Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011691.1 Kokia drynarioides strain JFW-HI SEQ_126685, 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: 126793
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 65 characters in sequence are not A, C, G, or T
Found at i:999 original size:23 final size:23
Alignment explanation
Indices: 900--984 Score: 125
Period size: 23 Copynumber: 3.7 Consensus size: 23
890 ACGCAAGTAC
*
900 GCTTACTGTTTCTCACTTCGTGT
1 GCTTACTGTTTCGCACTTCGTGT
*
923 GCTTACTGTTTTGCACTTCGTGT
1 GCTTACTGTTTCGCACTTCGTGT
* * *
946 GCTTACTGTTTCGTACTTTGTAT
1 GCTTACTGTTTCGCACTTCGTGT
969 GCTTACTGTTTCGCAC
1 GCTTACTGTTTCGCAC
985 CTTGTGTCCC
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 55 1.00
ACGTcount: A:0.11, C:0.24, G:0.19, T:0.47
Consensus pattern (23 bp):
GCTTACTGTTTCGCACTTCGTGT
Found at i:999 original size:46 final size:46
Alignment explanation
Indices: 903--999 Score: 117
Period size: 46 Copynumber: 2.1 Consensus size: 46
893 CAAGTACGCT
* * * *
903 TACTGTTTCTCACTTCGTGTGCTTACTGTTTTGCACTTCGTGTGCT
1 TACTGTTTCTCACTTCGTATGCTTACTGTTTCGCACTTCGTGTCCC
*
949 TACTGTTTCGT-ACTTTGTATGCTTACTGTTTCGCACCTT-GTGTCCC
1 TACTGTTTC-TCACTTCGTATGCTTACTGTTTCGCA-CTTCGTGTCCC
995 TACTG
1 TACTG
1000 ATTTGCGCTA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
46 40 0.91
47 4 0.09
ACGTcount: A:0.10, C:0.25, G:0.19, T:0.46
Consensus pattern (46 bp):
TACTGTTTCTCACTTCGTATGCTTACTGTTTCGCACTTCGTGTCCC
Found at i:1022 original size:69 final size:68
Alignment explanation
Indices: 900--1030 Score: 149
Period size: 69 Copynumber: 1.9 Consensus size: 68
890 ACGCAAGTAC
* * * * * * *
900 GCTTACTGTTTCTCACTTCGTGTGCTTACTGTTTTGCACTTCGTGTGCTTACTGTTTCGTACTTT
1 GCTTACTGTTTCGCACTTCGTGTCCCTACTGATTTGCACTTCGTGCGCCTACTGATT-GTACTTT
965 GTAT
65 GTAT
*
969 GCTTACTGTTTCGCACCTT-GTGTCCCTACTGATTTGCGCTAT-GTGCGCCTACTGATTGTACT
1 GCTTACTGTTTCGCA-CTTCGTGTCCCTACTGATTTGCACT-TCGTGCGCCTACTGATTGTACT
1031 GTGTGTGCCT
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
68 5 0.10
69 43 0.83
70 4 0.08
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.44
Consensus pattern (68 bp):
GCTTACTGTTTCGCACTTCGTGTCCCTACTGATTTGCACTTCGTGCGCCTACTGATTGTACTTTG
TAT
Found at i:1054 original size:23 final size:22
Alignment explanation
Indices: 987--1067 Score: 90
Period size: 23 Copynumber: 3.6 Consensus size: 22
977 TTTCGCACCT
* * *
987 TGTGTCCCTACTGATTTGCGCTA
1 TGTGTGCCTACTGA-TTGCACTG
* *
1010 TGTGCGCCTACTGATTGTACTG
1 TGTGTGCCTACTGATTGCACTG
1032 TGTGTGCCTACTAGATTGCACTG
1 TGTGTGCCTACT-GATTGCACTG
*
1055 TGTGTGCTTACTG
1 TGTGTGCCTACTG
1068 TTTCCCTAGC
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
22 17 0.35
23 32 0.65
ACGTcount: A:0.14, C:0.22, G:0.26, T:0.38
Consensus pattern (22 bp):
TGTGTGCCTACTGATTGCACTG
Found at i:14770 original size:28 final size:28
Alignment explanation
Indices: 14737--14798 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
14727 ATCGCTCTGA
* *
14737 TAGAGCGATACTCTGCTTACAGCTCGAG
1 TAGAGCGATAATCTACTTACAGCTCGAG
** * *
14765 TAGAGCTTTAATCTATTTACAGCTCGGG
1 TAGAGCGATAATCTACTTACAGCTCGAG
14793 TAGAGC
1 TAGAGC
14799 TTTGACCTAT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (28 bp):
TAGAGCGATAATCTACTTACAGCTCGAG
Found at i:14830 original size:28 final size:28
Alignment explanation
Indices: 14753--14830 Score: 111
Period size: 28 Copynumber: 2.8 Consensus size: 28
