Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009960.1 Kokia drynarioides strain JFW-HI SEQ_124708, 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: 79543
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.35
Found at i:333 original size:20 final size:21
Alignment explanation
Indices: 308--350 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
298 TACTTACTAC
308 TACTAAC-AACAAAATAAAAT
1 TACTAACTAACAAAATAAAAT
* *
328 TACTAACTAGCAAAATTAAAT
1 TACTAACTAACAAAATAAAAT
349 TA
1 TA
351 AAGTAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.58, C:0.14, G:0.02, T:0.26
Consensus pattern (21 bp):
TACTAACTAACAAAATAAAAT
Found at i:523 original size:12 final size:12
Alignment explanation
Indices: 508--532 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
498 AAATTAAAAT
508 ATTTTAAAATTA
1 ATTTTAAAATTA
520 ATTTTAAAATTA
1 ATTTTAAAATTA
532 A
1 A
533 CCATACTTAA
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):
ATTTTAAAATTA
Found at i:4183 original size:15 final size:15
Alignment explanation
Indices: 4133--4194 Score: 58
Period size: 15 Copynumber: 4.2 Consensus size: 15
4123 TTTTAAAAAA
4133 TATTTATATA-TTTT
1 TATTTATATATTTTT
**
4147 TATTT-TAATATTTAA
1 TATTTAT-ATATTTTT
*
4162 TAATTATATATTTTT
1 TATTTATATATTTTT
4177 TATTTAT-TGATTTTT
1 TATTTATAT-ATTTTT
4192 TAT
1 TAT
4195 ATAGTCATCT
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
13 1 0.03
14 9 0.24
15 27 0.71
16 1 0.03
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.68
Consensus pattern (15 bp):
TATTTATATATTTTT
Found at i:7739 original size:2 final size:2
Alignment explanation
Indices: 7732--7761 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
7722 AACTTTAATT
7732 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
7762 CACCAAATTT
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):
TA
Found at i:25990 original size:2 final size:2
Alignment explanation
Indices: 25983--26012 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
25973 TTTATTTTAT
25983 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
26013 AAATTTTAGA
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):
TA
Found at i:27741 original size:3 final size:3
Alignment explanation
Indices: 27733--27766 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
27723 GACATTTTGA
27733 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
27767 AGTTTACTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:29078 original size:21 final size:21
Alignment explanation
Indices: 29033--29076 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
29023 AAATTTAAAA
*
29033 TTTAGTAATTATACTTTTATT
1 TTTAGAAATTATACTTTTATT
*
29054 TTTAGAAATTTTA-TTTTATT
1 TTTAGAAATTATACTTTTATT
29074 TTT
1 TTT
29077 TAAATTTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.66
Consensus pattern (21 bp):
TTTAGAAATTATACTTTTATT
Found at i:30218 original size:323 final size:326
Alignment explanation
Indices: 29484--30361 Score: 1374
Period size: 323 Copynumber: 2.7 Consensus size: 326
29474 TGTTAAAACT
* * * * * *
29484 TTGAAATCTCAAGCGAAGTTTAAAATATGATCTTTTTACAC--AACTCATTTCGCATGATTTTCA
1 TTGAAATTTCGAGCGAAGTTTAAAATACGATCCTTTGACACATAACTTATTTCGCATGATTTTCA
*
29547 AAAATCAAATTTGAAG-AAAATGTCCGTGTGTTTCAAATTTCTCAGAGAATTGAAGTCGTGTCCA
66 AAAATCAAATTTGAAGAAAAATGTCCGTGTGTTTCGAATTTCTCAGAGAATTGAAGTCGTGTCCA
* * *
29611 ACACGTTATGGCACGACATTCTCGGAATTTCGAAATTGAAAGAAATTTTAAAAGGTTTTAAAAAG
131 ACACGTTAGGGCACGACATTCTCGGAATTTCGAAATTGAAAGAAAATTTGAAAGGTTTTAAAAAG
* *
29676 GATATTCGATCGTGTGAATTATAC-AAATATCACACCCAGCATGTTAGGACATGTTTTTTTCGAA
196 GATATTCGATCGCGTGAATTATACGAAA-ATCACACCCAGCATATTAGGACATGTTTTTTTCGAA
*
29740 GTTTTCACACGAAAGGATATTGCCTCGGTTTTTTGTTTAAAATTATTTATGTATTTTTTTTTGAG
260 GTTTTCACACGAAAGGATATTGCCTCGGTTTTTTGTTTAAAATTATTTATGTA-TTTTTTCTGAG
29805 AAC
324 AAC
29808 TTGAAATTTCGAGCGAAGTTTAAAATACGATCCTTTGACACATAACTTATTTCGCATGATTTTCA
1 TTGAAATTTCGAGCGAAGTTTAAAATACGATCCTTTGACACATAACTTATTTCGCATGATTTTCA
*
29873 AAAATCAAATTTGAAGAAAAATGTCCGTGTGTTTCGAATTTCTCAAAGAATTGAAGTCGTGTCCA
