Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002161.1 Hibiscus syriacus cultivar Beakdansim tig00004413_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: 164381
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:1437 original size:21 final size:20
Alignment explanation
Indices: 1397--1438 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
1387 TAACAAAAAA
* *
1397 AAATATTATAATTTATAATT
1 AAATAATATAATTTAAAATT
1417 AAATAATATATATTTAAAATT
1 AAATAATATA-ATTTAAAATT
1438 A
1 A
1439 TTCCTAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
AAATAATATAATTTAAAATT
Found at i:24650 original size:227 final size:218
Alignment explanation
Indices: 24256--24688 Score: 697
Period size: 227 Copynumber: 1.9 Consensus size: 218
24246 TTATCTATCC
*
24256 TTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATCTTTAGTTAATATTGT
1 TTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATATTTAGTTAATATTGT
*
24321 TAAATTTAAAATCTAAATAATTTTATAAAATATCAAAACAATCAAATAATTTTGTGTAAATGAAA
66 TAAATTTAAAATCTAAATAATTTTATAAAATATCAAAACAATCAAATAATTTTGTGCAAATGAAA
*
24386 TTATTAAATTAATATGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTATA
131 TTATTAAATTAATATGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACA
24451 TAACTTTCAAAAAGTATATATCAT
196 TAACTTT-AAAAAGTATATATCAT
* *
24475 TTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGGTTAATA
1 TTTTATAAAAGTGTCCATACTTATTTCACTG-TG-AAA-ATATAT-TTATTATATTTAGTTAATA
*
24540 TTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTTTGTGC
62 TTGTTAAATTTAAAATCTAAAT-A-ATTTTATAAAATATCAAAACAATCAAAT--AATTTTGTGC
* *
24605 AAATTAAATTATTAAATTAATATTGTAGGTGG-AAACATGAAACACTATTAAATAAATTGAAACA
123 AAATGAAATTATTAAATTAATA-TGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACA
24669 TAAATTACATAACTTTAAAA
187 TAAATTACATAACTTTAAAA
24689 GCAGTTTTAA
Statistics
Matches: 197, Mismatches: 8, Indels: 11
0.91 0.04 0.05
Matches are distributed among these distances:
219 31 0.16
220 2 0.01
221 3 0.02
222 5 0.03
223 38 0.19
224 1 0.01
225 28 0.14
226 4 0.02
227 76 0.39
228 9 0.05
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.39
Consensus pattern (218 bp):
TTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATATTTAGTTAATATTGT
TAAATTTAAAATCTAAATAATTTTATAAAATATCAAAACAATCAAATAATTTTGTGCAAATGAAA
TTATTAAATTAATATGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACA
TAACTTTAAAAAGTATATATCAT
Found at i:24774 original size:20 final size:19
Alignment explanation
Indices: 24751--24796 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
24741 CGATATACCA
24751 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
24771 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
24791 GGTAAA
1 GGTAAA
24797 TTTAAAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:27071 original size:12 final size:12
Alignment explanation
Indices: 27054--27106 Score: 70
Period size: 12 Copynumber: 4.4 Consensus size: 12
27044 GGTCGCAGAA
*
27054 GATGAAGTTGAC
1 GATGAAGATGAC
27066 GATGAAGATGAC
1 GATGAAGATGAC
*
27078 GATGATGATGAC
1 GATGAAGATGAC
* *
27090 GATGATGATGAT
1 GATGAAGATGAC
27102 GATGA
1 GATGA
27107 TGAAGATGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 38 1.00
ACGTcount: A:0.36, C:0.06, G:0.34, T:0.25
Consensus pattern (12 bp):
GATGAAGATGAC
Found at i:27086 original size:3 final size:3
Alignment explanation
Indices: 27066--27119 Score: 72
Period size: 3 Copynumber: 18.0 Consensus size: 3
27056 TGAAGTTGAC
* * * *
27066 GAT GAA GAT GAC GAT GAT GAT GAC GAT GAT GAT GAT GAT GAT GAA GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
27114 GAT GAT
1 GAT GAT
27120 CCAAACAAGT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.37, C:0.04, G:0.33, T:0.26
Consensus pattern (3 bp):
GAT
Found at i:27087 original size:18 final size:18
Alignment explanation
Indices: 27051--27119 Score: 72
Period size: 18 Copynumber: 4.0 Consensus size: 18
27041 AGCGGTCGCA
* *
27051 GAAGATGAAGTTGACGAT
1 GAAGATGAAGATGATGAT
*
27069 GAAGATGACGATGATGAT
1 GAAGATGAAGATGATGAT
*
27087 GACGAT---GATGATGAT
1 GAAGATGAAGATGATGAT
*
27102 GATGATGAAGATGATGAT
1 GAAGATGAAGATGATGAT
27120 CCAAACAAGT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
15 14 0.33
18 29 0.67
ACGTcount: A:0.38, C:0.04, G:0.33, T:0.25
Consensus pattern (18 bp):
GAAGATGAAGATGATGAT
Found at i:27107 original size:12 final size:12
Alignment explanation
Indices: 27062--27119 Score: 80
Period size: 12 Copynumber: 4.8 Consensus size: 12
27052 AAGATGAAGT
*
27062 TGACGATGAAGA
1 TGACGATGATGA
27074 TGACGATGATGA
1 TGACGATGATGA
27086 TGACGATGATGA
1 TGACGATGATGA
*
27098 TGATGATGATGA
1 TGACGATGATGA
* *