14743 GATACTCTGC
* * *
14753 TTACAGCTCGAGTAGAGCTTTAATCTAT
1 TTACAGCTCGGGTAGAGCTTTGACCTAT
14781 TTACAGCTCGGGTAGAGCTTTGACCTAT
1 TTACAGCTCGGGTAGAGCTTTGACCTAT
* *
14809 TTATAGCTCGGGTAAAGCTTTG
1 TTACAGCTCGGGTAGAGCTTTG
14831 GTCTGCTTAC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (28 bp):
TTACAGCTCGGGTAGAGCTTTGACCTAT
Found at i:26731 original size:136 final size:137
Alignment explanation
Indices: 26212--26895 Score: 907
Period size: 138 Copynumber: 5.0 Consensus size: 137
26202 AAGGAACTAC
* * *
26212 ATTCTTTACAAAAGAATATTAACTTT-CATATCTTTTATATTTTGATCGAAATTAATTTATATAA
1 ATTCTTTCCAAAAGAATATTAA-TTTCCATATCTTTTATATTTTGA-CCAAATTAATTAATATAA
* * *
26276 CTGTTTATATTAATAAATTTGATAAAATATATACAATTAATATTTTGTATGAATCAAATTCATAT
64 TTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATTCATAT
26341 ATTAATTAT
129 ATTAATTAT
* * * * *
26350 ATTCTTTACAAAAGAATGTTAGTTTCCATGTCTTTTATATTTTAACCAAAATTAATTAATATAAA
1 ATTCTTTCCAAAAGAATATTAATTTCCATATCTTTTATATTTTGACC-AAATTAATTAATAT-AA
* **
26415 TT-TTAATATTAATAAATTCAATAAAATATATACAATTAATATTTTGTATGAATCAAATTCATAT
64 TTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATTCATAT
26479 ATTAATTAT
129 ATTAATTAT
* * * * * *
26488 ATTCTTTTCAAAAGAATATTAATTTCCATCTCTTTTATATTTTGATCGAAATTAATCAAAATAAC
1 ATTCTTTCCAAAAGAATATTAATTTCCATATCTTTTATATTTTGA-CCAAATTAATTAATATAAT
** * * * ** *
26553 TCCTTATATTAATAAACTT-GGTAAAATATGTACAATTTATATTTTTTATGAATCCCATTCATAA
65 TGTTTATATTAATAAA-TTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATTCATAT
26617 ATTAATTAT
129 ATTAATTAT
* * *
26626 ATTC-TTCCAAAAAAATATTAATTTCCATGTCTTTCATATTTTGACCAAATTAATTAATATAATT
1 ATTCTTTCCAAAAGAATATTAATTTCCATATCTTTTATATTTTGACCAAATTAATTAATATAATT
*
26690 GTTTATATTAATAAATTCGGT-AAATATTATACAATTAATATTTAGTATGAATCAAATTCATATA
66 GTTTATATTAATAAATTCGGTAAAATA-TATACAATTAATATTTTGTATGAATCAAATTCATATA
26754 TTAATTAT
130 TTAATTAT
* *
26762 ATTC-TTCTCAAAA-AATATTAATTTCTATATCGTTTATATTTTGACCGAAATTAATTAATATAA
1 ATTCTTTC-CAAAAGAATATTAATTTCCATATCTTTTATATTTTGACC-AAATTAATTAATATAA
* *
26825 TTGTTTATATTAATAAATTCGGTAAAATATATACAATTAGTA-TTTATATGAATCAAATTCATAT
64 TTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATTCATAT
26889 ATTAATT
129 ATTAATT
26896 TGATTCATGT
Statistics
Matches: 482, Mismatches: 53, Indels: 24
0.86 0.09 0.04
Matches are distributed among these distances:
135 7 0.01
136 133 0.28
137 99 0.21
138 237 0.49
139 6 0.01
ACGTcount: A:0.41, C:0.09, G:0.05, T:0.45
Consensus pattern (137 bp):
ATTCTTTCCAAAAGAATATTAATTTCCATATCTTTTATATTTTGACCAAATTAATTAATATAATT
GTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATTCATATAT
TAATTAT
Found at i:26759 original size:70 final size:71
Alignment explanation
Indices: 26685--26895 Score: 162
Period size: 70 Copynumber: 3.1 Consensus size: 71
26675 TTAATTAATA
26685 TAATTGTTTATATTAATAAATTCGGTAAATAT-TATACAATTAATATTTAGTATGAATCAAATTC
1 TAATTGTTTATATTAATAAATTCGGTAAATATATATACAATTAATATTTAGTATGAATCAAATTC
26749 ATATAT
66 ATATAT
* * * * * * * * *
26755 TAATTATATTCT-TCTCAAAAAATAT---T-AATTTCTATATC-GTTTATATTTTG-ACCGAAAT
1 TAATTGT-TTATAT-T-AATAAAT-TCGGTAAATATATATA-CAATTAATATTTAGTA-TG-AAT
*
26813 -TAATT-A-ATA-
59 CAAATTCATATAT
*
26822 TAATTGTTTATATTAATAAATTCGGTAAA-ATATATACAATTAGTATTTA-TATGAATCAAATTC
1 TAATTGTTTATATTAATAAATTCGGTAAATATATATACAATTAATATTTAGTATGAATCAAATTC
26885 ATATAT
66 ATATAT
26891 TAATT
1 TAATT
26896 TGATTCATGT
Statistics
