Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009343.1 Hibiscus syriacus cultivar Beakdansim tig00113123_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: 2141224
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 11
Found at i:761150 original size:25 final size:25
Alignment explanation
Indices: 761122--761169 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
761112 GATAAGTGAC
* *
761122 GGTAGATGAATATATAAAGGAAAAA
1 GGTAGATGAAGAAATAAAGGAAAAA
*
761147 GGTAGTTGAAGAAATAAAGGAAA
1 GGTAGATGAAGAAATAAAGGAAA
761170 GAAAGGTTAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.27, T:0.19
Consensus pattern (25 bp):
GGTAGATGAAGAAATAAAGGAAAAA
Found at i:763754 original size:23 final size:23
Alignment explanation
Indices: 763728--763784 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 23
763718 TGGCACTCCA
763728 GTGCATTTATACGCAGCACTACG
1 GTGCATTTATACGCAGCACTACG
* * ** *
763751 GTGCAATTCTACGTGGCACTTCG
1 GTGCATTTATACGCAGCACTACG
*
763774 GTGTATTTATA
1 GTGCATTTATA
763785 TGAGCTGTGG
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (23 bp):
GTGCATTTATACGCAGCACTACG
Found at i:764659 original size:69 final size:69
Alignment explanation
Indices: 764548--764685 Score: 233
Period size: 69 Copynumber: 2.0 Consensus size: 69
764538 TGTCTCTCTC
*
764548 TTGATGCTCTATGATCTTCGAGTGGAGTGATTCAGTGATTCAGAAATGATTGTGCTTGATCAATC
1 TTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCAGAAATGATTGTGCTTGATCAATC
764613 TCAT
66 TCAT
* *
764617 TTGATGCTCTATGATCTTCGAG-GAAAGTGGTTCAGTGATTCAGAAATGATTGTTCTTGATCAAT
1 TTGATGCTCTATGATCTTCGAGTG-AAGTGATTCAGTGATTCAGAAATGATTGTGCTTGATCAAT
764681 CTCAT
65 CTCAT
764686 AGTTTGAACC
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
68 1 0.02
69 64 0.98
ACGTcount: A:0.25, C:0.14, G:0.22, T:0.38
Consensus pattern (69 bp):
TTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCAGAAATGATTGTGCTTGATCAATC
TCAT
Found at i:764795 original size:1 final size:1
Alignment explanation
Indices: 764757--764787 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
764747 GTTTTTTCTC
*
764757 TTTTTATTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
764788 CTCTTTTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.03, C:0.00, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:767898 original size:14 final size:15
Alignment explanation
Indices: 767881--767918 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
767871 AATAGAGAAG
* *
767881 ATAAAATAAA-ACGA
1 ATAAAAGAAAGACAA
767895 ATAAAAGAAAGACAA
1 ATAAAAGAAAGACAA
767910 ATAAAAGAA
1 ATAAAAGAA
767919 TAATAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.74, C:0.05, G:0.11, T:0.11
Consensus pattern (15 bp):
ATAAAAGAAAGACAA
Found at i:767984 original size:4 final size:4
Alignment explanation
Indices: 767975--768019 Score: 56
Period size: 4 Copynumber: 10.8 Consensus size: 4
767965 ACCTAAAGAA
767975 AAAT AAAT AAAT AAAAT AAA- AGACAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT -AAAT AAAT A-A-AT AAAT AAAT AAAT AAAT AAA
768020 GTCCATAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
3 1 0.03
4 29 0.78
5 6 0.16
6 1 0.03
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (4 bp):
AAAT
Found at i:767989 original size:34 final size:31
Alignment explanation
Indices: 767908--768019 Score: 86
Period size: 33 Copynumber: 3.5 Consensus size: 31
767898 AAAGAAAGAC
* *
767908 AAATAAA-AGAATAATAATAAAATAACGAT-AAC
1 AAATAAATA-AATAAAAATAAAA-AAC-ATAAAA
* *
767940 AAGTAAATTAAATAAAAATAAAGAAACCTAAAGAA
1 AAATAAA-TAAATAAAAATAAA-AAACAT-AA-AA
* *
767975 AAATAAATAAAT-AAAATAAAAGACATAAAT
1 AAATAAATAAATAAAAATAAAAAACATAAAA
768005 AAATAAATAAATAAA
1 AAATAAATAAATAAA
768020 GTCCATAAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 15
0.74 0.09 0.17
Matches are distributed among these distances:
30 13 0.20
31 4 0.06
32 11 0.17
33 22 0.34
34 8 0.12
35 7 0.11
ACGTcount: A:0.71, C:0.04, G:0.05, T:0.19
Consensus pattern (31 bp):
AAATAAATAAATAAAAATAAAAAACATAAAA
Found at i:767993 original size:9 final size:9
Alignment explanation
Indices: 767974--768050 Score: 52
Period size: 9 Copynumber: 8.7 Consensus size: 9
767964 AACCTAAAGA
767974 AAAATAAAT
1 AAAATAAAT
767983 -AAATAAAAT
1 AAAAT-AAAT
* *
767992 AAAAGACAT
1 AAAATAAAT
768001 -AAATAAAT
1 AAAATAAAT
768009 -AAATAAAT
1 AAAATAAAT
* **
768017 AAAGTCCAT
1 AAAATAAAT
*
768026 AAAAGCAAAT
1 AAAA-TAAAT
*
768036 GAAATAAAT
1 AAAATAAAT
768045 AAAATA
1 AAAATA
768051 CTAGAAAATA
Statistics
Matches: 50, Mismatches: 14, Indels: 8
0.69 0.19 0.11
Matches are distributed among these distances:
8 18 0.36
9 24 0.48
10 8 0.16
ACGTcount: A:0.70, C:0.05, G:0.05, T:0.19
Consensus pattern (9 bp):
AAAATAAAT
Found at i:768400 original size:14 final size:15
Alignment explanation
Indices: 768381--768419 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
768371 AAATATGCGT
*
768381 ATAAATAAAATTA-A
1 ATAAATAAAATAATA
768395 ATAAATAAAATAATA
1 ATAAATAAAATAATA
*
768410 ATAATTAAAA
1 ATAAATAAAA
768420 CGTAAATGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
ATAAATAAAATAATA
Found at i:775005 original size:13 final size:13
Alignment explanation
Indices: 774987--775012 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
774977 GATCAGCTTG
774987 CACAGGTAATTTT
1 CACAGGTAATTTT
775000 CACAGGTAATTTT
1 CACAGGTAATTTT
775013 TGGTGTAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
CACAGGTAATTTT
Found at i:777178 original size:43 final size:43
Alignment explanation
Indices: 777058--777180 Score: 176
Period size: 42 Copynumber: 2.9 Consensus size: 43
777048 TTTAGTGGCG
* *
777058 TTTGTTCCCAAAACGCCGTTATATGTCTCAACCTTATGCGACA
1 TTTGTTCCCAAAATGCCGTTATATGTCTCAACCTTTTGCGACA
* **
777101 TTTGTT-CCAAAATGCCGTTATATATCTCAACCTTTTGCTTCA
1 TTTGTTCCCAAAATGCCGTTATATGTCTCAACCTTTTGCGACA
**
777143 TTTGTTCCCAAAATGCCACTATATGTCTCAACCTTTTG
1 TTTGTTCCCAAAATGCCGTTATATGTCTCAACCTTTTG
777181 TGGCGTTTAT
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
42 37 0.52
43 34 0.48
ACGTcount: A:0.24, C:0.26, G:0.11, T:0.38
Consensus pattern (43 bp):
TTTGTTCCCAAAATGCCGTTATATGTCTCAACCTTTTGCGACA
Found at i:780239 original size:51 final size:51
Alignment explanation
Indices: 780143--780308 Score: 156
Period size: 51 Copynumber: 3.3 Consensus size: 51
780133 CAACAAGGAA
* * * * * * *
780143 TAAAATGAAATAAAATAAAA-AATAGTAGCCAAATAAAAAATAAACAGTGAC
1 TAAAAT-ACATAAAATAAAAGAACAATAACCAAATCAGAAACAAACAGTGAC
* ** *
780194 TAAGATACATAAAATGGAAGAACAATAACCAAATTAGAAACAAACAGTGAC
1 TAAAATACATAAAATAAAAGAACAATAACCAAATCAGAAACAAACAGTGAC
* * * *
780245 TAAAATGCATAAAATAAAAGAACAATAGCTAAATCAGAAATAAACAGTGA-
1 TAAAATACATAAAATAAAAGAACAATAACCAAATCAGAAACAAACAGTGAC
*
780295 TCAAAATGCATAAA
1 T-AAAATACATAAA
780309 TTGAAAGTAT
Statistics
Matches: 95, Mismatches: 18, Indels: 4
0.81 0.15 0.03
Matches are distributed among these distances:
50 11 0.12
51 84 0.88
ACGTcount: A:0.60, C:0.11, G:0.11, T:0.17
Consensus pattern (51 bp):
TAAAATACATAAAATAAAAGAACAATAACCAAATCAGAAACAAACAGTGAC
Found at i:782423 original size:36 final size:36
Alignment explanation
Indices: 782375--782443 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 36
782365 GCGTTTAAAG
*
782375 GGAAAACTATCTCAAGCGAGATAAAATTTGTTTTTA
1 GGAAAACAATCTCAAGCGAGATAAAATTTGTTTTTA
* * *
782411 GGAAAACAATCTCAAGTGAGATCAATTTTGTTT
1 GGAAAACAATCTCAAGCGAGATAAAATTTGTTT
782444 CAAGTGAAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (36 bp):
GGAAAACAATCTCAAGCGAGATAAAATTTGTTTTTA
Found at i:782455 original size:36 final size:36
Alignment explanation
Indices: 782375--782452 Score: 93
Period size: 36 Copynumber: 2.1 Consensus size: 36
782365 GCGTTTAAAG
* **
782375 GGAAAACTATCTCAAGCGAGATAAAATTTGTTTTTA
1 GGAAAACAATCTCAAGCGAGATAAAATTTGTTTCAA
* * *
782411 GGAAAACAATCTCAAGTGAGATCAATTTTGTTTCAA
1 GGAAAACAATCTCAAGCGAGATAAAATTTGTTTCAA
782447 GTGAAA
1 G-GAAA
782453 CAAATTCGAA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
36 31 0.89
37 4 0.11
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.31
Consensus pattern (36 bp):
GGAAAACAATCTCAAGCGAGATAAAATTTGTTTCAA
Found at i:782478 original size:102 final size:103
Alignment explanation
Indices: 782295--782527 Score: 249
Period size: 102 Copynumber: 2.3 Consensus size: 103
782285 GAGTGGAAAG
* * * * *
782295 AAATTTGTTACAAGAGAAGCTATCTCAGGTGAGATAATATTTTGTTTAGAGGGAAACAATTTCAA
1 AAATTTGTTTCAAGAGAAACAATCTCAAGTGAGATAATATTTTGTTTAGAGGGAAACAAATTCAA
* *
782360 AATTTGCGTTTAAAGGGAAAACTATCTCAAGCGAGAT-A
66 AATTTGCGCTTAAAGGG-AAACTAGCTCAAGCGAGATGA
** * *
782398 AAATTTGTTTTTAG-GAAAACAATCTCAAGTGAGATCA-ATTTTGTTTCA-AGTGAAACAAATTC
1 AAATTTGTTTCAAGAG-AAACAATCTCAAGTGAGATAATATTTTGTTT-AGAGGGAAACAAATTC
* * * * * *
782460 GAAATTTGGGCTTCAAGGGGAACTGGCTTAAGCGAGATGA
64 AAAATTTGCGCTTAAAGGGAAACTAGCTCAAGCGAGATGA
*
782500 AACTTTGTTTCAAGAGAAACAATCTCAA
1 AAATTTGTTTCAAGAGAAACAATCTCAA
782528 AGGCTTATAT
Statistics
Matches: 106, Mismatches: 20, Indels: 9
0.79 0.15 0.07