27110 AGATGATGAT
1 TGACGATGAT
27120 CCAAACAAGT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 43 1.00
ACGTcount: A:0.36, C:0.05, G:0.33, T:0.26
Consensus pattern (12 bp):
TGACGATGATGA
Found at i:29094 original size:183 final size:182
Alignment explanation
Indices: 28534--29233 Score: 1207
Period size: 181 Copynumber: 3.9 Consensus size: 182
28524 CTTTCAACAT
** * * *
28534 ATTATAATAAAATAGGTAAATTTGCAATATAACCGGTAT-AATATACCGGTTTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
28598 GGTCTACAACCTATATCGACACTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAA
66 GGTCTACAACCTATATCGACACTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAA
28663 ATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
131 ATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
*
28715 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATATCGGTTTTA-GCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
28779 GGTCTAC-ACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACAC-TTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
28843 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
130 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
*
28896 ATTATAATGTAATAGATAATTTTATAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
*
28961 GGCCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACAC-TTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
* * *
29026 AATGTGTCGATACGATTTAAAAAAGTATCGACATTTACACATCGAAACCCAGA
130 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
*
29079 TTTATAATGTAATAGATAATTTTGTAATA-AACCGGTATAAATATACCGGTTTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
*
29143 GGTCTACAACCTATATCGACAC-TTT-ATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAA
66 GGTCTACAACCTATATCGACACTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAA
*
29206 ATGTGTCGATACCATTT-AAAAAGTGTCG
131 ATGTGTCGATACGATTTAAAAAAGTGTCG
29234 GTAATTTTAA
Statistics
Matches: 497, Mismatches: 18, Indels: 11
0.94 0.03 0.02
Matches are distributed among these distances:
178 10 0.02
179 53 0.11
180 17 0.03
181 198 0.40
182 85 0.17
183 134 0.27
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (182 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
GGTCTACAACCTATATCGACACTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAA
ATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
Found at i:31684 original size:25 final size:25
Alignment explanation
Indices: 31650--31719 Score: 95
Period size: 25 Copynumber: 2.8 Consensus size: 25
31640 AAATTCGCAG
31650 TACATATTTAGGTATGTACAATAAC
1 TACATATTTAGGTATGTACAATAAC
****
31675 TACATATTTAGGTATGTTTGTTAAC
1 TACATATTTAGGTATGTACAATAAC
*
31700 TACATATTTAGGTATATACA
1 TACATATTTAGGTATGTACA
31720 TCTTTTGAGT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.41
Consensus pattern (25 bp):
TACATATTTAGGTATGTACAATAAC
Found at i:32048 original size:22 final size:22
Alignment explanation
Indices: 32001--32048 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
31991 AAATTACATA
32001 ACTTTTTAAAAAAGTATCGATC
1 ACTTTTTAAAAAAGTATCGATC
*
32023 -CTTTTTATAAAAAGTATGGA-C
1 ACTTTTTA-AAAAAGTATCGATC
32044 ACTTT
1 ACTTT
32049 CAATATAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 8 0.35
22 15 0.65
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (22 bp):
ACTTTTTAAAAAAGTATCGATC
Found at i:32096 original size:22 final size:23
Alignment explanation
Indices: 32066--32128 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
32056 ATAGGTAAAC
*
32066 ATATGATGTAATAGGTAGC-CCT
1 ATATAATGTAATAGGTAGCGCCT
* **
32088 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCCT
32111 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
32129 TGGTTATATT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
22 17 0.49
23 18 0.51
ACGTcount: A:0.37, C:0.06, G:0.21, T:0.37
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCCT
Found at i:32135 original size:23 final size:23
Alignment explanation
Indices: 32087--32137 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
32077 TAGGTAGCCC
*
32087 TATATAATGTAATAGGTATCGTT
1 TATATAATGTAATAGGTATCGGT
32110 TATATAATGTAATAGGTAGT-GGT
1 TATATAATGTAATAGGTA-TCGGT
32133 TATAT
1 TATAT
32138 TGTAAAGTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 25 0.96
24 1 0.04
ACGTcount: A:0.35, C:0.02, G:0.20, T:0.43
Consensus pattern (23 bp):
TATATAATGTAATAGGTATCGGT
Found at i:32437 original size:25 final size:25
Alignment explanation
Indices: 32403--32453 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
32393 ACAACAAATC
*
32403 AATTAAACATTGTTGTGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
