Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005217.1 Hibiscus syriacus cultivar Beakdansim tig00011814_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: 131691
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:570 original size:116 final size:116
Alignment explanation
Indices: 432--994 Score: 614
Period size: 116 Copynumber: 5.0 Consensus size: 116
422 AACATAAAAA
* *
432 TATATATTTTATCTCATCTTAACTTTTAAAATTTAAT-AAATTGATCTGATTACT-CATTTGGTC
1 TATATATTTTATCTCATCTTAACTTTTAAAATTTAATAAAATTGATATAATTA-TACATTTGGTC
* * *
495 A-ATTAACTTATATATTCTATCAATTTAGTCCTAATTTTAATAAATTCGAACTT
65 ACTTTTACTTATATATTCTATCAATTTAGTCATAATTTTAATAAATT--AACTT
* * *
548 TTTATATTTTATCTCATCTTAACTTTTAAAATTT--TAAAATTTATATAATTACACATTTGGTCA
1 TATATATTTTATCTCATCTTAACTTTTAAAATTTAATAAAATTGATATAATTATACATTTGGTCA
* * **
611 CTTTTACTTTTATATTCTATC-ATTTAGTCGTAAAAATT-A-AAATTAA-TT
66 CTTTTACTTATATATTCTATCAATTTAGTCAT-AATTTTAATAAATTAACTT
* *
659 TATATATTTTATCTCATCTTAACTTTTAAAATTTAATAAAATTGATA-AAATATACATTTCGTCA
1 TATATATTTTATCTCATCTTAACTTTTAAAATTTAATAAAATTGATATAATTATACATTTGGTCA
*
723 CTTTTACTTATATATTCTATCAATTTAGTCATAATTTTAATAAATATTACTT
66 CTTTTACTTATATATTCTATCAATTTAGTCATAATTTTAATAAAT-TAACTT
* *
775 TATATTTTTTATCTTATCTTAAC-TTTAAAATTTAATAAAATTGATATAATTATACATTTGGTCA
1 TATATATTTTATCTCATCTTAACTTTTAAAATTTAATAAAATTGATATAATTATACATTTGGTCA
* * **
839 CTTTTAC------ATCCTA-CAATTTAGTAATAA--AAAATTAAAATTAA-TT
66 CTTTTACTTATATATTCTATCAATTTAGTCATAATTTTAA-T-AAATTAACTT
* * * * **
882 TATATATTTTATCTCATCTTAGCTTTTAAAATTTAATAAAATTAATATAATTACAAATTTCCATC
1 TATATATTTTATCTCATCTTAACTTTTAAAATTTAATAAAATTGATATAATTATACATTT-GGTC
* * *
947 ACTTGTACTT-TATATTCTATCAATTTA-TACCTAATTTTAAAAAATTAA
65 ACTTTTACTTATATATTCTATCAATTTAGT-CATAATTTTAATAAATTAA
995 AATTAATTTA
Statistics
Matches: 377, Mismatches: 45, Indels: 51
0.80 0.10 0.11
Matches are distributed among these distances:
107 24 0.06
108 36 0.10
109 26 0.07
110 5 0.01
111 35 0.09
112 40 0.11
113 20 0.05
114 16 0.04
115 74 0.20
116 99 0.26
117 2 0.01
ACGTcount: A:0.38, C:0.11, G:0.03, T:0.48
Consensus pattern (116 bp):
TATATATTTTATCTCATCTTAACTTTTAAAATTTAATAAAATTGATATAATTATACATTTGGTCA
CTTTTACTTATATATTCTATCAATTTAGTCATAATTTTAATAAATTAACTT
Found at i:760 original size:228 final size:220
Alignment explanation
Indices: 432--994 Score: 717
Period size: 228 Copynumber: 2.5 Consensus size: 220
422 AACATAAAAA
* * *
432 TATATATTTTATCTCATCTTAACTTTTAAAATTTAAT-AAATTGATCTGATTACTCATTTGGTCA
1 TATATATTTTATCTCATCTTAACTTTTAAAATTTAATAAAATTGATATAATTA--CATTTCGTCA
* * *
496 -ATTAACTTATATATTCTATCAATTTAGTCCTAATTTTAATAAATTCGAACTTTTTATATTTTAT
64 CTTTTACTTATATATTCTATCAATTTAGTCCTAATTTTAATAAATT--AACTTTATATATTTTAT
*
560 CTCATCTTAACTTTTAAAATTT-TAAAATTTATATAATTACACATTTGGTCACTTTTACTTTTAT
127 CTCATCTTAAC-TTTAAAATTTATAAAATTGATATAATTACACATTTGGTCACTTTTAC------
* **
624 ATTCTATC-ATTTAGTCGT-AAAAATTAAAATTAATT
185 ATCCTA-CAATTTAGTAATAAAAAATTAAAATTAATT
*
659 TATATATTTTATCTCATCTTAACTTTTAAAATTTAATAAAATTGATAAAATATACATTTCGTCAC
1 TATATATTTTATCTCATCTTAACTTTTAAAATTTAATAAAATTGATATAAT-TACATTTCGTCAC
* * *
724 TTTTACTTATATATTCTATCAATTTAGTCATAATTTTAATAAATATTACTTTATATTTTTTATCT
65 TTTTACTTATATATTCTATCAATTTAGTCCTAATTTTAATAAAT-TAACTTTATATATTTTATCT
* *
789 TATCTTAACTTTAAAATTTAATAAAATTGATATAATTATACATTTGGTCACTTTTACATCCTACA
129 CATCTTAACTTTAAAATTT-ATAAAATTGATATAATTACACATTTGGTCACTTTTACATCCTACA
854 ATTTAGTAATAAAAAATTAAAATTAATT
193 ATTTAGTAATAAAAAATTAAAATTAATT
* * *
882 TATATATTTTATCTCATCTTAGCTTTTAAAATTTAATAAAATTAATATAATTACAAATTTCCATC
1 TATATATTTTATCTCATCTTAACTTTTAAAATTTAATAAAATTGATATAATTAC--ATTT-CGTC
* *
947 ACTTGTACTT-TATATTCTATCAATTTA-TACCTAATTTTAAAAAATTAA
63 ACTTTTACTTATATATTCTATCAATTTAGT-CCTAATTTTAATAAATTAA
995 AATTAATTTA
Statistics
Matches: 300, Mismatches: 24, Indels: 28
0.85 0.07 0.08
Matches are distributed among these distances:
221 1 0.00
222 16 0.05
223 68 0.23
224 35 0.12
225 12 0.04
226 10 0.03
227 70 0.23
228 85 0.28
229 3 0.01
ACGTcount: A:0.38, C:0.11, G:0.03, T:0.48
Consensus pattern (220 bp):
TATATATTTTATCTCATCTTAACTTTTAAAATTTAATAAAATTGATATAATTACATTTCGTCACT
TTTACTTATATATTCTATCAATTTAGTCCTAATTTTAATAAATTAACTTTATATATTTTATCTCA
TCTTAACTTTAAAATTTATAAAATTGATATAATTACACATTTGGTCACTTTTACATCCTACAATT
TAGTAATAAAAAATTAAAATTAATT
Found at i:2280 original size:19 final size:21
Alignment explanation
Indices: 2228--2280 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 21
2218 TTATATTTAT
2228 ATTATAAAATTAGGCCCCTAAAA
1 ATTATAAAATTAGG--CCTAAAA
**
2251 ATTATTTAATTAGG-C-AAAA
1 ATTATAAAATTAGGCCTAAAA
2270 ATTATAAAATT
1 ATTATAAAATT
2281 GTAAGTAAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 13 0.50
20 1 0.04
23 12 0.46
ACGTcount: A:0.49, C:0.09, G:0.08, T:0.34
Consensus pattern (21 bp):
ATTATAAAATTAGGCCTAAAA
Found at i:2352 original size:20 final size:20
Alignment explanation
Indices: 2317--2359 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 20
2307 ATGAATAAAT
2317 TTAAATAAATTATATTA-TA
1 TTAAATAAATTATATTATTA
2336 TTAAATGAAA-TAGTATTATTA
1 TTAAAT-AAATTA-TATTATTA
2357 TTA
1 TTA
2360 TTATAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 8 0.38
20 8 0.38
21 5 0.24
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (20 bp):
TTAAATAAATTATATTATTA
Found at i:6236 original size:121 final size:121
Alignment explanation
Indices: 5951--6420 Score: 647
Period size: 121 Copynumber: 4.0 Consensus size: 121
5941 ATGACATGAC
* * **
5951 AATTTTAATTTATTAAAATTAGGACCAAATTGATAGAATATATAAGTAGAAA-TGACGAAATACG
1 AATTTTAATTTATTAAAATTAGGACTAAATTGATAGAATATATAAGTA-AAAGTGACCAAATGTG
* * *
6015 TAATTATATCAA-TTT-TTAAATCTTAAAATTTAAGATGAGAT-AAA-ATATAAATT
65 TAATTATATCAATTTTATTAAATTTTAAAAGTTAAGATGAGATAAAATATATAAAGT
* * *
6068 AATTTT-ACTT-TT----TTACGACTAAATTGATAGAATATAAAAGTAAAAGTGACCAAATGTGT
1 AATTTTAATTTATTAAAATTAGGACTAAATTGATAGAATATATAAGTAAAAGTGACCAAATGTGT
*
6127 AATTATATCAATTTTATTAAATTTTAAAAGTTAAGATGGGATAAAATATATAAAGT
66 AATTATATCAATTTTATTAAATTTTAAAAGTTAAGATGAGATAAAATATATAAAGT
* * *
6183 AATTTTAATTTATTAAAATTAGAACTAAATTGATAGAATATATCAGTAAAAGTGACGAAATGTGT
1 AATTTTAATTTATTAAAATTAGGACTAAATTGATAGAATATATAAGTAAAAGTGACCAAATGTGT
* * * *
6248 AATTATATCAATTTTATTAAATTTTAAAAATTAAGATAAGACAAATTATATAAAGT
66 AATTATATCAATTTTATTAAATTTTAAAAGTTAAGATGAGATAAAATATATAAAGT
* * * *
6304 AATTTTAATTTATTAAAATTAGGACTAAATTGATAGCATATACAAGTCAAACTGACCAAATGTGT
1 AATTTTAATTTATTAAAATTAGGACTAAATTGATAGAATATATAAGTAAAAGTGACCAAATGTGT
6369 AATTATATCAATTTTATTAAATTTTAAAAGTTAAGATGAGATAAATATATAT
66 AATTATATCAATTTTATTAAATTTTAAAAGTTAAGATGAGATAAA-ATATAT
6421 TTTTATGTTA
Statistics
Matches: 308, Mismatches: 33, Indels: 19
0.86 0.09 0.05
Matches are distributed among these distances:
110 3 0.01
111 48 0.16
112 3 0.01
113 23 0.07
114 3 0.01
115 16 0.05
116 6 0.02
117 8 0.03
121 193 0.63
122 5 0.02
ACGTcount: A:0.47, C:0.05, G:0.11, T:0.37
Consensus pattern (121 bp):
AATTTTAATTTATTAAAATTAGGACTAAATTGATAGAATATATAAGTAAAAGTGACCAAATGTGT