Matches: 102, Mismatches: 20, Indels: 39
0.63 0.12 0.24
Matches are distributed among these distances:
64 1 0.01
65 9 0.09
66 10 0.10
67 22 0.22
68 8 0.08
69 11 0.11
70 26 0.25
71 8 0.08
72 6 0.06
73 1 0.01
ACGTcount: A:0.42, C:0.07, G:0.06, T:0.45
Consensus pattern (71 bp):
TAATTGTTTATATTAATAAATTCGGTAAATATATATACAATTAATATTTAGTATGAATCAAATTC
ATATAT
Found at i:28596 original size:22 final size:23
Alignment explanation
Indices: 28550--28608 Score: 93
Period size: 22 Copynumber: 2.6 Consensus size: 23
28540 TTTAAGTGGA
*
28550 TGTGTTTGGAGGGTATATTTGGT
1 TGTGTTTGGAGGGTATAATTGGT
28573 TGTGTTTGGAGGGTA-AATTGGT
1 TGTGTTTGGAGGGTATAATTGGT
*
28595 TGTGTTTGGTGGGT
1 TGTGTTTGGAGGGT
28609 TATAGCTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
22 19 0.56
23 15 0.44
ACGTcount: A:0.12, C:0.00, G:0.42, T:0.46
Consensus pattern (23 bp):
TGTGTTTGGAGGGTATAATTGGT
Found at i:32799 original size:24 final size:23
Alignment explanation
Indices: 32765--32822 Score: 64
Period size: 22 Copynumber: 2.4 Consensus size: 23
32755 ACAGAAGAAC
* *
32765 AAGAAATAAAATAACTACAACCTA
1 AAGAAAGAAAA-AACTAAAACCTA
32789 AAGAAAG-AAAAACTAAAACCTA
1 AAGAAAGAAAAAACTAAAACCTA
32811 AATTGAAAGAAA
1 AA--GAAAGAAA
32823 GGAAATTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
22 13 0.45
23 3 0.10
24 11 0.38
25 2 0.07
ACGTcount: A:0.66, C:0.12, G:0.09, T:0.14
Consensus pattern (23 bp):
AAGAAAGAAAAAACTAAAACCTA
Found at i:32808 original size:22 final size:23
Alignment explanation
Indices: 32777--32822 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
32767 GAAATAAAAT
*
32777 AACTACAACCTAAA-GAAAGAAA
1 AACTAAAACCTAAATGAAAGAAA
32799 AACTAAAACCTAAATTGAAAGAAA
1 AACTAAAACCTAAA-TGAAAGAAA
32823 GGAAATTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 13 0.62
24 8 0.38
ACGTcount: A:0.63, C:0.15, G:0.09, T:0.13
Consensus pattern (23 bp):
AACTAAAACCTAAATGAAAGAAA
Found at i:33470 original size:16 final size:16
Alignment explanation
Indices: 33445--33476 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
33435 TGTCCTCAAG
*
33445 CAATCGAAAGAAAAAA
1 CAATCAAAAGAAAAAA
33461 CAATCAAAAGAAAAAA
1 CAATCAAAAGAAAAAA
33477 GACACTTGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.72, C:0.12, G:0.09, T:0.06
Consensus pattern (16 bp):
CAATCAAAAGAAAAAA
Found at i:36674 original size:23 final size:22
Alignment explanation
Indices: 36644--36787 Score: 125
Period size: 22 Copynumber: 6.4 Consensus size: 22
36634 TTTAAGTGGA
* *
36644 TGTGTTTGGAGCATATATTTAGT
1 TGTGTTTGGAG-GTATATTTGGT
*
36667 TGTGTTTGGAAGGTA-AATTGGT
1 TGTGTTTGG-AGGTATATTTGGT
36689 TGTGTTTGGAGGGTATATTTGGT
1 TGTGTTTGGA-GGTATATTTGGT
* *
36712 TGTG-TTGGAAGGTATGTATGGT
1 TGTGTTTGG-AGGTATATTTGGT
*
36734 TGTGTTTGGAGGGTA-AATTGGT
1 TGTGTTTGGA-GGTATATTTGGT
**
36756 TGTGTTTAAAGGCTATGA-TTGGT
1 TGTGTTTGGAGG-TAT-ATTTGGT
36779 TGTGTTTGG
1 TGTGTTTGG
36788 TGGGTCATAG
Statistics
Matches: 99, Mismatches: 13, Indels: 18
0.76 0.10 0.14
Matches are distributed among these distances:
21 3 0.03
22 51 0.52
23 42 0.42
24 3 0.03
ACGTcount: A:0.18, C:0.01, G:0.36, T:0.44
Consensus pattern (22 bp):
TGTGTTTGGAGGTATATTTGGT
Found at i:36693 original size:22 final size:22
Alignment explanation
Indices: 36665--36787 Score: 133
Period size: 22 Copynumber: 5.5 Consensus size: 22
36655 CATATATTTA
36665 GTTGTGTTTGGAAGGTAAATTG
1 GTTGTGTTTGGAAGGTAAATTG
* *