66 AAAATCAAATTTGAAGAAAAATGTCCGTGTGTTTCGAATTTCTCAGAGAATTGAAGTCGTGTCCA
* *
29938 ACACG-TAGGGTACGACATTCTCGGAATTTCGAAATTGAAAGAAAATTTGAAAGGTTTTAAAAAA
131 ACACGTTAGGGCACGACATTCTCGGAATTTCGAAATTGAAAGAAAATTTGAAAGGTTTTAAAAAG
* *
30002 GATATTCGATCGCGTGAATTATACGAAAATCACACCTAGCATATTAGGGCATG-TTTTTTCGAAG
196 GATATTCGATCGCGTGAATTATACGAAAATCACACCCAGCATATTAGGACATGTTTTTTTCGAAG
30066 TTTTCACACGAAAGGATATTGCCTCGGTTTTTTGTTTAAAATTATTTATGTA-TTTTTCTGAGAA
261 TTTTCACACGAAAGGATATTGCCTCGGTTTTTTGTTTAAAATTATTTATGTATTTTTTCTGAGAA
30130 C
326 C
* *
30131 TTGAAATTTCGAGCTAAGTTTAAAATACGATCCTTGGACACATAACTTATTTCGCATGATTTTCA
1 TTGAAATTTCGAGCGAAGTTTAAAATACGATCCTTTGACACATAACTTATTTCGCATGATTTTCA
* * * *
30196 AAAATCAAATTTGAAGAAAAATGCCCGTGTGTTTCGAATTTCTCGGGGAATTGAGGTCGTGTCCA
66 AAAATCAAATTTGAAGAAAAATGTCCGTGTGTTTCGAATTTCTCAGAGAATTGAAGTCGTGTCCA
* * * * * * * *
30261 ACACGTTAGGGCACAACGTTCTCGGAATTTTGAAATTGAAGGACACTTTGAAAGGTTTTGAAGAG
131 ACACGTTAGGGCACGACATTCTCGGAATTTCGAAATTGAAAGAAAATTTGAAAGGTTTTAAAAAG
**
30326 GATATTCGATCGCGCAAATTATACGAAAAATCACAC
196 GATATTCGATCGCGTGAATTATACG-AAAATCACAC
30362 TCAACACGTT
Statistics
Matches: 511, Mismatches: 37, Indels: 11
0.91 0.07 0.02
Matches are distributed among these distances:
323 140 0.27
324 108 0.21
325 73 0.14
326 136 0.27
327 54 0.11
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (326 bp):
TTGAAATTTCGAGCGAAGTTTAAAATACGATCCTTTGACACATAACTTATTTCGCATGATTTTCA
AAAATCAAATTTGAAGAAAAATGTCCGTGTGTTTCGAATTTCTCAGAGAATTGAAGTCGTGTCCA
ACACGTTAGGGCACGACATTCTCGGAATTTCGAAATTGAAAGAAAATTTGAAAGGTTTTAAAAAG
GATATTCGATCGCGTGAATTATACGAAAATCACACCCAGCATATTAGGACATGTTTTTTTCGAAG
TTTTCACACGAAAGGATATTGCCTCGGTTTTTTGTTTAAAATTATTTATGTATTTTTTCTGAGAA
C
Found at i:30759 original size:30 final size:30
Alignment explanation
Indices: 30723--30918 Score: 209
Period size: 30 Copynumber: 6.6 Consensus size: 30
30713 GGTTAAAACA
** *
30723 TAATTTTAAAAAAGTTTAAGGGTAAAAATG
1 TAATTTTGGAAAAGTTTAAGGGTCAAAATG
* * * *
30753 TGATTTT-GAAGGAGTTT-GGGGTCAAAAAG
1 TAATTTTGGAA-AAGTTTAAGGGTCAAAATG
* * * *
30782 TGATTTTGGAAAGGTTTAGGGGTCAAAGTG
1 TAATTTTGGAAAAGTTTAAGGGTCAAAATG
*
30812 TAATTTTGGAAAAGTTTAAGGGTCAAAATA
1 TAATTTTGGAAAAGTTTAAGGGTCAAAATG
* *
30842 CAATTTTGGAAAA-TTTAAGGGTTAAAATG
1 TAATTTTGGAAAAGTTTAAGGGTCAAAATG
*
30871 TAATTTTGGAAAAGTTTGAGGGTCAAAATG
1 TAATTTTGGAAAAGTTTAAGGGTCAAAATG
* *
30901 TAATTTTAGAGAAGTTTA
1 TAATTTTGGAAAAGTTTA
30919 GAGATCAAAA
Statistics
Matches: 138, Mismatches: 24, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
29 48 0.35
30 90 0.65
ACGTcount: A:0.38, C:0.03, G:0.25, T:0.34
Consensus pattern (30 bp):
TAATTTTGGAAAAGTTTAAGGGTCAAAATG
Found at i:30788 original size:59 final size:59
Alignment explanation
Indices: 30723--30918 Score: 200
Period size: 59 Copynumber: 3.3 Consensus size: 59
30713 GGTTAAAACA
* * *
30723 TAATTTTAAAAAAGTTTAAGGGTAAAAATGTGATTTT-GAAGGAGTTTGGGGTCAAAAAG
1 TAATTTTAGAAAAGTTTAAGGGTAAAAATGTAATTTTGGAA-AAGTTTGGGGTCAAAAAG
* * * * * * *
30782 TGATTTTGGAAAGGTTTAGGGGTCAAAGTGTAATTTTGGAAAAGTTTAAGGGTCAAAATA-
1 TAATTTTAGAAAAGTTTAAGGGTAAAAATGTAATTTTGGAAAAGTTT-GGGGTCAAAA-AG
* * * *
30842 CAATTTTGGAAAA-TTTAAGGGTTAAAATGTAATTTTGGAAAAGTTTGAGGGTCAAAATG
1 TAATTTTAGAAAAGTTTAAGGGTAAAAATGTAATTTTGGAAAAGTTTG-GGGTCAAAAAG
*
30901 TAATTTTAGAGAAGTTTA
1 TAATTTTAGAAAAGTTTA
30919 GAGATCAAAA
Statistics
Matches: 110, Mismatches: 21, Indels: 11
0.77 0.15 0.08
Matches are distributed among these distances:
59 83 0.75
60 26 0.24
61 1 0.01
ACGTcount: A:0.38, C:0.03, G:0.25, T:0.34
Consensus pattern (59 bp):
TAATTTTAGAAAAGTTTAAGGGTAAAAATGTAATTTTGGAAAAGTTTGGGGTCAAAAAG
Found at i:30818 original size:89 final size:89
Alignment explanation
Indices: 30723--30918 Score: 218
Period size: 89 Copynumber: 2.2 Consensus size: 89
30713 GGTTAAAACA
* *** * * *
30723 TAATTTTAAAAAAGTTTAAGGGTAAAAATGTGATTTT-GAAGGAGTTT-GGGGTCAAAAAGTGAT
1 TAATTTTAGAAAAGTTTAAGGGTAAAAATACAATTTTGGAA--AATTTAAGGGTCAAAAAGTAAT
* *
30786 TTTGGAAAGGTTT-AGGGGTCAAAGTG
64 TTTGGAAAAGTTTGA-GGGTCAAAATG
* * * *
30812 TAATTTTGGAAAAGTTTAAGGGTCAAAATACAATTTTGGAAAATTTAAGGGTTAAAATGTAATTT