AATTATATCAATTTTATTAAATTTTAAAAGTTAAGATGAGATAAAATATATAAAGT
Found at i:6384 original size:232 final size:223
Alignment explanation
Indices: 5951--6384 Score: 530
Period size: 232 Copynumber: 1.9 Consensus size: 223
5941 ATGACATGAC
*
5951 AATTTTAATTTATTAAAATTAGGACCAAATTGATAGAATATATAAGTAGAAATGACGAAATACGT
1 AATTTTAATTTATTAAAATTAGAACCAAATTGATAGAATATATAAGTAGAAATGACGAAATACGT
* * * *
6016 AATTATATCAATTTTTAAATCTTAAAATTTAAGATGAGATAAAATATAAATTAATTTTACTTTTT
66 AATTATATCAATTTTTAAATCTTAAAAATTAAGATAAGACAAAATATAAAGTAATTTTACTTTTT
*
6081 TACGACTAAATTGATAGAATATAAAAGTAAAAGTGACCAAATGTGTAATTATATCAATTTTATTA
131 TACGACTAAATTGATAGAATATAAAAGTAAAACTGACCAAATGTGTAATTATATC--------T-
6146 AATTTTAAAAGTTAAGATGGGATAAAATATATAAAGT
187 AATTTTAAAAGTTAAGATGGGATAAAATATATAAAGT
* * **
6183 AATTTTAATTTATTAAAATTAGAACTAAATTGATAGAATATATCAGTA-AAAGTGACGAAATGTG
1 AATTTTAATTTATTAAAATTAGAACCAAATTGATAGAATATATAAGTAGAAA-TGACGAAATACG
*
6247 TAATTATATCAATTTTATTAAATTTTAAAAATTAAGATAAGACAAATTATATAAAGTAATTTTAA
65 TAATTATATCAA-TTT-TTAAATCTTAAAAATTAAGATAAGACAAA--ATATAAAGTAATTTT-A
* * * * *
6312 TTTATTAAAATTAGGACTAAATTGATAGCATATACAAGTCAAACTGACCAAATGTGTAATTATAT
125 CTT-TT----TTACGACTAAATTGATAGAATATAAAAGTAAAACTGACCAAATGTGTAATTATAT
6377 C-AATTTTA
185 CTAATTTTA
6385 TTAAATTTTA
Statistics
Matches: 175, Mismatches: 16, Indels: 22
0.82 0.08 0.10
Matches are distributed among these distances:
231 3 0.02
232 74 0.42
233 3 0.02
234 25 0.14
236 14 0.08
237 3 0.02
238 2 0.01
242 51 0.29
ACGTcount: A:0.47, C:0.06, G:0.11, T:0.37
Consensus pattern (223 bp):
AATTTTAATTTATTAAAATTAGAACCAAATTGATAGAATATATAAGTAGAAATGACGAAATACGT
AATTATATCAATTTTTAAATCTTAAAAATTAAGATAAGACAAAATATAAAGTAATTTTACTTTTT
TACGACTAAATTGATAGAATATAAAAGTAAAACTGACCAAATGTGTAATTATATCTAATTTTAAA
AGTTAAGATGGGATAAAATATATAAAGT
Found at i:6446 original size:31 final size:30
Alignment explanation
Indices: 6432--6487 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
6422 TTTATGTTAT
6432 ATAAGAATAAAA-ATATATTTTTTAATAAAA
1 ATAAGAATAAAATATATA-TTTTTAATAAAA
6462 ATAAGAATAAAATATATA-TTTTAATA
1 ATAAGAATAAAATATATATTTTTAATA
6488 TTTAATAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
29 8 0.32
30 12 0.48
31 5 0.20
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.38
Consensus pattern (30 bp):
ATAAGAATAAAATATATATTTTTAATAAAA
Found at i:6495 original size:30 final size:31
Alignment explanation
Indices: 6411--6496 Score: 99
Period size: 29 Copynumber: 2.8 Consensus size: 31
6401 AAGATGAGAT
6411 AAATATATATTTT--TATGTTATATAAGAATAA
1 AAATATATATTTTAATAT-TTA-ATAAGAATAA
* **
6442 AAATATATTTTTTAATA-AAAATAAGAAT-A
1 AAATATATATTTTAATATTTAATAAGAATAA
6471 AAATATATATTTTAATATTTAATAAG
1 AAATATATATTTTAATATTTAATAAG
6497 TTAAGATAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
29 17 0.37
30 14 0.30
31 13 0.28
33 2 0.04
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (31 bp):
AAATATATATTTTAATATTTAATAAGAATAA
Found at i:19403 original size:3 final size:3
Alignment explanation
Indices: 19395--19495 Score: 103
Period size: 3 Copynumber: 33.7 Consensus size: 3
19385 TCCTGACTAC
* * * * * * *
19395 GAT GAT GAT GAT GAC GAC GAC GAG GAT GAT GAT GAT GAT GAC GAC GAG
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* * * *
19443 GAT GAT GAT GAT AAT GAT GAC GAG GAT GAT GAT GAT GAT GGT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
19491 GAT GA
1 GAT GA
19496 AAGTGAGGAA
Statistics
Matches: 85, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 85 1.00
ACGTcount: A:0.34, C:0.06, G:0.37, T:0.24
Consensus pattern (3 bp):
GAT
Found at i:19433 original size:27 final size:27
Alignment explanation
Indices: 19395--19489 Score: 136
Period size: 27 Copynumber: 3.5 Consensus size: 27
19385 TCCTGACTAC
*
19395 GATGATGATGATGACGACGACGAGGAT
1 GATGATGATGATGACGACGACGATGAT
*
19422 GATGATGATGATGACGACGAGGATGAT
1 GATGATGATGATGACGACGACGATGAT
* * *
19449 GATGATAATGATGACGAGGATGATGAT
1 GATGATGATGATGACGACGACGATGAT
*
19476 GATGATGGTGATGA
1 GATGATGATGATGA
19490 TGATGAAAGT
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 61 1.00
ACGTcount: A:0.34, C:0.06, G:0.37, T:0.23
Consensus pattern (27 bp):
GATGATGATGATGACGACGACGATGAT
Found at i:19495 original size:24 final size:24
Alignment explanation
Indices: 19395--19482 Score: 149
Period size: 24 Copynumber: 3.7 Consensus size: 24
19385 TCCTGACTAC
*
19395 GATGATGATGATGACGACGACGAG
1 GATGATGATGATGATGACGACGAG
19419 GATGATGATGATGATGACGACGAG
1 GATGATGATGATGATGACGACGAG
* *
19443 GATGATGATGATAATGATGACGAG
1 GATGATGATGATGATGACGACGAG
19467 GATGATGATGATGATG
1 GATGATGATGATGATG
19483 GTGATGATGA
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.34, C:0.07, G:0.36, T:0.23
Consensus pattern (24 bp):
GATGATGATGATGATGACGACGAG
Found at i:21559 original size:30 final size:29
Alignment explanation
Indices: 21523--21579 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
21513 GCTGCTGGAA
*
21523 ACCGGTTTAATCGGTTTTCAATCGGTTCTG
1 ACCGGTTTAATCGG-TTTCAACCGGTTCTG
*
21553 ACCGGTTTGATCGGTTTCAACCGGTTC
1 ACCGGTTTAATCGGTTTCAACCGGTTC
21580 GAACCGATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 12 0.48
30 13 0.52
ACGTcount: A:0.16, C:0.23, G:0.25, T:0.37
Consensus pattern (29 bp):
ACCGGTTTAATCGGTTTCAACCGGTTCTG
Found at i:21585 original size:29 final size:30
Alignment explanation
Indices: 21522--21596 Score: 91
Period size: 29 Copynumber: 2.5 Consensus size: 30
21512 GGCTGCTGGA
* *
21522 AACCGGTTTAATCGGTTTTCAATCGGTTCTG
1 AACCGGTTTGATCGG-TTTCAACCGGTTCTG
21553 -ACCGGTTTGATCGGTTTCAACCGGTTC-G
1 AACCGGTTTGATCGGTTTCAACCGGTTCTG
* *
21581 AACCGATTTGACCGGT
1 AACCGGTTTGATCGGT
21597 CTGACCCGAC
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
28 1 0.03
29 25 0.64
30 13 0.33
ACGTcount: A:0.19, C:0.23, G:0.25, T:0.33
Consensus pattern (30 bp):
AACCGGTTTGATCGGTTTCAACCGGTTCTG
Found at i:21615 original size:12 final size:12
Alignment explanation
Indices: 21598--21635 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
21588 TTGACCGGTC
21598 TGACCCGACCGT
1 TGACCCGACCGT
21610 TGACCCGACC--
1 TGACCCGACCGT
*
21620 CGACCCGACCGT
1 TGACCCGACCGT
21632 TGAC
1 TGAC
21636 AGTTGACCGT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 9 0.41
12 13 0.59
ACGTcount: A:0.18, C:0.45, G:0.24, T:0.13
Consensus pattern (12 bp):
TGACCCGACCGT
Found at i:28829 original size:9 final size:9
Alignment explanation
Indices: 28815--28911 Score: 50
Period size: 10 Copynumber: 10.0 Consensus size: 9
28805 GGCTGCTGGA
28815 AACCGGTTT
1 AACCGGTTT
28824 AACCGGTTTT
1 AACCGG-TTT
*
28834 CAACCAGTTCT
1 -AACCGGTT-T
* *
28845 GACTGGTTT
1 AACCGGTTT
* *
28854 CGACCGGTTCG
1 -AACCGGTT-T
28865 AACCGGTTT
1 AACCGGTTT
* *
28874 GACCGGTCTG
1 AACCGGT-TT
28884 AACCGGTTT
1 AACCGGTTT
* *
28893 GACCGGTCTG
1 AACCGGT-TT
28903 AACCGGTTT
1 AACCGGTTT
28912 GACCAGTCTG
Statistics
Matches: 65, Mismatches: 16, Indels: 14
0.68 0.17 0.15