Matches are distributed among these distances:
101 15 0.14
102 61 0.58
103 30 0.28
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (103 bp):
AAATTTGTTTCAAGAGAAACAATCTCAAGTGAGATAATATTTTGTTTAGAGGGAAACAAATTCAA
AATTTGCGCTTAAAGGGAAACTAGCTCAAGCGAGATGA
Found at i:782570 original size:66 final size:67
Alignment explanation
Indices: 782471--782629 Score: 212
Period size: 66 Copynumber: 2.4 Consensus size: 67
782461 AAATTTGGGC
* * * * *
782471 TTCAAGGGGAACTGGCTTAAGCGAGATGAAACTTTGTTTCAAGAGAAACAATCTCAAAGGCTTAT
1 TTCAAGAGAAACTGTCTCAAGCAAGATGAAACTTTGTTTCAAGAGAAACAATCTCAAAGGCTTAT
782536 AT
66 AT
** * *
782538 TTCAAGAGAAACTGTCTCAAGCAAGATG-AACTTTGTTTGGATAGAAACAATCTCAAAGGTTTAT
1 TTCAAGAGAAACTGTCTCAAGCAAGATGAAACTTTGTTTCAAGAGAAACAATCTCAAAGGCTTAT
*
782602 GT
66 AT
*
782604 TTCAAGAGAAACTGTCTCAAGTAAGA
1 TTCAAGAGAAACTGTCTCAAGCAAGA
782630 AAAAAATTTA
Statistics
Matches: 81, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
66 58 0.72
67 23 0.28
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (67 bp):
TTCAAGAGAAACTGTCTCAAGCAAGATGAAACTTTGTTTCAAGAGAAACAATCTCAAAGGCTTAT
AT
Found at i:782623 original size:30 final size:30
Alignment explanation
Indices: 782505--782615 Score: 89
Period size: 30 Copynumber: 3.5 Consensus size: 30
782495 GATGAAACTT
782505 TGTTTCAAGAGAAACAATCTCAAAGGCTTA
1 TGTTTCAAGAGAAACAATCTCAAAGGCTTA
* **
782535 TATTTCAAGAGAAACTGTCTCAAGCAAGATGAACTT-
1 TGTTTCAAGAGAAACAATCTC-A--AAG--G--CTTA
** * *
782571 TGTTTGGATAGAAACAATCTCAAAGGTTTA
1 TGTTTCAAGAGAAACAATCTCAAAGGCTTA
782601 TGTTTCAAGAGAAAC
1 TGTTTCAAGAGAAAC
782616 TGTCTCAAGT
Statistics
Matches: 60, Mismatches: 13, Indels: 16
0.67 0.15 0.18
Matches are distributed among these distances:
29 2 0.03
30 30 0.50
31 2 0.03
33 6 0.10
35 2 0.03
36 15 0.25
37 3 0.05
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (30 bp):
TGTTTCAAGAGAAACAATCTCAAAGGCTTA
Found at i:786978 original size:169 final size:168
Alignment explanation
Indices: 786699--787033 Score: 661
Period size: 169 Copynumber: 2.0 Consensus size: 168
786689 AACGGGAAAA
786699 AGGTACTCAAATTATCCTTGTTGTTGGTTCCCCCTTGGGCTAAATGCATTCATTAAATGAACTGG
1 AGGTACTCAAATTATCCTTGTTGTTGGTTCCCCCTTGGGCTAAATGCATTCATTAAATGAACTGG
786764 CTAGTGGCACATGTCTAAAACATGTAACTACTAAGTTGTGGCTGGCATCATGGTAAGGCTGAAGG
66 CTAGTGGCACATGTCTAAAACATGTAACTACTAAGTTGTGGCTGGCATCATGGTAAGGCTGAAGG
786829 TTCTGCATCTCGGAGCTCATGCACCTCTGTAGCCTGCGG
131 TTCTGCATCTCGGAGCTCATGCACC-CTGTAGCCTGCGG
786868 AGGTACTCAAATTATCCTTGTTGTTGGTTCCCCCTTGGGCTAAATGCATTCATTAAATGAACTGG
1 AGGTACTCAAATTATCCTTGTTGTTGGTTCCCCCTTGGGCTAAATGCATTCATTAAATGAACTGG
786933 CTAGTGGCACATGTCTAAAACATGTAACTACTAAGTTGTGGCTGGCATCATGGTAAGGCTGAAGG
66 CTAGTGGCACATGTCTAAAACATGTAACTACTAAGTTGTGGCTGGCATCATGGTAAGGCTGAAGG
786998 TTCTGCATCTCGGAGCTCATGCACCCTGTAGCCTGC
131 TTCTGCATCTCGGAGCTCATGCACCCTGTAGCCTGC
787034 CGGTATACCA
Statistics
Matches: 166, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
168 11 0.07
169 155 0.93
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (168 bp):
AGGTACTCAAATTATCCTTGTTGTTGGTTCCCCCTTGGGCTAAATGCATTCATTAAATGAACTGG
CTAGTGGCACATGTCTAAAACATGTAACTACTAAGTTGTGGCTGGCATCATGGTAAGGCTGAAGG
TTCTGCATCTCGGAGCTCATGCACCCTGTAGCCTGCGG
Found at i:798175 original size:2 final size:2
Alignment explanation
Indices: 798168--798196 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
798158 AAATAAATAA
798168 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
798197 AATTCATGAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:798334 original size:21 final size:20
Alignment explanation
Indices: 798272--798334 Score: 54
Period size: 23 Copynumber: 3.0 Consensus size: 20
798262 TTTAATTCAT
* *
798272 AAAATTATAATTGTTTTAAA
1 AAAATTATAATTATTTTTAA
* *
798292 AAAAATATGAATTTATAATTTAA
1 AAAATTAT-AA-TTAT-TTTTAA
798315 AAAATTATAATTAATTTTTA
1 AAAATTATAATT-ATTTTTA
798335 TTTAATTGTG
Statistics
Matches: 33, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
20 7 0.21
21 8 0.24
22 7 0.21
23 11 0.33
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.44
Consensus pattern (20 bp):
AAAATTATAATTATTTTTAA
Found at i:799710 original size:11 final size:11
Alignment explanation
Indices: 799694--799719 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
799684 TCATGTGTAA
799694 TTTTTAAATAT
1 TTTTTAAATAT
799705 TTTTTAAATAT
1 TTTTTAAATAT
799716 TTTT
1 TTTT
799720 AATAATTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTTTAAATAT
Found at i:813208 original size:25 final size:25
Alignment explanation
Indices: 813172--813269 Score: 101
Period size: 24 Copynumber: 4.0 Consensus size: 25
813162 GAGTCGAGGG
*
813172 TTCTACGCGGTCCTTTGAGACAAAT
1 TTCTACGCGGTCCTTCGAGACAAAT
* *
813197 TTCTACGTGGTCCTTCGGGACAAA-
1 TTCTACGCGGTCCTTCGAGACAAAT
* * *
813221 TTCTATGCAGTCCTTCGGGACAAA-
1 TTCTACGCGGTCCTTCGAGACAAAT
* * *
813245 TTCTACACAGTCCTTCGGGACAAAT
1 TTCTACGCGGTCCTTCGAGACAAAT
813270 CTATGTGGCA
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
24 43 0.67
25 21 0.33
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.30
Consensus pattern (25 bp):
TTCTACGCGGTCCTTCGAGACAAAT
Found at i:813233 original size:24 final size:24
Alignment explanation
Indices: 813206--813274 Score: 113
Period size: 24 Copynumber: 2.9 Consensus size: 24
813196 TTTCTACGTG
813206 GTCCTTCGGGACAAATTCTATGCA
1 GTCCTTCGGGACAAATTCTATGCA
**
813230 GTCCTTCGGGACAAATTCTACACA
1 GTCCTTCGGGACAAATTCTATGCA
813254 GTCCTTCGGGACAAA-TCTATG
1 GTCCTTCGGGACAAATTCTATG
813275 TGGCACTTCG
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
23 4 0.10
24 37 0.90
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (24 bp):
GTCCTTCGGGACAAATTCTATGCA
Found at i:819503 original size:20 final size:20
Alignment explanation
Indices: 819480--819534 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 20
819470 AGTAGTATTG
*
819480 ATACTAATATTGGGGTATCA
1 ATACTAATATTGAGGTATCA
* * * *
819500 ATACCAAGAGTAAGGTATCA
1 ATACTAATATTGAGGTATCA
*
819520 ATACTATTATTGAGG
1 ATACTAATATTGAGG
819535 ATGAAATTCC
Statistics
Matches: 25, Mismatches: 10, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (20 bp):
ATACTAATATTGAGGTATCA
Found at i:820018 original size:15 final size:15
Alignment explanation
Indices: 820000--820051 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
819990 TGTGTTATAA
*
820000 GTGAATATGCTCTAT
1 GTGAATATGATCTAT
* *
820015 GTGAATATGATTTAC
1 GTGAATATGATCTAT
* * *
820030 ATGAATGTGGTCTAT
1 GTGAATATGATCTAT
820045 GTGAATA
1 GTGAATA
820052 AAAGACATGT
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.31, C:0.08, G:0.23, T:0.38
Consensus pattern (15 bp):
GTGAATATGATCTAT
Found at i:820213 original size:24 final size:24
Alignment explanation
Indices: 820153--820231 Score: 115
Period size: 24 Copynumber: 3.3 Consensus size: 24
820143 GAGTCAAGAG
* *
820153 TTCTATGCGGTCATTCAGGACAAA
1 TTCTATGCGGTCCTTCGGGACAAA
*
820177 TTTCTATGTGGTCCTTCGGGACAAA
1 -TTCTATGCGGTCCTTCGGGACAAA
820202 TTCTATGCGGTCCTTCGGGACAAA
1 TTCTATGCGGTCCTTCGGGACAAA
820226 -TCTATG
1 TTCTATG
820232 TGGCACTTCA
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
23 6 0.12
24 23 0.46
25 21 0.42
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.33
Consensus pattern (24 bp):
TTCTATGCGGTCCTTCGGGACAAA
Found at i:821553 original size:27 final size:27
Alignment explanation
Indices: 821486--821556 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 27
821476 GAATTTATTA
* *
821486 AAAATGATTGAAATACCCTTGAGCTTT
1 AAAATGATTGAAATATCCTAGAGCTTT
* ***
821513 AAAATTACCAAAATATCCTA-AGACTTT
1 AAAATGATTGAAATATCCTAGAG-CTTT
821540 AAAATGATTGAAATATC
1 AAAATGATTGAAATATC
821557 ATCGAGTTCT
Statistics
Matches: 33, Mismatches: 10, Indels: 2
0.73 0.22 0.04
Matches are distributed among these distances:
26 2 0.06
27 31 0.94
ACGTcount: A:0.45, C:0.14, G:0.10, T:0.31
Consensus pattern (27 bp):
AAAATGATTGAAATATCCTAGAGCTTT
Found at i:823985 original size:30 final size:30
Alignment explanation
Indices: 823949--824051 Score: 143
Period size: 30 Copynumber: 3.4 Consensus size: 30
823939 TCCGAAGGAC
*
823949 CTATCCAGAGGTCATAAAGATCCTTGGCAA
1 CTATCCAGAGGTCATAAAGATCCTTGGTAA
* * *
823979 CTATCCAGAGGTAATAAAGATCATCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTTGGTAA
*
824009 CAATCCAGAGGTCATAAAGATCCTTGGTAA
1 CTATCCAGAGGTCATAAAGATCCTTGGTAA
* *
824039 CTGTCCATAGGTC
1 CTATCCAGAGGTC
824052 CCGAAGAACC
Statistics
Matches: 62, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 62 1.00
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTTGGTAA
Found at i:824068 original size:60 final size:60
Alignment explanation
Indices: 823951--824068 Score: 146
Period size: 60 Copynumber: 2.0 Consensus size: 60
823941 CGAAGGACCT
* * *
823951 ATCCAGAGGTCATAAAGATCCTTGGCAACTATCCAGAGGTAATAAAGATCATCGGTAACA
1 ATCCAGAGGTCATAAAGATCCTTGGCAACTATCCAGAGGTAACAAAGAACATAGGTAACA
* * * ** * *
824011 ATCCAGAGGTCATAAAGATCCTTGGTAACTGTCCATAGGTCCCGAAGAACCTAGGTAA
1 ATCCAGAGGTCATAAAGATCCTTGGCAACTATCCAGAGGTAACAAAGAACATAGGTAA