36687 GTTGTGTTTGGAGGGTATATTTG
1 GTTGTGTTTGGAAGGTA-AATTG
**
36710 GTTGTG-TTGGAAGGTATGTATG
1 GTTGTGTTTGGAAGGTAAAT-TG
*
36732 GTTGTGTTTGGAGGGTAAATTG
1 GTTGTGTTTGGAAGGTAAATTG
* *
36754 GTTGTGTTT-AAAGGCTATGATTG
1 GTTGTGTTTGGAAGG-TA-AATTG
36777 GTTGTGTTTGG
1 GTTGTGTTTGG
36788 TGGGTCATAG
Statistics
Matches: 83, Mismatches: 12, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
21 4 0.05
22 46 0.55
23 33 0.40
ACGTcount: A:0.17, C:0.01, G:0.38, T:0.44
Consensus pattern (22 bp):
GTTGTGTTTGGAAGGTAAATTG
Found at i:36708 original size:45 final size:45
Alignment explanation
Indices: 36644--36792 Score: 169
Period size: 45 Copynumber: 3.3 Consensus size: 45
36634 TTTAAGTGGA
** *
36644 TGTGTTTGGAGCATATATTTAGTTGTGTTTGGAAGGTAAATTGGT
1 TGTGTTTGGAGGGTATATTTGGTTGTGTTTGGAAGGTAAATTGGT
**
36689 TGTGTTTGGAGGGTATATTTGGTTGTG-TTGGAAGGTATGTATGGT
1 TGTGTTTGGAGGGTATATTTGGTTGTGTTTGGAAGGTAAAT-TGGT
* * *
36734 TGTGTTTGGAGGGTA-AATTGGTTGTGTTT-AAAGGCTATGATTGGT
1 TGTGTTTGGAGGGTATATTTGGTTGTGTTTGGAAGG-TA-AATTGGT
*
36779 TGTGTTTGGTGGGT
1 TGTGTTTGGAGGGT
36793 CATAGCTTTA
Statistics
Matches: 90, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
44 25 0.28
45 64 0.71
46 1 0.01
ACGTcount: A:0.17, C:0.01, G:0.37, T:0.44
Consensus pattern (45 bp):
TGTGTTTGGAGGGTATATTTGGTTGTGTTTGGAAGGTAAATTGGT
Found at i:39238 original size:2 final size:2
Alignment explanation
Indices: 39233--39257 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
39223 AATATATATA
39233 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
39258 ATTAATATGG
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:40835 original size:18 final size:18
Alignment explanation
Indices: 40808--40842 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
40798 CTACATCAAG
*
40808 TGTGAGCCTTATATGTCT
1 TGTGAACCTTATATGTCT
40826 TGTGAACCTTATATGTC
1 TGTGAACCTTATATGTC
40843 AACGAGCCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (18 bp):
TGTGAACCTTATATGTCT
Found at i:46832 original size:30 final size:29
Alignment explanation
Indices: 46772--46836 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
46762 GCTTTATTTT
* *
46772 AAAATTATTTTTTGACCTCAAACTATCCA
1 AAAATTATGTTTTGACCTCAAACTACCCA
*
46801 AAAATTATGTTTTGACC-CATAAACTGCCCA
1 AAAATTATGTTTTGACCTC--AAACTACCCA
46831 AAAATT
1 AAAATT
46837 CAAATTTGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 1 0.03
29 16 0.52
30 14 0.45
ACGTcount: A:0.40, C:0.20, G:0.06, T:0.34
Consensus pattern (29 bp):
AAAATTATGTTTTGACCTCAAACTACCCA
Found at i:46864 original size:30 final size:30
Alignment explanation
Indices: 46830--46906 Score: 102
Period size: 30 Copynumber: 2.6 Consensus size: 30
46820 TAAACTGCCC
*
46830 AAAAATTCAAATTTGATCC-CTAAACTTTTT
1 AAAAATTCAAATTTGA-CCTCTAAACTTTCT
**
46860 AAAAATTCTGATTTGACCTCTAAACTTTCT
1 AAAAATTCAAATTTGACCTCTAAACTTTCT
*
46890 AAAAGTTCAAATTTGAC
1 AAAAATTCAAATTTGAC
46907 TCAGTTTTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
29 2 0.05
30 38 0.95
ACGTcount: A:0.39, C:0.17, G:0.06, T:0.38
Consensus pattern (30 bp):
AAAAATTCAAATTTGACCTCTAAACTTTCT
Found at i:58138 original size:50 final size:50
Alignment explanation
Indices: 58075--58200 Score: 144
Period size: 50 Copynumber: 2.5 Consensus size: 50
58065 TCCTATACCT
* * *
58075 CTAAAGCTGTAGAGGAATGGATTAAAGTCGCAATGACAAATCTCATACAC
1 CTAAAGCTATAGAGGAATAGATTAAAGCCGCAATGACAAATCTCATACAC