Matches are distributed among these distances:
9 21 0.32
10 38 0.58
11 6 0.09
ACGTcount: A:0.18, C:0.26, G:0.27, T:0.30
Consensus pattern (9 bp):
AACCGGTTT
Found at i:28879 original size:19 final size:19
Alignment explanation
Indices: 28849--28922 Score: 114
Period size: 19 Copynumber: 3.8 Consensus size: 19
28839 AGTTCTGACT
28849 GGTTTCGACCGGT-TCGAACC
1 GGTTT-GACCGGTCT-GAACC
28869 GGTTTGACCGGTCTGAACC
1 GGTTTGACCGGTCTGAACC
28888 GGTTTGACCGGTCTGAACC
1 GGTTTGACCGGTCTGAACC
*
28907 GGTTTGACCAGTCTGA
1 GGTTTGACCGGTCTGA
28923 CCTGACCGAC
Statistics
Matches: 52, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
19 46 0.88
20 6 0.12
ACGTcount: A:0.16, C:0.26, G:0.31, T:0.27
Consensus pattern (19 bp):
GGTTTGACCGGTCTGAACC
Found at i:28897 original size:38 final size:39
Alignment explanation
Indices: 28836--28922 Score: 117
Period size: 38 Copynumber: 2.3 Consensus size: 39
28826 CCGGTTTTCA
*
28836 ACCAGTTCTG-ACTGGTTTCGACCGGT-TCGAACCGGTTTG
1 ACCAG-TCTGAACCGGTTTCGACCGGTCT-GAACCGGTTTG
*
28875 ACCGGTCTGAACCGGTTT-GACCGGTCTGAACCGGTTTG
1 ACCAGTCTGAACCGGTTTCGACCGGTCTGAACCGGTTTG
28913 ACCAGTCTGA
1 ACCAGTCTGA
28923 CCTGACCGAC
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
38 31 0.72
39 12 0.28
ACGTcount: A:0.17, C:0.26, G:0.29, T:0.28
Consensus pattern (39 bp):
ACCAGTCTGAACCGGTTTCGACCGGTCTGAACCGGTTTG
Found at i:28956 original size:17 final size:17
Alignment explanation
Indices: 28934--28971 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
28924 CTGACCGACC
28934 GACCCGACCCAACCGTT
1 GACCCGACCCAACCGTT
*
28951 GACCCGACCCGACCGTT
1 GACCCGACCCAACCGTT
28968 GACC
1 GACC
28972 GTTGACCGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.21, C:0.47, G:0.21, T:0.11
Consensus pattern (17 bp):
GACCCGACCCAACCGTT
Found at i:28973 original size:7 final size:7
Alignment explanation
Indices: 28961--28991 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
28951 GACCCGACCC
28961 GACCGTT
1 GACCGTT
28968 GACCGTT
1 GACCGTT
28975 GACCGTT
1 GACCGTT
*
28982 AACCGTT
1 GACCGTT
28989 GAC
1 GAC
28992 TTTCTTTGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.19, C:0.29, G:0.26, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:31829 original size:64 final size:66
Alignment explanation
Indices: 31670--31829 Score: 222
Period size: 65 Copynumber: 2.5 Consensus size: 66
31660 GAATAAATTG
* * *
31670 AACATCGAATGCATTTCATGGACCGATGCA-CATACTATGCATCGATGCACTCAGAGTTTTATGA
1 AACATCGAATGCATTTCATGCATCGATGCACCAGACTATGCATCGATGCACTCAGAGTTTTATGA
31734 A
66 A
*
31735 AACATCGAATGCATTTCATGCATCGATGCACCAGA-TATGCATCGATTCACTCAG-GCTATTT-T
1 AACATCGAATGCATTTCATGCATCGATGCACCAGACTATGCATCGATGCACTCAGAG-T-TTTAT
31797 G-A
64 GAA
*
31799 AACATCGAATGCATTTTATGCATCGATGCAC
1 AACATCGAATGCATTTCATGCATCGATGCAC
31830 TCTTAGTGCA
Statistics
Matches: 87, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
64 32 0.37
65 49 0.56
66 6 0.07
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (66 bp):
AACATCGAATGCATTTCATGCATCGATGCACCAGACTATGCATCGATGCACTCAGAGTTTTATGA
A
Found at i:32139 original size:17 final size:17
Alignment explanation
Indices: 32119--32157 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
32109 TTCAAGCCAA
32119 ATTTCCTTTCAATATTC
1 ATTTCCTTTCAATATTC
*
32136 ATTTTGCTTTCAATATTC
1 A-TTTCCTTTCAATATTC
32154 ATTT
1 ATTT
32158 TGCTTTCAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.23, C:0.18, G:0.03, T:0.56
Consensus pattern (17 bp):
ATTTCCTTTCAATATTC
Found at i:32147 original size:18 final size:18
Alignment explanation
Indices: 32124--32166 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
32114 GCCAAATTTC
32124 CTTTCAATATTCATTTTG
1 CTTTCAATATTCATTTTG
32142 CTTTCAATATTCATTTTG
1 CTTTCAATATTCATTTTG
32160 CTTTCAA
1 CTTTCAA
32167 GAACACAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.23, C:0.19, G:0.05, T:0.53
Consensus pattern (18 bp):
CTTTCAATATTCATTTTG
Found at i:37340 original size:23 final size:23
Alignment explanation
Indices: 37292--37402 Score: 145
Period size: 23 Copynumber: 4.9 Consensus size: 23
37282 ATGAATCCCT
*
37292 TTGAATGTGCATCGAT--ACACC
1 TTGAATGTGCACCGATGCACACC
* * **
37313 ATGAAAGTGCAGTGATGCACACC
1 TTGAATGTGCACCGATGCACACC
*
37336 TTGAATGTGCACCAATGCACACC
1 TTGAATGTGCACCGATGCACACC
37359 TTGAATGTGCACCGATGCACACC
1 TTGAATGTGCACCGATGCACACC
*
37382 TTGAATGTGCATCGATGCACA
1 TTGAATGTGCACCGATGCACA
37403 AGGCCATGCA
Statistics
Matches: 77, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
21 12 0.16
23 65 0.84
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.23
Consensus pattern (23 bp):
TTGAATGTGCACCGATGCACACC
Found at i:39592 original size:2 final size:2
Alignment explanation
Indices: 39585--39654 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
39575 CAGCTTAAGC
39585 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
39627 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
39655 ATCAATTTAC
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:40262 original size:46 final size:45
Alignment explanation
Indices: 40204--40310 Score: 137
Period size: 45 Copynumber: 2.4 Consensus size: 45
40194 TGCACATACT
*
40204 ATGCATCGATGCACTTAGAG-T-TTTATGAAAACATCGAATGCATTTG
1 ATGCATCGATGCACTCAG-GCTATTT-TG-AAACATCGAATGCATTTG
* *
40250 ATGTATCGATGCACTCAGGCTATTTTGAAACATCGAATGCATTTT
1 ATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCATTTG
*
40295 ATGCATCGGTGCACTC
1 ATGCATCGATGCACTC
40311 TTAGTGCACC
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
45 32 0.59
46 19 0.35
47 3 0.06
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.33
Consensus pattern (45 bp):
ATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCATTTG
Found at i:49199 original size:5 final size:5
Alignment explanation
Indices: 49189--49213 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
49179 ACCGGTCATA
49189 ACCCG ACCCG ACCCG ACCCG ACCCG
1 ACCCG ACCCG ACCCG ACCCG ACCCG
49214 TTTACCTGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.60, G:0.20, T:0.00
Consensus pattern (5 bp):
ACCCG
Found at i:49255 original size:18 final size:18
Alignment explanation
Indices: 49232--49269 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
49222 ACCCGTTTAT
49232 CCGACCAGTTGACCCGAC
1 CCGACCAGTTGACCCGAC
*
49250 CCGACCCGTTGACCCGAC
1 CCGACCAGTTGACCCGAC
49268 CC
1 CC
49270 ATTGACCCGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.18, C:0.50, G:0.21, T:0.11
Consensus pattern (18 bp):
CCGACCAGTTGACCCGAC
Found at i:49263 original size:8 final size:8
Alignment explanation
Indices: 49252--49316 Score: 68
Period size: 8 Copynumber: 8.5 Consensus size: 8
49242 GACCCGACCC
49252 GACCCGTT
1 GACCCGTT
49260 GACCC---
1 GACCCGTT
*
49265 GACCCATT
1 GACCCGTT
49273 GACCCGTT
1 GACCCGTT
49281 GA-CCGTT
1 GACCCGTT
49288 GACCCGTT
1 GACCCGTT
49296 GA-CCGTT
1 GACCCGTT
49303 GACCGGCGTT
1 GACC--CGTT
49313 GACC
1 GACC
49317 TTTGTTGACC
Statistics
Matches: 49, Mismatches: 1, Indels: 12