1 TAATTTTAGAAAAGTTTAAGGGTAAAAATACAATTTTGGAAAATTTAAGGGTCAAAAAGTAATTT
30877 TGGAAAAGTTTGAGGGTCAAAATG
66 TGGAAAAGTTTGAGGGTCAAAATG
*
30901 TAATTTTAGAGAAGTTTA
1 TAATTTTAGAAAAGTTTA
30919 GAGATCAAAA
Statistics
Matches: 89, Mismatches: 15, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
88 4 0.04
89 81 0.91
90 4 0.04
ACGTcount: A:0.38, C:0.03, G:0.25, T:0.34
Consensus pattern (89 bp):
TAATTTTAGAAAAGTTTAAGGGTAAAAATACAATTTTGGAAAATTTAAGGGTCAAAAAGTAATTT
TGGAAAAGTTTGAGGGTCAAAATG
Found at i:30927 original size:30 final size:30
Alignment explanation
Indices: 30804--30947 Score: 105
Period size: 30 Copynumber: 4.9 Consensus size: 30
30794 GGTTTAGGGG
* * * * *
30804 TCAAAGTGTAATTTTGGAAAAGTTTAAGGG
1 TCAAAATGTAATTTTAGAGAAGTTTGAGGA
** * * * *
30834 TCAAAATACAATTTTGGA-AAATTTAAGGG
1 TCAAAATGTAATTTTAGAGAAGTTTGAGGA
* * * *
30863 TTAAAATGTAATTTTGGAAAAGTTTGAGGG
1 TCAAAATGTAATTTTAGAGAAGTTTGAGGA
30893 TCAAAATGTAATTTTAGAGAAGTTT-AGAGA
1 TCAAAATGTAATTTTAGAGAAGTTTGAG-GA
* *
30923 TCAAAATTTGATTTTAG-GAAGTTTG
1 TCAAAATGTAATTTTAGAGAAGTTTG
30948 GTGGTTGCCT
Statistics
Matches: 96, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
29 34 0.35
30 62 0.65
ACGTcount: A:0.39, C:0.03, G:0.22, T:0.35
Consensus pattern (30 bp):
TCAAAATGTAATTTTAGAGAAGTTTGAGGA
Found at i:31066 original size:29 final size:29
Alignment explanation
Indices: 31017--31074 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
31007 TTGAGTGAGG
*
31017 GACTAAATTGTAAAAATTTAAAATTATTA
1 GACTAAATTGTAAAAATTTAAAAATATTA
31046 GACTAAATTGTAATAAA-TTAAAAATATTA
1 GACTAAATTGTAA-AAATTTAAAAATATTA
31075 CAAAAGGACT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 24 0.89
30 3 0.11
ACGTcount: A:0.53, C:0.03, G:0.07, T:0.36
Consensus pattern (29 bp):
GACTAAATTGTAAAAATTTAAAAATATTA
Found at i:31681 original size:2 final size:2
Alignment explanation
Indices: 31668--31719 Score: 81
Period size: 2 Copynumber: 27.0 Consensus size: 2
31658 AATCAAGATG
*
31668 TA TA TT TA TA TA TA TA TA -A T- 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
31708 TA TA TA TA TA TA
1 TA TA TA TA TA TA
31720 ATTATGTACA
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 2 0.04
2 44 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31802 original size:62 final size:62
Alignment explanation
Indices: 31736--31871 Score: 139
Period size: 62 Copynumber: 2.2 Consensus size: 62
31726 TACATGCATG
* ** * **
31736 TATATATATAAAAATCATAAGAAGGATGTATATCTATTTACATATATATGTA-TGTGTGCGTA
1 TATATATATAAAAAT-AAAAGAAAAATGTATATCTATGTACATATATACATACTGTGTGCGTA
* * * * *
31798 TATATAAAGTAAAAATAAAATAAAAATGTATATCTATGTATATATGTACATACGTGTGTGTGTA
1 TATATATA-TAAAAATAAAAGAAAAATGTATATCTATGTACATATATACATAC-TGTGTGCGTA
31862 TATATATATA
1 TATATATATA
31872 TGTATATATG
Statistics
Matches: 59, Mismatches: 12, Indels: 5
0.78 0.16 0.07
Matches are distributed among these distances:
62 34 0.58
63 9 0.15
64 16 0.27
ACGTcount: A:0.43, C:0.05, G:0.13, T:0.38
Consensus pattern (62 bp):
TATATATATAAAAATAAAAGAAAAATGTATATCTATGTACATATATACATACTGTGTGCGTA
Found at i:32772 original size:76 final size:76
Alignment explanation
Indices: 32640--32797 Score: 226
Period size: 76 Copynumber: 2.1 Consensus size: 76
32630 GCTTCGACCC
* * *
32640 ACTTCTCTATATCTCATCAGGAAAAAGGGGTTTGAAAGTTTCACTCATATTTAGCTTCGCTTCAT
1 ACTTCTCTATATCTCATCAGGAAAAAGGGGTTTGAAAGTTTCACTCACATTGAGCTTCACTTCAT
32705 TGAATTAGTCT
66 TGAATTAGTCT
* * * * *
32716 ACTTTTCTATATCTCATCAGGAAGATGGGGTTTGGAAGTTTCACTCACATTGAGCTTTACTTCAT
1 ACTTCTCTATATCTCATCAGGAAAAAGGGGTTTGAAAGTTTCACTCACATTGAGCTTCACTTCAT
*
32781 TGAATTGGTCT
66 TGAATTAGTCT
*
32792 ATTTCT
1 ACTTCT
32798 TTGTATTTCA
Statistics
Matches: 71, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
76 71 1.00
ACGTcount: A:0.25, C:0.18, G:0.17, T:0.40
Consensus pattern (76 bp):
ACTTCTCTATATCTCATCAGGAAAAAGGGGTTTGAAAGTTTCACTCACATTGAGCTTCACTTCAT
TGAATTAGTCT
Found at i:32815 original size:76 final size:76
Alignment explanation
Indices: 32640--32836 Score: 209
Period size: 76 Copynumber: 2.6 Consensus size: 76
32630 GCTTCGACCC
* * * * * * *