** * * * *
58125 CTAAAGCTATAGAGGGGTAGATTGAAGCCGCAATGGCGAATCTCATTCAC
1 CTAAAGCTATAGAGGAATAGATTAAAGCCGCAATGACAAATCTCATACAC
* **
58175 CTAAAGCTATGGAGGGGTAGATTAAA
1 CTAAAGCTATAGAGGAATAGATTAAA
58201 ACCCGTAGTA
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 65 1.00
ACGTcount: A:0.37, C:0.17, G:0.25, T:0.22
Consensus pattern (50 bp):
CTAAAGCTATAGAGGAATAGATTAAAGCCGCAATGACAAATCTCATACAC
Found at i:58393 original size:79 final size:79
Alignment explanation
Indices: 58309--58556 Score: 397
Period size: 79 Copynumber: 3.1 Consensus size: 79
58299 CCACATCCTG
*
58309 TCTTTTACCCCGACCATGGGGCAGATTGAAGCAATCCAATCTTTTACCCTAATTAGGGGGCAGAT
1 TCTTTTACCCCGACCATGGGGCAGATTGAAGCAATCCAATCTTTTACCCTAATTAGAGGGCAGAT
58374 TGAAGACCATCCAA
66 TGAAGACCATCCAA
* * * *
58388 TCTTTTACCCCGACCATGGGACAAATTGAAGCAATCCAACCTTTTATCCTAATTAGAGGGCAGAT
1 TCTTTTACCCCGACCATGGGGCAGATTGAAGCAATCCAATCTTTTACCCTAATTAGAGGGCAGAT
58453 TGAAGACCATCCAA
66 TGAAGACCATCCAA
* * ** * *
58467 TCTTTTACCCCGACCATGGGGTAGATTGAATCAATCCAATCTTTTACCCTAACCAAAGGGTAGAT
1 TCTTTTACCCCGACCATGGGGCAGATTGAAGCAATCCAATCTTTTACCCTAATTAGAGGGCAGAT
58532 TGAAGACCATCCAA
66 TGAAGACCATCCAA
58546 TCTTTTACCCC
1 TCTTTTACCCC
58557 TAAAGTTATA
Statistics
Matches: 154, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
79 154 1.00
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (79 bp):
TCTTTTACCCCGACCATGGGGCAGATTGAAGCAATCCAATCTTTTACCCTAATTAGAGGGCAGAT
TGAAGACCATCCAA
Found at i:58396 original size:40 final size:40
Alignment explanation
Indices: 58309--58555 Score: 239
Period size: 39 Copynumber: 6.2 Consensus size: 40
58299 CCACATCCTG
** *
58309 TCTTTTACCCCGACCATGGGGCAGATTGAAG-CAATCCAA
1 TCTTTTACCCTAACCAGGGGGCAGATTGAAGACAATCCAA
** *
58348 TCTTTTACCCTAATTAGGGGGCAGATTGAAGACCATCCAA
1 TCTTTTACCCTAACCAGGGGGCAGATTGAAGACAATCCAA
** * * *
58388 TCTTTTACCCCGACCATGGGACAAATTGAAG-CAATCCAA
1 TCTTTTACCCTAACCAGGGGGCAGATTGAAGACAATCCAA
* * ** * *
58427 CCTTTTATCCTAATTAGAGGGCAGATTGAAGACCATCCAA
1 TCTTTTACCCTAACCAGGGGGCAGATTGAAGACAATCCAA
** * * *
58467 TCTTTTACCCCGACCATGGGGTAGATTGAA-TCAATCCAA
1 TCTTTTACCCTAACCAGGGGGCAGATTGAAGACAATCCAA
** * *
58506 TCTTTTACCCTAACCAAAGGGTAGATTGAAGACCATCCAA
1 TCTTTTACCCTAACCAGGGGGCAGATTGAAGACAATCCAA
58546 TCTTTTACCC
1 TCTTTTACCC
58556 CTAAAGTTAT
Statistics
Matches: 163, Mismatches: 42, Indels: 5
0.78 0.20 0.02
Matches are distributed among these distances:
39 87 0.53
40 76 0.47
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (40 bp):
TCTTTTACCCTAACCAGGGGGCAGATTGAAGACAATCCAA
Found at i:59681 original size:2 final size:2
Alignment explanation
Indices: 59676--59706 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
59666 ACACACACAC
59676 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
59707 TTACTTTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:59716 original size:16 final size:16
Alignment explanation
Indices: 59679--59739 Score: 61
Period size: 16 Copynumber: 3.7 Consensus size: 16
59669 CACACACATA
*
59679 TATATATATATATATAT
1 TATAT-TATATTTATAT
59696 ATATATTATATTTACT-T
1 -TATATTATATTTA-TAT
* *
59713 TATATTTTACTTATAT
1 TATATTATATTTATAT
59729 TATATTATATT
1 TATATTATATT
59740 ATTATTTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
15 1 0.03
16 21 0.58
17 8 0.22
18 6 0.17
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (16 bp):
TATATTATATTTATAT
Found at i:59738 original size:10 final size:10
Alignment explanation
