Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007921.1 Hibiscus syriacus cultivar Beakdansim tig00110325_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: 892961
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:580052 original size:21 final size:21
Alignment explanation
Indices: 580028--580087 Score: 50
Period size: 21 Copynumber: 2.8 Consensus size: 21
580018 ACTTGTCTTA
*
580028 TTTAAGGTTTAGATTTTAGAT
1 TTTAAGGTTTAGATTTTAGAG
* * *
580049 TTTATA-ATTTATAATTTAGAG
1 TTTA-AGGTTTAGATTTTAGAG
*
580070 TTCAAGGTTTAGGATTTT
1 TTTAAGGTTTA-GATTTT
580088 GGGATTGTGA
Statistics
Matches: 28, Mismatches: 8, Indels: 5
0.68 0.20 0.12
Matches are distributed among these distances:
20 1 0.04
21 22 0.79
22 5 0.18
ACGTcount: A:0.30, C:0.02, G:0.17, T:0.52
Consensus pattern (21 bp):
TTTAAGGTTTAGATTTTAGAG
Found at i:580428 original size:17 final size:17
Alignment explanation
Indices: 580381--580440 Score: 52
Period size: 17 Copynumber: 3.6 Consensus size: 17
580371 ATAATCAATA
*
580381 AATTAAATTTCA-ATAAT
1 AATTAAAATTCATAT-AT
* * *
580398 TATTAAAAAT-ATATCT
1 AATTAAAATTCATATAT
*
580414 AATTTAAATTCATATAT
1 AATTAAAATTCATATAT
580431 AATTAAAATT
1 AATTAAAATT
580441 AATGTAGTTA
Statistics
Matches: 32, Mismatches: 9, Indels: 4
0.71 0.20 0.09
Matches are distributed among these distances:
16 9 0.28
17 23 0.72
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (17 bp):
AATTAAAATTCATATAT
Found at i:580735 original size:31 final size:31
Alignment explanation
Indices: 580697--580795 Score: 98
Period size: 31 Copynumber: 3.3 Consensus size: 31
580687 AACGGTTTAT
580697 GTATCATACTGGA-TATTTCAATAAAATATAA
1 GTATCATA-TGGACTATTTCAATAAAATATAA
* *
580728 GTATCATATTGACTATTTCGATAAAATATAA
1 GTATCATATGGACTATTTCAATAAAATATAA
* * * *
580759 GTACCATGTCGAATATTT---TAAAATATAA
1 GTATCATATGGACTATTTCAATAAAATATAA
*
580787 GTAACATAT
1 GTATCATAT
580796 TAGACATTTT
Statistics
Matches: 59, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
28 17 0.29
30 3 0.05
31 39 0.66
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.36
Consensus pattern (31 bp):
GTATCATATGGACTATTTCAATAAAATATAA
Found at i:580804 original size:28 final size:27
Alignment explanation
Indices: 580718--580806 Score: 79
Period size: 28 Copynumber: 3.1 Consensus size: 27
580708 GATATTTCAA
*
580718 TAAAATATAAGTATCATATTGACTATTT
1 TAAAATATAAGTAACATATTGAC-ATTT
* * * *
580746 CGATAAAATATAAGTACCATGTCGAATATTT
1 ---TAAAATATAAGTAACATATTG-ACATTT
580777 TAAAATATAAGTAACATATTAGACATTT
1 TAAAATATAAGTAACATATT-GACATTT
580805 TA
1 TA
580807 TCAAAGTACA
Statistics
Matches: 48, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
28 24 0.50
29 1 0.02
31 22 0.46
32 1 0.02
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.37
Consensus pattern (27 bp):
TAAAATATAAGTAACATATTGACATTT
Found at i:583714 original size:15 final size:15
Alignment explanation
Indices: 583694--583727 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
583684 TTCTTTCTTT
583694 GGATACATTCTTACA
1 GGATACATTCTTACA
*
583709 GGATACGTTCTTACA
1 GGATACATTCTTACA
583724 GGAT
1 GGAT
583728 CCTGCCTATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (15 bp):
GGATACATTCTTACA
Found at i:585271 original size:12 final size:12
Alignment explanation
Indices: 585254--585278 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
585244 TTTTAATAAA
585254 AAATAATATTTT
1 AAATAATATTTT
585266 AAATAATATTTT
1 AAATAATATTTT
585278 A
1 A
585279 TCAAAAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AAATAATATTTT
Found at i:594283 original size:2 final size:2
Alignment explanation
Indices: 594271--594331 Score: 113
Period size: 2 Copynumber: 30.5 Consensus size: 2
594261 TATTGTTTTC
*
594271 TA TA TA CA 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
594313 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
594332 TGTTTCTGTT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:596942 original size:43 final size:43
Alignment explanation
Indices: 596817--596944 Score: 213
Period size: 43 Copynumber: 3.0 Consensus size: 43
596807 ATTTAAGATG
* * *
596817 AGACTGAAAAGCAATAGTTTGGTATAACAGGGAGGGTTAATTG
1 AGACTGGAAAGCAATAGTTTGGTATAACAGGGAGGGTTACTTA
596860 AGACTGGAAAGCAATAGTTTGGTATAACAGGGAGGGTTACTTA
1 AGACTGGAAAGCAATAGTTTGGTATAACAGGGAGGGTTACTTA
596903 AGACTGGAAAGCAATAGTTTGGCT-TAACAGGGAGGGTTACTT
1 AGACTGGAAAGCAATAGTTTGG-TATAACAGGGAGGGTTACTT
596945 TGAAAACGAG
Statistics
Matches: 81, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
43 80 0.99
44 1 0.01
ACGTcount: A:0.34, C:0.09, G:0.30, T:0.26
Consensus pattern (43 bp):
AGACTGGAAAGCAATAGTTTGGTATAACAGGGAGGGTTACTTA
Found at i:599329 original size:21 final size:21
Alignment explanation
Indices: 599288--599329 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
599278 TTAATCTATA
* * *
599288 AAATATATATAATTTTTTAAT
1 AAATAAATATAATCTTATAAT
599309 AAATAAATATAATCTTATAAT
1 AAATAAATATAATCTTATAAT
599330 TATTTAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (21 bp):
AAATAAATATAATCTTATAAT
Found at i:603394 original size:63 final size:65
Alignment explanation
Indices: 603320--603473 Score: 199
Period size: 65 Copynumber: 2.4 Consensus size: 65
603310 AGGCCAATAT
* *
603320 CCTTCGCTGTGAAGTTGAA-AT-TG-ACTCTGAAACT-GGGAAGTTGTTTGTTGACAGCCAGCGG
1 CCTTCGTTGTGAAGTTGAACATGTGTACTCTGAAACTGGGGAA-TT-TTTGTTGACAACCAGCGG
603381 CC
64 CC
* ** *
603383 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTAAACTGGGGAATTTTTGTTGACAACCAGCGGCC
1 CCTTCGTTGTGAAGTTGAACATGTGTACTCTGAAACTGGGGAATTTTTGTTGACAACCAGCGGCC
*
603448 CCTTCGTTGTGAAGTTGAACTTGTGT
1 CCTTCGTTGTGAAGTTGAACATGTGT
603474 TGTCTTGAGT
Statistics
Matches: 81, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
63 18 0.22
64 1 0.01
65 47 0.58
66 10 0.12
67 5 0.06
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.34
Consensus pattern (65 bp):
CCTTCGTTGTGAAGTTGAACATGTGTACTCTGAAACTGGGGAATTTTTGTTGACAACCAGCGGCC
Found at i:603446 original size:65 final size:66
Alignment explanation
Indices: 603349--603479 Score: 230
Period size: 65 Copynumber: 2.0 Consensus size: 66
603339 ATTGACTCTG
*
603349 AAACTGGGAAGTTGTTTGTTGACAGCCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
1 AAACTGGGAAGTTGTTTGTTGACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
603414 T
66 T
603415 AAACTGGGGAA-TT-TTTGTTGACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTC
1 AAACT-GGGAAGTTGTTTGTTGACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTC
603478 TT
65 TT
603480 GAGTCCAATA
Statistics
Matches: 63, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
65 51 0.81
66 7 0.11
67 5 0.08
ACGTcount: A:0.19, C:0.18, G:0.27, T:0.35
Consensus pattern (66 bp):
AAACTGGGAAGTTGTTTGTTGACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
T
Found at i:603666 original size:235 final size:231
Alignment explanation
Indices: 603349--603805 Score: 731
Period size: 235 Copynumber: 2.0 Consensus size: 231
603339 ATTGACTCTG
* *
603349 AAACTGGGAAGTTGTTTGTTGACAGCCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
1 AAACTGGGAAGATGTTTGTTGACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * *
603414 TAAACTGGGGAATTTTTGTTGACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 GAAACTGGGAAATTTTTGTTAACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* *
603479 TG-AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGAC
131 TGAAGTCCAATATCCTTCGCTATGAAGTTGAAATT-G----G--ATTGGGAAATTGTTTGTTGAC
603543 AGCCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
