATAATGAAATA
Found at i:236134 original size:14 final size:14
Alignment explanation
Indices: 236086--236137 Score: 50
Period size: 14 Copynumber: 3.5 Consensus size: 14
236076 TTATATAGAT
* *
236086 AATAAAAATAATGA
1 AATAATAATAATAA
*
236100 AATAATAATTAAAACA
1 AATAATAA-TAATA-A
236116 TAATAATAATAATAA
1 -AATAATAATAATAA
236131 AATAATA
1 AATAATA
236138 TTGCAAATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
14 14 0.45
15 4 0.13
16 5 0.16
17 8 0.26
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (14 bp):
AATAATAATAATAA
Found at i:236135 original size:17 final size:17
Alignment explanation
Indices: 236084--236137 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 17
236074 ATTTATATAG
* *
236084 ATAATAAAAATAATGAA
1 ATAATAATAATAATAAA
*
236101 ATAATAAT--TAA-AAC
1 ATAATAATAATAATAAA
236115 ATAATAATAATAATAAA
1 ATAATAATAATAATAAA
236132 ATAATA
1 ATAATA
236138 TTGCAAATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
14 9 0.30
15 3 0.10
16 3 0.10
17 15 0.50
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (17 bp):
ATAATAATAATAATAAA
Found at i:237504 original size:3 final size:3
Alignment explanation
Indices: 237496--237568 Score: 67
Period size: 3 Copynumber: 24.3 Consensus size: 3
237486 ATATATATAT
* * * * *
237496 ATA ATA ATAA ATA ATA ATA AT- ATT ATT ATA TTA ATA ATA ATA TTT
1 ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
237541 ATA ATA ATA ATA ATT TTA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
237569 ACGAAAAATT
Statistics
Matches: 57, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
2 2 0.04
3 52 0.91
4 3 0.05
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (3 bp):
ATA
Found at i:237544 original size:12 final size:12
Alignment explanation
Indices: 237476--237549 Score: 50
Period size: 12 Copynumber: 6.4 Consensus size: 12
237466 ATGTAATTTG
*
237476 TAATATATAT-A
1 TAATATTTATAA
*
237487 TATATATATATAA
1 TA-ATATTTATAA
* *
237500 TAATAAATAATAA
1 TAAT-ATTTATAA
237513 TAATA-TTAT--
1 TAATATTTATAA
*
237522 T-ATATTAATAA
1 TAATATTTATAA
237533 TAATATTTATAA
1 TAATATTTATAA
237545 TAATA
1 TAATA
237550 ATAATTTTAA
Statistics
Matches: 50, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
8 3 0.06
9 4 0.08
11 6 0.12
12 25 0.50
13 12 0.24
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
TAATATTTATAA
Found at i:243133 original size:23 final size:24
Alignment explanation
Indices: 243093--243142 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
243083 CCACTACGGG
243093 CTATGAAATTTGTCCCGAAGGACCA
1 CTATGAAA-TTGTCCCGAAGGACCA
243118 CTATGAAA-TGTCCCGAAGGACCA
1 CTATGAAATTGTCCCGAAGGACCA
243141 CT
1 CT
243143 GTAAATCCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 17 0.68
25 8 0.32
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.22
Consensus pattern (24 bp):
CTATGAAATTGTCCCGAAGGACCA
Found at i:245293 original size:8 final size:8
Alignment explanation
Indices: 245278--245309 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
245268 CTTTTCATTT
245278 CTTTATTC
1 CTTTATTC
*
245286 CATTATTC
1 CTTTATTC
245294 CTTTATTC
1 CTTTATTC
245302 CTTTATTC
1 CTTTATTC
245310 ATTCCAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.16, C:0.25, G:0.00, T:0.59
Consensus pattern (8 bp):
CTTTATTC
Found at i:247420 original size:23 final size:24
Alignment explanation
Indices: 247380--247429 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
247370 CCATTACGGG
247380 CTATGAAATTTGTCCCGAAGGACCA
1 CTATGAAA-TTGTCCCGAAGGACCA
247405 CTATGAAA-TGTCCCGAAGGACCA
1 CTATGAAATTGTCCCGAAGGACCA
247428 CT
1 CT
247430 GTAAATCCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 17 0.68
25 8 0.32
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.22
Consensus pattern (24 bp):
CTATGAAATTGTCCCGAAGGACCA
Found at i:248952 original size:23 final size:24
Alignment explanation
Indices: 248926--248970 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
248916 TACTTCATTT
*
248926 AATAATTACCAATAA-TCCCTAAA
1 AATAATTACAAATAAGTCCCTAAA
* *
248949 AATATTTATAAATAAGTCCCTA
1 AATAATTACAAATAAGTCCCTA
248971 TATTTACAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 12 0.67
24 6 0.33
ACGTcount: A:0.49, C:0.18, G:0.02, T:0.31
Consensus pattern (24 bp):
AATAATTACAAATAAGTCCCTAAA
Found at i:256747 original size:215 final size:215
Alignment explanation
Indices: 256270--256748 Score: 793
Period size: 216 Copynumber: 2.2 Consensus size: 215
256260 ATTTTATGAA
* *
256270 AAATACAAATTT-AAGAATTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTA
1 AAATA-AAATTTGGAGAACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTA
256334 AACAACACACATTGATGAGGGATCAAATCGAAATAATTTAAATTATGAGTTTGAAATTAATACAA
65 AACAACACACATTGATGAGGGATCAAATCGAAATAATTTAAATTATGAGTTTGAAATTAATACAA
* *
256399 AAAAGTACTAAATTATACCCATTTAAAAAGTTATGAGCCAATTAAAAAATATAATTAAGTAATAA
130 AAAAGTACTAAATTATACCCATTTAAAAAGTTATGAGCCAATTAAAAAATAGAAATAAGTAATAA
*
256464 GTATGGATCAATTTTAGATGC
195 GTATGGATCAATTTCAGATGC
*
256485 AAATAAAATTTGGAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAA
1 AAATAAAATTTGGAGAACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAA
*
256550 ACAACACACATTGATGAGGGATCAAATCGAAATAATTTTAAATTGTGA-TATTGAAATTAATACA
66 ACAACACACATTGATGAGGGATCAAATCGAAATAA-TTTAAATTATGAGT-TTGAAATTAATACA
** * * *
256614 AAAAAGTGTTAAATTATACCCATTTAAAATGTTATGGGCCAATTTAAAAATAGAAATAAGTAATA
129 AAAAAGTACTAAATTATACCCATTTAAAAAGTTATGAGCCAATTAAAAAATAGAAATAAGTAATA
*
256679 AGTATGGGTCAATTTCAGATGC
194 AGTATGGATCAATTTCAGATGC
256701 AAATAAAATTTGGAGAACTAAATTGAACAAATATGAAATT-CAAATAAA
1 AAATAAAATTTGGAGAACTAAATTGAACAAATATGAAATTACAAATAAA
256749 TTAAACAACA
Statistics
Matches: 247, Mismatches: 14, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
214 6 0.02
215 99 0.40
216 142 0.57
ACGTcount: A:0.51, C:0.08, G:0.12, T:0.29
Consensus pattern (215 bp):
AAATAAAATTTGGAGAACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAA
ACAACACACATTGATGAGGGATCAAATCGAAATAATTTAAATTATGAGTTTGAAATTAATACAAA
AAAGTACTAAATTATACCCATTTAAAAAGTTATGAGCCAATTAAAAAATAGAAATAAGTAATAAG
TATGGATCAATTTCAGATGC
Found at i:256798 original size:6 final size:6
Alignment explanation
Indices: 256791--256872 Score: 119
Period size: 6 Copynumber: 13.7 Consensus size: 6
256781 TCATGGTTCA
* *
256791 TATTCA TATTCA TATTCG TATTCG TATTCG TATTCG TATTCG TATTCG
1 TATTCG TATTCG TATTCG TATTCG TATTCG TATTCG TATTCG TATTCG
* * *
256839 TATTCA TATTCG TATTCG TATTCT TATTCA TATT
1 TATTCG TATTCG TATTCG TATTCG TATTCG TATT
256873 TATATAAACT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 71 1.00
ACGTcount: A:0.22, C:0.16, G:0.10, T:0.52
Consensus pattern (6 bp):
TATTCG
Found at i:256910 original size:20 final size:20
Alignment explanation
Indices: 256885--256954 Score: 68
Period size: 22 Copynumber: 3.2 Consensus size: 20
256875 TATAAACTAC
256885 ATACTATAATTTATATTTAT
1 ATACTATAATTTATATTTAT
*
256905 ATACTATATTTTATACTATTTAT
1 ATACTATA-ATT-TA-TATTTAT
* *
256928 ATAAAATATAGTTTATATTTAT
1 AT--ACTATAATTTATATTTAT
256950 ATACT
1 ATACT
256955 CTATATATGA
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
20 10 0.24
21 2 0.05
22 11 0.27
23 11 0.27
24 2 0.05
25 5 0.12
ACGTcount: A:0.40, C:0.06, G:0.01, T:0.53
Consensus pattern (20 bp):
ATACTATAATTTATATTTAT
Found at i:256921 original size:12 final size:13
Alignment explanation
Indices: 256896--256945 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
256886 TACTATAATT
256896 TATATTTATATAC
1 TATATTTATATAC
256909 TATATTT-TATAC
1 TATATTTATATAC
* *
256921 TAT-TTATATAAAA
1 TATATT-TATATAC
256934 TATAGTTTATAT
1 TATA-TTTATAT
256946 TTATATACTC
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
11 2 0.07
12 9 0.30
13 13 0.43
14 4 0.13
15 2 0.07
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (13 bp):
TATATTTATATAC
Found at i:256936 original size:23 final size:22
Alignment explanation
Indices: 256889--256952 Score: 67
Period size: 23 Copynumber: 2.9 Consensus size: 22
256879 AACTACATAC
* **
256889 TATAATTTATATTTATATACTA
1 TATAGTTTATATTTATATAAAA
*
256911 TAT-TTTATACTATTTATATAAAA
1 TATAGTT-TA-TATTTATATAAAA
256934 TATAGTTTATATTTATATA
1 TATAGTTTATATTTATATA
256953 CTCTATATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
21 2 0.06
22 15 0.43
23 16 0.46
24 2 0.06
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.55
Consensus pattern (22 bp):
TATAGTTTATATTTATATAAAA
Found at i:256962 original size:33 final size:32
Alignment explanation
Indices: 256909--256975 Score: 89
Period size: 33 Copynumber: 2.1 Consensus size: 32
256899 ATTTATATAC
*
256909 TATATTTTATACTATTTATATAAAATATAGTT
1 TATATTTTATACTATATATATAAAATATAGTT
* * *
256941 TATATTTATATACTCTATATATGAACTATAGTT
1 TATATTT-TATACTATATATATAAAATATAGTT
256974 TA
1 TA
256976 CATATGAACT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 7 0.23
33 23 0.77
ACGTcount: A:0.39, C:0.06, G:0.04, T:0.51
Consensus pattern (32 bp):
TATATTTTATACTATATATATAAAATATAGTT
Found at i:256980 original size:18 final size:18
Alignment explanation
Indices: 256959--257041 Score: 66
Period size: 18 Copynumber: 4.7 Consensus size: 18
256949 TATACTCTAT
256959 ATATGAACTATAGTTTAC
1 ATATGAACTATAGTTTAC
* *
256977 ATATGAACTATAAATATAC
1 ATATGAACTAT-AGTTTAC
* *