Indices: 59679--59754 Score: 57
Period size: 11 Copynumber: 7.1 Consensus size: 10
59669 CACACACATA
59679 TATATATATAT
1 TATAT-TATAT
59690 ATATATATATAT
1 -TATAT-TATAT
59702 TATATT-TACTT
1 TATATTATA--T
*
59713 TATATTTTACT
1 TATATTATA-T
59724 TATATTATAT
1 TATATTATAT
59734 TATATTATTAT
1 TATATTA-TAT
*
59745 T-TTTTATAT
1 TATATTATAT
59754 T
1 T
59755 GAAACTAAAT
Statistics
Matches: 57, Mismatches: 3, Indels: 11
0.80 0.04 0.15
Matches are distributed among these distances:
9 6 0.11
10 13 0.23
11 25 0.44
12 13 0.23
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (10 bp):
TATATTATAT
Found at i:59745 original size:27 final size:25
Alignment explanation
Indices: 59697--59754 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 25
59687 TATATATATA
59697 TATATTATATTTACTTTATATTTTACT
1 TATATTATATTTACTTTATATTTT--T
59724 TATATTATA-TTA-TATTATTATTTTT
1 TATATTATATTTACT-TTA-TATTTTT
59749 TATATT
1 TATATT
59755 GAAACTAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
25 8 0.28
26 6 0.21
27 15 0.52
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (25 bp):
TATATTATATTTACTTTATATTTTT
Found at i:60521 original size:30 final size:30
Alignment explanation
Indices: 60485--60541 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
60475 TATTTTAAAA
60485 TTTTGACCCCCAAACTATCCAAAAATTATG
1 TTTTGACCCCCAAACTATCCAAAAATTATG
* **
60515 TTTTGACCCCTAAACTATTTAAAAATT
1 TTTTGACCCCCAAACTATCCAAAAATT
60542 CAAAATTAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.37, C:0.23, G:0.05, T:0.35
Consensus pattern (30 bp):
TTTTGACCCCCAAACTATCCAAAAATTATG
Found at i:60554 original size:30 final size:30
Alignment explanation
Indices: 60520--60605 Score: 120
Period size: 30 Copynumber: 2.9 Consensus size: 30
60510 TTATGTTTTG
*
60520 ACCCCTAAACTATT-TAAAAATTCAAAATTA
1 ACCCCTAAACT-TTCCAAAAATTCAAAATTA
* *
60550 ACCCCTAAACTTTCCAAAAATTCAAATTTG
1 ACCCCTAAACTTTCCAAAAATTCAAAATTA
*
60580 ACCCCTAAACTTCCCAAAAATTCAAA
1 ACCCCTAAACTTTCCAAAAATTCAAA
60606 CTAAACCCTC
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
29 2 0.04
30 49 0.96
ACGTcount: A:0.45, C:0.27, G:0.01, T:0.27
Consensus pattern (30 bp):
ACCCCTAAACTTTCCAAAAATTCAAAATTA
Found at i:60599 original size:60 final size:60
Alignment explanation
Indices: 60490--60605 Score: 146
Period size: 60 Copynumber: 1.9 Consensus size: 60
60480 TAAAATTTTG
** **
60490 ACCCCCAAACTATCCAAAAATTATGTTTTGACCCCTAAACTATTTAAAAATTCAAAATTA
1 ACCCCCAAACTATCCAAAAATTATAATTTGACCCCTAAACTATCCAAAAATTCAAAATTA
* *
60550 ACCCCTAAACTTTCCAAAAATTCA-AATTTGACCCCTAAACT-TCCCAAAAATTCAAA
1 ACCCCCAAACTATCCAAAAATT-ATAATTTGACCCCTAAACTAT-CCAAAAATTCAAA
60606 CTAAACCCTC
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
59 1 0.02
60 46 0.96
61 1 0.02
ACGTcount: A:0.43, C:0.27, G:0.03, T:0.28
Consensus pattern (60 bp):
ACCCCCAAACTATCCAAAAATTATAATTTGACCCCTAAACTATCCAAAAATTCAAAATTA
Found at i:60614 original size:29 final size:29
Alignment explanation
Indices: 60535--60614 Score: 106
Period size: 30 Copynumber: 2.7 Consensus size: 29
60525 TAAACTATTT
*
60535 AAAAATTCAAAATTAACCCCTAAACTTTCC
1 AAAAATTC-AAATTAACCCCTAAACTTCCC
*
60565 AAAAATTCAAATTTGACCCCTAAACTTCCC
1 AAAAATTCAAA-TTAACCCCTAAACTTCCC
* *
60595 AAAAATTCAAACTAAACCCT
1 AAAAATTCAAATTAACCCCT
60615 CAATTTTTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
29 9 0.20
30 35 0.80
ACGTcount: A:0.46, C:0.28, G:0.01, T:0.25