32640 ACTTCTCTATATCTCATCAGGAAAAAGGGGTTTGAAAGTTTCACTCATATTTAGCTTCGCTTCAT
1 ACTTTTCTATATCTCACCAGGAAGATGGGGTTTGAAAGTTTCACTCACATTGAGCTTCACTTCAT
32705 TGAATTAGTCT
66 TGAATTAGTCT
* * *
32716 ACTTTTCTATATCTCATCAGGAAGATGGGGTTTGGAAGTTTCACTCACATTGAGCTTTACTTCAT
1 ACTTTTCTATATCTCACCAGGAAGATGGGGTTTGAAAGTTTCACTCACATTGAGCTTCACTTCAT
*
32781 TGAATTGGTCT
66 TGAATTAGTCT
* * * * * * *
32792 A-TTTCTTTGTATTTCACCGGGAAGATGAGATTTGAAA-TTCCACTC
1 ACTTT-TCTATATCTCACCAGGAAGATGGGGTTTGAAAGTTTCACTC
32837 CACTCTGCTG
Statistics
Matches: 102, Mismatches: 18, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
75 10 0.10
76 92 0.90
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.39
Consensus pattern (76 bp):
ACTTTTCTATATCTCACCAGGAAGATGGGGTTTGAAAGTTTCACTCACATTGAGCTTCACTTCAT
TGAATTAGTCT
Found at i:33305 original size:155 final size:156
Alignment explanation
Indices: 33016--33381 Score: 491
Period size: 155 Copynumber: 2.4 Consensus size: 156
33006 CCTATTGCGA
* * * * *
33016 GGTAAGAGATTGGCTGACGGTGATCTGCCCCATGATCGGGGTAAAAGATCGAATGGTTACAATCT
1 GGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTACAATCT
* ** *
33081 GCCCTAGGCTCAAGATAAGAGATTGGCTGATGGTGATTTGCCTTACGCTCAGGGTAAAAGATCGA
66 GCCCTAGGCTCAAGATAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCAGGGTAAAAGATCGA
33146 ATGGCTGCAATCTACCCCAAGCACGG
131 ATGGCTGCAATCTACCCCAAGCACGG
* * * *
33172 GGTAAGAGATTGGCTGATGGTGATCTGCTCCAAGCTCGGCGTAAGAGATCGGATGGCTGCAATCT
1 GGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTACAATCT
* * ** * *
33237 GCCC-AGGCTCAAGGTAAGAGATTGGTTGATGGTGATCTGCCCCAAGCTTGGGGTAAAAGATTGG
66 GCCCTAGGCTCAAGATAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCAGGGTAAAAGATCGA
* *** *
33301 ATGGCTTCAATCTGTTCCAAGCTCGG
131 ATGGCTGCAATCTACCCCAAGCACGG
* *
33327 GGCAAGAGATTGGCTGATGGTGATCTACCCCAAGCTCGGGGTAAAAGATCGGATG
1 GGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATCGGATG
33382 ATTGTGATCT
Statistics
Matches: 181, Mismatches: 29, Indels: 1
0.86 0.14 0.00
Matches are distributed among these distances:
155 121 0.67
156 60 0.33
ACGTcount: A:0.26, C:0.20, G:0.31, T:0.23
Consensus pattern (156 bp):
GGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTACAATCT
GCCCTAGGCTCAAGATAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCAGGGTAAAAGATCGA
ATGGCTGCAATCTACCCCAAGCACGG
Found at i:33381 original size:78 final size:77
Alignment explanation
Indices: 33015--33414 Score: 431
Period size: 78 Copynumber: 5.1 Consensus size: 77
33005 CCCTATTGCG
* * * * * *
33015 AGGTAAGAGATTGGCTGACGGTGATCTGCCCCATGATCGGGGTAAAAGATCGAATGGTTACAATC
1 AGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTGCAATC
*
33080 TGCCCTAGGCTCA
66 TGCCC-AAGCTCA
* * ** * * *
33093 AGATAAGAGATTGGCTGATGGTGATTTGCCTTACGCTCAGGGTAAAAGATCGAATGGCTGCAATC
1 AGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTGCAATC
* * *
33158 TACCCCAAGCACG
66 T-GCCCAAGCTCA
* * * *
33171 GGGTAAGAGATTGGCTGATGGTGATCTGCTCCAAGCTCGGCGTAAGAGATCGGATGGCTGCAATC
1 AGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTGCAATC
*
33236 TGCCCAGGCTCA
66 TGCCCAAGCTCA
* * * *
33248 AGGTAAGAGATTGGTTGATGGTGATCTGCCCCAAGCTTGGGGTAAAAGATTGGATGGCTTCAATC
1 AGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTGCAATC
* *
33313 TGTTCCAAGCTCG
66 TG-CCCAAGCTCA
* * * ** **
33326 GGGCAAGAGATTGGCTGATGGTGATCTACCCCAAGCTCGGGGTAAAAGATCGGATGATTGTGATC
1 AGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTGCAATC
*
33391 TGCCTCAAGATCA
66 TGCC-CAAGCTCA
*
33404 GGGTAAGAGAT
1 AGGTAAGAGAT
33415 CGGATGGCTA
Statistics
Matches: 264, Mismatches: 55, Indels: 6
0.81 0.17 0.02
Matches are distributed among these distances:
77 67 0.25
78 194 0.73
79 3 0.01
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (77 bp):
AGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTGCAATC
TGCCCAAGCTCA
Found at i:33420 original size:117 final size:117
Alignment explanation
Indices: 33249--33573 Score: 400
Period size: 117 Copynumber: 2.8 Consensus size: 117
33239 CCAGGCTCAA
* * * * *
33249 GGTAAGAGATTGGTTGATGGTGATCTGCCCCAAGCTTGGGGTAAAAGATTGGATGGCTTCAATCT
1 GGTAAAAGATCGGATGATTGTGATCTGCCCCAAGCTTGGGGTAAAAGATCGGATGGCTTCAATCT