*
32428 AATTGAACATTGTTATGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
32453 A
1 A
32454 TTTGGAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (25 bp):
AATTAAACATTGTTATGGGTACATT
Found at i:32860 original size:18 final size:18
Alignment explanation
Indices: 32839--32875 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
32829 GTAATTGGAG
32839 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
32857 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
32875 T
1 T
32876 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:32883 original size:24 final size:24
Alignment explanation
Indices: 32831--32877 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
32821 TTTCATATGT
* *
32831 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
32855 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
32878 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:33178 original size:39 final size:39
Alignment explanation
Indices: 33135--33221 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
33125 TCCGATGCTC
*
33135 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
*
33174 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
33213 ATCAAAATC
1 ATCAAAATC
33222 TACAACTTGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.48, C:0.21, G:0.14, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
Found at i:33653 original size:22 final size:23
Alignment explanation
Indices: 33620--33690 Score: 83
Period size: 22 Copynumber: 3.2 Consensus size: 23
33610 AATAGGTAAC
*
33620 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
33643 ATAT-ATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
33665 ATATAATGT-ATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
33687 ATAT
1 ATAT
33691 TGTAAAGTGT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
22 34 0.81
23 8 0.19
ACGTcount: A:0.32, C:0.04, G:0.23, T:0.41
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:34341 original size:327 final size:330
Alignment explanation
Indices: 33733--34390 Score: 1216
Period size: 327 Copynumber: 2.0 Consensus size: 330
33723 CATACTTTTT
33733 TCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAAT
1 TCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAAT
*
33798 TATAGGCGTCTAATGATTTATTTTTTTCGTTACGATATATTATTATTAAATTAAAAATTCTAAAT
66 TATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATTATTATTAAATTAAAAATTCTAAAT
*
33863 ATTATTTATAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAATATT
131 ATTATTTATAAAAATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAATATT
*
33928 GTAGGTGGAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAGAAG
196 GTAGGTGGAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAGAAA
*
33993 TATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATAT-ATATAATGTAATAGGTAAATTTGC
261 TATCGATCCTTTTTATAAAAAGTATGAACACTTTCAATATAATATAATGTAATAGGTAAATTTGC
34057 AATGC
326 AATGC
34062 TCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAAT
1 TCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAAT
* *
34127 TATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATTATTATTAAATTAAAATTTTTAAAT
66 TATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATTATTATTAAATTAAAAATTCTAAAT
34192 A-T-TTTATAAAAATC-AAACAATCAAATAATTTTTTTGTGCAAATGAAATTATTAAATTAATAT
131 ATTATTTATAAAAATCAAAACAATCAAATAA-TTTTTTGTGCAAATGAAATTATTAAATTAATAT
34254 TGTAGGTGGAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAGAA
195 TGTAGGTGGAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAGAA
*
34319 ATATCGATCCTTTTTATAAAAAGTATGAACACTTTTAATATAATATAATGTAATAGGTAAATTTG
260 ATATCGATCCTTTTTATAAAAAGTATGAACACTTTCAATATAATATAATGTAATAGGTAAATTTG
34384 CAATGC
325 CAATGC
34390 T
1 T
34391 ATCGGTATAA
Statistics
Matches: 320, Mismatches: 7, Indels: 5
0.96 0.02 0.02
Matches are distributed among these distances:
326 14 0.04
327 147 0.46
328 31 0.10
329 128 0.40
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.39
Consensus pattern (330 bp):
TCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAAT
TATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATTATTATTAAATTAAAAATTCTAAAT
ATTATTTATAAAAATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATTAATATT
GTAGGTGGAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAGAAA
TATCGATCCTTTTTATAAAAAGTATGAACACTTTCAATATAATATAATGTAATAGGTAAATTTGC
AATGC
Found at i:34792 original size:42 final size:38
Alignment explanation
Indices: 34716--34795 Score: 106
Period size: 42 Copynumber: 2.0 Consensus size: 38
34706 AAATAATAAG
* *
34716 TATATTTAAAAAAATATTTCTTTAAAAATGTATTAAAT