824069 ACTATCCATA
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 48 1.00
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (60 bp):
ATCCAGAGGTCATAAAGATCCTTGGCAACTATCCAGAGGTAACAAAGAACATAGGTAACA
Found at i:825206 original size:24 final size:20
Alignment explanation
Indices: 825153--825229 Score: 75
Period size: 20 Copynumber: 3.7 Consensus size: 20
825143 TTTCTCTTGA
825153 AGTGCATCGATGCATTCAAC
1 AGTGCATCGATGCATTCAAC
*
825173 AGTGCATCGATGCATTCTTTAGC
1 AGTGCATCGATGCATTC---AAC
* *
825196 ATGTGCATCGATGCAGT-ACC
1 A-GTGCATCGATGCATTCAAC
*
825216 CGTGCATCGATGCA
1 AGTGCATCGATGCA
825230 CAAATCACCT
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
19 13 0.27
20 19 0.39
23 3 0.06
24 14 0.29
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (20 bp):
AGTGCATCGATGCATTCAAC
Found at i:825286 original size:64 final size:63
Alignment explanation
Indices: 825198--825358 Score: 180
Period size: 64 Copynumber: 2.5 Consensus size: 63
825188 TCTTTAGCAT
* * ** * * *
825198 GTGCATCGATGCAGTACCCGTGCATCGATGCACAAATCACCTTCGATGTTTTCATTTTAAGGG
1 GTGCATCGATGCACTTCCTATGCATCGATGCACAAATCACATTCGATGTTTCCATTTTAAGAG
* ** *
825261 GATGCATCGATGCAC-TCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCCATTTTAATAG
1 G-TGCATCGATGCACTTCC-TATGCATCGATGCACAAATCACATTCGATGTTTCCATTTTAAGAG
* *
825325 GTGCATCGATGCACTTCCTGTGCATCGATACACA
1 GTGCATCGATGCACTTCCTATGCATCGATGCACA
825359 CTGAACAATT
Statistics
Matches: 81, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
63 29 0.36
64 52 0.64
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.31
Consensus pattern (63 bp):
GTGCATCGATGCACTTCCTATGCATCGATGCACAAATCACATTCGATGTTTCCATTTTAAGAG
Found at i:828798 original size:30 final size:30
Alignment explanation
Indices: 828762--828864 Score: 161
Period size: 30 Copynumber: 3.4 Consensus size: 30
828752 TCCGAAGGAC
*
828762 CTATCCAAAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
828792 CTATCCAGAGGTTATAAAGATCCTCGCTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
828822 CAATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
828852 CTATCCATAGGTC
1 CTATCCAGAGGTC
828865 CCGAAGAACC
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 65 1.00
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:837262 original size:21 final size:21
Alignment explanation
Indices: 837236--837275 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
837226 TCCCCTTTGA
*
837236 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
837257 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
837276 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:839250 original size:17 final size:17
Alignment explanation
Indices: 839224--839259 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
839214 TGTTTCAACA
*
839224 TTTTGAATTGTTTGATT
1 TTTTGAATTGTTGGATT
*
839241 TTTTGGATTGTTGGATT
1 TTTTGAATTGTTGGATT
839258 TT
1 TT
839260 GGATTTATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.14, C:0.00, G:0.22, T:0.64
Consensus pattern (17 bp):
TTTTGAATTGTTGGATT
Found at i:846755 original size:22 final size:21
Alignment explanation
Indices: 846729--846771 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
846719 AAAATGTTGA
846729 AAAAAAATAGCAGTTCGAAAAAG
1 AAAAAAA-A-CAGTTCGAAAAAG
*
846752 AAAAAAAACTGTTCGAAAAA
1 AAAAAAAACAGTTCGAAAAA
846772 AAAGACATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
22 1 0.05
23 7 0.37
ACGTcount: A:0.63, C:0.09, G:0.14, T:0.14
Consensus pattern (21 bp):
AAAAAAAACAGTTCGAAAAAG
Found at i:855910 original size:22 final size:22
Alignment explanation
Indices: 855882--855948 Score: 106
Period size: 22 Copynumber: 3.2 Consensus size: 22
855872 AGAAGTTAAC
855882 ATTTTAAATTATTATTTTTATA
1 ATTTTAAATTATTATTTTTATA
855904 ATTTTAAATTATTATTTTTATA
1 ATTTTAAATTATTATTTTTATA
855926 ATTTTAAA--A-TATTTTTAT-
1 ATTTTAAATTATTATTTTTATA
855944 ATTTT
1 ATTTT
855949 CTTGGATATT
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
18 5 0.11
19 9 0.20
20 1 0.02
22 30 0.67
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
ATTTTAAATTATTATTTTTATA
Found at i:856031 original size:26 final size:24
Alignment explanation
Indices: 855992--856046 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 24
855982 AATTTTCAAT
855992 TATTTAATATTTTTTAAATATTTTTA
1 TATTTAATA-TTTTTAAA-ATTTTTA
*
856018 TATTTAAT-TATTTTATAATTTTTA
1 TATTTAATAT-TTTTAAAATTTTTA
856042 -ATTTA
1 TATTTA
856047 CTTTACATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 5 0.19
24 8 0.30
25 6 0.22
26 8 0.30
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (24 bp):
TATTTAATATTTTTAAAATTTTTA
Found at i:856137 original size:21 final size:20
Alignment explanation
Indices: 856113--856155 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
856103 AGAATTAAAT
856113 AAATACTAAATTTGTAAAAAA
1 AAAT-CTAAATTTGTAAAAAA
* *
856134 AAATCTAATTTTTTTAAAAAA
1 AAATCTAA-ATTTGTAAAAAA
856155 A
1 A
856156 TTAATCAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (20 bp):
AAATCTAAATTTGTAAAAAA
Found at i:857192 original size:29 final size:28
Alignment explanation
Indices: 857135--857195 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
857125 AGTTAAAAAA
* * *
857135 TAAATTTAAATTTTTTTATATTTTAAAT
1 TAAATTTAAATTTTTTCAAATTATAAAT
*
857163 TAAATTTAATATTTTTTCAAATCTATAATT
1 TAAATTTAA-ATTTTTTCAAAT-TATAAAT
857193 TAA
1 TAA
857196 TGATTATAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 9 0.33
29 10 0.37
30 8 0.30
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (28 bp):
TAAATTTAAATTTTTTCAAATTATAAAT
Found at i:857558 original size:2 final size:2
Alignment explanation
Indices: 857551--857580 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
857541 TTAGTGTTTG
857551 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
857581 CCAAATTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:858852 original size:31 final size:31
Alignment explanation
Indices: 858810--858869 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
858800 AACTTAAAAG
* *
858810 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
858841 AGTTTTACAATACTGAAATTTAAATAATT
1 AGTTTTACAATACTGAAATTTAAATAATT
858870 CATACAACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:859402 original size:20 final size:19
Alignment explanation
Indices: 859360--859403 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
859350 TTTTAATAAT
* *
859360 ATATAAAATAATTTATATG
1 ATATAAAATAATATATATA
*
859379 ATATAAAATTAATATCTATA
1 ATATAAAA-TAATATATATA
859399 ATATA
1 ATATA
859404 TATTAAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (19 bp):
ATATAAAATAATATATATA
Found at i:859435 original size:23 final size:26
Alignment explanation
Indices: 859383--859446 Score: 87
Period size: 24 Copynumber: 2.5 Consensus size: 26
859373 TATATGATAT
859383 AAAATTAATATCTATAATATATATTAA
1 AAAATTAATAT-TATAATATATATTAA
*
859410 AAAATTAATATT-TAATTTAT-TTAA
1 AAAATTAATATTATAATATATATTAA
*
859434 AAATTTAATATTA
1 AAAATTAATATTA
859447 AAATTAATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 15 0.44
25 7 0.21
26 1 0.03
27 11 0.32
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (26 bp):
AAAATTAATATTATAATATATATTAA
Found at i:859441 original size:24 final size:25
Alignment explanation
Indices: 859383--859446 Score: 78
Period size: 27 Copynumber: 2.5 Consensus size: 25
859373 TATATGATAT
859383 AAAATTAATATCTATAATATATATTAA
1 AAAATTAATAT-TATAATATATATT-A
*
859410 AAAATTAATATT-TAATTTAT-TTA
1 AAAATTAATATTATAATATATATTA
859433 AAAATTTAATATTA
1 AAAA-TTAATATTA
859447 AAATTAATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
23 5 0.15
24 10 0.29
25 7 0.21
26 1 0.03
27 11 0.32
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (25 bp):
AAAATTAATATTATAATATATATTA
Found at i:859482 original size:40 final size:36
Alignment explanation
Indices: 859410--859483 Score: 94
Period size: 40 Copynumber: 1.9 Consensus size: 36
859400 TATATATTAA
* *
859410 AAAATTAATATTTAATTTATTTAAAAATTTAATATT
1 AAAATTAATATTTAATTAATTTAAAAAATTAATATT
859446 AAAATTAATATCTATAATATAATATTAAAAAATTAATA
1 AAAATTAATAT-T-TAAT-TAAT-TTAAAAAATTAATA
859484 GGTAATTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 11 0.34
37 1 0.03
38 4 0.12
39 3 0.09
40 13 0.41
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (36 bp):
AAAATTAATATTTAATTAATTTAAAAAATTAATATT
Found at i:859495 original size:64 final size:64
Alignment explanation
Indices: 859382--859536 Score: 246
Period size: 64 Copynumber: 2.5 Consensus size: 64
859372 TTATATGATA
** *
859382 TAAAATTAATATCTATAATAT-ATATTAAAAAATTAATATTTAATTTATTTAAAAATTTAATAT
1 TAAAATTAATATCTATAATATAATATTAAAAAATTAATAGGTAATTTATTTAAAAAATTAATAT
859445 TAAAATTAATATCTATAATATAATATTAAAAAATTAATAGGTAATTTATTTAAAAAATTAATAT
1 TAAAATTAATATCTATAATATAATATTAAAAAATTAATAGGTAATTTATTTAAAAAATTAATAT
*
859509 TAAAATTAAAATC-A-AATATAATA-TAAAA
1 TAAAATTAATATCTATAATATAATATTAAAA
859537 TTAAATATAA
Statistics
Matches: 87, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