* * *
33314 GTTCCAAGCTCGGGGCAAGAGATTGGCTGATGGTGATCTACCCCAAGCTCGG
66 GTCCCAAGCTCGGGGTAAGAGATTGGCTGATGATGATCTACCCCAAGCTCGG
* * ** * *
33366 GGTAAAAGATCGGATGATTGTGATCTGCCTCAAGATCAGGGTAAGAGATCGGATGGCTACAATCT
1 GGTAAAAGATCGGATGATTGTGATCTGCCCCAAGCTTGGGGTAAAAGATCGGATGGCTTCAATCT
* * * * *
33431 ATCCCAAGCTCAGGGTAAGAGATTGGCTGATGATGATCTGCCTCAAGCTTGG
66 GTCCCAAGCTCGGGGTAAGAGATTGGCTGATGATGATCTACCCCAAGCTCGG
* ** * * *
33483 GGTAAAAGATCGGATGGCTT-CAATCTGCCCCAGGCTTGGGGTAAAAGATCGGATGACTTCAATT
1 GGTAAAAGATCGGAT-GATTGTGATCTGCCCCAAGCTTGGGGTAAAAGATCGGATGGCTTCAATC
*
33547 TGCCCCAAGCTCGGGGTAAGAGATTGG
65 TGTCCCAAGCTCGGGGTAAGAGATTGG
33574 AATCTTCAAT
Statistics
Matches: 173, Mismatches: 34, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
117 170 0.98
118 3 0.02
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.25
Consensus pattern (117 bp):
GGTAAAAGATCGGATGATTGTGATCTGCCCCAAGCTTGGGGTAAAAGATCGGATGGCTTCAATCT
GTCCCAAGCTCGGGGTAAGAGATTGGCTGATGATGATCTACCCCAAGCTCGG
Found at i:33509 original size:39 final size:39
Alignment explanation
Indices: 33127--33570 Score: 239
Period size: 39 Copynumber: 11.4 Consensus size: 39
33117 TTTGCCTTAC
* * * *
33127 GCTCAGGGTAAAAGATCGAATGGCTGCAATCTACCCCAA
1 GCTCGGGGTAAAAGATCGGATGGCTTCAATCTGCCCCAA
* * * * *
33166 GCACGGGGTAAGAGATTGGCTGATGG--T-GATCTGCTCCAA
1 GCTCGGGGTAAAAGA-T--CGGATGGCTTCAATCTGCCCCAA
* * * *
33205 GCTCGGCGTAAGAGATCGGATGGCTGCAATCTG-CCCAG
1 GCTCGGGGTAAAAGATCGGATGGCTTCAATCTGCCCCAA
** * * *
33243 GCTCAAGGTAAGAGATTGGTTGATGG--T-GATCTGCCCCAA
1 GCTCGGGGTAAAAGA-TCG--GATGGCTTCAATCTGCCCCAA
* * **
33282 GCTTGGGGTAAAAGATTGGATGGCTTCAATCTGTTCCAA
1 GCTCGGGGTAAAAGATCGGATGGCTTCAATCTGCCCCAA
* * * * *
33321 GCTCGGGGCAAGAGATTGGCTGATGG--T-GATCTACCCCAA
1 GCTCGGGGTAAAAGA-T--CGGATGGCTTCAATCTGCCCCAA
* ** *
33360 GCTCGGGGTAAAAGATCGGAT-GATTGTGATCTGCCTCAA
1 GCTCGGGGTAAAAGATCGGATGGCTT-CAATCTGCCCCAA
* * * * **
33399 GATCAGGGTAAGAGATCGGATGGCTACAATCTATCCCAA
1 GCTCGGGGTAAAAGATCGGATGGCTTCAATCTGCCCCAA
* * * * * * *
33438 GCTCAGGGTAAGAGATTGGCTGATG-AT-GATCTGCCTCAA
1 GCTCGGGGTAAAAGATCGGATG--GCTTCAATCTGCCCCAA
* *
33477 GCTTGGGGTAAAAGATCGGATGGCTTCAATCTGCCCCAG
1 GCTCGGGGTAAAAGATCGGATGGCTTCAATCTGCCCCAA
* * *
33516 GCTTGGGGTAAAAGATCGGATGACTTCAATTTGCCCCAA
1 GCTCGGGGTAAAAGATCGGATGGCTTCAATCTGCCCCAA
*
33555 GCTCGGGGTAAGAGAT
1 GCTCGGGGTAAAAGAT
33571 TGGAATCTTC
Statistics
Matches: 302, Mismatches: 78, Indels: 50
0.70 0.18 0.12
Matches are distributed among these distances:
35 1 0.00
36 15 0.05
37 2 0.01
38 26 0.09
39 237 0.78
40 5 0.02
41 6 0.02
42 10 0.03
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.23
Consensus pattern (39 bp):
GCTCGGGGTAAAAGATCGGATGGCTTCAATCTGCCCCAA
Found at i:41340 original size:50 final size:51
Alignment explanation
Indices: 41285--41386 Score: 188
Period size: 50 Copynumber: 2.0 Consensus size: 51
41275 AAGACCCGGA
41285 AATAATCAACTTTTGGCTTGACTCTCTTTTA-TTTTTAAAGTCCCCAGTGG
1 AATAATCAACTTTTGGCTTGACTCTCTTTTATTTTTTAAAGTCCCCAGTGG
*
41335 AATAATCAACTTTTGGCTTGACTCTCTTTTATTTTTTAAAGTTCCCAGTGG
1 AATAATCAACTTTTGGCTTGACTCTCTTTTATTTTTTAAAGTCCCCAGTGG
41386 A
1 A
41387 GTCGTCAAGC
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
50 31 0.62
51 19 0.38
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.43
Consensus pattern (51 bp):
AATAATCAACTTTTGGCTTGACTCTCTTTTATTTTTTAAAGTCCCCAGTGG
Found at i:42366 original size:323 final size:324
Alignment explanation
Indices: 41655--42531 Score: 1340
Period size: 323 Copynumber: 2.7 Consensus size: 324
41645 TGTTAAAACT
* * **
41655 TTGAAATCTT-GAGCGAAGTTTAAAATATGATCTTTTTACACATAACTTATTTCGCATGATTTTC
1 TTGAAAT-TTCGAGCGAAGTTTAAAATACGATCCTTGGACACATAACTTATTTCGCATGATTTTC
*
41719 AAAAATCAAATTTGAAG-AAAATGCCCGTGTGTTTCGAATTTCTTAGAGAATTGAAGTCGTGTCC
65 AAAAATCAAATTTGAAGAAAAATGCTCGTGTGTTTCGAATTTCTTAGAGAATTGAAGTCGTGTCC
*
41783 AACACGTTAGGGCACGACATTCTCGGAATTTCGAAATTGAAAGAAATTTTGAAAGGTTTTAAAAA
130 AATACGTTAGGGCACGACATTCTC-GAATTTCGAAATTGAAAGAAATTTTGAAAGGTTTTAAAAA
*
41848 AGATATTCGATCACGTGAATTATACGAAAATCACACCTAACATGTTAGGGCATGTTTTTTCGAAG