1 TATATTTAAAAAAATATTTATTTAAAAATATATTAAAT
34754 TATATTTAAAACAAATTATTGTATGTTAAAAATATATTAAAT
1 TATATTTAAAA-AAA-TATT-TAT-TTAAAAATATATTAAAT
34796 AAATTACTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
38 11 0.31
39 3 0.08
40 4 0.11
41 2 0.06
42 16 0.44
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.44
Consensus pattern (38 bp):
TATATTTAAAAAAATATTTATTTAAAAATATATTAAAT
Found at i:35578 original size:26 final size:26
Alignment explanation
Indices: 35544--35610 Score: 107
Period size: 26 Copynumber: 2.6 Consensus size: 26
35534 AATGAAGTTT
*
35544 AACTCGAACTCGAAATATAATATTAA
1 AACTTGAACTCGAAATATAATATTAA
*
35570 AACTTGAACTCGAAATATAATATTGA
1 AACTTGAACTCGAAATATAATATTAA
*
35596 AACTTAAACTCGAAA
1 AACTTGAACTCGAAA
35611 AGGCTTGAAC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.49, C:0.15, G:0.09, T:0.27
Consensus pattern (26 bp):
AACTTGAACTCGAAATATAATATTAA
Found at i:38583 original size:21 final size:21
Alignment explanation
Indices: 38493--38588 Score: 129
Period size: 21 Copynumber: 4.6 Consensus size: 21
38483 GTTTTCAGAT
*
38493 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
*
38514 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
* * *
38535 TCACAATGTGAACTTAGACTA
1 TCGCAATGCGAACTTCGACTA
*
38556 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
*
38577 TCGCAATACGAA
1 TCGCAATGCGAA
38589 TATGTAAATC
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 67 1.00
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (21 bp):
TCGCAATGCGAACTTCGACTA
Found at i:41398 original size:173 final size:171
Alignment explanation
Indices: 41098--41442 Score: 528
Period size: 173 Copynumber: 2.0 Consensus size: 171
41088 ACTCTTTCTG
* *
41098 TCAAATTTCATGCGAAAGAATGTGGAGAAATCAAACATTTTATTAGACTAAAAGTAGAATACATG
1 TCAAATTTCATGCGAAAGAACGTGGAGAAATCAAACATTTTATTAGACTAAAAGTAGAATACATA
* * *
41163 AAGAAAAGATTATTTTTGAGACAATAGAAATATACAAAGGTTTTTTTTTAACAAATGTATCTACT
66 AAGAAAAGATTATTTTTGAGACAATAAAAATATACAAAGGTTTTTTTTAAACAAAAGTATCTACT
* *
41228 ATGTGAATCCTAATCTAAAACTATGAACATAAGAAAGAAAATA
131 A--AGAATCCTAATCTAAAACAATGAACATAAGAAAGAAAATA
* * * * * * * *
41271 TCAAATTTCATGCTAATGAACGTGGATAAATTAAACATTTTCTTAGACTCAGAGTAGAATGCATA
1 TCAAATTTCATGCGAAAGAACGTGGAGAAATCAAACATTTTATTAGACTAAAAGTAGAATACATA
*
41336 AAGAAAATATTATTTTTGAGACAATAAAAATATACAAAGGTTTTTTTTAAACAAAAGTATCTACT
66 AAGAAAAGATTATTTTTGAGACAATAAAAATATACAAAGGTTTTTTTTAAACAAAAGTATCTACT
41401 AAGAATCCTAATCTAAAACAATGAACATAAGAAAGAAAATA
131 AAGAATCCTAATCTAAAACAATGAACATAAGAAAGAAAATA
41442 T
1 T
41443 TTAGAAGATG
Statistics
Matches: 156, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
171 39 0.25
173 117 0.75
ACGTcount: A:0.47, C:0.10, G:0.13, T:0.30
Consensus pattern (171 bp):
TCAAATTTCATGCGAAAGAACGTGGAGAAATCAAACATTTTATTAGACTAAAAGTAGAATACATA
AAGAAAAGATTATTTTTGAGACAATAAAAATATACAAAGGTTTTTTTTAAACAAAAGTATCTACT
AAGAATCCTAATCTAAAACAATGAACATAAGAAAGAAAATA
Found at i:44188 original size:17 final size:17
Alignment explanation
Indices: 44162--44196 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
44152 AATTCGTCCC
*
44162 CCTAATATAAAATTTTA
1 CCTAACATAAAATTTTA
44179 CCTAACATAAAATTTTA
1 CCTAACATAAAATTTTA
44196 C
1 C
44197 GTCCGCCCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.46, C:0.17, G:0.00, T:0.37
Consensus pattern (17 bp):
CCTAACATAAAATTTTA
Found at i:47231 original size:5 final size:5
Alignment explanation
Indices: 47199--47228 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
47189 TTACTTGCAC
*
47199 TTAAT TTAAT TTAAT TTAAT TTAAT CTAAT
1 TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT
47229 CTACATCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (5 bp):
TTAAT
Found at i:57240 original size:14 final size:14
Alignment explanation
Indices: 57218--57257 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
57208 TAGGTATGTC
57218 ATAAATTTAATTAA
1 ATAAATTTAATTAA
* *
57232 TTTAATTTAATTAA
1 ATAAATTTAATTAA
57246 ATAAATTTAATT
1 ATAAATTTAATT
57258 TTCAAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATAAATTTAATTAA
Found at i:59387 original size:31 final size:31
Alignment explanation
Indices: 59352--59414 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
59342 AATTTAGTGA
59352 ATTCAATATGTCCTTCTCACTAGGAACTCCC
1 ATTCAATATGTCCTTCTCACTAGGAACTCCC
59383 ATTCAATATGTCCTTCTCACTAGGAACTCCC
1 ATTCAATATGTCCTTCTCACTAGGAACTCCC
59414 A
1 A
59415 AACTCTTGGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.27, C:0.32, G:0.10, T:0.32
Consensus pattern (31 bp):
ATTCAATATGTCCTTCTCACTAGGAACTCCC
Found at i:70046 original size:116 final size:117
Alignment explanation
Indices: 69839--70069 Score: 385