61 5 0.06
62 9 0.10
63 22 0.25
64 51 0.59
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.41
Consensus pattern (64 bp):
TAAAATTAATATCTATAATATAATATTAAAAAATTAATAGGTAATTTATTTAAAAAATTAATAT
Found at i:859543 original size:12 final size:12
Alignment explanation
Indices: 859498--859548 Score: 54
Period size: 12 Copynumber: 4.3 Consensus size: 12
859488 ATTTATTTAA
859498 AAAATT-AATATT
1 AAAATTAAATA-T
859510 AAAATTAAA-AT
1 AAAATTAAATAT
*
859521 CAAA-TATAATAT
1 AAAATTA-AATAT
859533 AAAATTAAATAT
1 AAAATTAAATAT
859545 AAAA
1 AAAA
859549 CCTCTTTGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
10 2 0.06
11 6 0.18
12 21 0.64
13 4 0.12
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (12 bp):
AAAATTAAATAT
Found at i:860721 original size:18 final size:18
Alignment explanation
Indices: 860681--860723 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
860671 ATGTACTGTA
* * *
860681 CTTTTTACTATACTTTGT
1 CTTTTTACCATACTATAT
860699 C-TTTTACCATACTATAT
1 CTTTTTACCATACTATAT
860716 CTTTTTAC
1 CTTTTTAC
860724 TATATTTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.21, C:0.21, G:0.02, T:0.56
Consensus pattern (18 bp):
CTTTTTACCATACTATAT
Found at i:861023 original size:24 final size:23
Alignment explanation
Indices: 860996--861049 Score: 72
Period size: 24 Copynumber: 2.3 Consensus size: 23
860986 GTGCTCGACG
* *
860996 GCACTGATACAGAAGTGTATATTT
1 GCACTAATACAGAAGTGCATA-TT
*
861020 GCACTAATACAGGAGTGCATATT
1 GCACTAATACAGAAGTGCATATT
861043 GCACTAA
1 GCACTAA
861050 CATAGGATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 9 0.33
24 18 0.67
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (23 bp):
GCACTAATACAGAAGTGCATATT
Found at i:861056 original size:23 final size:24
Alignment explanation
Indices: 861004--861056 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
860994 CGGCACTGAT
* * *
861004 ACAGAAGTGTATATTTGCACTAAT
1 ACAGGAGTGCATATTTGCACTAAC
861028 ACAGGAGTGCATA-TTGCACTAAC
1 ACAGGAGTGCATATTTGCACTAAC
*
861051 ATAGGA
1 ACAGGA
861057 TCAAATGATC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 14 0.56
24 11 0.44
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (24 bp):
ACAGGAGTGCATATTTGCACTAAC
Found at i:861885 original size:17 final size:17
Alignment explanation
Indices: 861850--861885 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
861840 CTTTTCTATT
**
861850 ATATCTATAATTTTTTC
1 ATATCTATAATTTAGTC
861867 ATATCTATAATTTAGTC
1 ATATCTATAATTTAGTC
861884 AT
1 AT
861886 TTTGTCATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.33, C:0.11, G:0.03, T:0.53
Consensus pattern (17 bp):
ATATCTATAATTTAGTC
Found at i:870547 original size:15 final size:15
Alignment explanation
Indices: 870528--870583 Score: 76
Period size: 15 Copynumber: 3.7 Consensus size: 15
870518 TTCATGGGGT
* *
870528 AAGAAGACAACGTCT
1 AAGAAGAAAACGTCA
870543 AAGAAGAAAACGTCA
1 AAGAAGAAAACGTCA
*
870558 AAGAAGAAAATGTCA
1 AAGAAGAAAACGTCA
870573 AAGAAGGAAAA
1 AAGAA-GAAAA
870584 AGAAAGCATC
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
15 32 0.86
16 5 0.14
ACGTcount: A:0.59, C:0.11, G:0.21, T:0.09
Consensus pattern (15 bp):
AAGAAGAAAACGTCA
Found at i:874531 original size:39 final size:40
Alignment explanation
Indices: 874455--874537 Score: 109
Period size: 39 Copynumber: 2.1 Consensus size: 40
874445 AAAGAGAAAG
*
874455 AAAAGGAAGAGGGTAAAGGAGAAGGGACACTACAAA-GGA
1 AAAAGGAAGAGGGTAAAGGAGAAGGGACACGACAAAGGGA
*
874494 AAAAGGAAGAGGAG-AAAGGAGAAGTGACACCGA-AAAGGGA
1 AAAAGGAAGAGG-GTAAAGGAGAAGGGACA-CGACAAAGGGA
874534 AAAA
1 AAAA
874538 AGAAAGAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
39 29 0.74
40 10 0.26
ACGTcount: A:0.54, C:0.07, G:0.35, T:0.04
Consensus pattern (40 bp):
AAAAGGAAGAGGGTAAAGGAGAAGGGACACGACAAAGGGA
Found at i:876903 original size:2 final size:2
Alignment explanation
Indices: 876896--876920 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
876886 TGAATCTACA
876896 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
876921 ATTTACGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:877111 original size:85 final size:85
Alignment explanation
Indices: 876968--877190 Score: 290
Period size: 85 Copynumber: 2.6 Consensus size: 85
876958 GTCTTTTTTA
* * * *
876968 ATGACGTGTGCTTTAATGACACGCAATGTAAGTCATACATGTGTGTCATAAATTTATGACACACA
1 ATGACGGGGGCTTCAATGACACGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACACACA
877033 AATGTATGTCA-AGAAGATTT
66 AATGTATGTCATAGAA-ATTT
* *
877053 ATGACGGGGGCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACGCACA
1 ATGACGGGGGCTTCAATGACACGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACACACA
* ***
877118 AATGTGTGTCATCTTAATTT
66 AATGTATGTCATAGAAATTT
* *
877138 ATGACGGGGGCTTCAATGACACTCAATG-AACGTCATTA-ATGCGCGTCATAAAT
1 ATGACGGGGGCTTCAATGACACGCAATGTAA-GTCA-TACATGCGTGTCATAAAT
877191 GTGTGTCATA
Statistics
Matches: 122, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
84 2 0.02
85 117 0.96
86 3 0.02
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (85 bp):
ATGACGGGGGCTTCAATGACACGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACACACA
AATGTATGTCATAGAAATTT
Found at i:877184 original size:13 final size:13
Alignment explanation
Indices: 877168--877213 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
877158 ACTCAATGAA
*
877168 CGTCATTAATGCG
1 CGTCATAAATGCG
*
877181 CGTCATAAATGTG
1 CGTCATAAATGCG
*
877194 TGTCATAAATGCG
1 CGTCATAAATGCG
877207 CGTCATA
1 CGTCATA
877214 TATTTATGAC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (13 bp):
CGTCATAAATGCG
Found at i:877191 original size:26 final size:26
Alignment explanation
Indices: 877162--877213 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
877152 AATGACACTC
*
877162 AATGAACGTCATTAATGCGCGTCATA
1 AATGAACGTCATAAATGCGCGTCATA
***
877188 AATGTGTGTCATAAATGCGCGTCATA
1 AATGAACGTCATAAATGCGCGTCATA
877214 TATTTATGAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (26 bp):
AATGAACGTCATAAATGCGCGTCATA
Found at i:878246 original size:16 final size:17
Alignment explanation
Indices: 878227--878259 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
878217 TTAAAGATAC
*
878227 AGAGTTTTAGA-ATTGA
1 AGAGTTTAAGATATTGA
878243 AGAGTTTAAGATATTGA
1 AGAGTTTAAGATATTGA
878260 GGGTCGAGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.39, C:0.00, G:0.24, T:0.36
Consensus pattern (17 bp):
AGAGTTTAAGATATTGA
Found at i:878435 original size:83 final size:83
Alignment explanation
Indices: 878293--878572 Score: 330
Period size: 83 Copynumber: 3.4 Consensus size: 83
878283 ATTATGTGAA
* * * **
878293 ATGGCATAGATTCTCTGAATAATAATGGAAAATGATTCCCCTAGAACGCGTTTTTCATTTCGGAT
1 ATGGCATAGATTCTCTGAATAATAATGGAAAACGCTTCCCCTGGAACGCGCCTTTCATTTCGGAT
878358 AGGATGGAACACTATGAC
66 AGGATGGAACACTATGAC
* * * * *
878376 ATAGCATAGATTCTTTGAATAATAATGGAAAACGCTTCCCCTGGAATGTGCCTTTCATTTTGGAT
1 ATGGCATAGATTCTCTGAATAATAATGGAAAACGCTTCCCCTGGAACGCGCCTTTCATTTCGGAT
*
878441 AGGATGGAACACTATGAT
66 AGGATGGAACACTATGAC
* * * * * * * *
878459 ATGGTAGATATTCTCTAAATAAT-ATGGAAAATGCTT-CCTTGTAACACGCCTTTCATTTCGGAT
1 ATGGCATAGATTCTCTGAATAATAATGGAAAACGCTTCCCCTGGAACGCGCCTTTCATTTCGGAT
* * * *
878522 GGGACGAAACTCTATGAC
66 AGGATGGAACACTATGAC
*
878540 ATGGCAAAGATTCTCTGAATAATAATGGAAAAC
1 ATGGCATAGATTCTCTGAATAATAATGGAAAAC
878573 ACTATGCCAT
Statistics
Matches: 162, Mismatches: 34, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
81 53 0.33
82 20 0.12
83 89 0.55
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (83 bp):
ATGGCATAGATTCTCTGAATAATAATGGAAAACGCTTCCCCTGGAACGCGCCTTTCATTTCGGAT
AGGATGGAACACTATGAC
Found at i:879501 original size:27 final size:26
Alignment explanation
Indices: 879450--879501 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
879440 TGAACTATAA
* *
879450 AAACAACAAACCATAAACGTTACATT
1 AAACAACAAACCATAAACATGACATT
*
879476 AAACAACAAACTATTAAACATGACAT
1 AAACAACAAACCA-TAAACATGACAT
879502 GAAGCATACC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 12 0.55
27 10 0.45
ACGTcount: A:0.56, C:0.21, G:0.04, T:0.19
Consensus pattern (26 bp):
AAACAACAAACCATAAACATGACATT
Found at i:879861 original size:21 final size:21
Alignment explanation
Indices: 879828--879870 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
879818 GTCGTCGTCA
* *
879828 TCATCCTCTTCCTTCTCATAC
1 TCATCCTCATCCTCCTCATAC
* *
879849 TCATCGTCATCCTCCTCCTAC
1 TCATCCTCATCCTCCTCATAC
879870 T
1 T
879871 TCTATGAGGT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.14, C:0.44, G:0.02, T:0.40
Consensus pattern (21 bp):
TCATCCTCATCCTCCTCATAC
Found at i:889977 original size:3 final size:3
Alignment explanation
Indices: 889969--889996 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
889959 AGTTCTTTTA
889969 GGT GGT GGT GGT GGT GGT GGT GGT GGT G
1 GGT GGT GGT GGT GGT GGT GGT GGT GGT G
889997 CCATTGTTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.68, T:0.32
Consensus pattern (3 bp):
GGT
Found at i:900553 original size:18 final size:18