189 AGCCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
603586 AAACTGGGAA-AT-TTTGTTGACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
1 AAACTGGGAAGATGTTTGTTGACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
*
603649 GATACTGGGAAATTTTTGTTAACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 GAAACTGGGAAATTTTTGTTAACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* *
603714 TGAATTCCAATATCCTTCGCTATGAAGTTGAAATTGGATTGGGAAATTGTTTGTTGACAGTCAGC
131 TGAAGTCCAATATCCTTCGCTATGAAGTTGAAATTGGATTGGGAAATTGTTTGTTGACAGCCAGC
*
603779 GGCCCCTTTGTTGTGAAGTTGAACTTG
196 GGCCCCTTCGTTGTGAAGTTGAACTTG
603806 AGCTGTCTCG
Statistics
Matches: 208, Mismatches: 11, Indels: 10
0.91 0.05 0.04
Matches are distributed among these distances:
229 52 0.25
231 1 0.00
235 114 0.55
236 31 0.15
237 10 0.05
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.35
Consensus pattern (231 bp):
AAACTGGGAAGATGTTTGTTGACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
GAAACTGGGAAATTTTTGTTAACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
TGAAGTCCAATATCCTTCGCTATGAAGTTGAAATTGGATTGGGAAATTGTTTGTTGACAGCCAGC
GGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
Found at i:603701 original size:65 final size:65
Alignment explanation
Indices: 603491--603713 Score: 328
Period size: 64 Copynumber: 3.5 Consensus size: 65
603481 AGTCCAATAT
* * * * * *
603491 CCTTCGCTGTGAAGTTGAAATTG-G--CTCTGAAATTGGGAAGTTGTTTGTTGACAGCCAGCGGC
1 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGAAACTGGGAAATT-TTTGTTGACAACCAGCGGC
603553 C
65 C
*
603554 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTAAACTGGGAAA-TTTTGTTGACAACCAGCGGCC
1 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGAAACTGGGAAATTTTTGTTGACAACCAGCGGCC
* *
603618 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGATACTGGGAAATTTTTGTTAACAACCAGCGGCC
1 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGAAACTGGGAAATTTTTGTTGACAACCAGCGGCC
603683 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
1 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
603714 TGAATTCCAA
Statistics
Matches: 146, Mismatches: 10, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
63 21 0.14
64 61 0.42
65 52 0.36
66 12 0.08
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.35
Consensus pattern (65 bp):
CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGAAACTGGGAAATTTTTGTTGACAACCAGCGGCC
Found at i:604278 original size:36 final size:36
Alignment explanation
Indices: 604168--604285 Score: 100
Period size: 36 Copynumber: 3.3 Consensus size: 36
604158 AGAGAAACTG
* * *
604168 TCTCAAGGGAGACAAAGT-TTGTTTCAAGAAAAACTA
1 TCTCAAGCGAGACAAA-TCTTGTTTTAAGAAAAACAA
* * ** **
604204 TCTCAAGCGAGATAAAATCTTCTAGT--G-AAAACGG
1 TCTCAAGCGAGA-CAAATCTTGTTTTAAGAAAAACAA
604238 TCTCAAGCGAGACAAATCTTGTTTTAAGAAAAACAA
1 TCTCAAGCGAGACAAATCTTGTTTTAAGAAAAACAA
*
604274 TCTCAAGTGAGA
1 TCTCAAGCGAGA
604286 TAATCATCTG
Statistics
Matches: 62, Mismatches: 15, Indels: 10
0.71 0.17 0.11
Matches are distributed among these distances:
33 9 0.15
34 17 0.27
35 2 0.03
36 28 0.45
37 6 0.10
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.25
Consensus pattern (36 bp):
TCTCAAGCGAGACAAATCTTGTTTTAAGAAAAACAA
Found at i:605124 original size:22 final size:22
Alignment explanation
Indices: 605099--605141 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
605089 CATTTTTGTT
*
605099 CATTTGATGCTCAAAGGTTTGG
1 CATTGGATGCTCAAAGGTTTGG
605121 CATTGGATGCTCAAAGGTTTG
1 CATTGGATGCTCAAAGGTTTG
605142 TTGGGGTAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.14, G:0.28, T:0.35
Consensus pattern (22 bp):
CATTGGATGCTCAAAGGTTTGG
Found at i:605718 original size:22 final size:23
Alignment explanation
Indices: 605689--605741 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
605679 TCTTTGCATG
605689 TGCTTTTTGTCCCTTTTTCTTTTT
1 TGCTTTTTGT-CCTTTTTCTTTTT
* *
605713 T-CTTTTTGTTCTTTTTTTTTTT
1 TGCTTTTTGTCCTTTTTCTTTTT
605735 TGCTTTT
1 TGCTTTT
605742 GTTTTTTGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 12 0.46
23 13 0.50
24 1 0.04
ACGTcount: A:0.00, C:0.15, G:0.08, T:0.77
Consensus pattern (23 bp):
TGCTTTTTGTCCTTTTTCTTTTT
Found at i:605724 original size:16 final size:16
Alignment explanation
Indices: 605705--605736 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
605695 TTGTCCCTTT
605705 TTCTTTTTTCTTTTTG
1 TTCTTTTTTCTTTTTG
*
605721 TTCTTTTTTTTTTTTG
1 TTCTTTTTTCTTTTTG
605737 CTTTTGTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.00, C:0.09, G:0.06, T:0.84
Consensus pattern (16 bp):
TTCTTTTTTCTTTTTG
Found at i:605742 original size:22 final size:22
Alignment explanation
Indices: 605691--605761 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 22
605681 TTTGCATGTG
*
605691 CTTTTTGTCCCTTTTTCTTTTTT
1 CTTTTTGT-TCTTTTTCTTTTTT
*
605714 CTTTTTGTTCTTTTTTTTTTTT
1 CTTTTTGTTCTTTTTCTTTTTT
* *
605736 GC-TTTTGTT-TTTTGC-TTCTT
1 -CTTTTTGTTCTTTTTCTTTTTT
605756 CTTTTT
1 CTTTTT
605762 TGCCCTTTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
19 1 0.02
20 8 0.20
21 4 0.10
22 19 0.46
23 9 0.22
ACGTcount: A:0.00, C:0.15, G:0.07, T:0.77
Consensus pattern (22 bp):
CTTTTTGTTCTTTTTCTTTTTT
Found at i:605755 original size:30 final size:29
Alignment explanation
Indices: 605702--605762 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 29
605692 TTTTTGTCCC
* *
605702 TTTTTCTTTTTTCTTTTTGTTCTTTTTTT
1 TTTTTCTTTTGTCTTTTTGTTCTTCTTTT
605731 TTTTTGCTTTTGT-TTTTTGCTTCTTCTTTT
1 TTTTT-CTTTTGTCTTTTTG-TTCTTCTTTT
605761 TT
1 TT
605763 GCCCTTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 11 0.39
30 17 0.61
ACGTcount: A:0.00, C:0.11, G:0.07, T:0.82
Consensus pattern (29 bp):
TTTTTCTTTTGTCTTTTTGTTCTTCTTTT
Found at i:605762 original size:14 final size:13
Alignment explanation
Indices: 605710--605764 Score: 56
Period size: 13 Copynumber: 4.0 Consensus size: 13
605700 CCTTTTTCTT
*
605710 TTTTCTTTTTGTTC
1 TTTTCTTTTT-TGC
*
605724 TTTTTTTTTTTTGC
1 -TTTTCTTTTTTGC
*
605738 TTTTGTTTTTTGC
1 TTTTCTTTTTTGC
605751 TTCTTCTTTTTTGC
1 TT-TTCTTTTTTGC
605765 CCTTTTTATT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
13 14 0.40
14 12 0.34
15 9 0.26
ACGTcount: A:0.00, C:0.13, G:0.09, T:0.78
Consensus pattern (13 bp):
TTTTCTTTTTTGC
Found at i:605762 original size:16 final size:14
Alignment explanation
Indices: 605709--605762 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 14
605699 CCCTTTTTCT
605709 TTTTTCTTTTTGTTC
1 TTTTT-TTTTTGTTC
605724 TTTTTTTTTT-TTGC
1 TTTTTTTTTTGTT-C
605738 TTTTGTTTTTTGCTTC
1 TTTT-TTTTTTG-TTC
*
605754 TTCTTTTTT
1 TTTTTTTTT
605763 GCCCTTTTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
13 2 0.06
14 10 0.29
15 16 0.47
16 4 0.12
17 2 0.06
ACGTcount: A:0.00, C:0.11, G:0.07, T:0.81
Consensus pattern (14 bp):
TTTTTTTTTTGTTC
Found at i:607691 original size:5 final size:5
Alignment explanation
Indices: 607681--607709 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
607671 GCAAGTGATG
607681 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
607710 GAAAGATGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:610181 original size:3 final size:3
Alignment explanation
Indices: 610173--610226 Score: 90
Period size: 3 Copynumber: 17.7 Consensus size: 3
610163 TGTGTCTACA
610173 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T
*
610219 ATT TTT AT
1 ATT ATT AT
610227 GTTAATGTTA
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
3 45 0.94
4 3 0.06
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:621740 original size:13 final size:13