256996 -TA--AAGTTGATA-TTTAT
1 ATATGAA-CT-ATAGTTTAC
257012 ATATGAACTATAGTTTAC
1 ATATGAACTATAGTTTAC
*
257030 ATATGCACTATA
1 ATATGAACTATA
257042 TATATAAACT
Statistics
Matches: 50, Mismatches: 8, Indels: 14
0.69 0.11 0.19
Matches are distributed among these distances:
16 5 0.10
17 7 0.14
18 31 0.62
19 7 0.14
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.39
Consensus pattern (18 bp):
ATATGAACTATAGTTTAC
Found at i:257024 original size:86 final size:85
Alignment explanation
Indices: 256921--257142 Score: 247
Period size: 86 Copynumber: 2.6 Consensus size: 85
256911 TATTTTATAC
* * * * *
256921 TATTTATATAAAATATAGTTTATATTTATATACTCTATATATGAAC-TATAGTTTACATATGAAC
1 TATTTATATAAAATATAGTTTACA--TATACACTATATATATAAACATATAGTATACATATGAAC
256985 TATA-A-ATATACTAAAGTTGA
64 TATATATATATACTAAAGTTGA
* * *
257005 TATTTATATATGAACTATAGTTTACATATGCACTATATATATAAACTATATAGTATACATATGAC
1 TATTTATATA--AAATATAGTTTACATATACACTATATATATAAAC-ATATAGTATACATATGAA
*
257070 CTATATATATATACTATAGTTGA
63 CTATATATATATACTAAAGTTGA
** *
257093 TATTTATATACTATATAGTTTACATATGAC-CTATATATATATAC-TATAGT
1 TATTTATATAAAATATAGTTTACATAT-ACACTATATATATAAACATATAGT
257143 TTATATTTAT
Statistics
Matches: 117, Mismatches: 14, Indels: 14
0.81 0.10 0.10
Matches are distributed among these distances:
84 32 0.27
86 59 0.50
87 2 0.02
88 24 0.21
ACGTcount: A:0.41, C:0.09, G:0.07, T:0.43
Consensus pattern (85 bp):
TATTTATATAAAATATAGTTTACATATACACTATATATATAAACATATAGTATACATATGAACTA
TATATATATACTAAAGTTGA
Found at i:257052 original size:31 final size:31
Alignment explanation
Indices: 257009--257145 Score: 116
Period size: 33 Copynumber: 4.6 Consensus size: 31
256999 AGTTGATATT
*
257009 TATATATGAACTATAGTTTACATATG-CACTA
1 TATATATAAACTATAGTTTACATATGAC-CTA
*
257040 TATATATAAACTATATAGTATACATATGACCTA
1 TATATATAAAC--TATAGTTTACATATGACCTA
* *
257073 TATATATATACTATAG-TT-GATAT----T-
1 TATATATAAACTATAGTTTACATATGACCTA
257097 TATATACT--A-TATAGTTTACATATGACCTA
1 TATATA-TAAACTATAGTTTACATATGACCTA
*
257126 TATATATATACTATAGTTTA
1 TATATATAAACTATAGTTTA
257146 TATTTATATA
Statistics
Matches: 86, Mismatches: 6, Indels: 28
0.72 0.05 0.23
Matches are distributed among these distances:
22 5 0.06
23 3 0.03
24 10 0.12
25 2 0.02
28 2 0.02
29 10 0.12
30 2 0.02
31 24 0.28
33 27 0.31
34 1 0.01
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.42
Consensus pattern (31 bp):
TATATATAAACTATAGTTTACATATGACCTA
Found at i:257117 original size:53 final size:53
Alignment explanation
Indices: 257039--257155 Score: 198
Period size: 53 Copynumber: 2.2 Consensus size: 53
257029 CATATGCACT
* *
257039 ATATATATAAACTATATAGTATACATATGACCTATATATATATACTATAGTTG
1 ATATTTATATACTATATAGTATACATATGACCTATATATATATACTATAGTTG
* *
257092 ATATTTATATACTATATAGTTTACATATGACCTATATATATATACTATAGTTT
1 ATATTTATATACTATATAGTATACATATGACCTATATATATATACTATAGTTG
257145 ATATTTATATA
1 ATATTTATATA
257156 TATGTAGACA
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 60 1.00
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.44
Consensus pattern (53 bp):
ATATTTATATACTATATAGTATACATATGACCTATATATATATACTATAGTTG
Found at i:257206 original size:6 final size:6
Alignment explanation
Indices: 257189--257229 Score: 57
Period size: 6 Copynumber: 6.8 Consensus size: 6
257179 AACAATAAAA
*
257189 AATTAT -ATTAT AATTAT AATTAT TATTAT AAATTAT AATTA
1 AATTAT AATTAT AATTAT AATTAT AATTAT -AATTAT AATTA
257230 GTATTAGTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 5 0.16
6 21 0.68
7 5 0.16
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (6 bp):
AATTAT
Found at i:257224 original size:19 final size:17
Alignment explanation
Indices: 257189--257235 Score: 67
Period size: 19 Copynumber: 2.6 Consensus size: 17
257179 AACAATAAAA
257189 AATTATATTATAATTAT
1 AATTATATTATAATTAT
257206 AATTATTATTATAAATTAT
1 AATTA-TATTAT-AATTAT
257225 AATTAGTATTA
1 AATTA-TATTA
257236 GTATTAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 5 0.19
18 6 0.22
19 16 0.59
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (17 bp):
AATTATATTATAATTAT
Found at i:258344 original size:2 final size:2
Alignment explanation
Indices: 258337--258361 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
258327 TATTGATGTT
258337 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 T
258362 TGATTTATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:258400 original size:31 final size:30
Alignment explanation
Indices: 258356--258414 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
258346 ATATATATAT
* *
258356 ATATATTGATTTATTGTTGTTGATGTAAATG
1 ATATACTGATTTATTGTTG-TAATGTAAATG
*
258387 ATATACTGGTTTATTGTTGTAATGTAAA
1 ATATACTGATTTATTGTTGTAATGTAAA
258415 CTAACCATGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 8 0.32
31 17 0.68
ACGTcount: A:0.31, C:0.02, G:0.19, T:0.49
Consensus pattern (30 bp):
ATATACTGATTTATTGTTGTAATGTAAATG
Found at i:270184 original size:29 final size:29
Alignment explanation
Indices: 270149--270230 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
270139 AAACTAAATT
* *
270149 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
270178 GATGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
270207 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
270231 GTTAGGTGAG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 44 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:272789 original size:175 final size:171
Alignment explanation
Indices: 272501--272831 Score: 441
Period size: 175 Copynumber: 1.9 Consensus size: 171
272491 ATTATTATTT
* ** * *
272501 GCGCCTTTCTGCAAAGGGTATTAGATCGATAATATTTTTTAACGGTGTCTGACACGTAAATAAAA
1 GCGCCTTTCTACAAAGAATATTAAATCGATAATATTTTTTAACAGTGTCTGACACGTAAATAAAA
* * * * *
272566 AATAGGTTGTTTTTTCGATAAATACGTCGGAACATCCCCAATAGTAATACATTAGAACAAAC-CC
66 AATAGGATGATTTTTCGATAAATACGTCGCAACATCCCCAACAGTAATACATGAGAACAAACACC
272630 TCTCTTTCTATTCAACAAAAAGAAAGATGTAGATCATCATCC
131 -CTCTTTCTATTCAACAAAAAGAAAGATGTAGATCATCATCC
* * *
272672 GCGCCTTTCTACAAAGAATGTTAAATCGATAATATTTCCTTTAACAGTGTGTGACATGTAAATAA
1 GCGCCTTTCTACAAAGAATATTAAATCGATAATATTT--TTTAACAGTGTCTGACACGTAAAT--
* *
272737 AAAAAATAGGATGATTTTTCGATAAATACG-CTGCAACATGCCCAACAGTAATATATGAGAACAA
62 AAAAAATAGGATGATTTTTCGATAAATACGTC-GCAACATCCCCAACAGTAATACATGAGAACAA
* *
272801 ACACCCTCTTTCTATTCAGCAAAAGGAAAGA
126 ACACCCTCTTTCTATTCAACAAAAAGAAAGA
272832 CTCCCTCATC
Statistics
Matches: 137, Mismatches: 17, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
171 32 0.23
173 21 0.15
174 1 0.01
175 81 0.59
176 2 0.01
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (171 bp):
GCGCCTTTCTACAAAGAATATTAAATCGATAATATTTTTTAACAGTGTCTGACACGTAAATAAAA
AATAGGATGATTTTTCGATAAATACGTCGCAACATCCCCAACAGTAATACATGAGAACAAACACC
CTCTTTCTATTCAACAAAAAGAAAGATGTAGATCATCATCC
Found at i:273795 original size:19 final size:19
Alignment explanation
Indices: 273771--273811 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
273761 ATCAACTTCT
273771 CTTCCTTCCAGCAAAATGG
1 CTTCCTTCCAGCAAAATGG
273790 CTTCCTTCCAGCAAAATGG
1 CTTCCTTCCAGCAAAATGG
273809 CTT
1 CTT
273812 TGGAATCCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.24, C:0.32, G:0.15, T:0.29
Consensus pattern (19 bp):
CTTCCTTCCAGCAAAATGG
Found at i:275386 original size:281 final size:280
Alignment explanation
Indices: 274869--275430 Score: 1115
Period size: 281 Copynumber: 2.0 Consensus size: 280
274859 TCCGCCCCAA
274869 CAAACTGAGGGAGTAAAGAAGAACTCACCGTGGAATAAAGCCAGGACGTTAAAGTGATGTCCTGA
1 CAAACTGAGGGAGTAAAGAAGAACTCACCGTGGAATAAAGCCAGGACGTTAAAGTGATGTCCTGA
274934 GTAACAAAGACCTCAGTCTTCGTTCGGCACTTCAACTCCGTTGTCAAGAGTGACGTTGCCGGCGG
66 GTAACAAAGACCTCAGTCTTCGTTCGGCACTTCAACTCCGTTGTCAAGAGTGACGTTGCCGGCGG
274999 TGGAACCACCACACCAAGAAGCAGTTTCTCCAGGCGATGACTGCGAACTGCCAAGAGGGTCTGTT
131 TGGAACCACCACACCAAGAAGCAGTTTCTCCAGGCGATGACTGCGAACTGCCAAGAGGGTCTGTT
275064 GTTTCCATAATAGAAAGTTATATTCGTCCAACACGATATTAACACTTTTGTTGGTGAAAACCTTC
196 GTTTCCATAATAGAAAGTTATATTCGTCCAACACGATATTAACACTTTTGTTGGTGAAAACCTTC
275129 TCAGATCTAAAGCTAGAGAC
261 TCAGATCTAAAGCTAGAGAC
275149 CAAACTGAGGGAGTAAAGAAGAACTCACCGTGGAATAAAGCCAGGACGTTAAAGTGATGTCCTGA
1 CAAACTGAGGGAGTAAAGAAGAACTCACCGTGGAATAAAGCCAGGACGTTAAAGTGATGTCCTGA
275214 GTAACAAAGACCTCAGTCTTCGTTCGGCACTTCAACTCCGTTGTCAAGAGTGACCGTTGCCGGCG
66 GTAACAAAGACCTCAGTCTTCGTTCGGCACTTCAACTCCGTTGTCAAGAGTGA-CGTTGCCGGCG
275279 GTGGAACCACCACACCAAGAAGCAGTTTCTCCAGGCGATGACTGCGAACTGCCAAGAGGGTCTGT
130 GTGGAACCACCACACCAAGAAGCAGTTTCTCCAGGCGATGACTGCGAACTGCCAAGAGGGTCTGT
275344 TGTTTCCATAATAGAAAGTTATATTCGTCCAACACGATATTAACACTTTTGTTGGTGAAAACCTT
195 TGTTTCCATAATAGAAAGTTATATTCGTCCAACACGATATTAACACTTTTGTTGGTGAAAACCTT
275409 CTCAGATCTAAAGCTAGAGAC
260 CTCAGATCTAAAGCTAGAGAC
275430 C
1 C
275431 TCTGCCCTTA
Statistics
Matches: 281, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
280 118 0.42
281 163 0.58
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (280 bp):
CAAACTGAGGGAGTAAAGAAGAACTCACCGTGGAATAAAGCCAGGACGTTAAAGTGATGTCCTGA
GTAACAAAGACCTCAGTCTTCGTTCGGCACTTCAACTCCGTTGTCAAGAGTGACGTTGCCGGCGG
TGGAACCACCACACCAAGAAGCAGTTTCTCCAGGCGATGACTGCGAACTGCCAAGAGGGTCTGTT
GTTTCCATAATAGAAAGTTATATTCGTCCAACACGATATTAACACTTTTGTTGGTGAAAACCTTC
TCAGATCTAAAGCTAGAGAC
Found at i:275747 original size:180 final size:181