Period size: 116 Copynumber: 2.0 Consensus size: 117
69829 TAGGTTAATT
*
69839 GGCATGTCTTATTTGTATTTTCTATTAATGATCTAATAATTCTGCGCCTTTAAAATTTTAAATCT
1 GGCATGTCTTATTTGTATTTTCTATTAATGA-CTAATAATTCTGCACCTTTAAAATTTTAAATCT
69904 AACTTTCGAAGTTTACGCCCTTGATATAAATTTTTATATCCGTCCTTGAATATA
65 AACTTTCGAAGTTTACGCCCTTGATATAAATTTTT-TATCCGTCCTTGAATATA
* *
69958 GGCATGTCTTATTTGTATTTTCTATTAATG-GT-ATAATTTTGCACCTTTAAAATTTTAAATCTA
1 GGCATGTCTTATTTGTATTTTCTATTAATGACTAATAATTCTGCACCTTTAAAATTTTAAATCTA
* *
70021 ACTTTTGAAGTTTACGCCTTTGATATAAATTTTTTATCCGTCCTTGAAT
66 ACTTTCGAAGTTTACGCCCTTGATATAAATTTTTTATCCGTCCTTGAAT
70070 TTAGCTGGAA
Statistics
Matches: 107, Mismatches: 5, Indels: 4
0.92 0.04 0.03
Matches are distributed among these distances:
115 15 0.14
116 61 0.57
117 1 0.01
119 30 0.28
ACGTcount: A:0.28, C:0.15, G:0.11, T:0.46
Consensus pattern (117 bp):
GGCATGTCTTATTTGTATTTTCTATTAATGACTAATAATTCTGCACCTTTAAAATTTTAAATCTA
ACTTTCGAAGTTTACGCCCTTGATATAAATTTTTTATCCGTCCTTGAATATA
Found at i:73168 original size:30 final size:30
Alignment explanation
Indices: 73132--73210 Score: 122
Period size: 31 Copynumber: 2.6 Consensus size: 30
73122 CTTTTTCATT
73132 TAAGTACCTAAAGTATTTTTTTGGTCAAAA
1 TAAGTACCTAAAGTATTTTTTTGGTCAAAA
*
73162 TAAGTACCTAAAGTTATCTTTTTGGTCAAAA
1 TAAGTACCTAAAG-TATTTTTTTGGTCAAAA
* *
73193 TAGGTAACTAAAGTATTT
1 TAAGTACCTAAAGTATTT
73211 AATCTTTTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
30 17 0.39
31 27 0.61
ACGTcount: A:0.37, C:0.10, G:0.14, T:0.39
Consensus pattern (30 bp):
TAAGTACCTAAAGTATTTTTTTGGTCAAAA
Found at i:77820 original size:29 final size:29
Alignment explanation
Indices: 77777--77832 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
77767 TGTTTGTCGT
77777 AGGTCGCTGGAAGGGCATGGCGACCTACA
1 AGGTCGCTGGAAGGGCATGGCGACCTACA
*
77806 AGGTCGCCTGG-AGGGTATGGCGACCTA
1 AGGTCG-CTGGAAGGGCATGGCGACCTA
77833 TGTGTTGGGG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 21 0.84
30 4 0.16
ACGTcount: A:0.21, C:0.23, G:0.39, T:0.16
Consensus pattern (29 bp):
AGGTCGCTGGAAGGGCATGGCGACCTACA
Found at i:78008 original size:14 final size:14
Alignment explanation
Indices: 77971--78009 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
77961 CATCCGATGT
* *
77971 CATCCGACCAAGGG
1 CATCCGACCGAGGC
77985 CATCCGACCGAGGC
1 CATCCGACCGAGGC
77999 CATCCGACCGA
1 CATCCGACCGA
78010 ATTATGTGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.26, C:0.41, G:0.26, T:0.08
Consensus pattern (14 bp):
CATCCGACCGAGGC
Found at i:78053 original size:23 final size:23
Alignment explanation
Indices: 78023--78067 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
78013 ATGTGAGGGC
78023 ATGCGAGGACAGCCGAGCGAGCT
1 ATGCGAGGACAGCCGAGCGAGCT
* *
78046 ATGCGAGGGCATCCGAGCGAGC
1 ATGCGAGGACAGCCGAGCGAGC
78068 GAGCAAGGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.40, T:0.09
Consensus pattern (23 bp):
ATGCGAGGACAGCCGAGCGAGCT
Found at i:84663 original size:40 final size:40
Alignment explanation
Indices: 84608--84687 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
84598 ATTATCGACA
84608 AAGGAGGAGGTCTTTAAACTCTATTTTCAAATATCATTGT
1 AAGGAGGAGGTCTTTAAACTCTATTTTCAAATATCATTGT
84648 AAGGAGGAGGTCTTTAAACTCTATTTTCAAATATCATTGT
1 AAGGAGGAGGTCTTTAAACTCTATTTTCAAATATCATTGT
84688 GTTAATTTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (40 bp):
AAGGAGGAGGTCTTTAAACTCTATTTTCAAATATCATTGT
Found at i:88369 original size:21 final size:21
Alignment explanation
Indices: 88345--88492 Score: 124
Period size: 21 Copynumber: 7.0 Consensus size: 21
88335 TTCGTTGTGG
88345 TAGTCCAAGTTCGCGTTGCGA
1 TAGTCCAAGTTCGCGTTGCGA
* *
88366 TAGTCGAAGATCGCGTTGCGA
1 TAGTCCAAGTTCGCGTTGCGA
* * *
88387 TTTATTTCAAATT--CGTTGCGA
1 --TAGTCCAAGTTCGCGTTGCGA
*
88408 TAGTTCAAGTTCGCGTTGCGA
1 TAGTCCAAGTTCGCGTTGCGA
* * *
88429 TAGTCGAAGTTTGCGTTACGA
1 TAGTCCAAGTTCGCGTTGCGA
* *
88450 TTTATTCCAAGTT--CATTGCGA
1 --TAGTCCAAGTTCGCGTTGCGA
*
88471 TAGTCGAAGTTCGCGTTGCGA
1 TAGTCCAAGTTCGCGTTGCGA
88492 T
1 T
88493 TTATTCCAAA
Statistics
Matches: 99, Mismatches: 20, Indels: 16
0.73 0.15 0.12
Matches are distributed among these distances:
19 18 0.18
21 66 0.67
23 15 0.15
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (21 bp):
TAGTCCAAGTTCGCGTTGCGA
Found at i:88417 original size:63 final size:63
Alignment explanation
Indices: 88321--88492 Score: 233
Period size: 63 Copynumber: 2.8 Consensus size: 63
88311 ACTATCGCAA
* * *
88321 TACGA-TT-TTCCAAATTCGTTGTGGTAGTCCAAGTTCGCGTTGCGATAGTCGAAGATCGCGT
1 TACGATTTATTCCAAATTCGTTGCGATAGTTCAAGTTCGCGTTGCGATAGTCGAAGATCGCGT
* * * *
88382 TGCGATTTATTTCAAATTCGTTGCGATAGTTCAAGTTCGCGTTGCGATAGTCGAAGTTTGCGT