Alignment explanation
Indices: 900530--900574 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
900520 AATATTCTCA
*
900530 GTAATCTTATTCTCGCCG
1 GTAATCTTATTCTCACCG
* *
900548 GTAATCCTATTCTCACTG
1 GTAATCTTATTCTCACCG
900566 GTAATCTTA
1 GTAATCTTA
900575 CATTCCGTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.22, C:0.24, G:0.13, T:0.40
Consensus pattern (18 bp):
GTAATCTTATTCTCACCG
Found at i:901175 original size:17 final size:18
Alignment explanation
Indices: 901138--901225 Score: 88
Period size: 18 Copynumber: 4.7 Consensus size: 18
901128 TTTCTGAGAT
901138 AATTGGAATCTGTGAAGG
1 AATTGGAATCTGTGAAGG
*
901156 AATTAGAATCTGTCAGGAATTGG
1 AATTGGAATCTGT---GAA--GG
901179 AATTGGAATCTGTGAAGG
1 AATTGGAATCTGTGAAGG
* * *
901197 AATTGAAATTTGT-CAGG
1 AATTGGAATCTGTGAAGG
901214 AATTGGAATCTG
1 AATTGGAATCTG
901226 AATCTGAAAC
Statistics
Matches: 58, Mismatches: 7, Indels: 11
0.76 0.09 0.14
Matches are distributed among these distances:
17 13 0.22
18 25 0.43
20 3 0.05
21 3 0.05
23 14 0.24
ACGTcount: A:0.34, C:0.07, G:0.28, T:0.31
Consensus pattern (18 bp):
AATTGGAATCTGTGAAGG
Found at i:901187 original size:23 final size:23
Alignment explanation
Indices: 901154--901231 Score: 78
Period size: 23 Copynumber: 3.6 Consensus size: 23
901144 AATCTGTGAA
*
901154 GGAATTAGAATCTGTCAGGAATT
1 GGAATTGGAATCTGTCAGGAATT
901177 GGAATTGGAATCTGT---GAA--
1 GGAATTGGAATCTGTCAGGAATT
* *
901195 GGAATTGAAATTTGTCAGGAATT
1 GGAATTGGAATCTGTCAGGAATT
901218 GGAATCT-GAATCTG
1 GGAAT-TGGAATCTG
901232 AAACATGTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
18 13 0.30
20 3 0.07
21 3 0.07
23 24 0.55
24 1 0.02
ACGTcount: A:0.33, C:0.08, G:0.28, T:0.31
Consensus pattern (23 bp):
GGAATTGGAATCTGTCAGGAATT
Found at i:901195 original size:41 final size:41
Alignment explanation
Indices: 901138--901231 Score: 147
Period size: 41 Copynumber: 2.3 Consensus size: 41
901128 TTTCTGAGAT
901138 AATTGGAATCTGTGAAGGAATT-AGAATCTGTCAGGAATTGG
1 AATTGGAATCTGTGAAGGAATTGA-AATCTGTCAGGAATTGG
*
901179 AATTGGAATCTGTGAAGGAATTGAAATTTGTCAGGAATTGG
1 AATTGGAATCTGTGAAGGAATTGAAATCTGTCAGGAATTGG
901220 AATCT-GAATCTG
1 AAT-TGGAATCTG
901232 AAACATGTTT
Statistics
Matches: 50, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
41 48 0.96
42 2 0.04
ACGTcount: A:0.34, C:0.07, G:0.28, T:0.31
Consensus pattern (41 bp):
AATTGGAATCTGTGAAGGAATTGAAATCTGTCAGGAATTGG
Found at i:903881 original size:19 final size:19
Alignment explanation
Indices: 903857--903916 Score: 84
Period size: 19 Copynumber: 3.1 Consensus size: 19
903847 TTCTGATGCA
903857 GAAAGTATCGATACTCTTG
1 GAAAGTATCGATACTCTTG
* *
903876 GAAAGTATCAATACTCTGAG
1 GAAAGTATCGATACTCT-TG
903896 GTAAAGTATCGATACTCTTG
1 G-AAAGTATCGATACTCTTG
903916 G
1 G
903917 CCTGCAATCC
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
19 16 0.46
20 4 0.11
21 15 0.43
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (19 bp):
GAAAGTATCGATACTCTTG
Found at i:905189 original size:18 final size:17
Alignment explanation
Indices: 905135--905183 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
905125 TTGGACCCTT
* *
905135 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
905153 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
905171 AGTGCATTCGATG
1 AGTGCA-TCGATG
905184 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:905288 original size:65 final size:65
Alignment explanation
Indices: 905155--905314 Score: 177
Period size: 65 Copynumber: 2.5 Consensus size: 65
905145 TGCACTAAGA
* * *
905155 GTGCATCGATGCATCAAGTGCATTCGATG-TTTCAAAATAGCTAGAGTGCATCGATGCATGACTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATACCTACAGTGCATCGATGCATGACTG
*
905219 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAACAT-CCT-CAGTGCATCGGTGCATGGT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AA-ATACCTACAGTGCATCGATGCAT-G-
905282 A-T-
62 ACTG
* * * *
905284 GTGCATCAATACATGAAACGCATTCGATGTT
1 GTGCATCGATGCATCAAATGCATTCGATGTT
905315 CAATTTAATT
Statistics
Matches: 83, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
64 28 0.34
65 46 0.55
66 6 0.07
67 3 0.04
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.30
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATACCTACAGTGCATCGATGCATGACTG
Found at i:913968 original size:65 final size:64
Alignment explanation
Indices: 913773--913979 Score: 210
Period size: 65 Copynumber: 3.2 Consensus size: 64
913763 ACTAAGAGTT
* * * * * *
913773 CATCGATGCATCAAGTGCATTCGATGTTTCAAAATAGCTAAAGTGCATCGATGCAT-GACTGGTG
1 CATCGATGCATCAAATGCATTCGATGTTTCATAACATCT-CAGTGCATCGATGCATGGATTGGTG
*
913837 CATCGATGCATCAAATGCATTCGATGTTTTCATAACATCCTCAGTGCATCGGTGCATGG-TAT-G
1 CATCGATGCATCAAATGCATTCGATG-TTTCATAACAT-CTCAGTGCATCGATGCATGGAT-TGG
913900 TG
63 TG
* *
913902 CATCGATGCATGAAATGCATTCGATG-TTCAATTTA-AT-TCATGGTGCATCGATGCATGGATTG
1 CATCGATGCATCAAATGCATTCGATGTTTC-A-TAACATCTCA--GTGCATCGATGCATGGATTG
913964 GTG
62 GTG
*
913967 CATCGGTGCATCA
1 CATCGATGCATCA
913980 CTCTGAAAAA
Statistics
Matches: 121, Mismatches: 12, Indels: 19
0.80 0.08 0.12
Matches are distributed among these distances:
62 3 0.02
63 3 0.02
64 44 0.36
65 67 0.55
66 4 0.03
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (64 bp):
CATCGATGCATCAAATGCATTCGATGTTTCATAACATCTCAGTGCATCGATGCATGGATTGGTG
Found at i:915083 original size:18 final size:18
Alignment explanation
Indices: 915060--915094 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
915050 ACTGAATATT
*
915060 TGTCCCAAATGACCACTA
1 TGTCCCAAAGGACCACTA
*
915078 TGTCCCGAAGGACCACT
1 TGTCCCAAAGGACCACT
915095 GGTAATTCCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.34, G:0.17, T:0.20
Consensus pattern (18 bp):
TGTCCCAAAGGACCACTA
Found at i:915142 original size:24 final size:24
Alignment explanation
Indices: 915115--915164 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
915105 CGACTCTTGG
915115 CATGCCAATTATACTTATAGATCT
1 CATGCCAATTATACTTATAGATCT
*
915139 CATGCCAATTATACTTATAGCTCT
1 CATGCCAATTATACTTATAGATCT
915163 CA
1 CA
915165 CTTTAAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.32, C:0.24, G:0.08, T:0.36
Consensus pattern (24 bp):
CATGCCAATTATACTTATAGATCT
Found at i:925261 original size:3 final size:3
Alignment explanation
Indices: 925249--925314 Score: 125
Period size: 3 Copynumber: 22.3 Consensus size: 3
925239 TTATTGGCAC
925249 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
925296 TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT T
925315 GAAGAAAAAA
Statistics
Matches: 62, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 60 0.97
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:926543 original size:35 final size:36
Alignment explanation
Indices: 926502--926582 Score: 121
Period size: 35 Copynumber: 2.3 Consensus size: 36
926492 AACACAATCA
* *
926502 TCAATTACATTTTAAATCCT-AAATTCC-AAAATGCT
1 TCAATTACATTCTAAA-CCTCAAATTCCAAAAATACT
926537 TCAATTACATTCTAAACCTCAAATTCCAAAAATACT
1 TCAATTACATTCTAAACCTCAAATTCCAAAAATACT
926573 TCAATTACAT
1 TCAATTACAT
926583 ACCCAACCCC
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
34 3 0.07
35 22 0.52
36 17 0.40
ACGTcount: A:0.42, C:0.22, G:0.01, T:0.35
Consensus pattern (36 bp):
TCAATTACATTCTAAACCTCAAATTCCAAAAATACT
Found at i:926596 original size:36 final size:35
Alignment explanation
Indices: 926522--926598 Score: 100
Period size: 36 Copynumber: 2.2 Consensus size: 35
926512 TTTAAATCCT
* * * *
926522 AAATTCCAAAATGCTTCAATTACATTCTAAACCTC
1 AAATTCCAAAATACTTCAATTACATACCAAACCCC
*
926557 AAATTCCAAAAATACTTCAATTACATACCCAACCCC
1 AAATTCC-AAAATACTTCAATTACATACCAAACCCC
926593 AAATTC
1 AAATTC
926599 ATAATCCATT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
35 7 0.19
36 29 0.81
ACGTcount: A:0.43, C:0.29, G:0.01, T:0.27
Consensus pattern (35 bp):
AAATTCCAAAATACTTCAATTACATACCAAACCCC
Found at i:927253 original size:144 final size:146
Alignment explanation
Indices: 927077--927365 Score: 422
Period size: 144 Copynumber: 2.0 Consensus size: 146
927067 GAAACTATTT
* * * *
927077 AATTAGAATCAAATAATGTTATAGTATTATAAATATTTATAATTAAATTTAAACAAAAAATT-GA
1 AATTAGAACCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAA-AAAAAATTCGA
*
927141 AAATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAA-AAAAAAATCT-AGTCAACTA
65 AAATTCAATTCAATTCGACTTGATTTAAATTTTACAAACTCAAACAAAAAAATCTGAGTCAACTA
927204 TTTTATAAACTGAACTG
130 TTTTATAAACTGAACTG
* *
927221 AATTAGAACCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAATAGAAATTCGAA
1 AATTAGAACCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAAAAAAAATTCGAA
* ** *
927286 AATTCAATTCAATTCGACTTGATTTGAATTTTACAAACTCAAATCGAAAAACTTTTGAGTCAACT
66 AATTCAATTCAATTCGACTTGATTTAAATTTTACAAACTCAAA-C-AAAAAAATCTGAGTCAACT
*
927351 ATTTTATAATCTGAA
129 ATTTTATAAACTGAA
927366 TCGAGTATTT
Statistics
Matches: 128, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
143 6 0.05
144 93 0.73
147 7 0.05
148 22 0.17
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.36