Alignment explanation
Indices: 621722--621746 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
621712 TTGCTTCGTT
621722 AAATAATTTAATA
1 AAATAATTTAATA
621735 AAATAATTTAAT
1 AAATAATTTAAT
621747 GGGATAAGGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAATAATTTAATA
Found at i:624981 original size:21 final size:20
Alignment explanation
Indices: 624957--625007 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
624947 TATATTAATC
624957 ATAATATAAATTAAAAATATT
1 ATAATATAAATT-AAAATATT
* *
624978 ATAATAATATATTAATATATT
1 ATAAT-ATAAATTAAAATATT
*
624999 ATAAAATAA
1 ATAATATAA
625008 TATTTAAACT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 3 0.12
21 16 0.64
22 6 0.24
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
ATAATATAAATTAAAATATT
Found at i:626660 original size:21 final size:21
Alignment explanation
Indices: 626634--626696 Score: 108
Period size: 21 Copynumber: 3.0 Consensus size: 21
626624 AGTCGAGGGT
626634 TACAGTGGTCATTCGGGACAA
1 TACAGTGGTCATTCGGGACAA
*
626655 TACAGTGGTCCTTCGGGACAA
1 TACAGTGGTCATTCGGGACAA
*
626676 TATAGTGGTCATTCGGGACAA
1 TACAGTGGTCATTCGGGACAA
626697 ATTTCATATG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (21 bp):
TACAGTGGTCATTCGGGACAA
Found at i:627043 original size:19 final size:19
Alignment explanation
Indices: 627019--627056 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
627009 CAGAAATGAT
627019 ATATGTTTTATATGATATG
1 ATATGTTTTATATGATATG
627038 ATATGTTTTATATGATATG
1 ATATGTTTTATATGATATG
627057 TAGCAGGGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.53
Consensus pattern (19 bp):
ATATGTTTTATATGATATG
Found at i:627137 original size:22 final size:22
Alignment explanation
Indices: 627109--627171 Score: 81
Period size: 22 Copynumber: 2.9 Consensus size: 22
627099 TAACATTCGG
*
627109 TATTGTTTACGGTACTGTTCAC
1 TATTGTTCACGGTACTGTTCAC
** *
627131 TATTGTTCATAGTACTGTTCAT
1 TATTGTTCACGGTACTGTTCAC
*
627153 TAATGTTCACGGTACTGTT
1 TATTGTTCACGGTACTGTT
627172 TATACCATAT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.21, C:0.16, G:0.17, T:0.46
Consensus pattern (22 bp):
TATTGTTCACGGTACTGTTCAC
Found at i:646374 original size:2 final size:2
Alignment explanation
Indices: 646367--646402 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
646357 CTGTTCTCAT
*
646367 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
646403 GTGGTCATAC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
TA
Found at i:650643 original size:39 final size:39
Alignment explanation
Indices: 650597--650674 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
650587 GTAAATAAAG
*
650597 ATGGAAAATACAAAGATCAAAACTACATTAATTGGTTTT
1 ATGGAAAATACAAAAATCAAAACTACATTAATTGGTTTT
650636 ATGGAAAATACAAAAATCAAAACTACATTAATTGGTTTT
1 ATGGAAAATACAAAAATCAAAACTACATTAATTGGTTTT
650675 CTTGTCCAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.31
Consensus pattern (39 bp):
ATGGAAAATACAAAAATCAAAACTACATTAATTGGTTTT
Found at i:653149 original size:10 final size:10
Alignment explanation
Indices: 653114--653148 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
653104 AGAATGAGAA
653114 ATATAAATAT
1 ATATAAATAT
*
653124 AAATAAATAT
1 ATATAAATAT
*
653134 ATATATATAT
1 ATATAAATAT
653144 ATATA
1 ATATA
653149 TGTGTGTGTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (10 bp):
ATATAAATAT
Found at i:655100 original size:16 final size:16
Alignment explanation
Indices: 655079--655109 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
655069 GTCGAGTGTA
655079 GATGAGTACAATTAAC
1 GATGAGTACAATTAAC
*
655095 GATGAGTACCATTAA
1 GATGAGTACAATTAA
655110 ATTAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.13, G:0.19, T:0.26
Consensus pattern (16 bp):
GATGAGTACAATTAAC
Found at i:660944 original size:20 final size:20
Alignment explanation
Indices: 660908--660951 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
660898 ATTTATAATT
* *
660908 TTAATGATATAATTAAAATA
1 TTAATGATAAAATTAAAAAA
660928 TTAAT-ATAAAATATAAAAAA
1 TTAATGATAAAAT-TAAAAAA
660948 TTAA
1 TTAA
660952 AATTTAAAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (20 bp):
TTAATGATAAAATTAAAAAA
Found at i:668509 original size:59 final size:59
Alignment explanation
Indices: 668388--668513 Score: 137
Period size: 59 Copynumber: 2.1 Consensus size: 59
668378 TTTGGGAATG
* * * * * * **
668388 TAAAATTAGAACGTTTAAAAATTTAGAGATTAGTTTAAAATGAGAATATACTTTGAGGA
1 TAAAATTAGAACGTTTAAAAATTTACAGACTAGTTTAAAATGAAAAAATAATTTAAAAA
* * *
668447 TAAAATTAGAATG-TTAAAAAGTTTACAGACTAGTTTAGAATTAAAAAATAATTTAAAAA
1 TAAAATTAGAACGTTTAAAAA-TTTACAGACTAGTTTAAAATGAAAAAATAATTTAAAAA
668506 TAAAATTA
1 TAAAATTA
668514 AAATATTTAA
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
58 7 0.13
59 48 0.87
ACGTcount: A:0.51, C:0.03, G:0.13, T:0.33
Consensus pattern (59 bp):
TAAAATTAGAACGTTTAAAAATTTACAGACTAGTTTAAAATGAAAAAATAATTTAAAAA
Found at i:674613 original size:35 final size:35
Alignment explanation
Indices: 674574--674645 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
674564 TCAAGACTTT
*
674574 TTCGATAAAAGTTAATACTTAATAAATATTTTTAA
1 TTCGATAAAAGTTAATACTTAATAAATATTTTAAA
674609 TTCGATAAAAGTTAATACTTAATAAATATTTTAAA
1 TTCGATAAAAGTTAATACTTAATAAATATTTTAAA
674644 TT
1 TT
674646 TTAGTTCTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.43
Consensus pattern (35 bp):
TTCGATAAAAGTTAATACTTAATAAATATTTTAAA
Found at i:682875 original size:27 final size:27
Alignment explanation
Indices: 682845--682909 Score: 121
Period size: 27 Copynumber: 2.4 Consensus size: 27
682835 AATAAATTAG
*
682845 TTTTAAAAAATCGTTCTTATAATAGAT
1 TTTTATAAAATCGTTCTTATAATAGAT
682872 TTTTATAAAATCGTTCTTATAATAGAT
1 TTTTATAAAATCGTTCTTATAATAGAT
682899 TTTTATAAAAT
1 TTTTATAAAAT
682910 TAAATACAGA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.48
Consensus pattern (27 bp):
TTTTATAAAATCGTTCTTATAATAGAT
Found at i:682879 original size:13 final size:13
Alignment explanation
Indices: 682861--682906 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
682851 AAAATCGTTC
682861 TTATAATAGATTT
1 TTATAATAGATTT
682874 TTATAA-A-ATCGTT
1 TTATAATAGAT--TT
682887 CTTATAATAGATTT
1 -TTATAATAGATTT
682901 TTATAA
1 TTATAA
682907 AATTAAATAC
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
11 2 0.07
12 1 0.04
13 14 0.50
14 8 0.29
15 1 0.04
16 2 0.07
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.50
Consensus pattern (13 bp):
TTATAATAGATTT
Found at i:705394 original size:19 final size:19
Alignment explanation
Indices: 705364--705419 Score: 94
Period size: 19 Copynumber: 2.9 Consensus size: 19
705354 ATGTATTTAA
*
705364 TAAAATAATATTTTATAAT
1 TAAAAAAATATTTTATAAT
*
705383 TAGAAAAATATTTTATAAT
1 TAAAAAAATATTTTATAAT
705402 TAAAAAAATATTTTATAA
1 TAAAAAAATATTTTATAA
705420 CTTTTAATAG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
TAAAAAAATATTTTATAAT
Found at i:707172 original size:75 final size:75
Alignment explanation
Indices: 707073--707220 Score: 197
Period size: 75 Copynumber: 2.0 Consensus size: 75
707063 TTATTGTATT
* * * * * *
707073 TAAACAATACAATATCTAAAATTTAATGCTATTTGATATAATTTGTCCATTCCTACATCTATTTC
1 TAAACAATACAATATCTAAAATTTAATGATATATAATATAATTTATCCATACCTACACCTATTTC
707138 TAATTATACC
66 TAATTATACC
* * * * *
707148 TAAATAATATAATGTCTAAAATTTAATTATATATAATATAATTTATCTATACCTACACCTATTTC
1 TAAACAATACAATATCTAAAATTTAATGATATATAATATAATTTATCCATACCTACACCTATTTC
707213 TAATTATA
66 TAATTATA
707221 TGTTTTAAGT
Statistics
Matches: 62, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
75 62 1.00
ACGTcount: A:0.41, C:0.14, G:0.03, T:0.43