1 TACGATTTATTCCAAATTCGTTGCGATAGTTCAAGTTCGCGTTGCGATAGTCGAAGATCGCGT
* *
88445 TACGATTTATTCCAAGTTCATTGCGATAG-TCGAAGTTCGCGTTGCGAT
1 TACGATTTATTCCAAATTCGTTGCGATAGTTC-AAGTTCGCGTTGCGAT
88493 TTATTCCAAA
Statistics
Matches: 97, Mismatches: 11, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
61 4 0.04
62 4 0.04
63 89 0.92
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (63 bp):
TACGATTTATTCCAAATTCGTTGCGATAGTTCAAGTTCGCGTTGCGATAGTCGAAGATCGCGT
Found at i:88469 original size:42 final size:42
Alignment explanation
Indices: 88423--88516 Score: 152
Period size: 42 Copynumber: 2.2 Consensus size: 42
88413 CAAGTTCGCG
* *
88423 TTGCGATAGTCGAAGTTTGCGTTACGATTTATTCCAAGTTCA
1 TTGCGATAGTCGAAGTTCGCGTTACGATTTATTCCAAATTCA
* *
88465 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTACGATTTATTCCAAATTCA
88507 TTGCGATAGT
1 TTGCGATAGT
88517 TCAAAATCGC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.37
Consensus pattern (42 bp):
TTGCGATAGTCGAAGTTCGCGTTACGATTTATTCCAAATTCA
Found at i:94551 original size:10 final size:10
Alignment explanation
Indices: 94532--94583 Score: 90
Period size: 10 Copynumber: 5.4 Consensus size: 10
94522 CACATAAGAT
94532 AATT-CTTTA
1 AATTACTTTA
94541 AATTACTTTA
1 AATTACTTTA
94551 AATTACTTTA
1 AATTACTTTA
94561 AATT-CTTTA
1 AATTACTTTA
94570 AATTACTTTA
1 AATTACTTTA
94580 AATT
1 AATT
94584 CTTGTTATAT
Statistics
Matches: 41, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
9 13 0.32
10 28 0.68
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.52
Consensus pattern (10 bp):
AATTACTTTA
Found at i:94568 original size:19 final size:19
Alignment explanation
Indices: 94532--94586 Score: 94
Period size: 19 Copynumber: 2.9 Consensus size: 19
94522 CACATAAGAT
94532 AATT-CTTTAAATTACTTTA
1 AATTACTTTAAATT-CTTTA
94551 AATTACTTTAAATTCTTTA
1 AATTACTTTAAATTCTTTA
94570 AATTACTTTAAATTCTT
1 AATTACTTTAAATTCTT
94587 GTTATATATA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
19 26 0.74
20 9 0.26
ACGTcount: A:0.36, C:0.11, G:0.00, T:0.53
Consensus pattern (19 bp):
AATTACTTTAAATTCTTTA
Found at i:107414 original size:18 final size:19
Alignment explanation
Indices: 107379--107414 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
107369 ATAATTTAAT
*
107379 CTTTAAAAATGTGTGTATG
1 CTTTAAAAATGTGAGTATG
107398 CTTTAAAAATGT-AGTAT
1 CTTTAAAAATGTGAGTAT
107415 TTTATGCTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.36, C:0.06, G:0.17, T:0.42
Consensus pattern (19 bp):
CTTTAAAAATGTGAGTATG
Found at i:107911 original size:61 final size:59
Alignment explanation
Indices: 107749--108021 Score: 243
Period size: 60 Copynumber: 4.5 Consensus size: 59
107739 GTTTATATAT
* * *
107749 TTTTAAACATTTTAATTTCATCCCTAAATTATAACTATCATACTAGATTAGTCCTCAAAC
1 TTTTGAACATTTTAATTTCATCCC-AAATTATAACTATCATTCTAAATTAGTCCTCAAAC
* * * * * *
107809 TTTTGAATATTTTAGTTAT-GTCCCCAAACTATGA-TATTCATTCTAAATCAGTCCTCAAAAAC
1 TTTTGAACATTTTAATT-TCAT-CCCAAATTATAACTA-TCATTCTAAATTAGTCCTC--AAAC
* *
107871 -TTTGAACATTTCAATTTCATCCCTAAATTATAACTATCATTCTAGATTAGTCCTCAAAC
1 TTTTGAACATTTTAATTTCATCCC-AAATTATAACTATCATTCTAAATTAGTCCTCAAAC
* * * * *
107930 TTTTGAATATTTTAGTTAT-ATCCACAAACTT-TGATCT-TCATTCTAAATTAGTCCTCGAAT
1 TTTTGAACATTTTAATT-TCATCC-CAAA-TTAT-AACTATCATTCTAAATTAGTCCTCAAAC
**
107990 TTTTGAACATTTCGATTTCATCCCAAATTATA
1 TTTTGAACATTTTAATTTCATCCCAAATTATA
108022 TGTATATACT
Statistics
Matches: 170, Mismatches: 28, Indels: 32
0.74 0.12 0.14
Matches are distributed among these distances:
58 3 0.02
59 12 0.07
60 100 0.59
61 49 0.29
62 6 0.04
ACGTcount: A:0.33, C:0.19, G:0.06, T:0.41
Consensus pattern (59 bp):
TTTTGAACATTTTAATTTCATCCCAAATTATAACTATCATTCTAAATTAGTCCTCAAAC
Found at i:107970 original size:121 final size:120
Alignment explanation
Indices: 107754--108021 Score: 421
Period size: 121 Copynumber: 2.2 Consensus size: 120
107744 TATATTTTTA
*
107754 AACATTTTAATTTCATCCCTAAATTATAACTATCATACTAGATTAGTCCTCAAACTTTTGAATAT
1 AACATTTCAATTTCATCCCTAAATTATAACTATCATACTAGATTAGTCCTCAAACTTTTGAATAT
* *
107819 TTTAGTTATGTCCCCAAACTATGATATTCATTCTAAATCAGTCCTCAAAAACTTTG
66 TTTAGTTATATCCACAAACTATGATATTCATTCTAAATCAGTCCTC-AAAACTTTG
*
107875 AACATTTCAATTTCATCCCTAAATTATAACTATCATTCTAGATTAGTCCTCAAACTTTTGAATAT
1 AACATTTCAATTTCATCCCTAAATTATAACTATCATACTAGATTAGTCCTCAAACTTTTGAATAT
* * * * **
107940 TTTAGTTATATCCACAAACTTTGATCTTCATTCTAAATTAGTCCTCGAATTTTTG
66 TTTAGTTATATCCACAAACTATGATATTCATTCTAAATCAGTCCTCAAAACTTTG
*
107995 AACATTTCGATTTCATCCC-AAATTATA
1 AACATTTCAATTTCATCCCTAAATTATA
108022 TGTATATACT
Statistics
Matches: 136, Mismatches: 11, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
119 8 0.06