0.79 0.02 0.19
Matches are distributed among these distances:
5 5 0.10
7 14 0.29
8 22 0.45
10 8 0.16
ACGTcount: A:0.15, C:0.37, G:0.26, T:0.22
Consensus pattern (8 bp):
GACCCGTT
Found at i:49269 original size:13 final size:13
Alignment explanation
Indices: 49203--49252 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
49193 GACCCGACCC
49203 GACCCGACCCGTT
1 GACCCGACCCGTT
* *
49216 TACCTGACCCGTT
1 GACCCGACCCGTT
* * *
49229 TATCCGACCAGTT
1 GACCCGACCCGTT
49242 GACCCGACCCG
1 GACCCGACCCG
49253 ACCCGTTGAC
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.18, C:0.42, G:0.20, T:0.20
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:49274 original size:13 final size:13
Alignment explanation
Indices: 49247--49278 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
49237 CAGTTGACCC
*
49247 GACCCGACCCGTT
1 GACCCGACCCATT
49260 GACCCGACCCATT
1 GACCCGACCCATT
49273 GACCCG
1 GACCCG
49279 TTGACCGTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.19, C:0.47, G:0.22, T:0.12
Consensus pattern (13 bp):
GACCCGACCCATT
Found at i:49288 original size:7 final size:7
Alignment explanation
Indices: 49271--49307 Score: 56
Period size: 7 Copynumber: 5.0 Consensus size: 7
49261 ACCCGACCCA
49271 TTGACCCG
1 TTGA-CCG
49279 TTGACCG
1 TTGACCG
49286 TTGACCCG
1 TTGA-CCG
49294 TTGACCG
1 TTGACCG
49301 TTGACCG
1 TTGACCG
49308 GCGTTGACCT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 17 0.61
8 11 0.39
ACGTcount: A:0.14, C:0.32, G:0.27, T:0.27
Consensus pattern (7 bp):
TTGACCG
Found at i:49291 original size:15 final size:15
Alignment explanation
Indices: 49271--49316 Score: 74
Period size: 15 Copynumber: 2.9 Consensus size: 15
49261 ACCCGACCCA
49271 TTGACCCGTTGACCG
1 TTGACCCGTTGACCG
49286 TTGACCCGTTGACCG
1 TTGACCCGTTGACCG
49301 TTGACCGGCGTTGACC
1 TTGACC--CGTTGACC
49317 TTTGTTGACC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
15 21 0.72
17 8 0.28
ACGTcount: A:0.13, C:0.33, G:0.28, T:0.26
Consensus pattern (15 bp):
TTGACCCGTTGACCG
Found at i:50621 original size:18 final size:18
Alignment explanation
Indices: 50595--50629 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
50585 TCGAAAGGAC
*
50595 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
50613 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
50630 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:52188 original size:31 final size:30
Alignment explanation
Indices: 52118--52191 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 30
52108 TAATGTGACA
*
52118 CTTAGGTAGGCTCTGCGGCCCTGAGATCATT
1 CTTAGGTAGGC-CTGCGGCCCTAAGATCATT
** **
52149 CTCGGGTAGGCCTGCGGCCCTAAGATGTGTT
1 CTTAGGTAGGCCTGCGGCCCTAAGAT-CATT
52180 CTTAGGTAGGCC
1 CTTAGGTAGGCC
52192 CCACGGCCCC
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
30 14 0.40
31 21 0.60
ACGTcount: A:0.15, C:0.26, G:0.32, T:0.27
Consensus pattern (30 bp):
CTTAGGTAGGCCTGCGGCCCTAAGATCATT
Found at i:54235 original size:5 final size:5
Alignment explanation
Indices: 54225--54249 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
54215 ACCGGTCATA
54225 ACCCG ACCCG ACCCG ACCCG ACCCG
1 ACCCG ACCCG ACCCG ACCCG ACCCG
54250 TTTACCTGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.60, G:0.20, T:0.00
Consensus pattern (5 bp):
ACCCG
Found at i:54291 original size:18 final size:18
Alignment explanation
Indices: 54268--54305 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
54258 ACCCGTTTAT
54268 CCGACCAGTTGACCCGAC
1 CCGACCAGTTGACCCGAC
*
54286 CCGACCCGTTGACCCGAC
1 CCGACCAGTTGACCCGAC
54304 CC
1 CC
54306 ATTGACCCGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.18, C:0.50, G:0.21, T:0.11
Consensus pattern (18 bp):
CCGACCAGTTGACCCGAC
Found at i:54299 original size:8 final size:8
Alignment explanation
Indices: 54288--54352 Score: 68
Period size: 8 Copynumber: 8.5 Consensus size: 8
54278 GACCCGACCC
54288 GACCCGTT
1 GACCCGTT
54296 GACCC---
1 GACCCGTT
*
54301 GACCCATT
1 GACCCGTT
54309 GACCCGTT
1 GACCCGTT
54317 GA-CCGTT
1 GACCCGTT
54324 GACCCGTT
1 GACCCGTT
54332 GA-CCGTT
1 GACCCGTT
54339 GACCGGCGTT
1 GACC--CGTT
54349 GACC
1 GACC
54353 TTTGTTGACC
Statistics
Matches: 49, Mismatches: 1, Indels: 12
0.79 0.02 0.19
Matches are distributed among these distances:
5 5 0.10
7 14 0.29
8 22 0.45
10 8 0.16
ACGTcount: A:0.15, C:0.37, G:0.26, T:0.22
Consensus pattern (8 bp):
GACCCGTT
Found at i:54305 original size:13 final size:13
Alignment explanation
Indices: 54239--54288 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
54229 GACCCGACCC
54239 GACCCGACCCGTT
1 GACCCGACCCGTT
* *
54252 TACCTGACCCGTT
1 GACCCGACCCGTT
* * *
54265 TATCCGACCAGTT
1 GACCCGACCCGTT
54278 GACCCGACCCG
1 GACCCGACCCG
54289 ACCCGTTGAC
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.18, C:0.42, G:0.20, T:0.20
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:54310 original size:13 final size:13
Alignment explanation
Indices: 54283--54314 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
54273 CAGTTGACCC
*
54283 GACCCGACCCGTT
1 GACCCGACCCATT
54296 GACCCGACCCATT
1 GACCCGACCCATT
54309 GACCCG
1 GACCCG
54315 TTGACCGTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.19, C:0.47, G:0.22, T:0.12
Consensus pattern (13 bp):
GACCCGACCCATT
Found at i:54324 original size:7 final size:7
Alignment explanation
Indices: 54307--54343 Score: 56
Period size: 7 Copynumber: 5.0 Consensus size: 7
54297 ACCCGACCCA
54307 TTGACCCG
1 TTGA-CCG
54315 TTGACCG
1 TTGACCG
54322 TTGACCCG
1 TTGA-CCG
54330 TTGACCG
1 TTGACCG
54337 TTGACCG
1 TTGACCG
54344 GCGTTGACCT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 17 0.61
8 11 0.39
ACGTcount: A:0.14, C:0.32, G:0.27, T:0.27
Consensus pattern (7 bp):
TTGACCG
Found at i:54327 original size:15 final size:15
Alignment explanation
Indices: 54307--54352 Score: 74
Period size: 15 Copynumber: 2.9 Consensus size: 15
54297 ACCCGACCCA
54307 TTGACCCGTTGACCG
1 TTGACCCGTTGACCG
54322 TTGACCCGTTGACCG
1 TTGACCCGTTGACCG
54337 TTGACCGGCGTTGACC
1 TTGACC--CGTTGACC
54353 TTTGTTGACC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
15 21 0.72
17 8 0.28
ACGTcount: A:0.13, C:0.33, G:0.28, T:0.26
Consensus pattern (15 bp):
TTGACCCGTTGACCG
Found at i:55658 original size:18 final size:18
Alignment explanation
Indices: 55632--55666 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
55622 TCGAAAGGAC
*
55632 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
55650 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
55667 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:57225 original size:31 final size:30
Alignment explanation
Indices: 57155--57228 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 30
57145 TAATGTGACA
*
57155 CTTAGGTAGGCTCTGCGGCCCTGAGATCATT
1 CTTAGGTAGGC-CTGCGGCCCTAAGATCATT
** **
57186 CTCGGGTAGGCCTGCGGCCCTAAGATGTGTT
1 CTTAGGTAGGCCTGCGGCCCTAAGAT-CATT