Consensus pattern (75 bp):
TAAACAATACAATATCTAAAATTTAATGATATATAATATAATTTATCCATACCTACACCTATTTC
TAATTATACC
Found at i:719571 original size:14 final size:14
Alignment explanation
Indices: 719552--719644 Score: 141
Period size: 14 Copynumber: 6.5 Consensus size: 14
719542 GGGGGTATAA
719552 TTCGCCACCTGTAT
1 TTCGCCACCTGTAT
719566 TTCGCCACCTGTAT
1 TTCGCCACCTGTAT
* *
719580 CTCGCCATCTGTAT
1 TTCGCCACCTGTAT
*
719594 TTTGCCACCTGTAT
1 TTCGCCACCTGTAT
719608 TTCGCCACCTGTAT
1 TTCGCCACCTGTAT
719622 AATTCGCCACCTGTAT
1 --TTCGCCACCTGTAT
719638 TTCGCCA
1 TTCGCCA
719645 TCTAACTCTA
Statistics
Matches: 71, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
14 57 0.80
16 14 0.20
ACGTcount: A:0.16, C:0.34, G:0.14, T:0.35
Consensus pattern (14 bp):
TTCGCCACCTGTAT
Found at i:722196 original size:443 final size:433
Alignment explanation
Indices: 721323--722201 Score: 1566
Period size: 436 Copynumber: 2.0 Consensus size: 433
721313 AAGATAATTC
*
721323 TCAATATTTGATACAGAACACTCACACTTCTAGTATTTCTGGTGCTAGAATCGGAAACTCGAGAA
1 TCAATATTTGATACAGAACACTCACAATTCTAGTATTTCTGGTGCTAGAATCGGAAACTCGAGAA
*
721388 TAACAATAATTCATTTACATCTAAGATATCGCTTGGTTGATATTCTCAATTCTTATATTAACTCG
66 TAACAATAATTCATTTACATC--AGATATCGCTTGGTTCATATTCTCAATTCTTATATTAACTCG
721453 GTACGGTGGAAATAAAATTCAAAATATGAGGAAATAGAAGAGTAAAATATTTTATTAATTAGACA
129 GTACGGTGGAAATAAAATTCAAAATATGAGGAAATAGAAGAGTAAAATATTTTATTAATTAGACA
721518 TTAGCCCATTTAATTGAATTATTGTTGTTTTTTTACTTTTTTAATATTCTTAAAATGATTACAAT
194 TTAGCCCATTTAATTGAATTATTGTTGTTTTTTTACTTTTTTAATATTCTTAAAATGATTACAAT
721583 GTAACATATGTATTTTTAACTGTTTACATCTATTAAAATAACTGTTTGAAGGTTAGAGATTCTAA
259 GTAACATATGTATTTTTAACTGTTTACATCTATTAAAATAACTGTTTGAAGGTTAGAGATTCTAA
721648 AAAACAAGTCTCTTTTTATTATTAAGATTATTTGTAAGTTAGTAGATTTAGTGGTGTATGTGCCA
324 AAAACAAGTCTCTTTTTATTATTAAGATTATTTGTAAGTTAGTAGATTTAGTGGTGTATGTGCCA
721713 AATTTCTAAGTTATATAGTATATATACATTATAAAGTTTATATGTA
389 AATTTCTAAGTTATATAG-ATATATACATTATAAAGTTTATATGTA
*
721759 TCAATATTTGATACAGAACACTCACAATTCTAGTATTTCTGGTGCTCGAATCTGGAAACTCGAAG
1 TCAATATTTGATACAGAACACTCACAATTCTAGTATTTCTGGTGCTAGAATC-GGAAACTCG-AG
721824 AATAACAATAATTCATTTACCATC-GATATCGCTTGGTTCATATTCTCAATTCTTATATTAACTC
64 AATAACAATAATTCATTTA-CATCAGATATCGCTTGGTTCATATTCTCAATTCTTATATTAACTC
721888 GGTACGGTGGAAATAAAATTCAAAATATGAGGAAATAGAATGAGTAAAATATATTTTATTAATTA
128 GGTACGGTGGAAATAAAATTCAAAATATGAGGAAATAGAA-GAGT-AAA-ATATTTTATTAATTA
721953 GACATTAGCCCAATTTTAATTGAATTATTTGTTGTTTTTTTACTTTTTTTAATATTCTTAAAATG
190 GACATTAGCCC-A-TTTAATTGAATTA-TTGTTGTTTTTTTAC-TTTTTTAATATTCTTAAAATG
722018 ATTACAATGTAACATATGTATTTTTAACTGTTTACATCTATTAAAATAACTGTTTGAA-GTTAGA
251 ATTACAATGTAACATATGTATTTTTAACTGTTTACATCTATTAAAATAACTGTTTGAAGGTTAGA
722082 GATTCTAAAAAACAAGTCTCTTTTTTATTATTAAGATTATTTGTTAAGTTAAGTAGATTTAGTGG
316 GATTCTAAAAAACAAGTCTC-TTTTTATTATTAAGATTATTTG-TAAGTT-AGTAGATTTAGTGG
722147 TGTATGTGCCAAATTTCTAAGTTATATAG-TATATACATTATAAAGTTTATATGTA
378 TGTATGTGCCAAATTTCTAAGTTATATAGATATATACATTATAAAGTTTATATGTA
722202 ATTTAGAGAG
Statistics
Matches: 427, Mismatches: 3, Indels: 19
0.95 0.01 0.04
Matches are distributed among these distances:
436 129 0.30
437 13 0.03
438 24 0.06
439 30 0.07
440 1 0.00
441 13 0.03
442 41 0.10
443 127 0.30
444 6 0.01
445 43 0.10
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.41
Consensus pattern (433 bp):
TCAATATTTGATACAGAACACTCACAATTCTAGTATTTCTGGTGCTAGAATCGGAAACTCGAGAA
TAACAATAATTCATTTACATCAGATATCGCTTGGTTCATATTCTCAATTCTTATATTAACTCGGT
ACGGTGGAAATAAAATTCAAAATATGAGGAAATAGAAGAGTAAAATATTTTATTAATTAGACATT
AGCCCATTTAATTGAATTATTGTTGTTTTTTTACTTTTTTAATATTCTTAAAATGATTACAATGT
AACATATGTATTTTTAACTGTTTACATCTATTAAAATAACTGTTTGAAGGTTAGAGATTCTAAAA
AACAAGTCTCTTTTTATTATTAAGATTATTTGTAAGTTAGTAGATTTAGTGGTGTATGTGCCAAA
TTTCTAAGTTATATAGATATATACATTATAAAGTTTATATGTA
Found at i:723977 original size:16 final size:16
Alignment explanation
Indices: 723956--723991 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
723946 TGTGTCATGC
723956 AAGTTAAAAGTGTTGG
1 AAGTTAAAAGTGTTGG
723972 AAGTTAAAAGTGTTGG
1 AAGTTAAAAGTGTTGG
723988 AAGT
1 AAGT
723992 ATACATGGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.31, T:0.31
Consensus pattern (16 bp):
AAGTTAAAAGTGTTGG
Found at i:727860 original size:2 final size:2
Alignment explanation
Indices: 727853--727897 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
727843 TATGGCTTAC
727853 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
727895 AT A
1 AT A
727898 GTGTATTAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:729642 original size:2 final size:2
Alignment explanation
Indices: 729635--729663 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
729625 TTGCTCTATT
729635 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
729664 GATGGCGCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:734268 original size:111 final size:109
Alignment explanation
Indices: 734085--734305 Score: 424
Period size: 111 Copynumber: 2.0 Consensus size: 109
734075 GAAATGCTGC
734085 ACGAGGGCATCGGACACCCGAGAGTATGGCCAGTTCTATATCGAACTCACCGGCGATATTGGTGC
1 ACGAGGGCATCGGACACCCGAGAGTATGGCCAGTTCTATATCGAACTCACCGGCGATATTGGTGC
734150 TCGCCTCGTCAAAGAAAAATAGTTCAACGCTTATTAAATGAAAA
66 TCGCCTCGTCAAAGAAAAATAGTTCAACGCTTATTAAATGAAAA
734194 ACGAGGGCATCGGACACCCCGAGAGTATGCGCCAGTTCTATATCGAACTCACCGGCGATATTGGT
1 ACGAGGGCATCGGACA-CCCGAGAGTATG-GCCAGTTCTATATCGAACTCACCGGCGATATTGGT
734259 GCTCGCCTCGTCAAAGAAAAATAGTTCAACGCTTATTAAATGAAAA
64 GCTCGCCTCGTCAAAGAAAAATAGTTCAACGCTTATTAAATGAAAA
734305 A
1 A
734306 TCCCGTGTTG
Statistics
Matches: 110, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
109 16 0.15
110 12 0.11
111 82 0.75
ACGTcount: A:0.32, C:0.24, G:0.23, T:0.22
Consensus pattern (109 bp):
ACGAGGGCATCGGACACCCGAGAGTATGGCCAGTTCTATATCGAACTCACCGGCGATATTGGTGC
TCGCCTCGTCAAAGAAAAATAGTTCAACGCTTATTAAATGAAAA
Found at i:743931 original size:13 final size:13
Alignment explanation
Indices: 743913--743939 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
743903 TTGAATTAAG
743913 TCATTGTTTTTAT
1 TCATTGTTTTTAT
743926 TCATTGTTTTTAT
1 TCATTGTTTTTAT
743939 T
1 T
743940 GAATAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.07, G:0.07, T:0.70
Consensus pattern (13 bp):
TCATTGTTTTTAT
Found at i:745089 original size:68 final size:68
Alignment explanation
Indices: 744977--745112 Score: 236
Period size: 68 Copynumber: 2.0 Consensus size: 68
744967 CAGAGGAAAG
*
744977 GGGCATTGGTTATGTGAGGGACTGGAGGCGTAATTCTACCCATTTGCAGCCCTTAATACCAACTT
1 GGGCATTGGTTATGTGAGGGACCGGAGGCGTAATTCTACCCATTTGCAGCCCTTAATACCAACTT
745042 AAC
66 AAC
* * *
745045 GGGCATTGGTTATGTGAGGGACCGGAGGCGTAATTCTACTCATTTGCAGCCTTTAATGCCAACTT
1 GGGCATTGGTTATGTGAGGGACCGGAGGCGTAATTCTACCCATTTGCAGCCCTTAATACCAACTT
745110 AAC
66 AAC
745113 ACGGAAACAA
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
68 64 1.00
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (68 bp):
GGGCATTGGTTATGTGAGGGACCGGAGGCGTAATTCTACCCATTTGCAGCCCTTAATACCAACTT
AAC
Found at i:746819 original size:33 final size:31
Alignment explanation
Indices: 746769--746832 Score: 76
Period size: 33 Copynumber: 2.0 Consensus size: 31
746759 ACGTCATAAG
*
746769 CATATTTATCAATATGTTCGTTTAATGTTTACC
1 CATATTTATCAATATGTT--TTTAATATTTACC
*
746802 CATATTTGTCTAA-ATGTTTTTAATATTTACC
1 CATATTTATC-AATATGTTTTTAATATTTACC
746833 GGCATGTTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 12 0.43
33 14 0.50
34 2 0.07
ACGTcount: A:0.28, C:0.14, G:0.08, T:0.50
Consensus pattern (31 bp):
CATATTTATCAATATGTTTTTAATATTTACC
Found at i:748560 original size:22 final size:23