Consensus pattern (146 bp):
AATTAGAACCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAAAAAAAATTCGAA
AATTCAATTCAATTCGACTTGATTTAAATTTTACAAACTCAAACAAAAAAATCTGAGTCAACTAT
TTTATAAACTGAACTG
Found at i:927578 original size:35 final size:35
Alignment explanation
Indices: 927539--927615 Score: 102
Period size: 35 Copynumber: 2.2 Consensus size: 35
927529 GTTGAGCATG
* *
927539 TAATTGAAGTATTTTGGAATTTT-AGGTTTATAATA
1 TAATTGAAGCATTTTGG-ATTTTGAGGTTTAGAATA
* *
927574 TAATTGAAGCATTTTGGATTTTGGGGTTTAGAATG
1 TAATTGAAGCATTTTGGATTTTGAGGTTTAGAATA
927609 TAATTGA
1 TAATTGA
927616 TGATTGTGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
34 5 0.14
35 32 0.86
ACGTcount: A:0.31, C:0.01, G:0.22, T:0.45
Consensus pattern (35 bp):
TAATTGAAGCATTTTGGATTTTGAGGTTTAGAATA
Found at i:928022 original size:29 final size:28
Alignment explanation
Indices: 927990--928044 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
927980 TTAAAATCGA
* *
927990 TACAACTTAATTTTTTTAATTTAAATTAG
1 TACAAATTAA-TTTATTAATTTAAATTAG
*
928019 TACAAATTGATTTATTAATTTAAATT
1 TACAAATTAATTTATTAATTTAAATT
928045 GATTTAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 15 0.65
29 8 0.35
ACGTcount: A:0.40, C:0.05, G:0.04, T:0.51
Consensus pattern (28 bp):
TACAAATTAATTTATTAATTTAAATTAG
Found at i:931079 original size:23 final size:23
Alignment explanation
Indices: 931060--931166 Score: 106
Period size: 23 Copynumber: 4.7 Consensus size: 23
931050 ACACGTTCAT
931060 GAACATGTTCATTTAGCGTTCGC
1 GAACATGTTCATTTAGCGTTCGC
* * * *
931083 GAATATGCTCGTTTATCGTTCGC
1 GAACATGTTCATTTAGCGTTCGC
* *
931106 GAACATGTTCATTTAACGTTCGT
1 GAACATGTTCATTTAGCGTTCGC
* * * *
931129 GAACATATTCGTTTGGCGTTCAC
1 GAACATGTTCATTTAGCGTTCGC
* *
931152 GAAAATGCTCATTTA
1 GAACATGTTCATTTA
931167 TATATGTTCA
Statistics
Matches: 64, Mismatches: 20, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 64 1.00
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (23 bp):
GAACATGTTCATTTAGCGTTCGC
Found at i:931141 original size:46 final size:46
Alignment explanation
Indices: 931044--931166 Score: 129
Period size: 46 Copynumber: 2.7 Consensus size: 46
931034 CGTTTAGAGT
* * * * *
931044 TCGTTTACACGTTCATGAACATGTTCATTTAGCGTTCGCGAATATGC
1 TCGTTTA-GCGTTCACGAACATGTTCATTTAACGTTCGCGAACATAC
* * * *
931091 TCGTTTATCGTTCGCGAACATGTTCATTTAACGTTCGTGAACATAT
1 TCGTTTAGCGTTCACGAACATGTTCATTTAACGTTCGCGAACATAC
* * *
931137 TCGTTTGGCGTTCACGAAAATGCTCATTTA
1 TCGTTTAGCGTTCACGAACATGTTCATTTA
931167 TATATGTTCA
Statistics
Matches: 63, Mismatches: 13, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
46 56 0.89
47 7 0.11
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (46 bp):
TCGTTTAGCGTTCACGAACATGTTCATTTAACGTTCGCGAACATAC
Found at i:931615 original size:45 final size:44
Alignment explanation
Indices: 931565--931671 Score: 145
Period size: 38 Copynumber: 2.5 Consensus size: 44
931555 ATAAACAATT
*
931565 AGCAGTAACATAAACATTTAAAGTAAAGAATTGTAAAACGAAATC
1 AGCAGTAACATAAACATTTAAAGT-AAGAATAGTAAAACGAAATC
*
931610 AGCAGTAACATAAACA--T----TAAGAATAGTAAAACGAAATT
1 AGCAGTAACATAAACATTTAAAGTAAGAATAGTAAAACGAAATC
931648 AGCAGTAACATAAACATTTAAAGT
1 AGCAGTAACATAAACATTTAAAGT
931672 TAGAGCACAT
Statistics
Matches: 54, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
38 34 0.63
39 1 0.02
40 1 0.02
43 1 0.02
44 1 0.02
45 16 0.30
ACGTcount: A:0.53, C:0.11, G:0.13, T:0.22
Consensus pattern (44 bp):
AGCAGTAACATAAACATTTAAAGTAAGAATAGTAAAACGAAATC
Found at i:931661 original size:22 final size:22
Alignment explanation
Indices: 931598--931661 Score: 52
Period size: 22 Copynumber: 3.2 Consensus size: 22
931588 TAAAGAATTG
*
931598 TAAAACGAAATCAGCAGTAACA
1 TAAAACGAAATTAGCAGTAACA
*
931620 T-AAAC---ATTA--AG-AATA
1 TAAAACGAAATTAGCAGTAACA
931635 GTAAAACGAAATTAGCAGTAACA
1 -TAAAACGAAATTAGCAGTAACA
931658 TAAA
1 TAAA
931662 CATTTAAAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 16
0.62 0.06 0.32
Matches are distributed among these distances:
15 3 0.10
16 3 0.10
17 4 0.13
18 3 0.10
20 4 0.13
21 4 0.13
22 7 0.23
23 3 0.10
ACGTcount: A:0.56, C:0.12, G:0.12, T:0.19
Consensus pattern (22 bp):
TAAAACGAAATTAGCAGTAACA
Found at i:932901 original size:22 final size:22
Alignment explanation
Indices: 932873--932936 Score: 59
Period size: 22 Copynumber: 3.2 Consensus size: 22
932863 GTAAAAAAAT
932873 TAAACGAGCTTATTCATGAACA
1 TAAACGAGCTTATTCATGAACA
* *
932895 TAAACGAAC-GATT--T--A-A
1 TAAACGAGCTTATTCATGAACA
*
932911 TAAACGAGCTTGTTCATGAACA
1 TAAACGAGCTTATTCATGAACA
932933 TAAA
1 TAAA
932937 TGAATCGAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 12
0.65 0.10 0.25
Matches are distributed among these distances:
16 9 0.29
17 3 0.10
19 2 0.06
21 4 0.13
22 13 0.42
ACGTcount: A:0.44, C:0.16, G:0.14, T:0.27
Consensus pattern (22 bp):
TAAACGAGCTTATTCATGAACA
Found at i:946274 original size:15 final size:14
Alignment explanation
Indices: 946255--946305 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 14
946245 TATTAGTTAA
946255 TTAATAAATTAAAT
1 TTAATAAATTAAAT
946269 ATTAATAAAAATTAAAT
1 -TTAAT--AAATTAAAT
946286 TATAA-AAATTAAAT
1 T-TAATAAATTAAAT
946300 TTAATA
1 TTAATA
946306 TAATAAAATG
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
13 3 0.09
14 11 0.34
15 5 0.16
16 1 0.03
17 12 0.38
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
TTAATAAATTAAAT
Found at i:946292 original size:14 final size:14
Alignment explanation
Indices: 946273--946300 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
946263 TTAAATATTA
946273 ATAAAAATTAAATT
1 ATAAAAATTAAATT
946287 ATAAAAATTAAATT
1 ATAAAAATTAAATT
946301 TAATATAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
ATAAAAATTAAATT
Found at i:946452 original size:3 final size:3
Alignment explanation
Indices: 946444--946482 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
946434 AATCAATAAT
946444 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
946483 AACTGCCAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:951398 original size:87 final size:87
Alignment explanation
Indices: 951298--951486 Score: 306
Period size: 87 Copynumber: 2.2 Consensus size: 87
951288 TTTGGTTCAC
**
951298 GGAATGTAAGATTACCAGTGAGAATATAAGATTGTCAGGGAATAAGATTACTGAGAATATTGTAT
1 GGAATGTAAGATTACCAGTGAGAATATAAGATTACCAGGGAATAAGATTACTGAGAATATTGTAT
*
951363 TTTATGTTTGGTTGGTTTAGCA
66 TTTATGTTTGGTTGGTTTAACA
* * *
951385 GGAATATAAGATTACCAGTGGGAATATAAGATTACCAGGGAATAAGATTACTGGGAATATTGTAT
1 GGAATGTAAGATTACCAGTGAGAATATAAGATTACCAGGGAATAAGATTACTGAGAATATTGTAT
*
951450 TTTGTGTTTGGTTGGTTTAACA
66 TTTATGTTTGGTTGGTTTAACA
*
951472 TGAATGTAAGATTAC
1 GGAATGTAAGATTAC
951487 ATGTTTGGTT
Statistics
Matches: 93, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
87 93 1.00
ACGTcount: A:0.34, C:0.06, G:0.25, T:0.35
Consensus pattern (87 bp):
GGAATGTAAGATTACCAGTGAGAATATAAGATTACCAGGGAATAAGATTACTGAGAATATTGTAT
TTTATGTTTGGTTGGTTTAACA
Found at i:951410 original size:20 final size:20
Alignment explanation
Indices: 951385--951422 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
951375 TGGTTTAGCA
951385 GGAATATAAGATTACCAGTG
1 GGAATATAAGATTACCAGTG
951405 GGAATATAAGATTACCAG
1 GGAATATAAGATTACCAG
951423 GGAATAAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.11, G:0.24, T:0.24
Consensus pattern (20 bp):
GGAATATAAGATTACCAGTG
Found at i:951435 original size:16 final size:19
Alignment explanation
Indices: 951385--951428 Score: 72
Period size: 20 Copynumber: 2.3 Consensus size: 19
951375 TGGTTTAGCA
951385 GGAATATAAGATTACCAGTG
1 GGAATATAAGATTACCAG-G
951405 GGAATATAAGATTACCA-G
1 GGAATATAAGATTACCAGG
951423 GGAATA
1 GGAATA
951429 AGATTACTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 7 0.29
20 17 0.71
ACGTcount: A:0.43, C:0.09, G:0.25, T:0.23
Consensus pattern (19 bp):
GGAATATAAGATTACCAGG
Found at i:951443 original size:15 final size:16
Alignment explanation
Indices: 951390--951435 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 16
951380 TAGCAGGAAT
951390 ATAAGATTACCAGTGGGAA
1 ATAAGATTACCA--GGG-A
951409 TATAAGATTACCAGGGA
1 -ATAAGATTACCAGGGA
951426 ATAAGATTAC
1 ATAAGATTAC
951436 TGGGAATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 10 0.38
17 1 0.04
18 3 0.12
20 12 0.46
ACGTcount: A:0.43, C:0.11, G:0.22, T:0.24
Consensus pattern (16 bp):
ATAAGATTACCAGGGA
Found at i:952427 original size:22 final size:22
Alignment explanation
Indices: 952399--952445 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
952389 CTTGCTTTTA
*
952399 TGAGCCTTAAATGAGTCAAAAT
1 TGAGCCTTAAACGAGTCAAAAT
952421 TGAGCCTTAAACGAGTCAAAAT
1 TGAGCCTTAAACGAGTCAAAAT
952443 TGA
1 TGA
952446 CCATCCAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (22 bp):
TGAGCCTTAAACGAGTCAAAAT
Found at i:953118 original size:21 final size:21
Alignment explanation
Indices: 953092--953143 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
953082 CCAGAATGGG
953092 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