Alignment explanation
Indices: 275445--275805 Score: 715
Period size: 180 Copynumber: 2.0 Consensus size: 181
275435 CCCTTACAGC
275445 CTCACCGGAAACAGAATCGTGTGACGGTATCACGAGCAGCAAACCTCACAAAAAAGAAGAAAAAA
1 CTCACCGGAAACAGAATCGTGTGACGGTATCACGAGCAGCAAACCTCACAAAAAAGAAGAAAAAA
275510 GACACAACACTCAAGAACCAAATAGAGGCTCCAGAGATCGAAAAGCTCTTGATACCATGTTGAAT
66 GACACAACACTCAAGAACCAAATAGAGGCTCCAGAGATCGAAAAGCTCTTGATACCATGTTGAAT
275575 ATTCAAAGAAACATCACAAGATTTTATTGAATTAAGAAAATA-GCGTGACT
131 ATTCAAAGAAACATCACAAGATTTTATTGAATTAAGAAAATAGGCGTGACT
275625 CTCACCGGAAACAGAATCGTGTGACGGTATCACGAGCAGCAAACCTCACAAAAAAGAAGAAAAAA
1 CTCACCGGAAACAGAATCGTGTGACGGTATCACGAGCAGCAAACCTCACAAAAAAGAAGAAAAAA
275690 GACACAACACTCAAGAACCAAATAGAGGCTCCAGAGATCGAAAAGCTCTTGATACCATGTTGAAT
66 GACACAACACTCAAGAACCAAATAGAGGCTCCAGAGATCGAAAAGCTCTTGATACCATGTTGAAT
275755 ATTCAAAGAAACATCACAAGATTTTATTGAATTAAGAAAATAGGCGTGACT
131 ATTCAAAGAAACATCACAAGATTTTATTGAATTAAGAAAATAGGCGTGACT
275806 TACAAAGCTA
Statistics
Matches: 180, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
180 172 0.96
181 8 0.04
ACGTcount: A:0.44, C:0.20, G:0.18, T:0.18
Consensus pattern (181 bp):
CTCACCGGAAACAGAATCGTGTGACGGTATCACGAGCAGCAAACCTCACAAAAAAGAAGAAAAAA
GACACAACACTCAAGAACCAAATAGAGGCTCCAGAGATCGAAAAGCTCTTGATACCATGTTGAAT
ATTCAAAGAAACATCACAAGATTTTATTGAATTAAGAAAATAGGCGTGACT
Found at i:276826 original size:85 final size:85
Alignment explanation
Indices: 276683--276853 Score: 333
Period size: 85 Copynumber: 2.0 Consensus size: 85
276673 TCCTTTCCCC
276683 TTTCCTCTTAATAAGATTAATGATTAAAATAAATCAACTTCAGAATTATTGCTTAAATAAATAAT
1 TTTCCTCTTAATAAGATTAATGATTAAAATAAATCAACTTCAGAATTATTGCTTAAATAAATAAT
*
276748 TTACTCTTCTTTAATTTATA
66 TTACTCTTATTTAATTTATA
276768 TTTCCTCTTAATAAGATTAATGATTAAAATAAATCAACTTCAGAATTATTGCTTAAATAAATAAT
1 TTTCCTCTTAATAAGATTAATGATTAAAATAAATCAACTTCAGAATTATTGCTTAAATAAATAAT
276833 TTACTCTTATTTAATTTATA
66 TTACTCTTATTTAATTTATA
276853 T
1 T
276854 ATCCATAACT
Statistics
Matches: 85, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 85 1.00
ACGTcount: A:0.40, C:0.11, G:0.05, T:0.44
Consensus pattern (85 bp):
TTTCCTCTTAATAAGATTAATGATTAAAATAAATCAACTTCAGAATTATTGCTTAAATAAATAAT
TTACTCTTATTTAATTTATA
Found at i:277551 original size:18 final size:19
Alignment explanation
Indices: 277507--277552 Score: 62
Period size: 17 Copynumber: 2.5 Consensus size: 19
277497 TATGATGTGA
277507 AAAATAATATTAATTATTGT
1 AAAATAATA-TAATTATTGT
277527 -AAA-AATATAATTATT-T
1 AAAATAATATAATTATTGT
277543 AAAATAATAT
1 AAAATAATAT
277553 CTAACTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
16 1 0.04
17 11 0.46
18 9 0.38
19 3 0.12
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (19 bp):
AAAATAATATAATTATTGT
Found at i:279553 original size:15 final size:15
Alignment explanation
Indices: 279519--279568 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
279509 TATATATATT
*
279519 TATAATAATAAT-AA
1 TATATTAATAATAAA
279533 TAATATTAATAATAAA
1 T-ATATTAATAATAAA
279549 TATATTGAA-AATAAA
1 TATATT-AATAATAAA
*
279564 CATAT
1 TATAT
279569 AAAATTAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
14 1 0.03
15 25 0.81
16 5 0.16
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (15 bp):
TATATTAATAATAAA
Found at i:281489 original size:3 final size:3
Alignment explanation
Indices: 281483--281570 Score: 67
Period size: 3 Copynumber: 29.7 Consensus size: 3
281473 TTTATTATAT
* *
281483 TAA TAA TAA TAA TAA TAA TAAA TAA -AA TAA -AA TAT TTA TAA TAA
1 TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
281527 TAT TTA TAA TAA TAT TTA TAA TAAA TAA -AA CTAA TAA TAA -AA TA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA -TAA TAA TAA TAA TA
281571 TAAATAAAAA
Statistics
Matches: 66, Mismatches: 12, Indels: 14
0.72 0.13 0.15
Matches are distributed among these distances:
2 8 0.12
3 50 0.76
4 8 0.12
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:282087 original size:18 final size:18
Alignment explanation
Indices: 282028--282087 Score: 52
Period size: 18 Copynumber: 3.2 Consensus size: 18
282018 GTTGAACAAG
282028 TTCTTCTCATTATGAACT
1 TTCTTCTCATTATGAACT
**
282046 CCTTCTTCCTC-TTA-GATAAG
1 --TTCTT-CTCATTATGA-ACT
282066 TTCTTCTCATTATGAACT
1 TTCTTCTCATTATGAACT
282084 TTCT
1 TTCT
282088 CTGGAAAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
17 3 0.09
18 13 0.41
19 4 0.12
20 9 0.28
21 3 0.09
ACGTcount: A:0.20, C:0.25, G:0.07, T:0.48
Consensus pattern (18 bp):
TTCTTCTCATTATGAACT
Found at i:282639 original size:22 final size:22
Alignment explanation
Indices: 282614--282676 Score: 99
Period size: 22 Copynumber: 2.9 Consensus size: 22
282604 AAATCCGATA
* * *
282614 AATCTTTCTTCTTTGAAAAGAG
1 AATCTATCATCTTTGAAAACAG
282636 AATCTATCATCTTTGAAAACAG
1 AATCTATCATCTTTGAAAACAG
282658 AATCTATCATCTTTGAAAA
1 AATCTATCATCTTTGAAAA
282677 ATGAAGATGT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.37
Consensus pattern (22 bp):
AATCTATCATCTTTGAAAACAG
Found at i:283046 original size:22 final size:22
Alignment explanation
Indices: 283021--283063 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
283011 TTATATGAAA
*
283021 GAATAAATTGAATTTCGAAAAT
1 GAATAAATTGAATTTAGAAAAT
*
283043 GAATAAATTGATTTTAGAAAA
1 GAATAAATTGAATTTAGAAAA
283064 AATAAACTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.51, C:0.02, G:0.14, T:0.33
Consensus pattern (22 bp):
GAATAAATTGAATTTAGAAAAT
Found at i:283394 original size:6 final size:6
Alignment explanation
Indices: 283383--283414 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
283373 TGACCCTCAT
283383 TTTTCA TTTTCA TTTT-- TTTTCA TTTTCA TTTT
1 TTTTCA TTTTCA TTTTCA TTTTCA TTTTCA TTTT
283415 TTTTCTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
4 4 0.17
6 20 0.83
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.75
Consensus pattern (6 bp):
TTTTCA
Found at i:283424 original size:16 final size:16
Alignment explanation
Indices: 283382--283423 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
283372 TTGACCCTCA
283382 TTTTTCATTTTCATTT
1 TTTTTCATTTTCATTT
283398 TTTTTCATTTTCATTT
1 TTTTTCATTTTCATTT
283414 TTTTTC-TTTT
1 TTTTTCATTTT
283424 TTCTTCTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 4 0.15
16 22 0.85
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTTCATTTTCATTT
Found at i:294094 original size:30 final size:27
Alignment explanation
Indices: 294054--294107 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
294044 ACATTAAAAG
*
294054 ATAAT-ATATATATAAATATTATGAAA
1 ATAATAATATATATAAAAATTATGAAA
*
294080 ATAATAAGTATATATAAAAATTTTGAAA
1 ATAATAA-TATATATAAAAATTATGAAA
294108 GGAAAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 5 0.21
27 1 0.04
28 18 0.75
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (27 bp):
ATAATAATATATATAAAAATTATGAAA
Found at i:294967 original size:3 final size:3
Alignment explanation
Indices: 294959--294983 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
294949 ATATATATTT
294959 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
294984 ATATATTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:296380 original size:3 final size:3
Alignment explanation
Indices: 296374--296456 Score: 66
Period size: 3 Copynumber: 27.7 Consensus size: 3
296364 TTTATTATAT
* *
296374 TAA TAA TAA TAA TAA TAAA TAA TAAA TAA TAA -AA TAA -AA TAT TTA
1 TAA TAA TAA TAA TAA T-AA TAA T-AA TAA TAA TAA TAA TAA TAA TAA
* *
296419 TAA TAA TAT TTA TAA TAAA TAA -AA CTAA TAA TAA -AA TA
1 TAA TAA TAA TAA TAA T-AA TAA TAA -TAA TAA TAA TAA TA
296457 TAAATAAAAA
Statistics
Matches: 64, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
2 8 0.12
3 45 0.70
4 11 0.17
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:296396 original size:7 final size:7
Alignment explanation
Indices: 296374--296406 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
296364 TTTATTATAT
296374 TAAT-AA
1 TAATAAA
296380 TAAT-AA
1 TAATAAA
296386 TAATAAA
1 TAATAAA
296393 TAATAAA
1 TAATAAA
296400 TAATAAA
1 TAATAAA
296407 ATAAAATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 10 0.38
7 16 0.62
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (7 bp):
TAATAAA
Found at i:296422 original size:42 final size:45
Alignment explanation
Indices: 296370--296462 Score: 120
Period size: 42 Copynumber: 2.1 Consensus size: 45
296360 TAAATTTATT
*
296370 ATATTAATAATAATA-ATAATAAATAATA-AATAATAAAATA-AA
1 ATATTAATAATAATATATAATAAATAAAACAATAATAAAATATAA
*
296412 ATATTTATAATAATATTTATAATAAATAAAACTAATAATAAAATATAA
1 ATATTAATAATAATA--TATAATAAATAAAAC-AATAATAAAATATAA
296460 ATA
1 ATA
296463 AAAACAAATT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
42 14 0.33
45 12 0.28
47 12 0.28
48 5 0.12
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (45 bp):
ATATTAATAATAATATATAATAAATAAAACAATAATAAAATATAA
Found at i:297605 original size:21 final size:23
Alignment explanation
Indices: 297579--297620 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
297569 CTTTCCTTTC
297579 TTTAAA-AAATAAATA-ATATTA
1 TTTAAACAAATAAATATATATTA
*
297600 TTTAAACAAATATATATATAT
1 TTTAAACAAATAAATATATAT
297621 ATGTGTGTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 8 0.44
23 4 0.22
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (23 bp):