Alignment explanation
Indices: 748532--748579 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
748522 TCTCTCTACA
* *
748532 AATTTTATAAATTC-ATTTTTTT
1 AATTTTAAAAAATCTATTTTTTT
*
748554 AATTTTAAAAAATCTGTTTTTTT
1 AATTTTAAAAAATCTATTTTTTT
748577 AAT
1 AAT
748580 ATAAAATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.58
Consensus pattern (23 bp):
AATTTTAAAAAATCTATTTTTTT
Found at i:751999 original size:13 final size:13
Alignment explanation
Indices: 751971--752004 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
751961 ATCATCACAT
751971 ATAAATAAAATAAA
1 ATAAA-AAAATAAA
*
751985 ATAAAAAACTAAA
1 ATAAAAAAATAAA
751998 ATAAAAA
1 ATAAAAA
752005 GGGGTAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (13 bp):
ATAAAAAAATAAA
Found at i:760686 original size:18 final size:19
Alignment explanation
Indices: 760651--760688 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
760641 GTGTTTTTTT
*
760651 AAATACTATGATGATTATA
1 AAATAATATGATGATTATA
*
760670 AAATAATAT-ATGTTTATA
1 AAATAATATGATGATTATA
760688 A
1 A
760689 TTTTTACTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.50, C:0.03, G:0.08, T:0.39
Consensus pattern (19 bp):
AAATAATATGATGATTATA
Found at i:768986 original size:14 final size:14
Alignment explanation
Indices: 768967--769011 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
768957 TGTTGTTGTA
768967 ATTTTACTAAAATT
1 ATTTTACTAAAATT
*
768981 A-TTT--TAAAATA
1 ATTTTACTAAAATT
768992 ATTTTACTAAAATT
1 ATTTTACTAAAATT
769006 ATTTTA
1 ATTTTA
769012 AAATAATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
11 7 0.27
12 3 0.12
13 3 0.12
14 13 0.50
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.51
Consensus pattern (14 bp):
ATTTTACTAAAATT
Found at i:768988 original size:11 final size:11
Alignment explanation
Indices: 768974--769022 Score: 53
Period size: 11 Copynumber: 4.2 Consensus size: 11
768964 GTAATTTTAC
*
768974 TAAAATTATTT
1 TAAAATAATTT
768985 TAAAATAATTTT
1 TAAAATAA-TTT
*
768997 ACTAAAATTATTT
1 --TAAAATAATTT
769010 TAAAATAATTT
1 TAAAATAATTT
769021 TA
1 TA
769023 TTTATACGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
11 19 0.59
12 3 0.09
13 3 0.09
14 7 0.22
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (11 bp):
TAAAATAATTT
Found at i:768999 original size:25 final size:25
Alignment explanation
Indices: 768965--769022 Score: 116
Period size: 25 Copynumber: 2.3 Consensus size: 25
768955 GTTGTTGTTG
768965 TAATTTTACTAAAATTATTTTAAAA
1 TAATTTTACTAAAATTATTTTAAAA
768990 TAATTTTACTAAAATTATTTTAAAA
1 TAATTTTACTAAAATTATTTTAAAA
769015 TAATTTTA
1 TAATTTTA
769023 TTTATACGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (25 bp):
TAATTTTACTAAAATTATTTTAAAA
Found at i:773293 original size:18 final size:18
Alignment explanation
Indices: 773270--773311 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
773260 TTCAAGCACA
773270 AGACACCACCTAACATGC
1 AGACACCACCTAACATGC
773288 AGACACCACCTAACATGC
1 AGACACCACCTAACATGC
*
773306 CGACAC
1 AGACAC
773312 TCAATTTGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.38, C:0.40, G:0.12, T:0.10
Consensus pattern (18 bp):
AGACACCACCTAACATGC
Found at i:773541 original size:23 final size:22
Alignment explanation
Indices: 773514--773557 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
773504 TGATTATTTT
773514 ATTATA-ATTTTTAAATATTTATA
1 ATTATATA-TTTTAAA-ATTTATA
*
773537 ATTATTTATTTTAAAATTTAT
1 ATTATATATTTTAAAATTTAT
773558 TAAGCGGTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 6 0.32
23 12 0.63
24 1 0.05
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
ATTATATATTTTAAAATTTATA
Found at i:775599 original size:10 final size:10
Alignment explanation
Indices: 775580--775609 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
775570 TTCACCACAA
775580 CAAATCCTCT
1 CAAATCCTCT
*
775590 CAAATTCTCT
1 CAAATCCTCT
775600 CAAATCCTCT
1 CAAATCCTCT
775610 AAAAAACCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.30, C:0.37, G:0.00, T:0.33
Consensus pattern (10 bp):
CAAATCCTCT
Found at i:775666 original size:17 final size:18
Alignment explanation
Indices: 775646--775679 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
775636 ATTTATAAGG
775646 ATATTTTATTA-TATTTA
1 ATATTTTATTAGTATTTA
*
775663 ATATTTTGTTAGTATTT
1 ATATTTTATTAGTATTT
775680 TATTTAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTTATTAGTATTTA
Found at i:775723 original size:16 final size:16
Alignment explanation
Indices: 775664--775723 Score: 52
Period size: 16 Copynumber: 3.6 Consensus size: 16
775654 TTATATTTAA
*
775664 TATTTTGTTAGTATTT
1 TATTTTTTTAGTATTT
775680 TATTTAATTATT-GTATTAT
1 TATTT--TT-TTAGTATT-T
775699 T-TATTTTTTAGTATTT
1 TAT-TTTTTTAGTATTT
775715 TATTTTTTT
1 TATTTTTTT
775724 GCAGTTATAA
Statistics
Matches: 36, Mismatches: 1, Indels: 14
0.71 0.02 0.27
Matches are distributed among these distances:
16 15 0.42
17 8 0.22
18 7 0.19
19 6 0.17
ACGTcount: A:0.22, C:0.00, G:0.07, T:0.72
Consensus pattern (16 bp):
TATTTTTTTAGTATTT
Found at i:777301 original size:10 final size:11
Alignment explanation
Indices: 777280--777323 Score: 56
Period size: 10 Copynumber: 4.0 Consensus size: 11
777270 AGAATTTTGA
777280 AAAATATTTAT
1 AAAATATTTAT
777291 AAAAT-TTTAT
1 AAAATATTTAT
777301 -AAATATTTAT
1 AAAATATTTAT
777311 AACTAATATTTAT
1 AA--AATATTTAT
777324 TTTTCAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
9 4 0.14
10 10 0.34
11 6 0.21
13 9 0.31
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (11 bp):
AAAATATTTAT
Found at i:778094 original size:30 final size:32
Alignment explanation
Indices: 778032--778096 Score: 82
Period size: 30 Copynumber: 2.1 Consensus size: 32
778022 TAATTAAATC
* *
778032 TTAAAATGATAATATAATAAAATGTTAGATAT
1 TTAAAATAATAATATAATAAAATGTTAAATAT
778064 TTAAAATAATAA-A-AATAATAAT-TTAAATAT
1 TTAAAATAATAATATAATAA-AATGTTAAATAT
778094 TTA
1 TTA
778097 TTATTAAATC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 15 0.50
31 4 0.13
32 11 0.37
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (32 bp):
TTAAAATAATAATATAATAAAATGTTAAATAT
Found at i:779954 original size:17 final size:16
Alignment explanation
Indices: 779916--779946 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
779906 ATTTTATCCT
*
779916 TATAAAATTAGTATTA
1 TATAAAATTAATATTA
779932 TATAAAATTAATATT
1 TATAAAATTAATATT
779947 TGTATAAATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (16 bp):
TATAAAATTAATATTA
Found at i:780854 original size:35 final size:37
Alignment explanation
Indices: 780783--780856 Score: 125
Period size: 37 Copynumber: 2.0 Consensus size: 37
780773 CAAAAATTGA
780783 AGAAGAAAAGTTTGATGCTTTTCTATACATGTTTGGTG
1 AGAAGAAAAGTTTGATGCTTTTC-ATACATGTTTGGTG
780821 AGAAG-AAAGTTTGATGCTTTTC-TACATGTTTGGTG
1 AGAAGAAAAGTTTGATGCTTTTCATACATGTTTGGTG
780856 A
1 A
780857 TTTCTGGGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
35 14 0.39
37 17 0.47
38 5 0.14
ACGTcount: A:0.28, C:0.08, G:0.24, T:0.39
Consensus pattern (37 bp):
AGAAGAAAAGTTTGATGCTTTTCATACATGTTTGGTG
Found at i:788849 original size:4 final size:4
Alignment explanation
Indices: 788840--788866 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
788830 CAATGCATGT
788840 ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATA
788867 CATAGTTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:789526 original size:60 final size:59
Alignment explanation
Indices: 789366--789548 Score: 149
Period size: 60 Copynumber: 3.1 Consensus size: 59
789356 CGTATAGTTT
* * * ** *