953113 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
953134 GGGAATCGAT
1 GGGAATCGAT
953144 TATTATGACC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.23
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:953283 original size:19 final size:19
Alignment explanation
Indices: 953242--953288 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
953232 GCCTCGGGGG
**
953242 TACTGTTCAAACAGTAATT
1 TACTGTTCAAACAGTAAAA
*
953261 TACTGTTCAAATAGTAAAA
1 TACTGTTCAAACAGTAAAA
*
953280 TACTATTCA
1 TACTGTTCA
953289 TAAAAACATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.40, C:0.15, G:0.09, T:0.36
Consensus pattern (19 bp):
TACTGTTCAAACAGTAAAA
Found at i:953385 original size:29 final size:31
Alignment explanation
Indices: 953353--953412 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
953343 AAATTTTGAA
*
953353 TAAATTCAATT-AAGTCCAAATA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
953382 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
953413 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.35
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:955365 original size:19 final size:20
Alignment explanation
Indices: 955338--955377 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
955328 GCTTGATTTC
955338 TTTTGATTA-AAAAATAATA
1 TTTTGATTAGAAAAATAATA
*
955357 TTTTTATTAGTAAAAATAATA
1 TTTTGATTAG-AAAAATAATA
955378 AAAAATATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 8 0.44
21 10 0.56
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (20 bp):
TTTTGATTAGAAAAATAATA
Found at i:956840 original size:14 final size:14
Alignment explanation
Indices: 956821--956862 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
956811 TATAAGATAC
*
956821 TATTTCCATTACCA
1 TATTTCCATCACCA
956835 TATTTCCATCACCA
1 TATTTCCATCACCA
**
956849 T-CCTCCATCACCA
1 TATTTCCATCACCA
956862 T
1 T
956863 TCGCGCCCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
13 11 0.44
14 14 0.56
ACGTcount: A:0.26, C:0.38, G:0.00, T:0.36
Consensus pattern (14 bp):
TATTTCCATCACCA
Found at i:961501 original size:15 final size:16
Alignment explanation
Indices: 961478--961510 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
961468 TTTGATAACA
961478 TTCTATCCAT-TTCAT
1 TTCTATCCATGTTCAT
*
961493 TTCTTTCCATGTTCAT
1 TTCTATCCATGTTCAT
961509 TT
1 TT
961511 TCATTTCTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.15, C:0.24, G:0.03, T:0.58
Consensus pattern (16 bp):
TTCTATCCATGTTCAT
Found at i:963788 original size:148 final size:149
Alignment explanation
Indices: 963491--963788 Score: 564
Period size: 148 Copynumber: 2.0 Consensus size: 149
963481 ACTTATTCTC
963491 GCCTCCGTTGTCTGAAATATCTTCTCCCATTTTCCTTCTGGCTGAAACAAAATCATATTCTTCTT
1 GCCTCCGTTGTCTG-AATATCTTCTCCCATTTTCCTTCTGGCTGAAACAAAATCATATTCTTCTT
963556 CGATTTGGCCAGAGTTGTTGCAAGGAGATTCCATTACTGCTCCAACAAACTTCTTCTTCTGTGGA
65 CGATTTGGCCAGAGTTGTTGCAAGGAGATTCCATTACTGCTCCAACAAACTTCTTCTTCTGTGGA
963621 GCCGAGCAAGGAGAAATGAG
130 GCCGAGCAAGGAGAAATGAG
963641 GCCTCCGTTGTCTG-A-ATCTTCTCCCATTTTTCCTTCTGGCTGAAACAAAATCATATTCTTCTT
1 GCCTCCGTTGTCTGAATATCTTCTCCCA-TTTTCCTTCTGGCTGAAACAAAATCATATTCTTCTT
963704 CGATTTGGCCAGAGTTGTTGCAAGGAGATTCCATTACTGCTCCAACAAACTTCTTCTTCTGTGGA
65 CGATTTGGCCAGAGTTGTTGCAAGGAGATTCCATTACTGCTCCAACAAACTTCTTCTTCTGTGGA
963769 GCCGAGCAAGGAGAAATGAG
130 GCCGAGCAAGGAGAAATGAG
963789 CCCGCAGACT
Statistics
Matches: 147, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
147 11 0.07
148 122 0.83
150 14 0.10
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.32
Consensus pattern (149 bp):
GCCTCCGTTGTCTGAATATCTTCTCCCATTTTCCTTCTGGCTGAAACAAAATCATATTCTTCTTC
GATTTGGCCAGAGTTGTTGCAAGGAGATTCCATTACTGCTCCAACAAACTTCTTCTTCTGTGGAG
CCGAGCAAGGAGAAATGAG
Found at i:966190 original size:21 final size:21
Alignment explanation
Indices: 966151--966191 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
966141 AAAAAAATTA
* **
966151 TATATAAATTTTATTAAAAAG
1 TATATAAATTTAAAAAAAAAG
966172 TATATAAATTTAAAAAAAAA
1 TATATAAATTTAAAAAAAAA
966192 TATTTTCGAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (21 bp):
TATATAAATTTAAAAAAAAAG
Found at i:975367 original size:16 final size:16
Alignment explanation
Indices: 975338--975395 Score: 98
Period size: 16 Copynumber: 3.6 Consensus size: 16
975328 ATCGAATGAT
* *
975338 GCCACGTGTCACTAAC
1 GCCACATGTTACTAAC
975354 GCCACATGTTACTAAC
1 GCCACATGTTACTAAC
975370 GCCACATGTTACTAAC
1 GCCACATGTTACTAAC
975386 GCCACATGTT
1 GCCACATGTT
975396 GTGCCACATG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 40 1.00
ACGTcount: A:0.28, C:0.33, G:0.16, T:0.24
Consensus pattern (16 bp):
GCCACATGTTACTAAC
Found at i:975739 original size:27 final size:26
Alignment explanation
Indices: 975709--975769 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 26
975699 TATTAATTAC
975709 ATTTTATTTTTAACTTAATTTAAAAA
1 ATTTTATTTTTAACTTAATTTAAAAA
**
975735 TATTTTATTTTTATGTTAATTTAAAAA
1 -ATTTTATTTTTAACTTAATTTAAAAA
975762 A-TTTATTT
1 ATTTTATTT
975770 ATGCTCAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
25 7 0.22
26 1 0.03
27 24 0.75
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (26 bp):
ATTTTATTTTTAACTTAATTTAAAAA
Found at i:975842 original size:30 final size:30
Alignment explanation
Indices: 975789--975962 Score: 142
Period size: 30 Copynumber: 5.9 Consensus size: 30
975779 TATTTTGAAG
* * *
975789 TTAAGATAAGAATAAAATATATTTAATAAT
1 TTAAAATAATAATATAATATATTTAATAAT
* *
975819 TTAAAATAATAATATAATGTATTTAATAAA
1 TTAAAATAATAATATAATATATTTAATAAT
* * *
975849 TTAAGATAA-AATAT-ATACATTGAA-AAT
1 TTAAAATAATAATATAATATATTTAATAAT
* *
975876 TTAAAATAATAATAGAATATATTTTAATAGT
1 TTAAAATAATAATATAATATA-TTTAATAAT
* * *
975907 TTAGATAAGAATAATAT-ATATATTT-TTAAC
1 TTA-A-AATAATAATATAATATATTTAATAAT
* * *
975937 TTAAAATAAAAATAAAATATTTTTAA
1 TTAAAATAATAATATAATATATTTAA
975963 ATTAAGTTAA
Statistics
Matches: 111, Mismatches: 25, Indels: 16
0.73 0.16 0.11
Matches are distributed among these distances:
27 10 0.09
28 19 0.17
29 17 0.15
30 42 0.38
31 8 0.07
32 6 0.05
33 9 0.08
ACGTcount: A:0.55, C:0.01, G:0.05, T:0.39
Consensus pattern (30 bp):
TTAAAATAATAATATAATATATTTAATAAT
Found at i:975883 original size:57 final size:61
Alignment explanation
Indices: 975789--975920 Score: 166
Period size: 57 Copynumber: 2.2 Consensus size: 61
975779 TATTTTGAAG
* * * *
975789 TTAAGATAAGAATAAAATATATTTAATAATTTAAAATAATAATATAATGTA-TTTAATAAA
1 TTAAGATAAGAATAAAATACATTGAATAATTTAAAATAATAATAGAATATATTTTAATAAA
* *
975849 TTAAGATAA-AAT-ATATACATTGAA-AATTTAAAATAATAATAGAATATATTTTAAT-AG
1 TTAAGATAAGAATAAAATACATTGAATAATTTAAAATAATAATAGAATATATTTTAATAAA
*
975906 TTTAGATAAGAATAA
1 TTAAGATAAGAATAA
975921 TATATATATT
Statistics
Matches: 62, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
57 31 0.50
58 18 0.29
59 4 0.06
60 9 0.15
ACGTcount: A:0.55, C:0.01, G:0.07, T:0.37
Consensus pattern (61 bp):
TTAAGATAAGAATAAAATACATTGAATAATTTAAAATAATAATAGAATATATTTTAATAAA
Found at i:977081 original size:22 final size:22
Alignment explanation
Indices: 977034--977083 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 22
977024 ACCTATAATT
977034 ATAAATTAGTTAAAAATTTAAAG
1 ATAAATTAGTTAAAAA-TTAAAG
*
977057 ATAAATTATTTAAAAA-TAAAGG
1 ATAAATTAGTTAAAAATTAAA-G
977079 ATAAA
1 ATAAA
977084 CTATACCAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 4 0.16
22 6 0.24
23 15 0.60
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (22 bp):
ATAAATTAGTTAAAAATTAAAG
Found at i:977925 original size:20 final size:19
Alignment explanation
Indices: 977893--977930 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
977883 AATGAAATTT
*
977893 TATTTCTAATTTATAAATA
1 TATTTCTAATTTACAAATA
977912 TATTTCTAATTTTACAAAT
1 TATTTCTAA-TTTACAAAT
977931 TGAGAAATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (19 bp):
TATTTCTAATTTACAAATA
Found at i:981006 original size:34 final size:32
Alignment explanation
Indices: 980968--981064 Score: 86
Period size: 34 Copynumber: 2.9 Consensus size: 32
980958 TGAAAAGGAT
980968 TTTATTTTTATTTGTTTATTTATTTTTATAAGTA
1 TTTATTTTTATTTGTTTATTTATTTTT-T-AGTA
* * *
981002 TTTATGTTAATTTGTATTCATTTAATTTTTAGTA
1 TTTATTTTTATTTGT-TT-ATTTATTTTTTAGTA
* * * *
981036 TTGTCTTTGTGTTCGTTTATTTATTTTTT
1 TT-TATTTTTATTTGTTTATTTATTTTTT
981065 CGGAGAACTA
Statistics
Matches: 50, Mismatches: 10, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
33 10 0.20
34 21 0.42
35 10 0.20
36 9 0.18
ACGTcount: A:0.20, C:0.03, G:0.09, T:0.68
Consensus pattern (32 bp):
TTTATTTTTATTTGTTTATTTATTTTTTAGTA
Found at i:982353 original size:15 final size:15
Alignment explanation
Indices: 982333--982366 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
982323 CTAGCCCTTG
982333 GCTATAGAAAACTTA
1 GCTATAGAAAACTTA
982348 GCTATAGAAAACTTA
1 GCTATAGAAAACTTA
982363 GCTA
1 GCTA
982367 AGTATTATAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.26
Consensus pattern (15 bp):
GCTATAGAAAACTTA
Found at i:985305 original size:26 final size:29