TTTAAACAAATAAATATATATTA
Found at i:297616 original size:2 final size:2
Alignment explanation
Indices: 297609--297664 Score: 58
Period size: 2 Copynumber: 28.0 Consensus size: 2
297599 ATTTAAACAA
* * * * * *
297609 AT AT AT AT AT AT AT GT GT GT GT AT GT AT GT 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
297651 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
297665 GACTAAGATG
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (2 bp):
AT
Found at i:297691 original size:11 final size:12
Alignment explanation
Indices: 297672--297708 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
297662 TATGACTAAG
297672 ATGAAAATAATA
1 ATGAAAATAATA
297684 AT-AAAATAATA
1 ATGAAAATAATA
*
297695 ATGAAAGTAATA
1 ATGAAAATAATA
297707 AT
1 AT
297709 TTAAATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.48
12 12 0.52
ACGTcount: A:0.65, C:0.00, G:0.08, T:0.27
Consensus pattern (12 bp):
ATGAAAATAATA
Found at i:299001 original size:15 final size:15
Alignment explanation
Indices: 298981--299018 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
298971 TAATTTATTA
*
298981 GGTCGATTCTGGTTG
1 GGTCGATTCTAGTTG
298996 GGTCGATTCTAGTTG
1 GGTCGATTCTAGTTG
*
299011 GGCCGATT
1 GGTCGATT
299019 TTGTAATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.11, C:0.16, G:0.37, T:0.37
Consensus pattern (15 bp):
GGTCGATTCTAGTTG
Found at i:299363 original size:22 final size:23
Alignment explanation
Indices: 299302--299364 Score: 62
Period size: 21 Copynumber: 2.9 Consensus size: 23
299292 CATTTGAAAA
*
299302 CATCCTGCACTGTAGGTCTTATG
1 CATCTTGCACTGTAGGTCTTATG
* * *
299325 GA--TGGCCCTG-AGGTCTTAT-
1 CATCTTGCACTGTAGGTCTTATG
299344 CATCTTGCACTGTAGGTCTTA
1 CATCTTGCACTGTAGGTCTTA
299365 CAGATGACCC
Statistics
Matches: 30, Mismatches: 7, Indels: 7
0.68 0.16 0.16
Matches are distributed among these distances:
19 1 0.03
20 9 0.30
21 11 0.37
22 8 0.27
23 1 0.03
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.35
Consensus pattern (23 bp):
CATCTTGCACTGTAGGTCTTATG
Found at i:299512 original size:45 final size:45
Alignment explanation
Indices: 299410--299513 Score: 147
Period size: 45 Copynumber: 2.3 Consensus size: 45
299400 CTCGAAGGCT
* *
299410 TTTTGAAAACATAATACACTGAAAGTCTTATAGATGACCCGAAGG
1 TTTTGAAAACATCATACACTGAAAGTCTTACAGATGACCCGAAGG
* * *
299455 TTTTGATAACATCATGCACT-AAAGGTCTTACAGATGACCCGGAGG
1 TTTTGAAAACATCATACACTGAAA-GTCTTACAGATGACCCGAAGG
299500 TTTTGAAAACATCA
1 TTTTGAAAACATCA
299514 AAAAGCTCCC
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
44 3 0.06
45 49 0.94
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.28
Consensus pattern (45 bp):
TTTTGAAAACATCATACACTGAAAGTCTTACAGATGACCCGAAGG
Found at i:299566 original size:121 final size:120
Alignment explanation
Indices: 299357--299589 Score: 342
Period size: 121 Copynumber: 1.9 Consensus size: 120
299347 CTTGCACTGT
* * *
299357 AGGTCTTACAGATGACCCAGAGGTTTTGAAATATCAAAAAGCTCTCGAAGGCTTTTTGAAAACAT
1 AGGTCTTACAGATGACCCAGAGGTTTTGAAACATCAAAAAGCTCTCCAAGGCTTTTTAAAAACAT
* * *
299422 AATACACTGAAAGTCTTATAGATGACCCGAAGGTTTTGATAACATCATGCACTAA
66 AATACACTGAAAGTCTTACAGATGACCCGAAGGCTTTGAAAACATCATGCACTAA
*
299477 AGGTCTTACAGATGACCCGGAGGTTTTGAAAACATCAAAAAGCTC-CCAATGGCTTTTTAAAAAC
1 AGGTCTTACAGATGACCCAGAGGTTTTG-AAACATCAAAAAGCTCTCCAA-GGCTTTTTAAAAAC
* * * *
299541 ATCATGCGCTGAAGGTCTTACAGATGACCCGAAGGCTTTGAAAACATCA
64 ATAATACACTGAAAGTCTTACAGATGACCCGAAGGCTTTGAAAACATCA
299590 AAAATCTCCC
Statistics
Matches: 100, Mismatches: 11, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
120 30 0.30
121 70 0.70
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (120 bp):
AGGTCTTACAGATGACCCAGAGGTTTTGAAACATCAAAAAGCTCTCCAAGGCTTTTTAAAAACAT
AATACACTGAAAGTCTTACAGATGACCCGAAGGCTTTGAAAACATCATGCACTAA
Found at i:299588 original size:76 final size:76
Alignment explanation
Indices: 299462--299665 Score: 300
Period size: 76 Copynumber: 2.7 Consensus size: 76
299452 AGGTTTTGAT
* * *
299462 AACATCATGCACTAAAGGTCTTACAGATGACCCGGAGGTTTTGAAAACATCAAAAAGCTCCCAAT
1 AACATCATGCACTGAAGGTCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCAAA
299527 GGCTTTTTAAA
66 GGCTTTTTAAA
* * *
299538 AACATCATGCGCTGAAGGTCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAATCTCCCAAA
1 AACATCATGCACTGAAGGTCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCAAA
*
299603 GGCTTTTTGAA
66 GGCTTTTTAAA
* * * **
299614 AACATCCTTCACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAACATCA
1 AACATCATGCACTGAAGGTCTTACAGATGACCCGAAGGTTTTGAAAACATCA
299666 TGCACTGTAG
Statistics
Matches: 114, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
76 114 1.00
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (76 bp):
AACATCATGCACTGAAGGTCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCAAA
GGCTTTTTAAA
Found at i:299661 original size:121 final size:121
Alignment explanation
Indices: 299531--299786 Score: 368
Period size: 121 Copynumber: 2.1 Consensus size: 121
299521 CCCAATGGCT
* * * *
299531 TTTTAAAAACATCATGCGCTGAAGGTCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAATC
1 TTTTGAAAACATCATGCACTGAAGGTCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGC
* * * * **
299596 TCCCAAAGGCTTTTTGAAAACATCCTTCACTGTAGGTCTTATGGATGACCCGAAGG
66 TCCCGAAGGATTTTTGAAAACATCCTGCACTGAAGGTCTTACAGATGACCCGAAGG
* * *
299652 TTTTGAAAACATCATGCACTGTAGGTCTTACATATGACCCAAAGGTTTTGAAAACATCAAAAAGC
1 TTTTGAAAACATCATGCACTGAAGGTCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGC
* *
299717 TCCCGAAGGCTTTTTGAAAACATCCTGCACTGAAGGTCTTACAGATGACCCAAAGG
66 TCCCGAAGGATTTTTGAAAACATCCTGCACTGAAGGTCTTACAGATGACCCGAAGG
*
299773 TTTTGATAACATCA
1 TTTTGAAAACATCA
299787 AAAAGCTCCC
Statistics
Matches: 121, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
121 121 1.00
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (121 bp):
TTTTGAAAACATCATGCACTGAAGGTCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGC
TCCCGAAGGATTTTTGAAAACATCCTGCACTGAAGGTCTTACAGATGACCCGAAGG
Found at i:299672 original size:45 final size:45
Alignment explanation
Indices: 299597--299710 Score: 156
Period size: 45 Copynumber: 2.5 Consensus size: 45
299587 TCAAAAATCT
* * **
299597 CCCAAAGGCTTTTTGAAAACATCCTTCACTGTAGGTCTTATGGATGA
1 CCCAAAGG--TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGA
* *
299644 CCCGAAGGTTTTGAAAACATCATGCACTGTAGGTCTTACATATGA
1 CCCAAAGGTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGA
299689 CCCAAAGGTTTTGAAAACATCA
1 CCCAAAGGTTTTGAAAACATCA
299711 AAAAGCTCCC
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
45 53 0.88
47 7 0.12
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (45 bp):
CCCAAAGGTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGA
Found at i:299691 original size:197 final size:196
Alignment explanation
Indices: 299344--299864 Score: 706
Period size: 197 Copynumber: 2.6 Consensus size: 196
299334 GAGGTCTTAT
* * * * *
299344 CATCTTGCACTGTAGGTCTTACAGATGACCCAGAGGTTTTG-AAATATCAAAAAGCTCTCGAAGG
1 CATCATGCACTGAAGGTCTTACAGATGACCCA-AGGTTTTGAAAACATCAAAAAGCTCCCAAAGG
* * *
299408 CTTTTTGAAAACATAATACACTGAAAGTCTTATAGATGACCCGAAGGTTTTGATAACATCATGCA
65 CTTTTTGAAAACATCATACACTGAAGGTCTTATAGATGACCCGAAGGTTTTGAAAACATCATGCA
**
299473 CTAAAGGTCTTACAGATGACCCGGAGGTTTTGAAAACATCAAAAAGCTCCC-AATGGCTTTTTAA
130 CTAAAGGTCTTACAGATGACCCAAAGGTTTTGAAAACATCAAAAAGCTCCCGAA-GGCTTTTTAA
299537 AAA
194 AAA
* * *
299540 CATCATGCGCTGAAGGTCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAATCTCCCAAAGG
1 CATCATGCACTGAAGGTCTTACAGATGACCC-AAGGTTTTGAAAACATCAAAAAGCTCCCAAAGG
* * * *
299605 CTTTTTGAAAACATCCTTCACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAACATCATGCA
65 CTTTTTGAAAACATCATACACTGAAGGTCTTATAGATGACCCGAAGGTTTTGAAAACATCATGCA
** * *
299670 CTGTAGGTCTTACATATGACCCAAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGAA
130 CTAAAGGTCTTACAGATGACCCAAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTAAA
299735 AA
195 AA
* *
299737 CATCCTGCACTGAAGGTCTTACAGATGACCCAAAGGTTTTGATAACATCAAAAAGCTCCCAAAGG
1 CATCATGCACTGAAGGTCTTACAGATGACCC-AAGGTTTTGAAAACATCAAAAAGCTCCCAAAGG
* * * * *
299802 TTTTTTTTGAAAATATCATGA-ATTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCA
65 --CTTTTTGAAAACATCAT-ACACTGAAGGTCTTATAGATGACCCGAAGGTTTTGAAAACATCA
299865 AAAAATCTCC
Statistics
Matches: 283, Mismatches: 36, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
196 35 0.12
197 195 0.69
198 2 0.01
199 51 0.18
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.27
Consensus pattern (196 bp):
CATCATGCACTGAAGGTCTTACAGATGACCCAAGGTTTTGAAAACATCAAAAAGCTCCCAAAGGC
TTTTTGAAAACATCATACACTGAAGGTCTTATAGATGACCCGAAGGTTTTGAAAACATCATGCAC
TAAAGGTCTTACAGATGACCCAAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTAAAA
A
Found at i:299733 original size:76 final size:76
Alignment explanation
Indices: 299644--300018 Score: 529
Period size: 76 Copynumber: 4.9 Consensus size: 76
299634 TTATGGATGA
* * * *
299644 CCCGAAGG--TTTTGAAAACATCATGCACTGTAGGTCTTACATATGACCCAAAGGTTTTGAAAAC
1 CCCGAAGGCTTTTTGAAAACATCCTGCACTGAAGGTCTTACAGATGACCCGAAGGTTTTGAAAAC
299707 ATCAAAAAGCT
66 ATCAAAAAGCT
* *
299718 CCCGAAGGCTTTTTGAAAACATCCTGCACTGAAGGTCTTACAGATGACCCAAAGGTTTTGATAAC
1 CCCGAAGGCTTTTTGAAAACATCCTGCACTGAAGGTCTTACAGATGACCCGAAGGTTTTGAAAAC