194 GGATATTCGATCACGTGAATTATACGAAAATCACACCTAACATGTTAGGGCATGTTTTTTCGAAG
* *
41913 TTTTCACACGAAAGGATATTGCCTCGGTTTTTTTGTTTAAAATTATTTATGTATTTTTTTGAGAA
259 TTTTCACAAGAAAGAATATTGCCTCGGTTTTTTTGTTTAAAATTATTTATGTATTTTTTTGAGAA
41978 C
324 C
* * * *
41979 TTGAAATTTCGAGCAAAGTTTAAAATACGATCCTTGGACAC--AACTTATTGCACATTATTTTCA
1 TTGAAATTTCGAGCGAAGTTTAAAATACGATCCTTGGACACATAACTTATTTCGCATGATTTTCA
* *
42042 AAAATCAAATTTGAAGAAAAATGCTCGTGTATTTCGAATTTCTTAGAGAATTGAAGTTGTGTCCA
66 AAAATCAAATTTGAAGAAAAATGCTCGTGTGTTTCGAATTTCTTAGAGAATTGAAGTCGTGTCCA
42107 ATACGTTAGGGCACGACATTCTCAGAATTTCGAAATTGAAAGAAATTTTGAAAGGTTTTAAAAAG
131 ATACGTTAGGGCACGACATTCTC-GAATTTCGAAATTGAAAGAAATTTTGAAAGGTTTTAAAAAG
* * *
42172 GATATTCGATCACGTGAATTACACGAAAATCACATCC-AGCATGTTAGGGCATGTTTTTTTGAAG
195 GATATTCGATCACGTGAATTATACGAAAATCACA-CCTAACATGTTAGGGCATGTTTTTTCGAAG
*
42236 TTTTCACAAGAAAGAATATTGCCTTGG-TTTTTTGTTTAAAATTATTTATGTA-TTTTTTGAGAA
259 TTTTCACAAGAAAGAATATTGCCTCGGTTTTTTTGTTTAAAATTATTTATGTATTTTTTTGAGAA
42299 C
324 C
* * *
42300 TTGAAATTTCGAGCGAAGTTTAAAATACGATCCTTGGACACATAATTTATTTCGTATGACTTTCA
1 TTGAAATTTCGAGCGAAGTTTAAAATACGATCCTTGGACACATAACTTATTTCGCATGATTTTCA
42365 AAAATCAAATTTGAAGAAAAATGCTCGTGTGTTTCGAATTTCTTAGAGAATTG-AGATCGTGTCC
66 AAAATCAAATTTGAAGAAAAATGCTCGTGTGTTTCGAATTTCTTAGAGAATTGAAG-TCGTGTCC
* * * * * * *
42429 AATACGTTAGGGCACGACGTTCTCGAAATTTTGAAATTGAAGGACACTTTGAAAGGTTTTGAAGA
130 AATACGTTAGGGCACGACATTCTCG-AATTTCGAAATTGAAAGAAATTTTGAAAGGTTTTAAAAA
* *
42494 GGATATTCAAT-AGCGCGAATTATACGAAAAATCACACC
194 GGATATTCGATCA-CGTGAATTATACG-AAAATCACACC
42532 CTGCACGTTT
Statistics
Matches: 505, Mismatches: 39, Indels: 19
0.90 0.07 0.03
Matches are distributed among these distances:
321 52 0.10
322 64 0.13
323 345 0.68
324 44 0.09
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.35
Consensus pattern (324 bp):
TTGAAATTTCGAGCGAAGTTTAAAATACGATCCTTGGACACATAACTTATTTCGCATGATTTTCA
AAAATCAAATTTGAAGAAAAATGCTCGTGTGTTTCGAATTTCTTAGAGAATTGAAGTCGTGTCCA
ATACGTTAGGGCACGACATTCTCGAATTTCGAAATTGAAAGAAATTTTGAAAGGTTTTAAAAAGG
ATATTCGATCACGTGAATTATACGAAAATCACACCTAACATGTTAGGGCATGTTTTTTCGAAGTT
TTCACAAGAAAGAATATTGCCTCGGTTTTTTTGTTTAAAATTATTTATGTATTTTTTTGAGAAC
Found at i:42973 original size:30 final size:30
Alignment explanation
Indices: 42939--43110 Score: 188
Period size: 30 Copynumber: 5.8 Consensus size: 30
42929 GAGTTTGTGA
* *
42939 TCAAAATGTGATTTTGGAAAGGTTTAAGGG
1 TCAAAATGTAATTTTGGAAAAGTTTAAGGG
* *
42969 TCAAAGTGAAATTTTGGAAAAGTTTAAGGG
1 TCAAAATGTAATTTTGGAAAAGTTTAAGGG
* * *
42999 TCAAAATGTAATTTTAGAAAATTTTAGGGG
1 TCAAAATGTAATTTTGGAAAAGTTTAAGGG
* *
43029 TTAAAATGTAATTTTGAAAAAG-TT-AGGG
1 TCAAAATGTAATTTTGGAAAAGTTTAAGGG
* *
43057 TCAAAATGTAATTTT-AAAGAAGTTTAGGGG
1 TCAAAATGTAATTTTGGAA-AAGTTTAAGGG
* * *
43087 TCAAAATATGATTTTAGAAAAGTT
1 TCAAAATGTAATTTTGGAAAAGTT
43111 CAGTGGTTGC
Statistics
Matches: 119, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
27 3 0.03
28 20 0.17
29 4 0.03
30 90 0.76
31 2 0.02
ACGTcount: A:0.40, C:0.03, G:0.23, T:0.34
Consensus pattern (30 bp):
TCAAAATGTAATTTTGGAAAAGTTTAAGGG
Found at i:43108 original size:58 final size:58
Alignment explanation
Indices: 42939--43110 Score: 188
Period size: 58 Copynumber: 2.9 Consensus size: 58
42929 GAGTTTGTGA
* * * * *
42939 TCAAAATGTGATTTTGGAAAGGTTTAAGGGTCAAAGTGA-AATTTTGGAAAAGTTTAAGGG
1 TCAAAATGTAATTTTAGAAAAGTTTAGGGGTCAAAAT-ATAATTTT-GAAAAG-TTAAGGG
* * *
42999 TCAAAATGTAATTTTAGAAAATTTTAGGGGTTAAAATGTAATTTTGAAAAAGTT-AGGG
1 TCAAAATGTAATTTTAGAAAAGTTTAGGGGTCAAAATATAATTTTG-AAAAGTTAAGGG
*
43057 TCAAAATGTAATTTTA-AAGAAGTTTAGGGGTCAAAATATGATTTTAGAAAAGTT
1 TCAAAATGTAATTTTAGAA-AAGTTTAGGGGTCAAAATATAATTTT-GAAAAGTT
43111 CAGTGGTTGC
Statistics
Matches: 96, Mismatches: 12, Indels: 10
0.81 0.10 0.08
Matches are distributed among these distances:
57 2 0.02
58 49 0.51
59 4 0.04
60 41 0.43
ACGTcount: A:0.40, C:0.03, G:0.23, T:0.34
Consensus pattern (58 bp):
TCAAAATGTAATTTTAGAAAAGTTTAGGGGTCAAAATATAATTTTGAAAAGTTAAGGG
Found at i:43763 original size:12 final size:12
Alignment explanation
Indices: 43748--43773 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