Consensus pattern (29 bp):
AAAAATTCAAATTAACCCCTAAACTTCCC
Found at i:61936 original size:23 final size:23
Alignment explanation
Indices: 61910--61958 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
61900 TGGGCAACTA
61910 TAGTTATTGGTCAACTACAATTT
1 TAGTTATTGGTCAACTACAATTT
* *
61933 TAGTTATTGGTCAATTTCAATTT
1 TAGTTATTGGTCAACTACAATTT
61956 TAG
1 TAG
61959 CAGTGAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.47
Consensus pattern (23 bp):
TAGTTATTGGTCAACTACAATTT
Found at i:62673 original size:11 final size:11
Alignment explanation
Indices: 62633--62675 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
62623 CTAACCGAAA
62633 CACCACC-CTAC
1 CACCACCAC-AC
*
62644 CACCACCATAC
1 CACCACCACAC
*
62655 AACCACCACAC
1 CACCACCACAC
62666 CACCACCACA
1 CACCACCACA
62676 TCAAAACCGT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.37, C:0.58, G:0.00, T:0.05
Consensus pattern (11 bp):
CACCACCACAC
Found at i:66704 original size:93 final size:94
Alignment explanation
Indices: 66588--66778 Score: 312
Period size: 93 Copynumber: 2.0 Consensus size: 94
66578 CAATCCAACA
* * *
66588 ATTCTTTAACTTCTTTTAATTTGGCCACTCTCTTCATTTTTCATTCTATCTTGACCTCATTTTGT
1 ATTCTTTAACTTATTTTAATTTGGCCACTCTCTTCACTTTTCATTCCATCTTGACCTCATTTTGT
*
66653 TTGATTTTGAATTTCAGCACTCCAATTGT
66 TTGATTTTGAATTTCAACACTCCAATTGT
* * *
66682 ATTC-TTAACTTATTTTAATTTGGCCCCTCTCTTCACTTTTCGTTCCATTTTGACCTCATTTTGT
1 ATTCTTTAACTTATTTTAATTTGGCCACTCTCTTCACTTTTCATTCCATCTTGACCTCATTTTGT
66746 TTGATTTTGAATTTCAACACTCCAATTGT
66 TTGATTTTGAATTTCAACACTCCAATTGT
66775 ATTC
1 ATTC
66779 CTAATAAGAA
Statistics
Matches: 90, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
93 86 0.96
94 4 0.04
ACGTcount: A:0.19, C:0.22, G:0.08, T:0.50
Consensus pattern (94 bp):
ATTCTTTAACTTATTTTAATTTGGCCACTCTCTTCACTTTTCATTCCATCTTGACCTCATTTTGT
TTGATTTTGAATTTCAACACTCCAATTGT
Found at i:76678 original size:13 final size:14
Alignment explanation
Indices: 76649--76678 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
76639 TTCAATACAT
76649 TGACATTTAACCTC
1 TGACATTTAACCTC
76663 TGACATTTAA-CTC
1 TGACATTTAACCTC
76676 TGA
1 TGA
76679 TTGCATTGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (14 bp):
TGACATTTAACCTC
Found at i:98419 original size:26 final size:28
Alignment explanation
Indices: 98362--98420 Score: 77
Period size: 26 Copynumber: 2.2 Consensus size: 28
98352 CGAAGGGGTT
* *
98362 TAAAGGAACAATGAAAGGAAAAAATAAT
1 TAAAGGAACAACGAAAGGAAAAAATAAA
*
98390 TAAAGGAA-AACGAGAGG-AAAAATAAA
1 TAAAGGAACAACGAAAGGAAAAAATAAA
98416 TAAAG
1 TAAAG
98421 AGGACAGGTC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 13 0.46
27 7 0.25
28 8 0.29
ACGTcount: A:0.64, C:0.03, G:0.20, T:0.12
Consensus pattern (28 bp):
TAAAGGAACAACGAAAGGAAAAAATAAA
Found at i:98569 original size:30 final size:29
Alignment explanation
Indices: 98534--98616 Score: 96
Period size: 30 Copynumber: 2.8 Consensus size: 29
98524 ATAATAGATG
98534 GAAAAAATTTAAGTATCAATTTA-AGATAA
1 GAAAAAATTTAAGTATCAATTTAGAGA-AA
*
98563 AAAAAAATTATAAGTATCAATTTAGAAGAAA
1 GAAAAAATT-TAAGTATCAATTTAG-AGAAA
* *
98594 TGAATAAATTTAAATATCAATTT
1 -GAAAAAATTTAAGTATCAATTT
98617 CATATTTAAC
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
29 8 0.17
30 14 0.30
31 14 0.30
32 10 0.22
ACGTcount: A:0.55, C:0.04, G:0.08, T:0.33
Consensus pattern (29 bp):
GAAAAAATTTAAGTATCAATTTAGAGAAA