57217 CTTAGGTAGGCC
1 CTTAGGTAGGCC
57229 CCACGGCCCC
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
30 14 0.40
31 21 0.60
ACGTcount: A:0.15, C:0.26, G:0.32, T:0.27
Consensus pattern (30 bp):
CTTAGGTAGGCCTGCGGCCCTAAGATCATT
Found at i:62603 original size:21 final size:21
Alignment explanation
Indices: 62579--62626 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
62569 GCCTCTACCT
62579 CGGCCTCTGAATCCTCGTCCA
1 CGGCCTCTGAATCCTCGTCCA
62600 CGGCCTCTGAATCCTCGTCCA
1 CGGCCTCTGAATCCTCGTCCA
62621 CGGCCT
1 CGGCCT
62627 GATGCTGGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.12, C:0.44, G:0.21, T:0.23
Consensus pattern (21 bp):
CGGCCTCTGAATCCTCGTCCA
Found at i:63740 original size:2 final size:2
Alignment explanation
Indices: 63733--63757 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
63723 GCTACAAATT
63733 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
63758 TATATATATA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:63762 original size:2 final size:2
Alignment explanation
Indices: 63757--63783 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
63747 ACACACACAC
63757 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
63784 ATAAACCGCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:71837 original size:20 final size:21
Alignment explanation
Indices: 71814--71891 Score: 70
Period size: 20 Copynumber: 3.7 Consensus size: 21
71804 TTGGTGCAGA
*
71814 GGGAATCGATACCCCCATGA-
1 GGGAACCGATACCCCCATGAG
* *
71834 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATACCCCC-ATG-AG
* *
71857 GGGAACCGATTCCCCCCT-AG
1 GGGAACCGATACCCCCATGAG
*
71877 GGGAATCGATACCCC
1 GGGAACCGATACCCC
71892 ATAGGGTTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
20 29 0.59
21 2 0.04
22 2 0.04
23 16 0.33
ACGTcount: A:0.24, C:0.33, G:0.26, T:0.17
Consensus pattern (21 bp):
GGGAACCGATACCCCCATGAG
Found at i:71896 original size:19 final size:20
Alignment explanation
Indices: 71855--71897 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
71845 CCCCCTTTGA
* *
71855 AGGGGAACCGATTCCCCCCT
1 AGGGGAACCGATTACCCCAT
*
71875 AGGGGAATCGA-TACCCCAT
1 AGGGGAACCGATTACCCCAT
71894 AGGG
1 AGGG
71898 TTTTGGATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.26, C:0.30, G:0.30, T:0.14
Consensus pattern (20 bp):
AGGGGAACCGATTACCCCAT
Found at i:76027 original size:20 final size:20
Alignment explanation
Indices: 76004--76085 Score: 74
Period size: 20 Copynumber: 4.0 Consensus size: 20
75994 GTTTCCAATT
*
76004 TCACAACGCGAATATGTAAA
1 TCACAACGCGAATTTGTAAA
** * **
76024 TCACATTGCGATTTTCCAAA
1 TCACAACGCGAATTTGTAAA
* *
76044 TTCGCAACGCGAATCTGTAAA
1 -TCACAACGCGAATTTGTAAA
*
76065 TCGCAACGCGAATTTGTAAA
1 TCACAACGCGAATTTGTAAA
76085 T
1 T
76086 TGCAACACAG
Statistics
Matches: 47, Mismatches: 14, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
20 34 0.72
21 13 0.28
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (20 bp):
TCACAACGCGAATTTGTAAA
Found at i:76086 original size:41 final size:40
Alignment explanation
Indices: 76007--76091 Score: 98
Period size: 41 Copynumber: 2.1 Consensus size: 40
75997 TCCAATTTCA
** *
76007 CAACGCGAATATGTAAATCACATTGCGATTTTCCAAATTCG
1 CAACGCGAATATGTAAATCACAACGCGAATTTCCAAATT-G
* * **
76048 CAACGCGAATCTGTAAATCGCAACGCGAATTTGTAAATTG
1 CAACGCGAATATGTAAATCACAACGCGAATTTCCAAATTG
76088 CAAC
1 CAAC
76092 ACAGAAGTCA
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
40 5 0.14
41 32 0.86
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.26
Consensus pattern (40 bp):
CAACGCGAATATGTAAATCACAACGCGAATTTCCAAATTG
Found at i:76109 original size:40 final size:41
Alignment explanation
Indices: 76065--76170 Score: 130
Period size: 40 Copynumber: 2.7 Consensus size: 41
76055 AATCTGTAAA
* * *
76065 TCGCAACGCGAATTTGT-AAATT-GCAACACAGAAGTCAAAT
1 TCGCAACGCG-AGTAGTCAAATTCGCAACACAAAAGTCAAAT
76105 TCGCAACGCG-GTAGTCAAATTCGCAACACAAAAGTCAAAT
1 TCGCAACGCGAGTAGTCAAATTCGCAACACAAAAGTCAAAT
* *
76145 TCGCAATGCGA-TAGTCAAATCCGCAA
1 TCGCAACGCGAGTAGTCAAATTCGCAA
76171 TGTGAATAGT
Statistics
Matches: 58, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
38 3 0.05
39 5 0.09
40 50 0.86
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.20
Consensus pattern (41 bp):
TCGCAACGCGAGTAGTCAAATTCGCAACACAAAAGTCAAAT
Found at i:76172 original size:20 final size:20
Alignment explanation
Indices: 76040--76170 Score: 101
Period size: 20 Copynumber: 6.5 Consensus size: 20
76030 TGCGATTTTC
*
76040 CAAATTCGCAACGCGAATCTGT
1 CAAATTCGCAACGCG-AT-AGT
*
76062 -AAA-TCGCAACGCGAATTTGT
1 CAAATTCGCAACGCG-A-TAGT
*
76082 -AAATT-GCAACACAGA-AGT
1 CAAATTCGCAACGC-GATAGT
*
76100 CAAATTCGCAACGCGGTAGT
1 CAAATTCGCAACGCGATAGT
* * *
76120 CAAATTCGCAACACAAAAGT
1 CAAATTCGCAACGCGATAGT
*
76140 CAAATTCGCAATGCGATAGT
1 CAAATTCGCAACGCGATAGT
*
76160 CAAATCCGCAA
1 CAAATTCGCAA
76171 TGTGAATAGT
Statistics
Matches: 90, Mismatches: 13, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
18 2 0.02
19 6 0.07
20 76 0.84
21 6 0.07
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.20
Consensus pattern (20 bp):
CAAATTCGCAACGCGATAGT
Found at i:76190 original size:21 final size:20
Alignment explanation
Indices: 76145--76211 Score: 73
Period size: 20 Copynumber: 3.3 Consensus size: 20
76135 AAAGTCAAAT
* *
76145 TCGCAATGCG-ATAGTCAAA
1 TCGCAATGTGAATAGTAAAA
76164 TCCGCAATGTGAATAGTAAAAA
1 T-CGCAATGTGAATAGT-AAAA
**
76186 TCGCAACATGAATAGTAAAA
1 TCGCAATGTGAATAGTAAAA
76206 TCGCAA
1 TCGCAA
76212 CGAATCTATA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
19 1 0.02
20 18 0.44
21 18 0.44
22 4 0.10
ACGTcount: A:0.43, C:0.18, G:0.18, T:0.21
Consensus pattern (20 bp):
TCGCAATGTGAATAGTAAAA
Found at i:76601 original size:21 final size:21
Alignment explanation
Indices: 76575--76662 Score: 117
Period size: 20 Copynumber: 4.3 Consensus size: 21
76565 GCGATTTTCT
*
76575 GATTTTCTAAAGTCGCGTTGC
1 GATTTTCTAAATTCGCGTTGC
*
76596 GATTTTC-CAATTCGCGTTGC
1 GATTTTCTAAATTCGCGTTGC
* *
76616 GATTTTCCAAATTCACGTTGC
1 GATTTTCTAAATTCGCGTTGC
*
76637 GATTTT-TCAATTCGCGTTGC
1 GATTTTCTAAATTCGCGTTGC
76657 GATTTT
1 GATTTT
76663 ACTATTTACG
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
20 35 0.59
21 24 0.41
ACGTcount: A:0.18, C:0.20, G:0.19, T:0.42
Consensus pattern (21 bp):
GATTTTCTAAATTCGCGTTGC
Found at i:76612 original size:20 final size:20
Alignment explanation
Indices: 76590--76702 Score: 136
Period size: 20 Copynumber: 5.6 Consensus size: 20
76580 TCTAAAGTCG
* *
76590 CGTTGCGATTTTCCAATTCG
1 CGTTGCGATTTTACAATTCA
*
76610 CGTTGCGATTTTCCAAATTCA
1 CGTTGCGATTTTAC-AATTCA
* *
76631 CGTTGCGATTTTTCAATTCG
1 CGTTGCGATTTTACAATTCA
* *
76651 CGTTGCGATTTTACTATTTA
1 CGTTGCGATTTTACAATTCA
*
76671 CGTTGCGATTTTACTATTCA
1 CGTTGCGATTTTACAATTCA
*
76691 CGCTGCGATTTT
1 CGTTGCGATTTT
76703 GGAAACTGAG
Statistics
Matches: 83, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
20 65 0.78
21 18 0.22