120 24 0.18
121 104 0.76
ACGTcount: A:0.34, C:0.20, G:0.06, T:0.40
Consensus pattern (120 bp):
AACATTTCAATTTCATCCCTAAATTATAACTATCATACTAGATTAGTCCTCAAACTTTTGAATAT
TTTAGTTATATCCACAAACTATGATATTCATTCTAAATCAGTCCTCAAAACTTTG
Found at i:108563 original size:2 final size:2
Alignment explanation
Indices: 108556--108586 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
108546 TGACACATGA
108556 AT AT AT AT AT AT AT AT AT AT AT AT ACT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
108587 TAGTTAATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:108767 original size:60 final size:60
Alignment explanation
Indices: 108640--108792 Score: 166
Period size: 60 Copynumber: 2.5 Consensus size: 60
108630 AATTGGTCTT
* * * *
108640 TAAACTTTTAAATATTCTCATTTCATCCCCAAACTACGAATCTTATTATAAATTAGTCCT
1 TAAACTTTTAAATATTCTAATTTCATCCCTAAACTAAGAATCTTATTATAAATTAGTCCC
* * * * *
108700 TAAACTTTTAAACATTCTAATTTCATCCCTAAACTAAGACTCTCT-TTCTAATTTGGTCCC
1 TAAACTTTTAAATATTCTAATTTCATCCCTAAACTAAGAATCT-TATTATAAATTAGTCCC
** *
108760 TGGACTTTTTAATATT-TCAATTTCATCCCTAAA
1 TAAACTTTTAAATATTCT-AATTTCATCCCTAAA
108793 TTAATCCAAA
Statistics
Matches: 78, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
59 1 0.01
60 76 0.97
61 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (60 bp):
TAAACTTTTAAATATTCTAATTTCATCCCTAAACTAAGAATCTTATTATAAATTAGTCCC
Found at i:131982 original size:29 final size:26
Alignment explanation
Indices: 131924--131978 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
131914 CAACATGCGC
*
131924 AAATTATAAAATGATTTATTATTATT
1 AAATCATAAAATGATTTATTATTATT
131950 AAATCATAAAATGATTTATTATTATT
1 AAATCATAAAATGATTTATTATTATT
131976 AAA
1 AAA
131979 AAATAAAACA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (26 bp):
AAATCATAAAATGATTTATTATTATT
Found at i:131984 original size:26 final size:26
Alignment explanation
Indices: 131929--131986 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
131919 TGCGCAAATT
**
131929 ATAAAATGATTTATTATTATTAAATC
1 ATAAAATGATTTATTATTATTAAAAA
131955 ATAAAATGATTTATTATTATTAAAAA
1 ATAAAATGATTTATTATTATTAAAAA
131981 ATAAAA
1 ATAAAA
131987 CAGGTTTTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.41
Consensus pattern (26 bp):
ATAAAATGATTTATTATTATTAAAAA
Found at i:132582 original size:32 final size:31
Alignment explanation
Indices: 132545--132621 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
132535 TGGGGCTACG
*
132545 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** ** *
132577 GGGCCTACCCGAGAATGATCTCAGGGTCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
132608 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
132622 GTCACATTAG
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.16
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:138198 original size:21 final size:21
Alignment explanation
Indices: 138152--138205 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
138142 GATTTTGACT
*
138152 ATCGCATTGCGATTTTCCAAA
1 ATCGCATTGCGATTTTACAAA
* * *
138173 TTCGCGTTGCGATTTTAGAAA
1 ATCGCATTGCGATTTTACAAA
*
138194 ATCGCAATGCGA
1 ATCGCATTGCGA
138206 ATATGTAAAT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.31
Consensus pattern (21 bp):
ATCGCATTGCGATTTTACAAA
Found at i:138257 original size:81 final size:81
Alignment explanation
Indices: 138110--138258 Score: 185
Period size: 82 Copynumber: 1.8 Consensus size: 81
138100 AATGACCAAC
* * ** * *
138110 AAAATCGCAATGCGATCTCTAAATCGCAACGCGATTTTGACTATCGCATTGCGATTTTCCAAATT
1 AAAATCGCAATGCGATATCTAAATCGCAACGCGATCTCCACTATCGCAATGCGAGTTTCCAAATT
138175 CGCGTTGCGATTTTAG
66 CGCGTTGCGATTTTAG
* * *
138191 AAAATCGCAATGCGAATATGTAAATCGCAACGCGATCTCCAGTATCGCAAAT-C-AGTTTCCAGA
1 AAAATCGCAATGCG-ATATCTAAATCGCAACGCGATCTCCACTATCGC-AATGCGAGTTTCCAAA
138254 TTCGC
64 TTCGC
138259 AACGCGATTC
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
81 27 0.47
82 28 0.49
83 2 0.04
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.28
Consensus pattern (81 bp):
AAAATCGCAATGCGATATCTAAATCGCAACGCGATCTCCACTATCGCAATGCGAGTTTCCAAATT
CGCGTTGCGATTTTAG
Found at i:138266 original size:81 final size:81
Alignment explanation
Indices: 138110--138307 Score: 179
Period size: 81 Copynumber: 2.4 Consensus size: 81
138100 AATGACCAAC
* * ** * *
138110 AAAATCGCAATGCGATCTCTAAATCGCAACGCGATTTTGACTATCGCATTGCGATTTTCCAAATT
1 AAAATCGCAATGCGATATCTAAATCGCAACGCGATCTCCACTATCGCAATGCGAGTTTCCAAATT
***
138175 CGCGTTGCGATTTTAG
66 CGCAACGCGATTTTAG
* * *
138191 AAAATCGCAATGCGAATATGTAAATCGCAACGCGATCTCCAGTATCGCAAAT-C-AGTTTCCAGA
1 AAAATCGCAATGCG-ATATCTAAATCGCAACGCGATCTCCACTATCGC-AATGCGAGTTTCCAAA
*
138254 TTCGCAACGCGATTCT-G