43738 ATCTATTTAC
43748 ATATATATATGT
1 ATATATATATGT
43760 ATATATATATGT
1 ATATATATATGT
43772 AT
1 AT
43774 GTGCGCATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (12 bp):
ATATATATATGT
Found at i:43782 original size:76 final size:77
Alignment explanation
Indices: 43702--43847 Score: 199
Period size: 76 Copynumber: 1.9 Consensus size: 77
43692 ATATATACAT
* * * *
43702 GCATGTATATATA-TAAAAATCATAAA-AAAGATGTATATCTATTTACATA-TATATATGTATAT
1 GCATGTATATAAAGTAAAAAT-A-AAATAAAAATGTATATCTATTTACATAGTACATACGTATAT
43764 ATATATGTATGTGC
64 ATATATGTATGTGC
*
43778 GCATGTATATAAAGTAAAAATAAAATAAAAATGTATATCTATTTATATATGTACATACGTATATA
1 GCATGTATATAAAGTAAAAATAAAATAAAAATGTATATCTATTTACATA-GTACATACGTATATA
43843 TATAT
65 TATAT
43848 ATATAATAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
75 3 0.05
76 34 0.56
77 7 0.11
78 17 0.28
ACGTcount: A:0.46, C:0.06, G:0.10, T:0.38
Consensus pattern (77 bp):
GCATGTATATAAAGTAAAAATAAAATAAAAATGTATATCTATTTACATAGTACATACGTATATAT
ATATGTATGTGC
Found at i:44548 original size:62 final size:62
Alignment explanation
Indices: 44432--44548 Score: 139
Period size: 61 Copynumber: 1.9 Consensus size: 62
44422 TAGTATAATA
* * * * *
44432 ACAAATTTAGCTCTCGAATGTTTACAGATTCTGTCAATTAGTCTTAATTCTAAAAAAATTCT
1 ACAAATTTAGCTCTCGAATCTTCACAAATTCTATCAATTAGGCTTAATTCTAAAAAAATTCT
* * *
44494 ACAAATTTAGCTCTC-AA-CTTCATAAATTCTATCAATTTAGGCTTGATTCTTAAAA
1 ACAAATTTAGCTCTCGAATCTTCACAAATTCTATCAA-TTAGGCTTAATTCTAAAAA
44549 TTTTAACGTT
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
60 13 0.28
61 18 0.39
62 15 0.33
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (62 bp):
ACAAATTTAGCTCTCGAATCTTCACAAATTCTATCAATTAGGCTTAATTCTAAAAAAATTCT
Found at i:47838 original size:31 final size:30
Alignment explanation
Indices: 47792--47873 Score: 114
Period size: 30 Copynumber: 2.7 Consensus size: 30
47782 AATTAAAAAT
47792 AAAAATAA-TTTAATAATTTTATTATT-TCAA
1 AAAAATAATTTTAATAATTTTA-TATTCT-AA
*
47822 AAAAATAATTTTAATAATTTTATATTCTTA
1 AAAAATAATTTTAATAATTTTATATTCTAA
*
47852 AAATATAATTTTAATAATTTTA
1 AAAAATAATTTTAATAATTTTA
47874 AAATCATTTG
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
30 34 0.71
31 14 0.29
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (30 bp):
AAAAATAATTTTAATAATTTTATATTCTAA
Found at i:47859 original size:21 final size:22
Alignment explanation
Indices: 47835--47877 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
47825 AATAATTTTA
47835 ATAATTTT-AT-ATTCTTAAAAT
1 ATAATTTTAATAATT-TTAAAAT
47856 ATAATTTTAATAATTTTAAAAT
1 ATAATTTTAATAATTTTAAAAT
47878 CATTTGCTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 8 0.40
22 9 0.45
23 3 0.15
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (22 bp):
ATAATTTTAATAATTTTAAAAT
Found at i:51606 original size:3 final size:3
Alignment explanation
Indices: 51598--51625 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
51588 AGGAGATACA
51598 CAT CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT C
51626 TCCTTGTAAT
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:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:52988 original size:15 final size:17
Alignment explanation
Indices: 52968--53007 Score: 57
Period size: 15 Copynumber: 2.5 Consensus size: 17
52958 AAATTTTTAA
52968 AAATTATAAAAAT-AT-
1 AAATTATAAAAATAATG
*
52983 AAATTATTAAAATAATG
1 AAATTATAAAAATAATG
53000 AAATTATA
1 AAATTATA
53008 TTTTACGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 12 0.57
16 2 0.10
17 7 0.33
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (17 bp):
AAATTATAAAAATAATG
Found at i:54866 original size:16 final size:16
Alignment explanation
Indices: 54845--54875 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
54835 TATATACTTA
54845 ATATTATTAAATAATG
1 ATATTATTAAATAATG
*
54861 ATATTATTATATAAT
1 ATATTATTAAATAAT
54876 CATTTTTCTT
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:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (16 bp):
ATATTATTAAATAATG
Found at i:56587 original size:25 final size:26
Alignment explanation