ACGTcount: A:0.18, C:0.21, G:0.18, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTACAATTCA
Found at i:76635 original size:41 final size:41
Alignment explanation
Indices: 76575--76702 Score: 150
Period size: 41 Copynumber: 3.1 Consensus size: 41
76565 GCGATTTTCT
* * * *
76575 GATTTTCTAAAGTCGCGTTGCGATTTTCCAATTCGCGTTGC
1 GATTTTCCAAATTCACGTTGCGATTTTACAATTCGCGTTGC
*
76616 GATTTTCCAAATTCACGTTGCGATTTTTCAATTCGCGTTGC
1 GATTTTCCAAATTCACGTTGCGATTTTACAATTCGCGTTGC
* * * * * *
76657 GATTTTAC-TATTTACGTTGCGATTTTACTATTCACGCTGC
1 GATTTTCCAAATTCACGTTGCGATTTTACAATTCGCGTTGC
76697 GATTTT
1 GATTTT
76703 GGAAACTGAG
Statistics
Matches: 76, Mismatches: 11, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
40 32 0.42
41 44 0.58
ACGTcount: A:0.19, C:0.20, G:0.18, T:0.43
Consensus pattern (41 bp):
GATTTTCCAAATTCACGTTGCGATTTTACAATTCGCGTTGC
Found at i:76662 original size:61 final size:60
Alignment explanation
Indices: 76587--76702 Score: 160
Period size: 61 Copynumber: 1.9 Consensus size: 60
76577 TTTTCTAAAG
* * * *
76587 TCGCGTTGCGATTTTCCAATTCGCGTTGCGATTTTCCAAATTCACGTTGCGATTTTTCAAT
1 TCGCGTTGCGATTTTACAATTCACGTTGCGATTTTAC-AATTCACGCTGCGATTTTTCAAT
* * *
76648 TCGCGTTGCGATTTTACTATTTACGTTGCGATTTTACTATTCACGCTGCGATTTT
1 TCGCGTTGCGATTTTACAATTCACGTTGCGATTTTACAATTCACGCTGCGATTTT
76703 GGAAACTGAG
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
60 16 0.33
61 32 0.67
ACGTcount: A:0.17, C:0.22, G:0.18, T:0.43
Consensus pattern (60 bp):
TCGCGTTGCGATTTTACAATTCACGTTGCGATTTTACAATTCACGCTGCGATTTTTCAAT
Found at i:82430 original size:221 final size:221
Alignment explanation
Indices: 82041--82459 Score: 669
Period size: 221 Copynumber: 1.9 Consensus size: 221
82031 AATTGTCCAT
* * *
82041 TCACATAGTTAACTATCTTCACTAAGGAATTTGTTCAAACACAAGGTACCATACAGCCACATGAG
1 TCACAGAGTTAACTATCTTCAATAAGGAATTTCTTCAAACACAAGGTACCATACAGCCACATGAG
* *
82106 CAGATATAAATACTAAAGCCTTAAATCGGACTGAATAATCGAGAAAGACAATCTAACTAGTCCTC
66 CAGATATAAATACTAAAACCGTAAATCGGACTGAATAATCGAGAAAGACAATCTAACTAGTCCTC
* ** *
82171 ACATACGCATAGGACATCCAAAGACATGCACACTAAGTTGTATACATATTTATACATACATAGTT
131 ACATACACATAGGACATCCAAAGACATGCACACTAAGTTACATACATATTTATACATACAAAGTT
82236 ACACACACATATCTATAAAGAATACA
196 ACACACACATATCTATAAAGAATACA
* * *
82262 TCACAGAGTTAACTATCTTCAATATGGAATTTCTTCAAACACAATGTACCATACAGCTACATGAG
1 TCACAGAGTTAACTATCTTCAATAAGGAATTTCTTCAAACACAAGGTACCATACAGCCACATGAG
*
82327 CAGATATAAATA-TGAAAACCGTAAATCGGATTGAATAATCGAGAAAGACAATCTAACTAGTCCT
66 CAGATATAAATACT-AAAACCGTAAATCGGACTGAATAATCGAGAAAGACAATCTAACTAGTCCT
** * *
82391 TGCATACACATAGGACATCCAAAGACGTGCACACTAAGTTACATACATATTTATACGTACAAAGT
130 CACATACACATAGGACATCCAAAGACATGCACACTAAGTTACATACATATTTATACATACAAAGT
82456 TACA
195 TACA
82460 TTATATACAG
Statistics
Matches: 180, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
220 1 0.01
221 179 0.99
ACGTcount: A:0.41, C:0.21, G:0.13, T:0.25
Consensus pattern (221 bp):
TCACAGAGTTAACTATCTTCAATAAGGAATTTCTTCAAACACAAGGTACCATACAGCCACATGAG
CAGATATAAATACTAAAACCGTAAATCGGACTGAATAATCGAGAAAGACAATCTAACTAGTCCTC
ACATACACATAGGACATCCAAAGACATGCACACTAAGTTACATACATATTTATACATACAAAGTT
ACACACACATATCTATAAAGAATACA
Found at i:84127 original size:30 final size:30
Alignment explanation
Indices: 84093--84153 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 30
84083 GGGCGGAGCT
*
84093 AGAAAATTTTATTTT-GGAG-GTCAAATTTAG
1 AGAAAA-TTTATTTTAGG-GTGTCAAAATTAG
84123 AGAAAATTTATTTTAGGGTGTCAAAATTAG
1 AGAAAATTTATTTTAGGGTGTCAAAATTAG
84153 A
1 A
84154 AATTGTATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 9 0.32
30 19 0.68
ACGTcount: A:0.39, C:0.03, G:0.20, T:0.38
Consensus pattern (30 bp):
AGAAAATTTATTTTAGGGTGTCAAAATTAG
Found at i:91679 original size:16 final size:15
Alignment explanation
Indices: 91638--91680 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
91628 CTTTGACCAC
91638 AGTCAATTTTTGAAA
1 AGTCAATTTTTGAAA
*
91653 AGTTAAAATTTTTGAAA
1 AG-T-CAATTTTTGAAA
91670 AGTCATATTTT
1 AGTCA-ATTTT
91681 ATGTTTTTCG
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
15 3 0.13
16 7 0.30
17 13 0.57
ACGTcount: A:0.40, C:0.05, G:0.12, T:0.44
Consensus pattern (15 bp):
AGTCAATTTTTGAAA
Found at i:93078 original size:24 final size:24
Alignment explanation
Indices: 93050--93152 Score: 134
Period size: 24 Copynumber: 4.3 Consensus size: 24
93040 ATATTTTATC
*
93050 TGATTTCTGTTCTGAATTCTGTTA
1 TGATTTCTGCTCTGAATTCTGTTA
* * *
93074 TGATTTCCGCTCTGAATTTTGTTC
1 TGATTTCTGCTCTGAATTCTGTTA
* *
93098 TAATTTATGCTCTGAATTCTGTTA
1 TGATTTCTGCTCTGAATTCTGTTA
* *
93122 TGATTTCTGCTCTGATTTCTGTTC
1 TGATTTCTGCTCTGAATTCTGTTA
93146 TGATTTC
1 TGATTTC
93153 GAATATCTCC
Statistics
Matches: 66, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 66 1.00
ACGTcount: A:0.16, C:0.17, G:0.16, T:0.52
Consensus pattern (24 bp):
TGATTTCTGCTCTGAATTCTGTTA
Found at i:93112 original size:48 final size:48
Alignment explanation
Indices: 93060--93151 Score: 150
Period size: 48 Copynumber: 1.9 Consensus size: 48
93050 TGATTTCTGT
93060 TCTGAATTCTGTTATGATTTCCGCTCTGAATTT-TGTTCTAATTTATGC
1 TCTGAATTCTGTTATGATTTCCGCTCTG-ATTTCTGTTCTAATTTATGC
* *
93108 TCTGAATTCTGTTATGATTTCTGCTCTGATTTCTGTTCTGATTT
1 TCTGAATTCTGTTATGATTTCCGCTCTGATTTCTGTTCTAATTT
93152 CGAATATCTC
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
47 4 0.10
48 37 0.90
ACGTcount: A:0.16, C:0.16, G:0.15, T:0.52
Consensus pattern (48 bp):
TCTGAATTCTGTTATGATTTCCGCTCTGATTTCTGTTCTAATTTATGC
Found at i:93149 original size:12 final size:12
Alignment explanation
Indices: 93048--93152 Score: 104
Period size: 12 Copynumber: 8.8 Consensus size: 12
93038 GAATATTTTA
93048 TCTGATTTCTGT
1 TCTGATTTCTGT
*
93060 TCTGAATTCTGT
1 TCTGATTTCTGT
* * *
93072 TATGATTTCCGC
1 TCTGATTTCTGT
93084 TCTGAATTT-TGT
1 TCTG-ATTTCTGT
* * *
93096 TCTAATTTATGC
1 TCTGATTTCTGT
*
93108 TCTGAATTCTGT
1 TCTGATTTCTGT
* *
93120 TATGATTTCTGC
1 TCTGATTTCTGT
93132 TCTGATTTCTGT
1 TCTGATTTCTGT
93144 TCTGATTTC
1 TCTGATTTC
93153 GAATATCTCC
Statistics
Matches: 72, Mismatches: 19, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
11 4 0.06
12 64 0.89
13 4 0.06
ACGTcount: A:0.15, C:0.17, G:0.15, T:0.52
Consensus pattern (12 bp):
TCTGATTTCTGT
Found at i:101270 original size:14 final size:14
Alignment explanation
Indices: 101251--101278 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
101241 CGTGAACGTC
101251 CGGTTATGTTCGTT
1 CGGTTATGTTCGTT
101265 CGGTTATGTTCGTT
1 CGGTTATGTTCGTT
101279 TATGTTCATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.14, G:0.29, T:0.50
Consensus pattern (14 bp):
CGGTTATGTTCGTT
Found at i:102380 original size:10 final size:10
Alignment explanation
Indices: 102365--102389 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
102355 GGTCTCCAAA
102365 GTTTATGTTC
1 GTTTATGTTC
102375 GTTTATGTTC
1 GTTTATGTTC
102385 GTTTA
1 GTTTA
102390 GTTATTAAAT
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:0.12, C:0.08, G:0.20, T:0.60