299783 ATCAAAAAGCT
66 ATCAAAAAGCT
* * * * * * *
299794 CCCAAAGGTTTTTTTTGAAAATATCATGAATTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAA
1 CCCGAAGG--CTTTTTGAAAACATCCTGCACTGAAGGTCTTACAGATGACCCGAAGGTTTTGAAA
*
299859 ACATCAAAAAATCT
64 ACATC-AAAAAGCT
*
299873 CCCGAAGGCTTTTTGAAAACATCCTGCACTAAAGGTCTTACAGATGACCCGAAGGTTTTGAAAAC
1 CCCGAAGGCTTTTTGAAAACATCCTGCACTGAAGGTCTTACAGATGACCCGAAGGTTTTGAAAAC
299938 ATCAAAAAGCT
66 ATCAAAAAGCT
* * **
299949 CCCGAAGGATTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGGACCCGAAGGTTTTGAAAA
1 CCCGAAGGCTTTTTGAAAACATCCTGCACTGAAGGTCTTACAGAT-GACCCGAAGGTTTTGAAAA
300014 CATCA
65 CATCA
300019 TGCACTGTAG
Statistics
Matches: 267, Mismatches: 28, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
74 8 0.03
76 116 0.43
77 77 0.29
78 52 0.19
79 14 0.05
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (76 bp):
CCCGAAGGCTTTTTGAAAACATCCTGCACTGAAGGTCTTACAGATGACCCGAAGGTTTTGAAAAC
ATCAAAAAGCT
Found at i:299933 original size:155 final size:153
Alignment explanation
Indices: 299652--300018 Score: 556
Period size: 155 Copynumber: 2.4 Consensus size: 153
299642 GACCCGAAGG
* *
299652 TTTTGAAAACATCATGCACTGTAGGTCTTACATATGACCCAAAGGTTTTGAAAACATC-AAAAAG
1 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAAG
* *
299716 CTCCCGAAGGCTTTTTGAAAACATCCTGCACTGAAGGTCTTACAGATGACCCAAAGGTTTTGATA
66 CTCCCGAAGGCTTTTTGAAAACATCCTGCACTAAAGGTCTTACAGATGACCCAAAGGTTTTGAAA
*
299781 ACATCAAAAAGCTCCCAAAGGTTTT
131 ACATCAAAAAGCTCCCAAAGG--AT
* * * * * *
299806 TTTTGAAAATATCATGAATTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAAT
1 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAAG
*
299871 CTCCCGAAGGCTTTTTGAAAACATCCTGCACTAAAGGTCTTACAGATGACCCGAAGGTTTTGAAA
66 CTCCCGAAGGCTTTTTGAAAACATCCTGCACTAAAGGTCTTACAGATGACCCAAAGGTTTTGAAA
*
299936 ACATCAAAAAGCTCCCGAAGGAT
131 ACATCAAAAAGCTCCCAAAGGAT
* **
299959 TTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGGACCCGAAGGTTTTGAAAACATCA
1 TTTTGAAAACATCATGCACTGTAGGTCTTACAGAT-GACCCGAAGGTTTTGAAAACATCA
300019 TGCACTGTAG
Statistics
Matches: 190, Mismatches: 21, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
153 28 0.15
154 75 0.39
155 87 0.46
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.27
Consensus pattern (153 bp):
TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAAG
CTCCCGAAGGCTTTTTGAAAACATCCTGCACTAAAGGTCTTACAGATGACCCAAAGGTTTTGAAA
ACATCAAAAAGCTCCCAAAGGAT
Found at i:300031 original size:122 final size:121
Alignment explanation
Indices: 299873--300139 Score: 426
Period size: 122 Copynumber: 2.2 Consensus size: 121
299863 CAAAAAATCT
* *
299873 CCCGAAGGCTTTTTGAAAACATCCTGCACTAAAGGTCTTACAGATGACCCGAAGGTTTTGAAAAC
1 CCCGAAGG--TTTTGAAAACATCATGCACTAAAGGTCTTACAGATGACCCCAAGGTTTTGAAAAC
* **
299938 ATCAAAAAGCTCCCGAAGGATTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGGA
64 ATCAAAAAGCTCCCGAAGGATTTTTGAAAACATCCTGCACTGAAGGTCTTACAGAT-GA
**
299997 CCCGAAGGTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCCAAGGTTTTGAAAACAT
1 CCCGAAGGTTTTGAAAACATCATGCACTAAAGGTCTTACAGATGACCCCAAGGTTTTGAAAACAT
*
300062 CAAAAAGCTCCCGAAGGATTTTTGATAACATCCTGCACTGAAGGTCTTACAGATGA
66 CAAAAAGCTCCCGAAGGATTTTTGAAAACATCCTGCACTGAAGGTCTTACAGATGA
*
300118 CCCGAAGGTTTTGATAACATCA
1 CCCGAAGGTTTTGAAAACATCA
300140 AAAAGCTCTC
Statistics
Matches: 134, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
121 23 0.17
122 103 0.77
124 8 0.06
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (121 bp):
CCCGAAGGTTTTGAAAACATCATGCACTAAAGGTCTTACAGATGACCCCAAGGTTTTGAAAACAT
CAAAAAGCTCCCGAAGGATTTTTGAAAACATCCTGCACTGAAGGTCTTACAGATGA
Found at i:300059 original size:45 final size:46
Alignment explanation
Indices: 299959--300063 Score: 167
Period size: 46 Copynumber: 2.3 Consensus size: 46
299949 CCCGAAGGAT
* ** *
299959 TTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGGACCCGAAGG
1 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGGACCCCAAGG
300005 TTTTGAAAACATCATGCACTGTAGGTCTTACAGAT-GACCCCAAGG
1 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGGACCCCAAGG
300050 TTTTGAAAACATCA
1 TTTTGAAAACATCA
300064 AAAAGCTCCC
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
45 23 0.42
46 32 0.58
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (46 bp):
TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGGACCCCAAGG
Found at i:300131 original size:76 final size:76
Alignment explanation
Indices: 299997--300268 Score: 415
Period size: 76 Copynumber: 3.6 Consensus size: 76
299987 TATGGATGGA
* *
299997 CCCGAAGG--TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCCAAGGTTTTGAAAAC
1 CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGTCTTACAGATGACCCGAAGGTTTTGAAAAC
300060 ATCAAAAAGCT
66 ATCAAAAAGCT
* * * *
300071 CCCGAAGGATTTTTGATAACATCCTGCACTGAAGGTCTTACAGATGACCCGAAGGTTTTGATAAC
1 CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGTCTTACAGATGACCCGAAGGTTTTGAAAAC
300136 ATCAAAAAGCT
66 ATCAAAAAGCT
* *
300147 CTCGAAGGCTTTTTGAAAACATCATGCACTGAAAGG-CTTACAGATGACCCGAAGGTTCTGAAAA
1 CCCGAAGGCTTTTTGAAAACATCATGCACTG-AAGGTCTTACAGATGACCCGAAGGTTTTGAAAA
300211 CATCAAAAAGCT
65 CATCAAAAAGCT
* * *
300223 CCCGAAGGCTTTTTAAAAACATCCTGCACTGAAAGTCTTACAGATG
1 CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGTCTTACAGATG
300269 TAGGAAATAG
Statistics
Matches: 179, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
74 8 0.04
75 3 0.02
76 164 0.92
77 4 0.02
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.25
Consensus pattern (76 bp):
CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGTCTTACAGATGACCCGAAGGTTTTGAAAAC
ATCAAAAAGCT
Found at i:300145 original size:198 final size:198
Alignment explanation
Indices: 299806--300215 Score: 626
Period size: 198 Copynumber: 2.1 Consensus size: 198
299796 CAAAGGTTTT
* * * *
299806 TTTTGAAAATATCATGAATTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAAT
1 TTTTGAAAACATCATGAACTGAAGGGCTTACAGATGACCCCAAGGTTTTGAAAACATCAAAAAAG
*
299871 CTCCCGAAGGCTTTTTGAAAACATCCTGCACTAAAGGTCTTACAGATGACCCGAAGGTTTTGAAA
66 CTCCCGAAGGATTTTTGAAAACATCCTGCACTAAAGGTCTTACAGATGACCCGAAGGTTTTGAAA
* * **
299936 ACATCAAAAAGCTCCCGAAGGATTTTTGAAAACATCCTGCACTG-TAGGTCTTATGGATGGACCC
131 ACATCAAAAAGCTCCCGAAGGATTTTTGAAAACATCATGCACTGAAAGG-CTTACAGAT-GACCC
300000 GAAGG
194 GAAGG
* * *
300005 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCCAAGGTTTTGAAAACATC-AAAAAG
1 TTTTGAAAACATCATGAACTGAAGGGCTTACAGATGACCCCAAGGTTTTGAAAACATCAAAAAAG
* * *
300069 CTCCCGAAGGATTTTTGATAACATCCTGCACTGAAGGTCTTACAGATGACCCGAAGGTTTTGATA
66 CTCCCGAAGGATTTTTGAAAACATCCTGCACTAAAGGTCTTACAGATGACCCGAAGGTTTTGAAA
* *
300134 ACATCAAAAAGCTCTCGAAGGCTTTTTGAAAACATCATGCACTGAAAGGCTTACAGATGACCCGA
131 ACATCAAAAAGCTCCCGAAGGATTTTTGAAAACATCATGCACTGAAAGGCTTACAGATGACCCGA
300199 AGG
196 AGG
*
300202 TTCTGAAAACATCA
1 TTTTGAAAACATCA
300216 AAAAGCTCCC
Statistics
Matches: 192, Mismatches: 18, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
197 23 0.12
198 114 0.59
199 55 0.29
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.26
Consensus pattern (198 bp):
TTTTGAAAACATCATGAACTGAAGGGCTTACAGATGACCCCAAGGTTTTGAAAACATCAAAAAAG
CTCCCGAAGGATTTTTGAAAACATCCTGCACTAAAGGTCTTACAGATGACCCGAAGGTTTTGAAA
ACATCAAAAAGCTCCCGAAGGATTTTTGAAAACATCATGCACTGAAAGGCTTACAGATGACCCGA
AGG
Found at i:301018 original size:22 final size:22
Alignment explanation
Indices: 300930--301009 Score: 142
Period size: 22 Copynumber: 3.6 Consensus size: 22
300920 AATAAAGCTT
*
300930 TCATCTTTGAAAAGAGAATATA
1 TCATCTTTGAAGAGAGAATATA
*
300952 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATATA
300974 TCATCTTTGAAGAGAGAATATA
1 TCATCTTTGAAGAGAGAATATA
300996 TCATCTTTGAAGAG
1 TCATCTTTGAAGAG
301010 TGTAGATATA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 55 1.00
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (22 bp):
TCATCTTTGAAGAGAGAATATA
Found at i:302577 original size:83 final size:83
Alignment explanation
Indices: 302470--302660 Score: 319
Period size: 83 Copynumber: 2.3 Consensus size: 83
302460 GTTTATGAGA
* * *
302470 GCTTTCAAAATGCCCCACATGGATCATTTATGTATGAATTAGACATTTAAAATGCCCCAACATTC
1 GCTTTCAAGATGTCCCACATGGATCATTTATGTATGAATTAGACATTCAAAATGCCCCAACATTC
302535 TATTTCTGGTTGATATGG
66 TATTTCTGGTTGATATGG
* * * *
302553 GCTTTCAAGATGTCCCACATGGATCATTTCTGTTTGAATTAGGCATTCAAAATGCCCTAACATTC
1 GCTTTCAAGATGTCCCACATGGATCATTTATGTATGAATTAGACATTCAAAATGCCCCAACATTC
302618 TATTTCTGGTTGATATGG
66 TATTTCTGGTTGATATGG
302636 GCTTTCAAGATGTCCCACATGGATC
1 GCTTTCAAGATGTCCCACATGGATC
302661 TTTCAGAATT
Statistics
Matches: 101, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
83 101 1.00
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.35
Consensus pattern (83 bp):
GCTTTCAAGATGTCCCACATGGATCATTTATGTATGAATTAGACATTCAAAATGCCCCAACATTC
TATTTCTGGTTGATATGG
Found at i:302602 original size:42 final size:42
Alignment explanation
Indices: 302473--302664 Score: 134
Period size: 41 Copynumber: 4.6 Consensus size: 42
302463 TATGAGAGCT
* *
302473 TTCAAAATGCCCCACATGGATCATTTAT-GTATGA-ATTAGACA
1 TTCAAAATGCCCCACATGGATCATTTCTGGT-TGATA-TAGGCA
* * *
302515 TTTAAAATGCCCCAACAT---TCTATTTCTGGTTGATATGGGCT
1 TTCAAAATGCCCC-ACATGGATC-ATTTCTGGTTGATATAGGCA
* * *