789366 GAGATAAAATTGGAATGTTCAAAAAGTTTGGGGACCAATTTAGAATGAAGGTCATGGTTTG
1 GAGATGAAATTGAAATATTC-AAAAGTTT-GGGACCAATTTAGAATGAAGGTCATAATTTA
* * * * * * *
789427 GGGATGAAATTGACATGTTCAAAAGGTTGATGACTAATTTAGAATGTTA-GTCATAATTTA
1 GAGATGAAATTGAAATATTCAAAAGTTTG-GGACCAATTTAGAATG-AAGGTCATAATTTA
* *
789487 GAGATGAAATTGAAATATTTAAAAGTTTAGGGACCAATTTA-AATG-AGGATCAT-ATTTT
1 GAGATGAAATTGAAATATTCAAAAGTTT-GGGACCAATTTAGAATGAAGG-TCATAATTTA
789545 GAGA
1 GAGA
789549 ACATATGATT
Statistics
Matches: 98, Mismatches: 19, Indels: 13
0.75 0.15 0.10
Matches are distributed among these distances:
57 1 0.01
58 9 0.09
59 9 0.09
60 61 0.62
61 18 0.18
ACGTcount: A:0.38, C:0.06, G:0.23, T:0.32
Consensus pattern (59 bp):
GAGATGAAATTGAAATATTCAAAAGTTTGGGACCAATTTAGAATGAAGGTCATAATTTA
Found at i:801649 original size:19 final size:19
Alignment explanation
Indices: 801625--801666 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
801615 GGTGATCCTC
* * *
801625 TCTCTCCTTTACTATTTTT
1 TCTCTCCATTAATATTCTT
801644 TCTCTCCATTAATATTCTT
1 TCTCTCCATTAATATTCTT
801663 TCTC
1 TCTC
801667 GCCTCCTCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.14, C:0.29, G:0.00, T:0.57
Consensus pattern (19 bp):
TCTCTCCATTAATATTCTT
Found at i:806686 original size:26 final size:27
Alignment explanation
Indices: 806657--806709 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
806647 TAATCTAACG
*
806657 AGAT-AAAATATTAA-ATTTATTAAATA
1 AGATAAAAAAATTAATATTT-TTAAATA
806683 AGATAAAAAAATTAATATTTTTAAATA
1 AGATAAAAAAATTAATATTTTTAAATA
806710 TTATGTTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 4 0.17
27 16 0.67
28 4 0.17
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (27 bp):
AGATAAAAAAATTAATATTTTTAAATA
Found at i:819316 original size:24 final size:24
Alignment explanation
Indices: 819289--819337 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
819279 GAGTCTTAAT
819289 TATTAAACGTTATAAAATAGTCAC
1 TATTAAACGTTATAAAATAGTCAC
819313 TATTAAACGTTATAAAATAGTCAC
1 TATTAAACGTTATAAAATAGTCAC
819337 T
1 T
819338 CGATTGTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.45, C:0.12, G:0.08, T:0.35
Consensus pattern (24 bp):
TATTAAACGTTATAAAATAGTCAC
Found at i:828143 original size:111 final size:111
Alignment explanation
Indices: 827949--828170 Score: 399
Period size: 111 Copynumber: 2.0 Consensus size: 111
827939 TAAGTTGTAA
827949 ACAAAATTAGCTAAAAATATGCATGCAAGAACAAAAAAATCTTGTAAGAGCATGAGAGAGTGTAC
1 ACAAAATTAGCTAAAAATATGCATGCAAGAACAAAAAAATCTTGTAAGAGCATGAGAGAGTGTAC
* *
828014 TAGAATGCATCATGCCAGTAGCAGCAACAGATCCCACGGTATTCAG
66 TAGAAGGCATCATGCCAGTAGCAGCAACAGATCCCACGCTATTCAG
*
828060 ACAAAATTAGCTAAAAATATGCATGCAAGAACAGAAAAATCTTGTAAGAGCATGAGAGAGTGTAC
1 ACAAAATTAGCTAAAAATATGCATGCAAGAACAAAAAAATCTTGTAAGAGCATGAGAGAGTGTAC
* *
828125 TAGAAGGCATCATGCCAGTAGCAGCAACTGATCCCATGCTATTCAG
66 TAGAAGGCATCATGCCAGTAGCAGCAACAGATCCCACGCTATTCAG
828171 CAATTTCGGA
Statistics
Matches: 106, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
111 106 1.00
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.20
Consensus pattern (111 bp):
ACAAAATTAGCTAAAAATATGCATGCAAGAACAAAAAAATCTTGTAAGAGCATGAGAGAGTGTAC
TAGAAGGCATCATGCCAGTAGCAGCAACAGATCCCACGCTATTCAG
Found at i:831280 original size:16 final size:16
Alignment explanation
Indices: 831259--831289 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
831249 TAATATTGAA
831259 ACTTGAACTCAAAAAG
1 ACTTGAACTCAAAAAG
831275 ACTTGAACTCAAAAA
1 ACTTGAACTCAAAAA
831290 AAATTAGAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.19, G:0.10, T:0.19
Consensus pattern (16 bp):
ACTTGAACTCAAAAAG
Found at i:840302 original size:26 final size:26
Alignment explanation
Indices: 840273--840328 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
840263 TTCCATGAAA
840273 CAACCAATACTTTCTATAGCACGATT
1 CAACCAATACTTTCTATAGCACGATT
840299 CAACCAATACTTTCTATAGCACGATT
1 CAACCAATACTTTCTATAGCACGATT
840325 CAAC
1 CAAC
840329 AATCCTCAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.36, C:0.29, G:0.07, T:0.29
Consensus pattern (26 bp):
CAACCAATACTTTCTATAGCACGATT
Found at i:842954 original size:79 final size:79
Alignment explanation
Indices: 842823--842981 Score: 291
Period size: 79 Copynumber: 2.0 Consensus size: 79
842813 CTATACGCCA
* *
842823 TACCTCTGTTTTCAATGTTTAGTTAAGACGGCTAGCACTCCATAAAGAGTTGCATACACATCCCA
1 TACCTCTGTTTTCAATGTTCAGTTAAGACGGCTAGCACTCCATAAACAGTTGCATACACATCCCA
842888 AGTCACAAGTATTG
66 AGTCACAAGTATTG
*
842902 TACCTCTGTTTTCATTGTTCAGTTAAGACGGCTAGCACTCCATAAACAGTTGCATACACATCCCA
1 TACCTCTGTTTTCAATGTTCAGTTAAGACGGCTAGCACTCCATAAACAGTTGCATACACATCCCA
842967 AGTCACAAGTATTG
66 AGTCACAAGTATTG
842981 T
1 T
842982 TAATTAATCT
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
79 77 1.00
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.31
Consensus pattern (79 bp):
TACCTCTGTTTTCAATGTTCAGTTAAGACGGCTAGCACTCCATAAACAGTTGCATACACATCCCA
AGTCACAAGTATTG
Found at i:843683 original size:20 final size:22
Alignment explanation
Indices: 843647--843688 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
843637 ATTATTTATA
843647 TTTTATCTTTATGTTTA-TTTT
1 TTTTATCTTTATGTTTACTTTT
843668 TTTTAT-TTCTAT-TTTACTTTT
1 TTTTATCTT-TATGTTTACTTTT
843689 AGAAAATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.14, C:0.07, G:0.02, T:0.76
Consensus pattern (22 bp):
TTTTATCTTTATGTTTACTTTT
Found at i:843689 original size:26 final size:26
Alignment explanation
Indices: 843632--843689 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 26
843622 AAACAATGCC
843632 CTTTTATTATTTATATTTTATCTTTA
1 CTTTTATTATTTATATTTTATCTTTA
* *
843658 -TGTTTATTTTTTTTATTTCTAT-TTTA
1 CT-TTTATTATTTATATTT-TATCTTTA
843684 CTTTTA
1 CTTTTA
843690 GAAAATAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
25 1 0.04
26 22 0.81
27 4 0.15
ACGTcount: A:0.19, C:0.07, G:0.02, T:0.72
Consensus pattern (26 bp):
CTTTTATTATTTATATTTTATCTTTA
Found at i:859428 original size:2 final size:2
Alignment explanation
Indices: 859423--859464 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
859413 ATTTTTTAAA
859423 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
859464 A
1 A
859465 AGGTTAATTA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:862955 original size:45 final size:45
Alignment explanation
Indices: 862891--862986 Score: 183
Period size: 45 Copynumber: 2.1 Consensus size: 45
862881 CCCATCTAAT
*
862891 TCATCTTCGCTATCATTAGCATCTCCAGCAGCATCTCCTCTCTCC
1 TCATCCTCGCTATCATTAGCATCTCCAGCAGCATCTCCTCTCTCC
862936 TCATCCTCGCTATCATTAGCATCTCCAGCAGCATCTCCTCTCTCC
1 TCATCCTCGCTATCATTAGCATCTCCAGCAGCATCTCCTCTCTCC
862981 TCATCC
1 TCATCC
862987 CTAGCAAATG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 50 1.00
ACGTcount: A:0.18, C:0.42, G:0.08, T:0.32
Consensus pattern (45 bp):
TCATCCTCGCTATCATTAGCATCTCCAGCAGCATCTCCTCTCTCC
Found at i:864096 original size:20 final size:21
Alignment explanation
Indices: 864071--864163 Score: 109
Period size: 21 Copynumber: 4.5 Consensus size: 21
864061 TTTTCCCAAT
*
864071 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* *
864091 TCGCAACGCGAATTGAGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
864112 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
864132 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
864153 TCGCAATGCGA
1 TCGCAATGCGA
864164 TACTGACTAT
Statistics
Matches: 60, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.47
21 32 0.53
ACGTcount: A:0.41, C:0.18, G:0.24, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:864114 original size:21 final size:20
Alignment explanation