Consensus pattern (10 bp):
GTTTATGTTC
Found at i:102586 original size:14 final size:14
Alignment explanation
Indices: 102567--102599 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
102557 ATAGTCTAAC
102567 GATTTACAAAGTAG
1 GATTTACAAAGTAG
102581 GATTTACAAAGTAG
1 GATTTACAAAGTAG
*
102595 TATTT
1 GATTT
102600 GTTCAGAGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.39, C:0.06, G:0.18, T:0.36
Consensus pattern (14 bp):
GATTTACAAAGTAG
Found at i:103091 original size:32 final size:32
Alignment explanation
Indices: 103049--103132 Score: 116
Period size: 32 Copynumber: 2.7 Consensus size: 32
103039 TTTTAAACGA
*
103049 TTCAACAATTTAATCCCTTCACGTGTATAAGT
1 TTCAACAATTTAATCCCTTCACATGTATAAGT
* * *
103081 TTCACCAATTTAACCCCTTCACATTTATAAGT
1 TTCAACAATTTAATCCCTTCACATGTATAAGT
*
103113 TTCATCAATTTAAT-CCTTCA
1 TTCAACAATTTAATCCCTTCA
103133 AACTCCGTTG
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
31 6 0.13
32 40 0.87
ACGTcount: A:0.31, C:0.25, G:0.05, T:0.39
Consensus pattern (32 bp):
TTCAACAATTTAATCCCTTCACATGTATAAGT
Found at i:103409 original size:23 final size:23
Alignment explanation
Indices: 103367--103411 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
103357 TGTTTGTGTT
*
103367 TGTTTGTTTATTATTCGCGAACA
1 TGTTTGTTTAATATTCGCGAACA
* *
103390 TGTTTGTTTAATGTTTGCGAAC
1 TGTTTGTTTAATATTCGCGAAC
103412 GTTTCATTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.11, G:0.20, T:0.49
Consensus pattern (23 bp):
TGTTTGTTTAATATTCGCGAACA
Found at i:103426 original size:23 final size:23
Alignment explanation
Indices: 103396--103469 Score: 69
Period size: 23 Copynumber: 3.2 Consensus size: 23
103386 AACATGTTTG
**
103396 TTTAATGTTTGCGAACGT-TTCA
1 TTTAATGTTCACGAACGTGTTCA
103418 TTTATATGTTCACGAACGTGTTCA
1 TTTA-ATGTTCACGAACGTGTTCA
** * * *
103442 TTTAGCGTTCACAAACATGTTCT
1 TTTAATGTTCACGAACGTGTTCA
103465 TTTAA
1 TTTAA
103470 AGTCCATTTA
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
22 4 0.10
23 30 0.71
24 8 0.19
ACGTcount: A:0.26, C:0.16, G:0.15, T:0.43
Consensus pattern (23 bp):
TTTAATGTTCACGAACGTGTTCA
Found at i:103519 original size:22 final size:22
Alignment explanation
Indices: 103474--103523 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
103464 TTTTAAAGTC
103474 CATTTAGCGTTCATTTAGTATT
1 CATTTAGCGTTCATTTAGTATT
* * *
103496 CATTTAGCGTTCGTTTATTGTT
1 CATTTAGCGTTCATTTAGTATT
103518 CATTTA
1 CATTTA
103524 TAAATTCAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.20, C:0.14, G:0.14, T:0.52
Consensus pattern (22 bp):
CATTTAGCGTTCATTTAGTATT
Found at i:103524 original size:11 final size:11
Alignment explanation
Indices: 103474--103523 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
103464 TTTTAAAGTC
*
103474 CATTTAGCGTT
1 CATTTAGTGTT
*
103485 CATTTAGTATT
1 CATTTAGTGTT
*
103496 CATTTAGCGTT
1 CATTTAGTGTT
* *
103507 CGTTTATTGTT
1 CATTTAGTGTT
103518 CATTTA
1 CATTTA
103524 TAAATTCAAT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 31 1.00
ACGTcount: A:0.20, C:0.14, G:0.14, T:0.52
Consensus pattern (11 bp):
CATTTAGTGTT
Found at i:103761 original size:12 final size:12
Alignment explanation
Indices: 103733--103778 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
103723 ATGAACATAA
103733 ATAAACGAG-TC
1 ATAAACGAGCTC
*
103744 GGTAAACGAGCTC
1 -ATAAACGAGCTC
103757 ATAAACGAGCTC
1 ATAAACGAGCTC
*
103769 ATAAATGAGC
1 ATAAACGAGC
103779 CTGTTTGTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
12 28 0.93
13 2 0.07
ACGTcount: A:0.41, C:0.20, G:0.22, T:0.17
Consensus pattern (12 bp):
ATAAACGAGCTC
Found at i:113425 original size:31 final size:31
Alignment explanation
Indices: 113387--113502 Score: 110
Period size: 31 Copynumber: 3.7 Consensus size: 31
113377 TAAGAAGAAC
113387 CTTGGGTAGGCTCTGAGGCCCCGAGATCTTT
1 CTTGGGTAGGCTCTGAGGCCCCGAGATCTTT
* * *
113418 CTTGGGTAGGCCCTGCA-GCCCTGAGATCATT
1 CTTGGGTAGGCTCTG-AGGCCCCGAGATCTTT
* * * *
113449 CTTAGGAAGGCTCCGTGGCCCCGA-ATAACTTT
1 CTTGGGTAGGCTCTGAGGCCCCGAGAT--CTTT
* *
113481 CTTGGGTAGGATCTGGGGCCCC
1 CTTGGGTAGGCTCTGAGGCCCC
113503 AAGGTATTCC
Statistics
Matches: 66, Mismatches: 15, Indels: 7
0.75 0.17 0.08
Matches are distributed among these distances:
30 2 0.03
31 43 0.65
32 21 0.32
ACGTcount: A:0.16, C:0.28, G:0.31, T:0.26
Consensus pattern (31 bp):
CTTGGGTAGGCTCTGAGGCCCCGAGATCTTT
Found at i:116820 original size:19 final size:20
Alignment explanation
Indices: 116796--116843 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
116786 ACCGATTTTC
*
116796 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
116815 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
116835 TTTTGAAAA
1 TTTTGAAAA
116844 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:118186 original size:11 final size:11
Alignment explanation
Indices: 118172--118203 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
118162 TTTTAATCTT
118172 AAAATAATTTC
1 AAAATAATTTC
118183 AAAATAATTTC
1 AAAATAATTTC
*
118194 AAAACAATTT
1 AAAATAATTT
118204 TATAAAGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.34
Consensus pattern (11 bp):
AAAATAATTTC
Found at i:120850 original size:49 final size:49
Alignment explanation
Indices: 120779--120885 Score: 133
Period size: 49 Copynumber: 2.2 Consensus size: 49
120769 TTTCCTCGAG
* * * *
120779 GGATCAATCCTTTGGTGAAGGGATCAATCAATGGCTATTGAAATCCAAC
1 GGATCGATCCCTTGCTGAAGGGATCAATCAATGGCTATTAAAATCCAAC
* * ** *
120828 GGATCGATCCCTTGCTGGAGGGATCGATCCTTGGCTATTAAAATCCAAG
1 GGATCGATCCCTTGCTGAAGGGATCAATCAATGGCTATTAAAATCCAAC
120877 GGATCGATC
1 GGATCGATC
120886 ATTTTTCAAG
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (49 bp):
GGATCGATCCCTTGCTGAAGGGATCAATCAATGGCTATTAAAATCCAAC
Found at i:122415 original size:21 final size:21
Alignment explanation
Indices: 122398--122476 Score: 61
Period size: 23 Copynumber: 3.5 Consensus size: 21
122388 ATAAATTGCA
122398 CCGAAGTG-CCACATAATTGTC
1 CCGAAG-GACCACATAATTGTC
*
122419 CCGAAGGACCACATAGGTTTGTC
1 CCGAAGGACCACATA--ATTGTC
* * *
122442 TCAAAGGACCACATAGGTTTTGTC
1 CCGAAGGACCACATA---ATTGTC
122466 CCGAAGGACCA
1 CCGAAGGACCA
122477 GATAGAACCC
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
20 1 0.02
21 13 0.27
23 18 0.38
24 16 0.33
ACGTcount: A:0.29, C:0.27, G:0.23, T:0.22
Consensus pattern (21 bp):
CCGAAGGACCACATAATTGTC
Found at i:122472 original size:24 final size:23
Alignment explanation
Indices: 122414--122481 Score: 100
Period size: 23 Copynumber: 2.9 Consensus size: 23
122404 TGCCACATAA
122414 TTGTCCCGAAGGACCACATAGGT
1 TTGTCCCGAAGGACCACATAGGT
* *
122437 TTGTCTCAAAGGACCACATAGGTT
1 TTGTCCCGAAGGACCACATAGG-T
*
122461 TTGTCCCGAAGGACCAGATAG
1 TTGTCCCGAAGGACCACATAG
122482 AACCCGCGAC
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
23 20 0.51
24 19 0.49
ACGTcount: A:0.28, C:0.24, G:0.25, T:0.24
Consensus pattern (23 bp):
TTGTCCCGAAGGACCACATAGGT
Found at i:122657 original size:13 final size:14