302556 TTCAAGATGTCCCACATGGATCATTTCTGTTTGA-ATTAGGCA
1 TTCAAAATGCCCCACATGGATCATTTCTGGTTGATA-TAGGCA
* * *
302598 TTCAAAATGCCCTAACAT---TCTATTTCTGGTTGATATGGGCT
1 TTCAAAATGCCC-CACATGGATC-ATTTCTGGTTGATATAGGCA
* *
302639 TTCAAGATGTCCCACATGGATC-TTTC
1 TTCAAAATGCCCCACATGGATCATTTC
302665 AGAATTGGGC
Statistics
Matches: 116, Mismatches: 20, Indels: 29
0.70 0.12 0.18
Matches are distributed among these distances:
40 12 0.10
41 51 0.44
42 41 0.35
43 12 0.10
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (42 bp):
TTCAAAATGCCCCACATGGATCATTTCTGGTTGATATAGGCA
Found at i:304333 original size:15 final size:16
Alignment explanation
Indices: 304308--304347 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
304298 ATTCAATTTC
*
304308 TCATCTTTTCCTTT-T
1 TCATTTTTTCCTTTAT
*
304323 TCCTTTTTTCCTTTAT
1 TCATTTTTTCCTTTAT
304339 TCATTTTTT
1 TCATTTTTT
304348 TTTTGTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.07, C:0.23, G:0.00, T:0.70
Consensus pattern (16 bp):
TCATTTTTTCCTTTAT
Found at i:306767 original size:14 final size:13
Alignment explanation
Indices: 306750--306835 Score: 57
Period size: 14 Copynumber: 6.2 Consensus size: 13
306740 AAATGTAATT
306750 ATGCAAATATGCAA
1 ATGCAAA-ATGCAA
*
306764 ATGCAAAACTGAAA
1 ATGCAAAA-TGCAA
* *
306778 ATG-TAAATACAA
1 ATGCAAAATGCAA
* *
306790 ACGTAAAAATGCAAA
1 ATG-CAAAATGC-AA
306805 GATGCAAAATGCAA
1 -ATGCAAAATGCAA
*
306819 ATGCAAAGATGTAA
1 ATGCAAA-ATGCAA
306833 ATG
1 ATG
306836 TAACATGAAA
Statistics
Matches: 56, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
12 5 0.09
13 11 0.20
14 29 0.52
15 9 0.16
16 2 0.04
ACGTcount: A:0.53, C:0.12, G:0.16, T:0.19
Consensus pattern (13 bp):
ATGCAAAATGCAA
Found at i:309807 original size:2 final size:2
Alignment explanation
Indices: 309798--309846 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
309788 CTAAGAAAAA
309798 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
309839 AT AT AT AT
1 AT AT AT AT
309847 TTTTAGGGTT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:314602 original size:29 final size:29
Alignment explanation
Indices: 314560--314623 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
314550 GGTTACAGAA
* * *
314560 TAAGATTACGGTGTTTGGTTGAGGGAATG
1 TAAGATCACAGTGTTTGATTGAGGGAATG
*
314589 TAAGATCACAGTGTTTGATTGAGTGAATG
1 TAAGATCACAGTGTTTGATTGAGGGAATG
314618 TAAGAT
1 TAAGAT
314624 TACCTTGAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.30, C:0.05, G:0.31, T:0.34
Consensus pattern (29 bp):
TAAGATCACAGTGTTTGATTGAGGGAATG
Found at i:316058 original size:34 final size:36
Alignment explanation
Indices: 316015--316114 Score: 152
Period size: 34 Copynumber: 2.8 Consensus size: 36
316005 TTCGTCCTAT
316015 AGGATTCAAACTCCTAAAAATAGGATAGAA-TT-TC
1 AGGATTCAAACTCCTAAAAATAGGATAGAATTTGTC
*
316049 AGGATTCAAACTCCTAAAAATAGGAT-GAAATTTTGTT
1 AGGATTCAAACTCCTAAAAATAGGATAG-AA-TTTGTC
316086 AGGATTCAAACTCCTAAAAATAGGATAGA
1 AGGATTCAAACTCCTAAAAATAGGATAGA
316115 GTTCTACTAT
Statistics
Matches: 60, Mismatches: 1, Indels: 7
0.88 0.01 0.10
Matches are distributed among these distances:
33 1 0.02
34 28 0.47
36 2 0.03
37 28 0.47
38 1 0.02
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.27
Consensus pattern (36 bp):
AGGATTCAAACTCCTAAAAATAGGATAGAATTTGTC
Found at i:316546 original size:18 final size:17
Alignment explanation
Indices: 316507--316549 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
316497 ATTATATGAA
316507 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
316523 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
316541 TATTATTAT
1 TATTATTAT
316550 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:316585 original size:61 final size:60
Alignment explanation
Indices: 316514--316636 Score: 169
Period size: 61 Copynumber: 2.0 Consensus size: 60
316504 GAATATTTTA
*
316514 TTCATTTATTTTTATTA-T-TCATGTTATTATTATTATATGTATATATATATATATAATTATT
1 TTCATTTATTTTT-TTACTAT-ATGTTATTATTATTATATATATATATATATATATAA-TATT
* * *
316575 TTCATTTATTTTTTTACTATATTTTATTATTATTATATATATATATATTTATTTAATATT
1 TTCATTTATTTTTTTACTATATGTTATTATTATTATATATATATATATATATATAATATT
316635 TT
1 TT
316637 ACTTATAAGT
Statistics
Matches: 56, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
60 9 0.16
61 46 0.82
62 1 0.02
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (60 bp):
TTCATTTATTTTTTTACTATATGTTATTATTATTATATATATATATATATATATAATATT
Found at i:317055 original size:2 final size:2
Alignment explanation
Indices: 317048--317092 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
317038 TAATACTTTG
317048 AT AT AT 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
317090 AT A
1 AT A
317093 CTTTACTATT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:321502 original size:22 final size:22
Alignment explanation
Indices: 321471--321527 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
321461 AAGCTACCCC
*
321471 ATCAATCCTTTGAGCATCAAAT
1 ATCAAACCTTTGAGCATCAAAT
321493 ATCAAACCTTTGAGCATCAAAT
1 ATCAAACCTTTGAGCATCAAAT
*
321515 -GCGAAACCTTTGA
1 ATC-AAACCTTTGA
321528 CCAAACACAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
21 1 0.03
22 31 0.97
ACGTcount: A:0.37, C:0.23, G:0.12, T:0.28
Consensus pattern (22 bp):
ATCAAACCTTTGAGCATCAAAT
Found at i:322467 original size:36 final size:36
Alignment explanation
Indices: 322424--322705 Score: 294
Period size: 36 Copynumber: 8.0 Consensus size: 36
322414 ACTAGAAGAG
322424 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
*
322460 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * *
322496 TTTCGTCTATCTTGAGACAGTTTCCCTTGAAATAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
*
322532 TTTTGTCTCTCTTAAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * * * *
322568 ------ATAT-TTGA-ATATGTTTTCTTTGAAACAAA
1 TTTTGTCTCTCTTGAGACA-GTTTCCCTTGAAACAAA
*** * ** * *
322597 TACCGTTTCTCTTGAGACAGTTTCTTTTGGAACTAAG
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAA
*
322634 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC-AA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
*
322669 TTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTT-GTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
322706 ATCTTTGAAT
Statistics
Matches: 203, Mismatches: 31, Indels: 23
0.79 0.12 0.09
Matches are distributed among these distances:
28 2 0.01
29 18 0.09
30 2 0.01
35 7 0.03
36 141 0.69
37 33 0.16
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (36 bp):
TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
Found at i:322467 original size:71 final size:72
Alignment explanation
Indices: 322382--322567 Score: 209
Period size: 72 Copynumber: 2.6 Consensus size: 72
322372 GTTTTTCTTA
* * * *
322382 AAACAAGA-TTTGTCTCGCTTGAGATC-GTTTTCACTAG-AA-GAGTTTTGTCTCTCTTGAGACA
1 AAACAA-ATTTTGTCTCGCTTGAGA-CAG-TTTCACTAGAAACAAATTTCGTCTATCTTGAGACA
322443 GTTTCCCTTG
63 GTTTCCCTTG
* * *
322453 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAGTT
1 AAACAAATTTTGTCTCGCTTGAGACAGTTTCACTAGAAACAAATTTCGTCTATCTTGAGACAGTT
322518 TCCCTTG
66 TCCCTTG
* * * * *
322525 AAATAAATTTTGTCTCTCTTAAGACAGTTTCCCTTGAAACAAA
1 AAACAAATTTTGTCTCGCTTGAGACAGTTTCACTAGAAACAAA
322568 ATATTTGAAT
Statistics
Matches: 101, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
70 9 0.09
71 24 0.24
72 68 0.67
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.38
Consensus pattern (72 bp):
AAACAAATTTTGTCTCGCTTGAGACAGTTTCACTAGAAACAAATTTCGTCTATCTTGAGACAGTT
TCCCTTG
Found at i:322697 original size:138 final size:137
Alignment explanation
Indices: 322467--322715 Score: 383
Period size: 138 Copynumber: 1.8 Consensus size: 137
322457 AAATTTTGTC
322467 TCTCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAATAAA
1 TCTCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAATAAA
*
322532 TTTTGTCTCTCTTAAGACAGTTTCCCTTGAAACAAAATATTTGAATATGTTTTCTTTGAAACAAA
66 TTTTGTCTATCTTAAGACAGTTTCCCTTGAAACAAAATATTTGAATATGTTTTCTTTGAAACAAA
322597 TACCGTT
131 TACCGTT
* * * * * * *
322604 TCTCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAA-CA
1 TCTCTTGAGACAGTTTCTCTTGAAAC-AAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAATAA
* *
322668 ATTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAAT
65 ATTTT-GTCTATCTTAAGACAGTTTCCCTTGAAACAAAATATTTGAAT
322716 TTATTTCTCC
Statistics
Matches: 100, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
137 30 0.30
138 70 0.70
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (137 bp):
TCTCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAATAAA
TTTTGTCTATCTTAAGACAGTTTCCCTTGAAACAAAATATTTGAATATGTTTTCTTTGAAACAAA
TACCGTT
Found at i:322732 original size:138 final size:137
Alignment explanation
Indices: 322467--322768 Score: 376
Period size: 138 Copynumber: 2.2 Consensus size: 137
322457 AAATTTTGTC
322467 TCTCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAATAAA
1 TCTCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAATAAA
* * *
322532 TTTTGTCTCTCTTAAGACAGTTTCCCTTGAAACAAAATATTTGAATATGTTTTCTTTGAAACAAA
66 TTTTGTCTATCTTAAGACAGTTTCCCTTGAAACAAAATATTTGAATATGTTTTCTCTAAAACAAA
322597 TACCGTT
131 TACCGTT
* * * * * * *
322604 TCTCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAA-CA
1 TCTCTTGAGACAGTTTCTCTTGAAAC-AAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAATAA
* *
322668 ATTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAAT-T-TATTTCTCCTAAAA
65 ATTTT-GTCTATCTTAAGACAGTTTCCCTTGAAACAAAATATTTGAATATGT-TTTCT-CTAAAA
*** *
322731 CAAATTTTGTC
127 CAAATACCGTT
* * *
322742 TCCCTTGAGGCAGTTACTCTTGAAACA
1 TCTCTTGAGACAGTTTCTCTTGAAACA
322769 CAAAATCTTC
Statistics
Matches: 140, Mismatches: 21, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
136 1 0.01
137 37 0.26
138 102 0.73
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (137 bp):
TCTCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAATAAA
TTTTGTCTATCTTAAGACAGTTTCCCTTGAAACAAAATATTTGAATATGTTTTCTCTAAAACAAA
TACCGTT
Found at i:322764 original size:65 final size:67
Alignment explanation
Indices: 322654--322820 Score: 189
Period size: 65 Copynumber: 2.5 Consensus size: 67
322644 CTTGAGACAG
* * ** * **
322654 TTTCTCTTGAAAC-AATTTTCGTCTATCTTGAGACAGTTTCCCTTG-AA-ACAAAATCTTTGAAT
1 TTTCTCCTAAAACAAATTTT-GTCTCCCTTGAGACAGTTACCCTTGAAACACAAAATCTTCAAAT
322716 TTA
65 TTA
* *
322719 TTTCTCCTAAAACAAATTTTGTCTCCCTTGAGGCAGTTACTCTTGAAACACAAAATCTTCAAATT
1 TTTCTCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTACCCTTGAAACACAAAATCTTCAAATT
322784 TA
66 TA
*
322786 TTTC-CCTTAAAACATAATTTTGTTTCCCTTGAGAC
1 TTTCTCC-TAAAACA-AATTTTGTCTCCCTTGAGAC
322821 CATTTCTCAT
Statistics
Matches: 86, Mismatches: 11, Indels: 7
0.83 0.11 0.07
Matches are distributed among these distances:
65 31 0.36
66 10 0.12
67 27 0.31
68 18 0.21
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.40
Consensus pattern (67 bp):
TTTCTCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTACCCTTGAAACACAAAATCTTCAAATT
TA
Found at i:323613 original size:43 final size:43
Alignment explanation
Indices: 323548--323656 Score: 164
Period size: 43 Copynumber: 2.5 Consensus size: 43
323538 ATTTCAGAGC
*
323548 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGATAACG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* * *
323591 CAATTTCAACGTCACAATGAAGGATATTGGACTTCAGACAACG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* *
323634 CAAGTTCAACTTCACGACGAAGG
1 CAATTTCAACTTCACAACGAAGG
323657 GACCGCTGCC
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 58 1.00
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.22
Consensus pattern (43 bp):
CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
Found at i:323710 original size:148 final size:149
Alignment explanation
Indices: 323480--323761 Score: 431
Period size: 148 Copynumber: 1.9 Consensus size: 149
323470 GCACTCGAGG
* **
323480 CAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAG
1 CAACACAAGTTCAACTTCACAACGAAGGGACCGCTGCCTGTCAACAAACAACTTCTCAATTTCAG
* * *
323545 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGATAACGCAATTTCAACGTCACAATG
66 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAAACAACGCAAGTTCAACGTCACAATG
323610 AAGGATATTGGACTTCAGA
131 AAGGATATTGGACTTCAGA
* *
323629 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCCTGTCAAC-AACAACTTCTCAATTTCAG
1 CAACACAAGTTCAACTTCACAACGAAGGGACCGCTGCCTGTCAACAAACAACTTCTCAATTTCAG
* * * * * *
323693 AGCTAATTTCAATTTCACAATGAAGGATATTGGACTTCAAACAACGCAAGTTCAACTTCACGATG
66 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAAACAACGCAAGTTCAACGTCACAATG
323758 AAGG
131 AAGG
323762 GACCGCTGCT
Statistics
Matches: 119, Mismatches: 14, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
148 79 0.66
149 40 0.34
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.23
Consensus pattern (149 bp):
CAACACAAGTTCAACTTCACAACGAAGGGACCGCTGCCTGTCAACAAACAACTTCTCAATTTCAG
AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAAACAACGCAAGTTCAACGTCACAATG
AAGGATATTGGACTTCAGA
Found at i:323711 original size:105 final size:105
Alignment explanation
Indices: 323591--324355 Score: 1146
Period size: 105 Copynumber: 7.3 Consensus size: 105
323581 CCAGATAACG
* *
323591 CAATTTCAACGTCACAATGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGAAG
*
323656 GGACCGCTGCCTGTCAACAACAACTTCTCAATTTCAGAGC
66 GGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGC
* * * * *
323696 TAATTTCAATTTCACAATGAAGGATATTGGACTTCAAACAACGCAAGTTCAACTTCACGATGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGAAG
323761 GGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGC
66 GGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGC
*
323801 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGAAG
323866 GGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGC
66 GGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGC
* * *
323906 CAATTTCAACTTCACAACGAAGGATATTGGACTTTAGACAATGCAAGTTCAACTTCACGATGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGAAG
* *
323971 GGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGC
66 GGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGC
* *
324011 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGAAG
* *
324076 GGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGC
66 GGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGC
*
324116 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGAAG
* **
324181 GGACCACTGCTTGTCAACAA-AA-TT-TC-A-TTCAGATT
66 GGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGC
* *
324216 CAATTTCAACTTCACAACGAAGGATATTGGAC-TCGAGACAACACAAGTTCAACTTCACAACGAA
1 CAATTTCAACTTCACAACGAAGGATATTGGACTTC-AGACAACGCAAGTTCAACTTCACGACGAA
* ** * * * * ** *
324280 TGGAAGGTTGGTTGTCAACAAACAATTTCCCGGTTCCAGAGC
65 GGGACCGCTGCTTGTCAAC-AACAACTTCTCAATTTCAGAGC
* *
324322 CAATTTCAACTTCACGACGGAGGATATTGGACTT
1 CAATTTCAACTTCACAACGAAGGATATTGGACTT
324356 GGAACAATGC
Statistics
Matches: 609, Mismatches: 43, Indels: 14
0.91 0.06 0.02
Matches are distributed among these distances:
99 1 0.00
100 77 0.13
101 3 0.00
102 3 0.00
103 4 0.01
104 3 0.00
105 482 0.79
106 35 0.06
107 1 0.00
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.23
Consensus pattern (105 bp):
CAATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGAAG
GGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGC
Found at i:324955 original size:34 final size:36
Alignment explanation
Indices: 324902--325000 Score: 134
Period size: 37 Copynumber: 2.8 Consensus size: 36
324892 TCGTCCTACT
*
324902 AGGATTCAAA-TCCTAAAAATAAGATAGAA-TT-TC
1 AGGATTCAAACTCCTAAAAATAGGATAGAATTTGTC
*
324935 AGGATTCAAACTCCTAAAAATAGGAT-GAAATTTTGTT
1 AGGATTCAAACTCCTAAAAATAGGATAG-AA-TTTGTC
324972 AGGATTCAAACTCCTAAAAATAGGATAGA
1 AGGATTCAAACTCCTAAAAATAGGATAGA
325001 GTTCTACTAT
Statistics
Matches: 58, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
33 11 0.19
34 16 0.28
36 2 0.03
37 28 0.48
38 1 0.02
ACGTcount: A:0.45, C:0.12, G:0.15, T:0.27
Consensus pattern (36 bp):
AGGATTCAAACTCCTAAAAATAGGATAGAATTTGTC
Found at i:325433 original size:18 final size:17
Alignment explanation
Indices: 325394--325436 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
325384 ATTATATGAA
325394 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
325410 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
325428 TATTATTAT
1 TATTATTAT
325437 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:325701 original size:10 final size:10
Alignment explanation
Indices: 325686--325740 Score: 58
Period size: 10 Copynumber: 5.3 Consensus size: 10
325676 TAACTTTATA
325686 ATTTTATATT
1 ATTTTATATT
325696 ATTTTATATT
1 ATTTTATATT
*
325706 ATTTT-TGTT
1 ATTTTATATT
*
325715 TTTTTATTCATT
1 ATTTTA-T-ATT
325727 ATTATTATATT
1 ATT-TTATATT
325738 ATT
1 ATT
325741 ATTTTCTTTG
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
9 7 0.19
10 15 0.41
11 7 0.19
12 5 0.14
13 3 0.08
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (10 bp):
ATTTTATATT
Found at i:328290 original size:15 final size:15
Alignment explanation
Indices: 328270--328315 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
328260 GATATAAATT
328270 AAATATTGTTAACTA
1 AAATATTGTTAACTA
328285 AAATATTGTTAAC--
1 AAATATTGTTAACTA
*
328298 ATA-ATTGTTAACTA
1 AAATATTGTTAACTA
328312 AAAT
1 AAAT
328316 GAAATATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
12 9 0.35
13 2 0.08
14 2 0.08
15 13 0.50
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.39
Consensus pattern (15 bp):
AAATATTGTTAACTA
Found at i:330510 original size:50 final size:50
Alignment explanation
Indices: 330345--330532 Score: 206
Period size: 50 Copynumber: 3.8 Consensus size: 50
330335 TTCATAATAC
* * *
330345 AAAAAATATAACACTTAACACATACTTACACTGGTGTAAGTGAATAAAAT
1 AAAAAATGTAACACTTAACACATACTTACACCGGTGTAAGTAAATAAAAT
* * * * *
330395 AAACAAGTGTAACATTTAACACATAC-TACAACGATGTAAGTGAAT---A-
1 AAA-AAATGTAACACTTAACACATACTTACACCGGTGTAAGTAAATAAAAT
* *
330441 AAAAAGTGTAGCACTTAACACATACTTACACCGGTGTAAGTAAATAAAAT
1 AAAAAATGTAACACTTAACACATACTTACACCGGTGTAAGTAAATAAAAT
* * **
330491 AAAAAATGTAACACTTAACACATATTTATACTAGTGTAAGTA
1 AAAAAATGTAACACTTAACACATACTTACACCGGTGTAAGTA
330533 TGTACATCTC
Statistics
Matches: 115, Mismatches: 17, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
45 20 0.17
46 19 0.17
47 1 0.01
49 1 0.01
50 55 0.48
51 19 0.17
ACGTcount: A:0.48, C:0.14, G:0.12, T:0.26
Consensus pattern (50 bp):
AAAAAATGTAACACTTAACACATACTTACACCGGTGTAAGTAAATAAAAT
Found at i:332338 original size:11 final size:11