Alignment explanation
Indices: 985270--985333 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
985260 TATAAAAGTA
*
985270 AAATATAATT-AAACAAT-GT-TTAAAAT
1 AAATAAAATTAAAACAATAGTATTAAAAT
*
985296 AAATAAAATTAAAACTATAGTATTAAAAT
1 AAATAAAATTAAAACAATAGTATTAAAAT
*
985325 GAATAAAAT
1 AAATAAAAT
985334 AATAAAACTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
26 9 0.28
27 6 0.19
28 2 0.06
29 15 0.47
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.31
Consensus pattern (29 bp):
AAATAAAATTAAAACAATAGTATTAAAAT
Found at i:987488 original size:112 final size:111
Alignment explanation
Indices: 987208--987756 Score: 655
Period size: 112 Copynumber: 5.0 Consensus size: 111
987198 ATAGAGTCGT
* * * * *
987208 GCAAAAGGTTGAACAAGCTCTTCTCATTATAAACTTCTTATTCC-TCTTCAGATAAGTTATTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
**
987272 ATTATGAACTTTCTCTGGAAAAGTTGATCCATTGAGTGATGAATTCA
66 ATTATGAACTTTC-CTGGAAAAGTTGATCCATCAAGTGATGAATTCA
* * * * * *
987319 ACACAAAGGTTTGAACAAATTTTTCTTATTATGAATTTCTTCTTCATTCTTCAGATGAGTTCTTC
1 GCA-AAAGG-TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
* * * * *
987384 TCATTATGAACTTTTCCTGGCAATGCTAATCCATCAAGTGATGAATTCG
64 TCATTATGAAC-TTTCCTGGAAAAGTTGATCCATCAAGTGATGAATTCA
987433 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTC-T-TC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
987496 ATTATGAAC-TTCCTATGGAAAAGTTGATCCATCAAGTGATGAATTCAA
66 ATTATGAACTTTCC--TGGAAAAGTTGATCCATCAAGTGATGAATTC-A
* * *
987544 GCAAAAGGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGACGAG---TTCT
1 GCAAAA-GGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* * *
987606 CATTATGAACTCTACCTGGAAATGTTGATCCATCGAGTGATGAATTCGA
65 CATTATGAACT-TTCCTGGAAAAGTTGATCCATCAAGTGATGAATTC-A
987655 GC-AAAGGTTGAACAAG---TTCTCATTATGAA---CTT-TT-CTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
987711 ATTATGAACTTCCTCTGGAAAAGTTGATCCA-CAAGTGATGAATTCA
66 ATTATGAACTTTC-CTGGAAAAGTTGATCCATCAAGTGATGAATTCA
987757 AATCTTTGCT
Statistics
Matches: 380, Mismatches: 42, Indels: 41
0.82 0.09 0.09
Matches are distributed among these distances:
101 12 0.03
102 3 0.01
103 18 0.05
104 31 0.08
106 13 0.03
108 4 0.01
109 10 0.03
110 42 0.11
111 52 0.14
112 100 0.26
113 36 0.09
114 55 0.14
115 4 0.01
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (111 bp):
GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTTTCCTGGAAAAGTTGATCCATCAAGTGATGAATTCA
Found at i:987605 original size:224 final size:221
Alignment explanation
Indices: 987208--987757 Score: 746
Period size: 224 Copynumber: 2.5 Consensus size: 221
987198 ATAGAGTCGT
* * *
987208 GCAAAAGGTTGAACAAGCTCTTCTCATTATAAACTTCTTATTCC-TCTTCAGATAAGTTATTCTC
1 GCAAAAGGTTGAACAAG-TCTTCTCATTATGAACTTCTT-TTCCTTCTTCAGATGAGTT-CTCTC
* ** * *
987272 ATTATGAACTTTCTCTGGAAAAGTTGATCCATTGAGTGATGAATTCAACACAAAGGTTTGAACAA
63 ATTATGAACTTCCTCTGGAAAAGTTGATCCATCAAGTGATGAATTCAACACAAAGGGTTAAACAA
* * * * * *
987337 ATTTTTCTTATTATGAATTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAACTTTTCCT
128 ATTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGACGAG---TTCTCATTATGAACTCTACCT
*
987402 GGCAATGCTAATCCATCAAGTGATGAATTCG-
190 GGAAATGCTAATCCATCAAGTGATGAATTCGA
987433 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT-TCA
1 GCAAAAGGTTGAACAAG-TCTTCTCATTATGAACTTCTT-TTCCTTCTTCAGATGAGTTCTCTCA
*
987497 TTATGAACTTCCTATGGAAAAGTTGATCCATCAAGTGATGAATTCAAGCA-AAAGGGTTAAACAA
64 TTATGAACTTCCTCTGGAAAAGTTGATCCATCAAGTGATGAATTCAA-CACAAAGGGTTAAACAA
*
987561 GTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGACGAGTTCTCATTATGAACTCTACCTGGA
128 ATTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGACGAGTTCTCATTATGAACTCTACCTGGA
* * *
987626 AATGTTGATCCATCGAGTGATGAATTCGA
193 AATGCTAATCCATCAAGTGATGAATTCGA
987655 GC-AAAGGTTGAACAAG--TTCTCATTATGAA---CTTTT-CTTCTTCAGATGAGTTCTTCTCAT
1 GCAAAAGGTTGAACAAGTCTTCTCATTATGAACTTCTTTTCCTTCTTCAGATGAGTTC-TCTCAT
987713 TATGAACTTCCTCTGGAAAAGTTGATCCA-CAAGTGATGAATTCAA
65 TATGAACTTCCTCTGGAAAAGTTGATCCATCAAGTGATGAATTCAA
987758 ATCTTTGCTA
Statistics
Matches: 297, Mismatches: 23, Indels: 21
0.87 0.07 0.06
Matches are distributed among these distances:
213 17 0.06
214 19 0.06
215 35 0.12
218 13 0.04
221 60 0.20
222 2 0.01
224 94 0.32
225 44 0.15
226 13 0.04
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (221 bp):
GCAAAAGGTTGAACAAGTCTTCTCATTATGAACTTCTTTTCCTTCTTCAGATGAGTTCTCTCATT
ATGAACTTCCTCTGGAAAAGTTGATCCATCAAGTGATGAATTCAACACAAAGGGTTAAACAAATT
CTTCTCATTATGAACTTCTTCTTCATTCTTCAGACGAGTTCTCATTATGAACTCTACCTGGAAAT
GCTAATCCATCAAGTGATGAATTCGA
Found at i:992835 original size:9 final size:9
Alignment explanation
Indices: 992823--992847 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
992813 CTTTCCTTTT
992823 TTTTTTTAA
1 TTTTTTTAA
992832 TTTTTTTAA
1 TTTTTTTAA
992841 TTTTTTT
1 TTTTTTT
992848 GATGAATGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (9 bp):
TTTTTTTAA
Found at i:993132 original size:2 final size:2
Alignment explanation
Indices: 993125--993175 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
993115 ACAACAAGGG
993125 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- 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
993166 AT AT AT AT AT
1 AT AT AT AT AT
993176 TTGAAAGGAT
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:997561 original size:24 final size:24
Alignment explanation
Indices: 997534--997593 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
997524 ATACATTAAA
997534 AATAAACTA-AAACATTAATAAAAT
1 AATAAA-TATAAACATTAATAAAAT
*
997558 AATATATATAAACATTAATAAAAT
1 AATAAATATAAACATTAATAAAAT
*
997582 AATATATATAAA
1 AATAAATATAAA
997594 TTTTGAAAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
23 2 0.06
24 32 0.94
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (24 bp):
AATAAATATAAACATTAATAAAAT
Found at i:997602 original size:22 final size:24
Alignment explanation
Indices: 997543--997593 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
997533 AAATAAACTA
997543 AAACATTAATAAAATAATATATAT
1 AAACATTAATAAAATAATATATAT
997567 AAACATTAATAAAATAATATATAT
1 AAACATTAATAAAATAATATATAT
997591 AAA
1 AAA
997594 TTTTGAAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (24 bp):
AAACATTAATAAAATAATATATAT
Found at i:999975 original size:3 final size:3
Alignment explanation
Indices: 999967--1000026 Score: 77
Period size: 3 Copynumber: 20.0 Consensus size: 3
999957 GGCCTGTTTG
* * *
999967 TAA TAA TAA TAA TAT TAA TAA TAA AAA TAAA TAA TAA T-A TAA TAG
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
1000012 TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA
1000027 AATGAAAAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
2 2 0.04
3 44 0.90
4 3 0.06
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1000973 original size:21 final size:21
Alignment explanation
Indices: 1000949--1000988 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1000939 CGCAATGGCC
*
1000949 GCAATAGCATCCGCGACGGCA
1 GCAATAGCACCCGCGACGGCA
*
1000970 GCAATAGCGCCCGCGACGG
1 GCAATAGCACCCGCGACGG
1000989 TCGCAATCAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.35, G:0.33, T:0.07
Consensus pattern (21 bp):
GCAATAGCACCCGCGACGGCA
Found at i:1000994 original size:21 final size:20
Alignment explanation
Indices: 1000948--1000995 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
1000938 CCGCAATGGC
*
1000948 CGCAATAGCATCCGCGACGG
1 CGCAATAGCACCCGCGACGG
*
1000968 CAGCAATAGCGCCCGCGACGG
1 C-GCAATAGCACCCGCGACGG
1000989 TCGCAAT
1 -CGCAAT
1000996 CACGATAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 1 0.04
21 22 0.92
22 1 0.04
ACGTcount: A:0.25, C:0.35, G:0.29, T:0.10
Consensus pattern (20 bp):
CGCAATAGCACCCGCGACGG
Found at i:1004966 original size:3 final size:3
Alignment explanation
Indices: 1004960--1004990 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1004950 ATTTTTACAC
1004960 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1004991 CCTCTCTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1006334 original size:15 final size:15
Alignment explanation
Indices: 1006316--1006345 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1006306 GGGAAAAAAG
1006316 GTTTCTTTTTCTACT
1 GTTTCTTTTTCTACT
1006331 GTTTCTTTTTCTACT
1 GTTTCTTTTTCTACT
1006346 CTCACTACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.07, C:0.20, G:0.07, T:0.67
Consensus pattern (15 bp):
GTTTCTTTTTCTACT
Found at i:1008190 original size:12 final size:12
Alignment explanation
Indices: 1008175--1008218 Score: 54
Period size: 12 Copynumber: 3.6 Consensus size: 12
1008165 CGGTTTTTTT
*
1008175 ACCGGATAAAAA
1 ACCGGTTAAAAA
1008187 ACCGGTTTGAAAAA
1 ACCGG-TT-AAAAA
1008201 ACC-GTTAAAAA
1 ACCGGTTAAAAA
1008212 ACCGGTT
1 ACCGGTT
1008219 TTTATCCGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
11 8 0.29
12 10 0.36
13 2 0.07
14 8 0.29
ACGTcount: A:0.45, C:0.18, G:0.18, T:0.18
Consensus pattern (12 bp):
ACCGGTTAAAAA
Done.