Alignment explanation
Indices: 122629--122659 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
122619 ATACACATTT
122629 CATAATCATGCACA
1 CATAATCATGCACA
122643 CATAATCAT-CACA
1 CATAATCATGCACA
122656 CATA
1 CATA
122660 GCTTAAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.45, C:0.29, G:0.03, T:0.23
Consensus pattern (14 bp):
CATAATCATGCACA
Found at i:124858 original size:289 final size:289
Alignment explanation
Indices: 124328--124906 Score: 1034
Period size: 289 Copynumber: 2.0 Consensus size: 289
124318 TGAGTTTTCC
124328 TTTACGCCCAAAACGAAGTAATTTCTTTCAAGGTGATACTTTTATGAACACTTTGTCACCTACTT
1 TTTACGCCCAAAACGAAGTAATTTCTTTCAAGGTGATACTTTTATGAACACTTTGTCACCTACTT
* *
124393 AAAATTCAATTTCTTTCCTCTTCAAATTGCATATGGCTTTTATCTGTCTGATGCCACTTTAAGAT
66 AAAATTCAATTTCTTTCCTCTTCAAATCGCATATGACTTTTATCTGTCTGATGCCACTTTAAGAT
*
124458 TATACTGGATTACCTGAACTTTTTCTTCAACTTCTTTAATCAAATATGGGCCATAAACTTCTCGA
131 TATACTGGATTACCTAAACTTTTTCTTCAACTTCTTTAATCAAATATGGGCCATAAACTTCTCGA
* * *
124523 TCTTTTAATTCATACCAATTAAGCAGTGTCCTGCACTTCTTTCCATACAATACTTCATACGGTGC
196 TCTTTTAATTCATACCAATTAAGCAGCGTCATGCACTTCCTTCCATACAATACTTCATACGGTGC
124588 CATTTTAATGCTTGATTGGTAACTGTTAT
261 CATTTTAATGCTTGATTGGTAACTGTTAT
* * *
124617 TTTATGCCCAAAACGAAGTACTTTCTTTCAAGGTGATACTTTTATGAACATTTTGTCACCTACTT
1 TTTACGCCCAAAACGAAGTAATTTCTTTCAAGGTGATACTTTTATGAACACTTTGTCACCTACTT
*
124682 AAAATTCAATTTCTTTCCTCTTCAAATCCGCGTATGACTTTTATCTGTCTGATGCCACTTTAAGA
66 AAAATTCAATTTCTTTCCTCTTCAAAT-CGCATATGACTTTTATCTGTCTGATGCCACTTTAAGA
124747 TTATACTGGATTACCTAAACTTTTTCTTCAACTTCTTTAATCAAATATGGGCCATAAACTTC-CG
130 TTATACTGGATTACCTAAACTTTTTCTTCAACTTCTTTAATCAAATATGGGCCATAAACTTCTCG
* *
124811 GTCTTTTAATTCATACCAATTAAGCGGCGTCATGCACTTCCTTCCATACAATACTTCATACGGTG
195 ATCTTTTAATTCATACCAATTAAGCAGCGTCATGCACTTCCTTCCATACAATACTTCATACGGTG
124876 CCATTTTAATGCTTGATTGGTAACTGTTAT
260 CCATTTTAATGCTTGATTGGTAACTGTTAT
124906 T
1 T
124907 ATGCAAATTT
Statistics
Matches: 277, Mismatches: 12, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
289 182 0.66
290 95 0.34
ACGTcount: A:0.27, C:0.21, G:0.12, T:0.40
Consensus pattern (289 bp):
TTTACGCCCAAAACGAAGTAATTTCTTTCAAGGTGATACTTTTATGAACACTTTGTCACCTACTT
AAAATTCAATTTCTTTCCTCTTCAAATCGCATATGACTTTTATCTGTCTGATGCCACTTTAAGAT
TATACTGGATTACCTAAACTTTTTCTTCAACTTCTTTAATCAAATATGGGCCATAAACTTCTCGA
TCTTTTAATTCATACCAATTAAGCAGCGTCATGCACTTCCTTCCATACAATACTTCATACGGTGC
CATTTTAATGCTTGATTGGTAACTGTTAT
Found at i:129417 original size:24 final size:24
Alignment explanation
Indices: 129360--129499 Score: 158
Period size: 24 Copynumber: 5.9 Consensus size: 24
129350 TGCCATATAA
* *
129360 TTGTCCCGTAGGACCACATAG-GT
1 TTGTCCCGAAGGACCACATAGATT
* *
129383 TTGTCCTGAAGGACCACACAGATT
1 TTGTCCCGAAGGACCACATAGATT
* *
129407 TTGTCCCGAAGGACCACACAGGTT
1 TTGTCCCGAAGGACCACATAGATT
*
129431 TTGTCCCGAAGGACCACATAGGTT
1 TTGTCCCGAAGGACCACATAGATT
* * *
129455 TTATCTCGAAGGACCATATA-ATT
1 TTGTCCCGAAGGACCACATAGATT
* *
129478 TTATCCCGAATGACCACATAGA
1 TTGTCCCGAAGGACCACATAGA
129500 ACCCTCGACT
Statistics
Matches: 101, Mismatches: 14, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
23 37 0.37
24 64 0.63
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.26
Consensus pattern (24 bp):
TTGTCCCGAAGGACCACATAGATT
Found at i:129444 original size:71 final size:71
Alignment explanation
Indices: 129360--129495 Score: 186
Period size: 71 Copynumber: 1.9 Consensus size: 71
129350 TGCCATATAA
* *
129360 TTGTCCCGTAGGACCACATAGGTTTGT-CCT-GAAGGACCACACAGATTTTGTCCCGAAGGACCA
1 TTGTCCCGAAGGACCACATAGGTTT-TACCTCGAAGGACCACACA-ATTTTATCCCGAAGGACCA
129423 CACAGGTT
64 CACAGGTT
* * * *
129431 TTGTCCCGAAGGACCACATAGGTTTTATCTCGAAGGACCATATAATTTTATCCCGAATGACCACA
1 TTGTCCCGAAGGACCACATAGGTTTTACCTCGAAGGACCACACAATTTTATCCCGAAGGACCACA
129496 TAGAACCCTC
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
70 1 0.02
71 45 0.79
72 11 0.19
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.26
Consensus pattern (71 bp):
TTGTCCCGAAGGACCACATAGGTTTTACCTCGAAGGACCACACAATTTTATCCCGAAGGACCACA
CAGGTT
Found at i:129465 original size:48 final size:48
Alignment explanation
Indices: 129363--129499 Score: 161
Period size: 47 Copynumber: 2.9 Consensus size: 48
129353 CATATAATTG
* * * *
129363 TCCCGTAGGACCACATAGG-TTTGTCCTGAAGGACCACACAGATTTTG
1 TCCCGAAGGACCACATAGGTTTTGTCCCGAAGGACCACATAGATTTTA
* *
129410 TCCCGAAGGACCACACAGGTTTTGTCCCGAAGGACCACATAGGTTTTA
1 TCCCGAAGGACCACATAGGTTTTGTCCCGAAGGACCACATAGATTTTA
* * * * *
129458 TCTCGAAGGACCATATA-ATTTTATCCCGAATGACCACATAGA
1 TCCCGAAGGACCACATAGGTTTTGTCCCGAAGGACCACATAGA
129500 ACCCTCGACT
Statistics
Matches: 76, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
47 38 0.50
48 38 0.50
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.25
Consensus pattern (48 bp):
TCCCGAAGGACCACATAGGTTTTGTCCCGAAGGACCACATAGATTTTA
Found at i:131629 original size:253 final size:254
Alignment explanation
Indices: 131100--131691 Score: 1043
Period size: 253 Copynumber: 2.3 Consensus size: 254
131090 CCCCCTTTCG
*
131100 GTATCGATATCATTTTCGACATACTGGAATTTCAAC-TGAAATTGGTATCAATACCTTACTCTTG
1 GTATCGATATCA-TTTCGACATACTGGAATTTCAACTTGAAATTGGTATCGATACCTTACTCTTG
**
131164 GTATCGATACTCCCCTTTCAGTATTGATACCTCCCTCAAGCAGTACAATACTGATCCTTGAATTC
65 GTATCGATACTCCCCTTTCAGTATCAATACCTCCCTCAAGCAGTACAATACTGATCCTTGAATTC
131229 TAATTGATTTAGCCTTGAAGTATCGGTTACTGTTCTTACAGTACCGATACCCTTGCCAAATTTAC
130 TAATTGATTTAGCCTTGAAGTATCGGTTACTGTTCTTACAGTACCGATACCCTTGCCAAATTTAC
131294 CATTCCATTTCGAATTTTAACCAAAACTTAACTAATCTCCTACTTTTACCTTCTTTATAC
195 CATTCCATTTCGAATTTTAACCAAAACTTAACTAATCTCCTACTTTTACCTTCTTTATAC
*
131354 GTATCGATATCATTTTGACATACTGGAATTTCAACTTGAAATT-GTATCGATACCTTACTCTTGG
1 GTATCGATATCATTTCGACATACTGGAATTTCAACTTGAAATTGGTATCGATACCTTACTCTTGG
* *
131418 TATCGATACTCCTCTTTCAGTATCAATACCTCCCTC-AGCAGTACCGATACTGATCCTTGAATTC
66 TATCGATACTCCCCTTTCAGTATCAATACCTCCCTCAAGCAGTA-CAATACTGATCCTTGAATTC
131482 TAATTGATTTAGCCTTGAAGTATCGG-TACTGTTCTTACAGTACCGATACCCTTGCCCGAAATTT
130 TAATTGATTTAGCCTTGAAGTATCGGTTACTGTTCTTACAGTACCGATACCCTTG-CC-AAATTT
131546 ACCATTCCATTTCGAATTTTAACCAAAACTTAACTAATCTCCTACTTTTACCTTCTTTATAC
193 ACCATTCCATTTCGAATTTTAACCAAAACTTAACTAATCTCCTACTTTTACCTTCTTTATAC
*
131608 GTATCGAT-TCATTTCGACATACTGGAATGTC-ACTTGAAATTGGTATCGATACCTTACTCTTGG
1 GTATCGATATCATTTCGACATACTGGAATTTCAACTTGAAATTGGTATCGATACCTTACTCTTGG
131671 TATCGATACTCCCCTTTCAGT
66 TATCGATACTCCCCTTTCAGT
Statistics
Matches: 324, Mismatches: 9, Indels: 11
0.94 0.03 0.03
Matches are distributed among these distances:
252 45 0.14
253 184 0.57
254 95 0.29
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.37
Consensus pattern (254 bp):
GTATCGATATCATTTCGACATACTGGAATTTCAACTTGAAATTGGTATCGATACCTTACTCTTGG
TATCGATACTCCCCTTTCAGTATCAATACCTCCCTCAAGCAGTACAATACTGATCCTTGAATTCT
AATTGATTTAGCCTTGAAGTATCGGTTACTGTTCTTACAGTACCGATACCCTTGCCAAATTTACC
ATTCCATTTCGAATTTTAACCAAAACTTAACTAATCTCCTACTTTTACCTTCTTTATAC
Done.