Alignment explanation
Indices: 332322--332348 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
332312 CATTTATTTT
332322 TAAAAAAATAA
1 TAAAAAAATAA
332333 TAAAAAAATAA
1 TAAAAAAATAA
332344 TAAAA
1 TAAAA
332349 TATATATTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (11 bp):
TAAAAAAATAA
Found at i:332990 original size:6 final size:6
Alignment explanation
Indices: 332974--333003 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
332964 TTCATATTAT
*
332974 ATTTTA GTTTTA ATTTTA ATTTTA ATTTTA
1 ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA
333004 TAATTTGTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (6 bp):
ATTTTA
Found at i:336650 original size:12 final size:12
Alignment explanation
Indices: 336633--336700 Score: 54
Period size: 12 Copynumber: 5.7 Consensus size: 12
336623 TATTATTAAT
336633 ATAATATATATA
1 ATAATATATATA
336645 ATAATAACGTATATA
1 ATAAT-A--TATATA
* *
336660 ATAA-AAACATA
1 ATAATATATATA
336671 TATAAT-TA-ATA
1 -ATAATATATATA
336682 AT-ATATATATA
1 ATAATATATATA
336693 ATAATATA
1 ATAATATA
336701 AACGGACAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 16
0.70 0.05 0.25
Matches are distributed among these distances:
9 2 0.04
10 4 0.09
11 12 0.27
12 15 0.33
13 2 0.04
15 10 0.22
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (12 bp):
ATAATATATATA
Found at i:336651 original size:15 final size:15
Alignment explanation
Indices: 336613--336700 Score: 92
Period size: 15 Copynumber: 5.9 Consensus size: 15
336603 ATATTATTTA
*
336613 ATAATACTAATAT-T
1 ATAATAATAATATAT
336627 ATTAAT-ATAATATAT
1 A-TAATAATAATATAT
**
336642 ATAATAATAACGTAT
1 ATAATAATAATATAT
* *
336657 ATAATAAAAACATAT
1 ATAATAATAATATAT
336672 ATAATTAATAATATAT
1 ATAA-TAATAATATAT
336688 AT-ATAATAATATA
1 ATAATAATAATATA
336701 AACGGACAAA
Statistics
Matches: 63, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
14 21 0.33
15 31 0.49
16 11 0.17
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (15 bp):
ATAATAATAATATAT
Found at i:337661 original size:22 final size:22
Alignment explanation
Indices: 337632--337726 Score: 181
Period size: 22 Copynumber: 4.3 Consensus size: 22
337622 AAAGCTTTCT
337632 ATCTTTGAAAAGAGAATCTATC
1 ATCTTTGAAAAGAGAATCTATC
*
337654 ACCTTTGAAAAGAGAATCTATC
1 ATCTTTGAAAAGAGAATCTATC
337676 ATCTTTGAAAAGAGAATCTATC
1 ATCTTTGAAAAGAGAATCTATC
337698 ATCTTTGAAAAGAGAATCTATC
1 ATCTTTGAAAAGAGAATCTATC
337720 ATCTTTG
1 ATCTTTG
337727 CATAATGTAG
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 71 1.00
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.33
Consensus pattern (22 bp):
ATCTTTGAAAAGAGAATCTATC
Found at i:342622 original size:21 final size:21
Alignment explanation
Indices: 342596--342651 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
342586 TTCTGGGCAG
342596 AGTGCATCGATGCACATTCAT
1 AGTGCATCGATGCACATTCAT
342617 AGTGCATCGATGCACATTCAT
1 AGTGCATCGATGCACATTCAT
342638 AGTGCATCGATGCA
1 AGTGCATCGATGCA
342652 TCAAGGTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (21 bp):
AGTGCATCGATGCACATTCAT
Found at i:342755 original size:64 final size:64
Alignment explanation
Indices: 342686--342904 Score: 212
Period size: 64 Copynumber: 3.5 Consensus size: 64
342676 TTGAAGGTGT
* **
342686 ATCGATGCATTAGTAGTGCATCGATGCA-CTCTTTTAA-AATAAAAACATCGAATGCAATTCATG
1 ATCGATGCATAAGTAGTGCATCGATGCATC-CCATTAATAAT-AAAACATCGAATGCAATTCATG
342749 C
64 C
* ** * * **
342750 ATCGATGCATAATTAAAGCATCGATGCATCCCATTAATAATGAAACATCGAATGTAATTGGTGC
1 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCATGC
* ** * * ** *
342814 ATCGATGCATAAGGAGTGCATCGATGCATCCCAGCAATAAT--AATATCGAATACCTTTTATGC
1 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCATGC
* *
342876 ACCGATGCATCAGTAGTGCATCGATGCAT
1 ATCGATGCATAAGTAGTGCATCGATGCAT
342905 ACCTTCATTA
Statistics
Matches: 127, Mismatches: 26, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
62 40 0.31
64 83 0.65
65 4 0.03
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.28
Consensus pattern (64 bp):
ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCATGC
Found at i:343253 original size:25 final size:24
Alignment explanation
Indices: 343225--343278 Score: 83
Period size: 23 Copynumber: 2.2 Consensus size: 24
343215 GTGATATGAT
343225 ATGATATGACATGTGATATGAGA-AC
1 ATGATATGA-A-GTGATATGAGATAC
343250 ATGATATGAAGTGATATGAGATAC
1 ATGATATGAAGTGATATGAGATAC
343274 ATGAT
1 ATGAT
343279 CACAAGAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
23 11 0.39
24 8 0.29
25 9 0.32
ACGTcount: A:0.41, C:0.06, G:0.24, T:0.30
Consensus pattern (24 bp):
ATGATATGAAGTGATATGAGATAC
Found at i:343408 original size:15 final size:15
Alignment explanation
Indices: 343390--343418 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
343380 GAGGATATAA
343390 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
343405 TAGTCCTTCGGGAT
1 TAGTCCTTCGGGAT
343419 ATAGGGGTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.31, T:0.34
Consensus pattern (15 bp):
TAGTCCTTCGGGATG
Found at i:346893 original size:21 final size:21
Alignment explanation
Indices: 346869--346910 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
346859 AGTTTATTTT
346869 TAAACTTTATTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
*
346890 TAAACTTTGTTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
346911 AACTTGAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.14, G:0.07, T:0.48
Consensus pattern (21 bp):
TAAACTTTATTTCAATTATCG
Found at i:346958 original size:33 final size:33
Alignment explanation
Indices: 346905--347007 Score: 165
Period size: 33 Copynumber: 3.2 Consensus size: 33
346895 TTTGTTTCAA
346905 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
346937 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
346970 TTATCAAACTTGGAAGTATTTAAGTATTTCAA-
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
347002 TTATCG
1 TTATCG
347008 TAAACTTTGT
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
32 16 0.24
33 50 0.76
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:347101 original size:15 final size:15
Alignment explanation
Indices: 347049--347104 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 15
347039 TTTAATAACA
*
347049 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
*
347064 TTATAACCGGTTTTT
1 TTAAAACCGGTTTTT
* *
347079 TAAAAAAACTGGTTTTT
1 T--TAAAACCGGTTTTT
347096 TTAAAACCG
1 TTAAAACCG
347105 AAACCGGTTA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
15 20 0.62
17 12 0.38
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.45
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:352372 original size:64 final size:64
Alignment explanation
Indices: 352258--352395 Score: 172
Period size: 64 Copynumber: 2.2 Consensus size: 64
352248 TTGAAGGTGT
* ** * *
352258 ATCGATGCATTAGTAGTGCATCGATGCACTCTTTTAAAATAAAAATATCGAATGCAATTCATGC
1 ATCGATGCATAAGTAGTGCATCGATGCACTCCATTAAAATAAAAACATCGAATGCAATACATGC
* **
352322 ATCGATGCATAAGTAGTGCATCGATGCA-TCCCATTAATAAT-GAAACATCGAATGCAATAGGTG
1 ATCGATGCATAAGTAGTGCATCGATGCACT-CCATTAA-AATAAAAACATCGAATGCAATACATG
352385 C
64 C
352386 ATCGATGCAT
1 ATCGATGCAT
352396 CCCAGCAATA
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
63 1 0.02
64 60 0.94
65 3 0.05
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (64 bp):
ATCGATGCATAAGTAGTGCATCGATGCACTCCATTAAAATAAAAACATCGAATGCAATACATGC
Found at i:352785 original size:12 final size:12
Alignment explanation
Indices: 352767--352802 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
352757 TATATATGTT
352767 CATGTGATATGA
1 CATGTGATATGA
*
352779 TATGTGATATGA
1 CATGTGATATGA
352791 CATGTGATATGA
1 CATGTGATATGA
352803 GAACATGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.36
Consensus pattern (12 bp):
CATGTGATATGA
Found at i:352824 original size:23 final size:26
Alignment explanation
Indices: 352767--352835 Score: 85
Period size: 24 Copynumber: 2.8 Consensus size: 26
352757 TATATATGTT
**
352767 CATGTGATAT--GATATGTGATATGA
1 CATGTGATATGAGATACATGATATGA
352791 CATGTGATATGAGA-ACATGATATGA
1 CATGTGATATGAGATACATGATATGA
352816 -A-GTGATATGAGATACATGAT
1 CATGTGATATGAGATACATGAT
352836 CACAAGAGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
23 11 0.28
24 18 0.45
25 9 0.22
26 2 0.05
ACGTcount: A:0.38, C:0.06, G:0.25, T:0.32
Consensus pattern (26 bp):
CATGTGATATGAGATACATGATATGA
Found at i:352965 original size:15 final size:15
Alignment explanation
Indices: 352947--352979 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
352937 GAGGGTATAA
352947 TAGTCCTTCAGGATG
1 TAGTCCTTCAGGATG
*
352962 TAGTCCTTCGGGATG
1 TAGTCCTTCAGGATG
352977 TAG
1 TAG
352980 GGGTCCTACG
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:0.18, G:0.30, T:0.33
Consensus pattern (15 bp):
TAGTCCTTCAGGATG
Found at i:357463 original size:14 final size:15
Alignment explanation
Indices: 357444--357476 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
357434 GAATCAATCT
357444 GGTTGGAT-TTCTCG
1 GGTTGGATCTTCTCG
357458 GGTTGGATCTTCTCG
1 GGTTGGATCTTCTCG
357473 GGTT
1 GGTT
357477 TGGTTTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.06, C:0.15, G:0.36, T:0.42
Consensus pattern (15 bp):
GGTTGGATCTTCTCG
Done.