Indices: 56532--56589 Score: 93
Period size: 25 Copynumber: 2.3 Consensus size: 26
56522 TTTATCTCAC
*
56532 TAAAATTTTGACGATTTTACACCCAG
1 TAAAATTTTGACGATTTTACACCAAG
56558 T-AAATTTTGACGATTTTAC-CCAAG
1 TAAAATTTTGACGATTTTACACCAAG
56582 TAAAATTT
1 TAAAATTT
56590 CAATAAAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 5 0.17
25 24 0.80
26 1 0.03
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (26 bp):
TAAAATTTTGACGATTTTACACCAAG
Found at i:58287 original size:19 final size:20
Alignment explanation
Indices: 58255--58292 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
58245 ATTTGAGTGT
58255 ACTTTATATAATTGCAATAA
1 ACTTTATATAATTGCAATAA
*
58275 ACTTTAT-TAATTGTAATA
1 ACTTTATATAATTGCAATA
58293 TTAAATATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.45
Consensus pattern (20 bp):
ACTTTATATAATTGCAATAA
Found at i:59299 original size:3 final size:3
Alignment explanation
Indices: 59291--59318 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
59281 GTGATTTTAT
59291 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
59319 AAAAATGAAA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:60100 original size:3 final size:3
Alignment explanation
Indices: 60092--60121 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
60082 CATCTCCATG
60092 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
60122 TAAGATAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:66962 original size:32 final size:33
Alignment explanation
Indices: 66925--67001 Score: 104
Period size: 33 Copynumber: 2.4 Consensus size: 33
66915 GATAGCATAT
* *
66925 AATATAATATT-GATGTAT-TTTATTTGGGTTTC
1 AATATAAT-TTAGATATATATTTAGTTGGGTTTC
*
66957 AATATAATTTAGATATCTATTTAGTTGGGTTTC
1 AATATAATTTAGATATATATTTAGTTGGGTTTC
66990 AATATAATTTAG
1 AATATAATTTAG
67002 CTCTAATAAC
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
31 2 0.05
32 13 0.32
33 25 0.62
ACGTcount: A:0.32, C:0.04, G:0.14, T:0.49
Consensus pattern (33 bp):
AATATAATTTAGATATATATTTAGTTGGGTTTC
Found at i:76160 original size:121 final size:121
Alignment explanation
Indices: 76033--76269 Score: 413
Period size: 121 Copynumber: 2.0 Consensus size: 121
76023 TGGAAGGTAT
*
76033 ACTATGCAAATTTAAATTTAAAATATTTTAAAGGTAAATTGGTAAAATATATATTATTAAGGGTA
1 ACTATGCAAATTTAAATTTAAAAGATTTTAAAGGTAAATTGGTAAAATATATATTATTAAGGGTA
* * *
76098 T-AAAAAAGGAAATTAAAAAGATTTAAAGGATGTGAGCTAAGAAGGGAAACCGCGTG
66 TAAAAAAAGGAAATT-AAAAGATTTAAAAGATATGAGCTAAGAAGAGAAACCGCGTG
*
76154 ACTATGCAATTTTAAATTTAAAAGATTTTAAAGGTAAATTGGTAAAATATATATTATTAAGGGTA
1 ACTATGCAAATTTAAATTTAAAAGATTTTAAAGGTAAATTGGTAAAATATATATTATTAAGGGTA
76219 TAAAAAAAGGAAATTAAAAGATTTAAAAGATATGAGCTAAGAAGAGAAACC
66 TAAAAAAAGGAAATTAAAAGATTTAAAAGATATGAGCTAAGAAGAGAAACC
76270 ATGTGTGTTT
Statistics
Matches: 110, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
121 97 0.88
122 13 0.12
ACGTcount: A:0.49, C:0.05, G:0.17, T:0.29
Consensus pattern (121 bp):
ACTATGCAAATTTAAATTTAAAAGATTTTAAAGGTAAATTGGTAAAATATATATTATTAAGGGTA
TAAAAAAAGGAAATTAAAAGATTTAAAAGATATGAGCTAAGAAGAGAAACCGCGTG
Found at i:78376 original size:32 final size:33
Alignment explanation
Indices: 78319--78381 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
78309 ACTTTCTAAA
* *
78319 ATTATGATAAAATATTATATTATTTATAAAAAT
1 ATTATGATAAAATATTAGATAATTTATAAAAAT
*
78352 ATTATGA-AAATTATTAGATAATTTATAAAA
1 ATTATGATAAAATATTAGATAATTTATAAAA
78382 CTTTTTTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 20 0.74
33 7 0.26
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (33 bp):
ATTATGATAAAATATTAGATAATTTATAAAAAT
Found at i:79479 original size:2 final size:2
Alignment explanation
Indices: 79467--79534 Score: 118
Period size: 2 Copynumber: 33.0 Consensus size: 2
79457 ATGATGCCAA
79467 AT AT GAT AT AT AT CAT 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
79511 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
79535 CATAATCTC
Statistics
Matches: 64, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
2 60 0.94
3 4 0.06
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (2 bp):
AT
Done.