Indices: 864071--864199 Score: 109
Period size: 20 Copynumber: 6.3 Consensus size: 20
864061 TTTTCCCAAT
*
864071 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
* *
864091 TCGCAACGCGAATTGAGAAAA
1 TCGCAATGCGAA-TAAGAAAA
*
864112 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
* **
864132 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGAAAA
* **
864153 TCGCAATGCG-ATACTGACTA
1 TCGCAATGCGAATA-AGAAAA
864173 TCGCAATGCGATAATAA-AAAA
1 TCGCAATGCG--AATAAGAAAA
864194 TCGCAA
1 TCGCAA
864200 CGAGATACTT
Statistics
Matches: 85, Mismatches: 18, Indels: 11
0.75 0.16 0.10
Matches are distributed among these distances:
19 1 0.01
20 42 0.49
21 39 0.46
23 3 0.04
ACGTcount: A:0.42, C:0.19, G:0.21, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATAAGAAAA
Found at i:864116 original size:41 final size:41
Alignment explanation
Indices: 864071--864163 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
864061 TTTTCCCAAT
864071 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGAAAA
*
864112 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGAAAA
864153 TCGCAATGCGA
1 TCGCAATGCGA
864164 TACTGACTAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.41, C:0.18, G:0.24, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGAGAAAA
Found at i:864176 original size:41 final size:41
Alignment explanation
Indices: 864090--864224 Score: 132
Period size: 41 Copynumber: 3.3 Consensus size: 41
864080 GAATAAGTAA
* *
864090 ATCGCAACGCGAATTGAGAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGAGAAAATCGCAATGCG-ATACTG-ACT
*
864131 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGAGAAAATCGCAATGCGATACTGACT
* * * * * *
864172 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGAGAAAATCGCAATGCGATACTGACT
*
864213 TTCGCAACGCGA
1 ATCGCAACGCGA
864225 TACTGACTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
40 4 0.05
41 73 0.92
42 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGAGAAAATCGCAATGCGATACTGACT
Found at i:864177 original size:20 final size:20
Alignment explanation
Indices: 864152--864246 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
864142 AATTGGGAAA
*
864152 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
864172 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
864193 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
864213 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
864233 TTCGCAACGCGATA
1 ATCGCAACGCGATA
864247 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:864461 original size:22 final size:22
Alignment explanation
Indices: 864434--864477 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
864424 CACTCTCTCA
*
864434 CCCATCTCCGACGAAATTCGTC
1 CCCATCTCCGACGAAATCCGTC
*
864456 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
864478 TATCTCCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.43, G:0.16, T:0.20
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:864779 original size:20 final size:20
Alignment explanation
Indices: 864756--864798 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
864746 GAAAGTCGAA
864756 TTCGCGTTGCGATTTTCATT
1 TTCGCGTTGCGATTTTCATT
*
864776 TTCGTGTTGCGATTTTCATT
1 TTCGCGTTGCGATTTTCATT
864796 TTC
1 TTC
864799 AGAAACTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.09, C:0.19, G:0.19, T:0.53
Consensus pattern (20 bp):
TTCGCGTTGCGATTTTCATT
Found at i:866144 original size:18 final size:18
Alignment explanation
Indices: 866117--866160 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
866107 CCACTTCGGA
*
866117 AGCCATCACCTCGCCCAG
1 AGCCATCACCTCACCCAG
*
866135 AGCTATCACCTCACCCAG
1 AGCCATCACCTCACCCAG
866153 AGCCATCA
1 AGCCATCA
866161 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.45, G:0.14, T:0.14
Consensus pattern (18 bp):
AGCCATCACCTCACCCAG
Found at i:866695 original size:19 final size:20
Alignment explanation
Indices: 866641--866696 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
866631 TAGTTTACTT
* *
866641 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
866661 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
*
866681 TCGCAATGC-GAAATGA
1 TCGCAACGCGGAAATGA
866697 AAATCGAAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 6 0.19
20 25 0.81
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.16
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:866740 original size:32 final size:33
Alignment explanation
Indices: 866680--866770 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
866670 GGAAATGGCT
* *
866680 ATCGCAATGCGAAATGAAAATCGAAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
866713 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
866745 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
866771 TGCGATTTGT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 31 0.56
33 24 0.44
ACGTcount: A:0.48, C:0.22, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:866847 original size:20 final size:19
Alignment explanation
Indices: 866822--866867 Score: 74
Period size: 20 Copynumber: 2.4 Consensus size: 19
866812 TCATTTCACA
866822 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTT-CGCG
*
866842 TTGCGATAGTCATTTCGCG
1 TTGCGATAGCCATTTCGCG
866861 TTGCGAT
1 TTGCGAT
866868 TTTAAGTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 11 0.44
20 14 0.56
ACGTcount: A:0.15, C:0.24, G:0.26, T:0.35
Consensus pattern (19 bp):
TTGCGATAGCCATTTCGCG
Found at i:868746 original size:14 final size:14
Alignment explanation
Indices: 868727--868762 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
868717 ATTGTTTAAT
868727 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
868741 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
868755 TGATTTGT
1 TGATTTGT
868763 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:868901 original size:19 final size:19
Alignment explanation
Indices: 868879--868946 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
868869 ATCGCAACGA
868879 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
868898 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
868917 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
868931 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
868947 TTTTCATTTC
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
14 11 0.24
15 1 0.02
16 2 0.04
17 2 0.04
19 30 0.65
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:868990 original size:20 final size:20
Alignment explanation
Indices: 868965--869021 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
868955 TCGCATTGCG
*
868965 ATTTTCTCATTGCGATAGCC
1 ATTTTCGCATTGCGATAGCC
*
868985 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCATTGCGATAGCC
* *
869005 ATTTTAGCGTTGCGATA
1 ATTTTCGCATTGCGATA
869022 TTCAAATGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (20 bp):
ATTTTCGCATTGCGATAGCC
Found at i:870105 original size:24 final size:24
Alignment explanation
Indices: 870078--870131 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
870068 GTATTCGAAA
* *
870078 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
870102 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
870126 TTTGAT
1 TTTGAT
870132 GTTGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:872658 original size:33 final size:33
Alignment explanation
Indices: 872614--872707 Score: 170
Period size: 33 Copynumber: 2.8 Consensus size: 33
872604 GGAAATTACT
*
872614 ATCGCATTGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