64 TTCGCAACGCGATTTTAG
** *
138271 ACTATCGCAACGCGATAATAC-ATAATCGCAACGCGAT
1 AAAATCGCAATGCGAT-AT-CTA-AATCGCAACGCGAT
138308 AATTCATAAT
Statistics
Matches: 95, Mismatches: 17, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
79 2 0.02
80 15 0.16
81 48 0.51
82 28 0.29
83 2 0.02
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.26
Consensus pattern (81 bp):
AAAATCGCAATGCGATATCTAAATCGCAACGCGATCTCCACTATCGCAATGCGAGTTTCCAAATT
CGCAACGCGATTTTAG
Found at i:138369 original size:21 final size:21
Alignment explanation
Indices: 138274--138363 Score: 112
Period size: 21 Copynumber: 4.3 Consensus size: 21
138264 GATTCTGACT
138274 ATCGCAACGCGATAATACATA
1 ATCGCAACGCGATAATACATA
*
138295 ATCGCAACGCGATAATTCATA
1 ATCGCAACGCGATAATACATA
**
138316 ATCGCAACGCGATTCTA-ACT-
1 ATCGCAACGCGATAATACA-TA
* *
138336 ATCGCAATGCGATAATACAAA
1 ATCGCAACGCGATAATACATA
138357 ATCGCAA
1 ATCGCAA
138364 TACGATTTTT
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
20 15 0.26
21 43 0.74
ACGTcount: A:0.40, C:0.24, G:0.14, T:0.21
Consensus pattern (21 bp):
ATCGCAACGCGATAATACATA
Found at i:138409 original size:19 final size:21
Alignment explanation
Indices: 138385--138425 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
138375 AAATTTACGT
138385 TAGTCCAA-ATT-CGTTGCGA
1 TAGTCCAAGATTACGTTGCGA
*
138404 TAGTCCAAGTTTACGTTGCGA
1 TAGTCCAAGATTACGTTGCGA
138425 T
1 T
138426 TTCTTAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 8 0.42
20 2 0.11
21 9 0.47
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (21 bp):
TAGTCCAAGATTACGTTGCGA
Found at i:146028 original size:30 final size:30
Alignment explanation
Indices: 145957--146018 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
145947 TCGACAAGTG
* *
145957 GTCCAAACAACCTATGCAGGTCGCCATGCAA
1 GTCC-AACGACCTATGCAGGTCACCATGCAA
* *
145988 GTCGAACGACCTGTGCAGGTCACCATGCAA
1 GTCCAACGACCTATGCAGGTCACCATGCAA
146018 G
1 G
146019 CCATGCGACC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
30 24 0.89
31 3 0.11
ACGTcount: A:0.29, C:0.31, G:0.24, T:0.16
Consensus pattern (30 bp):
GTCCAACGACCTATGCAGGTCACCATGCAA
Found at i:153634 original size:29 final size:29
Alignment explanation
Indices: 153589--153646 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
153579 GTGTTGGTCG
*
153589 TAGGTCGCCATGCCTTCCGGGCGACCTAC
1 TAGGTCGCCATGCCTTCCCGGCGACCTAC
* *
153618 TAGGTCGCCATGTCTTCCCGGCGAGCTAC
1 TAGGTCGCCATGCCTTCCCGGCGACCTAC
153647 AAGAGATTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.14, C:0.36, G:0.28, T:0.22
Consensus pattern (29 bp):
TAGGTCGCCATGCCTTCCCGGCGACCTAC
Found at i:153709 original size:23 final size:23
Alignment explanation
Indices: 153682--153732 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
153672 CTCAACAATC
153682 CGAGGCCA-TCCGAACGAGCTATG
1 CGAGGCCAGT-CGAACGAGCTATG
* *
153705 CGAGGGCAGTCGAGCGAGCTATG
1 CGAGGCCAGTCGAACGAGCTATG
*
153728 GGAGG
1 CGAGG
153733 GAATCCGAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 23 0.96
24 1 0.04
ACGTcount: A:0.24, C:0.24, G:0.41, T:0.12
Consensus pattern (23 bp):
CGAGGCCAGTCGAACGAGCTATG
Found at i:153741 original size:23 final size:24
Alignment explanation
Indices: 153689--153741 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 24
153679 ATCCGAGGCC
*
153689 ATCCGAACGAGCTATGCGAGGGCA
1 ATCCGAGCGAGCTATGCGAGGGCA
* *
153713 GT-CGAGCGAGCTATGGGAGGG-A
1 ATCCGAGCGAGCTATGCGAGGGCA
153735 ATCCGAG
1 ATCCGAG
153742 GGCAGCCGAG
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
22 2 0.08
23 21 0.88
24 1 0.04
ACGTcount: A:0.26, C:0.21, G:0.40, T:0.13
Consensus pattern (24 bp):
ATCCGAGCGAGCTATGCGAGGGCA
Found at i:153752 original size:33 final size:33
Alignment explanation
Indices: 153705--153774 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 33
153695 ACGAGCTATG
* *
153705 CGAGGGCAGTCGAGCGAGCTATGGGAGGGAATC
1 CGAGGGCAGCCGAGCGAGCTATGCGAGGGAATC
*
153738 CGAGGGCAGCCGAGCGAGCTATGCGAGGGCATC
1 CGAGGGCAGCCGAGCGAGCTATGCGAGGGAATC
153771 CGAG
1 CGAG
153775 CGAGCGAGCA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.23, C:0.23, G:0.44, T:0.10
Consensus pattern (33 bp):
CGAGGGCAGCCGAGCGAGCTATGCGAGGGAATC
Found at i:153836 original size:29 final size:29
Alignment explanation
Indices: 153790--153845 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
153780 GAGCAAGGGT
*
153790 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGGGCATGGCGACCTACA
153819 AGGTCGCCCGGAGGGCATGGCGACCTA
1 AGGTCGCCCGGAGGGCATGGCGACCTA
153846 TGTGTTGGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.20, C:0.30, G:0.38, T:0.12
Consensus pattern (29 bp):
AGGTCGCCCGGAGGGCATGGCGACCTACA
Done.