872647 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
872680 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
872708 CGAATTTAAT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.43, C:0.19, G:0.24, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:872705 original size:19 final size:19
Alignment explanation
Indices: 872614--872711 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
872604 GGAAATTACT
*
872614 ATCGCATTGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
872633 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
872647 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
872666 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
872680 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
872699 ATCGCAACGCGAA
1 ATCGCAATGCGAA
872712 TTTAATTTCG
Statistics
Matches: 61, Mismatches: 8, Indels: 20
0.69 0.09 0.22
Matches are distributed among these distances:
14 19 0.31
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 30 0.49
ACGTcount: A:0.43, C:0.19, G:0.24, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:872729 original size:19 final size:19
Alignment explanation
Indices: 872707--872769 Score: 81
Period size: 19 Copynumber: 3.3 Consensus size: 19
872697 AAATCGCAAC
*
872707 GCGAATTTAATTTCGCGTT
1 GCGATTTTAATTTCGCGTT
*
872726 GCGATTTTCATTTTCGCGTT
1 GCGATTTT-AATTTCGCGTT
* *
872746 GCGATTTTCATTTCGCATT
1 GCGATTTTAATTTCGCGTT
872765 GCGAT
1 GCGAT
872770 AGTACTTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
19 20 0.53
20 18 0.47
ACGTcount: A:0.16, C:0.19, G:0.21, T:0.44
Consensus pattern (19 bp):
GCGATTTTAATTTCGCGTT
Found at i:872742 original size:20 final size:19
Alignment explanation
Indices: 872716--872769 Score: 90
Period size: 20 Copynumber: 2.8 Consensus size: 19
872706 CGCGAATTTA
872716 ATTTCGCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTTTC
872735 ATTTTCGCGTTGCGATTTTC
1 A-TTTCGCGTTGCGATTTTC
*
872755 ATTTCGCATTGCGAT
1 ATTTCGCGTTGCGAT
872770 AGTACTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
19 14 0.42
20 19 0.58
ACGTcount: A:0.13, C:0.20, G:0.20, T:0.46
Consensus pattern (19 bp):
ATTTCGCGTTGCGATTTTC
Found at i:872892 original size:14 final size:14
Alignment explanation
Indices: 872873--872909 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
872863 CATCAATTAA
872873 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
872887 ACAAATCACCTTTT
1 ACAAATCAACTTTT
872901 ACAAATCAA
1 ACAAATCAA
872910 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:874348 original size:42 final size:42
Alignment explanation
Indices: 874302--874385 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
874292 CGATGACAGT
* * *
874302 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
874344 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
874386 CGAGTCGGGC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.23, C:0.17, G:0.39, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:876444 original size:19 final size:19
Alignment explanation
Indices: 876380--876512 Score: 114
Period size: 20 Copynumber: 7.1 Consensus size: 19
876370 TCTTTTGGTT
* *
876380 GAAATGAAAATCGCAACGA
1 GAAATGACAATCGCAACGC
*
876399 GATAATGAGAATCGCAACGC
1 GA-AATGACAATCGCAACGC
*
876419 GGAAATGACTATCGCAACGC
1 -GAAATGACAATCGCAACGC
* *
876439 GAAATGACTATCGCGAC-C
1 GAAATGACAATCGCAACGC
876457 ---A-GACAATCGCAACGC
1 GAAATGACAATCGCAACGC
*
876472 GAAATGAAAATCGCAATCGC
1 GAAATGACAATCGCAA-CGC
* * *
876492 GAAATAAAAATCGCAATGC
1 GAAATGACAATCGCAACGC
876511 GA
1 GA
876513 TTTTTGTTTC
Statistics
Matches: 96, Mismatches: 10, Indels: 16
0.79 0.08 0.13
Matches are distributed among these distances:
14 10 0.10
15 2 0.02
18 2 0.02
19 32 0.33
20 48 0.50
21 2 0.02
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.14
Consensus pattern (19 bp):
GAAATGACAATCGCAACGC
Found at i:877110 original size:20 final size:20
Alignment explanation
Indices: 877085--877137 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
877075 GCGCTATGTA
877085 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
877105 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
877125 TATCTCGTTGCGA
1 AATCGCGTTGCGA
877138 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:877198 original size:41 final size:41
Alignment explanation
Indices: 877106--877200 Score: 102
Period size: 41 Copynumber: 2.3 Consensus size: 41
877096 GAAAGTCAGA
* * * * ** *
877106 ATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAAT
*
877147 ATCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTT-CCAAT
877189 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
877201 TTACTTATTC
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
41 42 0.95
42 2 0.05
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (41 bp):
ATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAAT
Found at i:877382 original size:19 final size:19
Alignment explanation
Indices: 877310--877379 Score: 122
Period size: 19 Copynumber: 3.7 Consensus size: 19
877300 CGATAATGGA
*
877310 GATCGCGTTGCGAATTAGC
1 GATCGCATTGCGAATTAGC
877329 GATCGCATTGCGAATTAGC
1 GATCGCATTGCGAATTAGC
*
877348 GATCGCATTGCGATTTAGC
1 GATCGCATTGCGAATTAGC
877367 GATCGCATTGCGA
1 GATCGCATTGCGA
877380 TTTTATTGGT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 49 1.00
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (19 bp):
GATCGCATTGCGAATTAGC
Found at i:877858 original size:25 final size:25
Alignment explanation
Indices: 877812--877867 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 25
877802 TATATTTCTT
*
877812 TATATTTTTCATATATGAAATACATA
1 TATATTTTTCATATAT-AAATACACA
877838 TATATTTCTTCATATAT-AATACACA
1 TATATTT-TTCATATATAAATACACA
877863 TATAT
1 TATAT
877868 CATGCAAAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 12 0.43
26 7 0.25
27 9 0.32
ACGTcount: A:0.41, C:0.11, G:0.02, T:0.46
Consensus pattern (25 bp):
TATATTTTTCATATATAAATACACA
Found at i:883908 original size:20 final size:21
Alignment explanation
Indices: 883883--883922 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
883873 CCAGAAATAT
*
883883 TAAAAA-ATTAATATTTTAAA
1 TAAAAATAATAATATTTTAAA
883903 TAAAAATAATAATATTTTAA
1 TAAAAATAATAATATTTTAA
883923 GTAATTCCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAAAATAATAATATTTTAAA
Found at i:888681 original size:23 final size:23
Alignment explanation
Indices: 888592--888682 Score: 103
Period size: 23 Copynumber: 3.9 Consensus size: 23
888582 TCAAATTTGA
* *
888592 ATTCTGTTATGATACCTGACCTGG
1 ATTCTGATATGATACTTGA-CTGG
* *
888616 ATTCTGATCTGATA-TTCACATGG
1 ATTCTGATATGATACTTGAC-TGG
* *
888639 ATTCTGATCTGATACATGACTGG
1 ATTCTGATATGATACTTGACTGG
888662 ATTCTGATATGATACTTGACT
1 ATTCTGATATGATACTTGACT
888683 TGAATTATGT
Statistics
Matches: 57, Mismatches: 8, Indels: 5
0.81 0.11 0.07
Matches are distributed among these distances:
22 1 0.02
23 41 0.72
24 15 0.26
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.38
Consensus pattern (23 bp):
ATTCTGATATGATACTTGACTGG
Found at i:888806 original size:35 final size:35
Alignment explanation
Indices: 888758--888832 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
888748 TGGAGGAAGA
* *
888758 TTACTTGGAGGTTCCTCAGTTGTGTGCTCAGGGCC
1 TTACTTAGAGGTTCCTCAGCTGTGTGCTCAGGGCC
* *
888793 TTACTTAGCGGTTCCTCGGCTGTGTGCTCAGGGCC
1 TTACTTAGAGGTTCCTCAGCTGTGTGCTCAGGGCC
888828 TTACT
1 TTACT
888833 GGACGTGAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.11, C:0.25, G:0.29, T:0.35
Consensus pattern (35 bp):
TTACTTAGAGGTTCCTCAGCTGTGTGCTCAGGGCC
Done.