Found at i:107295 original size:22 final size:22
Alignment explanation
Indices: 107223--107295 Score: 60
Period size: 22 Copynumber: 3.3 Consensus size: 22
107213 ATAAATTAAC
* *
107223 AAAAA-TATATTTAAATTTAATA
1 AAAAATTATAATTAAATTT-GTA
*
107245 ATAAAATTATAATTATATTTGTA
1 A-AAAATTATAATTAAATTTGTA
**
107268 CTAAATTATAATTAAATCTT-TA
1 AAAAATTATAATTAAAT-TTGTA
107290 AAAAAT
1 AAAAAT
107296 ATGTAGAGTA
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
22 21 0.52
23 8 0.20
24 11 0.28
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.42
Consensus pattern (22 bp):
AAAAATTATAATTAAATTTGTA
Found at i:107729 original size:26 final size:28
Alignment explanation
Indices: 107652--107729 Score: 90
Period size: 27 Copynumber: 2.9 Consensus size: 28
107642 TACTAAATTA
* *
107652 TTTAAATATAATTTAT-TATATTTAAGT
1 TTTAAAAATAATTTATATATAATTAAGT
* * *
107679 TTTTAAAATATTTTATATATCATTAA-T
1 TTTAAAAATAATTTATATATAATTAAGT
107706 TTTAAAAATAATTTATAT-TAATTA
1 TTTAAAAATAATTTATATATAATTA
107730 CTTAAAAAAT
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
26 5 0.12
27 30 0.71
28 7 0.17
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (28 bp):
TTTAAAAATAATTTATATATAATTAAGT
Found at i:110735 original size:23 final size:25
Alignment explanation
Indices: 110695--110741 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 25
110685 TTTCTTAGAT
110695 TTAGGTTTTTAGTCATTT-CTTTTC
1 TTAGGTTTTTAGTCATTTCCTTTTC
* *
110719 TTAGG-TTTTATTTATTTCCTTTT
1 TTAGGTTTTTAGTCATTTCCTTTT
110742 TTCTTGTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.13, C:0.11, G:0.11, T:0.66
Consensus pattern (25 bp):
TTAGGTTTTTAGTCATTTCCTTTTC
Found at i:112504 original size:23 final size:23
Alignment explanation
Indices: 112459--112504 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
112449 AACAGAACTA
* *
112459 AAATTTTGAGAGAAAATATAAAT
1 AAATTTTGAGAGAAAACAAAAAT
* *
112482 AAATTTTGAGAGAGAGCAAAAAT
1 AAATTTTGAGAGAAAACAAAAAT
112505 GGTTGTTCTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.54, C:0.02, G:0.17, T:0.26
Consensus pattern (23 bp):
AAATTTTGAGAGAAAACAAAAAT
Found at i:112617 original size:21 final size:21
Alignment explanation
Indices: 112593--112647 Score: 83
Period size: 22 Copynumber: 2.6 Consensus size: 21
112583 GAAATTTAAA
112593 ACAAACATAATGAGGAGAGTT
1 ACAAACATAATGAGGAGAGTT
*
112614 ACAAAACATTATGAGGAGAGTT
1 AC-AAACATAATGAGGAGAGTT
*
112636 ACAGACATAATG
1 ACAAACATAATG
112648 TTTTGTAGGT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
21 10 0.33
22 20 0.67
ACGTcount: A:0.47, C:0.11, G:0.22, T:0.20
Consensus pattern (21 bp):
ACAAACATAATGAGGAGAGTT
Found at i:117699 original size:21 final size:21
Alignment explanation
Indices: 117675--117729 Score: 92
Period size: 22 Copynumber: 2.6 Consensus size: 21
117665 GAAATTTAAA
117675 ACAAACATAATGAGGAGAGTT
1 ACAAACATAATGAGGAGAGTT
*
117696 ACAAAACATTATGAGGAGAGTT
1 AC-AAACATAATGAGGAGAGTT
117718 ACAAACATAATG
1 ACAAACATAATG
117730 TTTTGTAGGT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
21 11 0.35
22 20 0.65
ACGTcount: A:0.49, C:0.11, G:0.20, T:0.20
Consensus pattern (21 bp):
ACAAACATAATGAGGAGAGTT
Found at i:120664 original size:6 final size:6
Alignment explanation
Indices: 120655--120715 Score: 56
Period size: 6 Copynumber: 10.5 Consensus size: 6
120645 ATTTGTTTAA
* * *
120655 AAATTT AAATTT -ATTTT AAATTT AAATTT -AATTT AAGTTT AAAATT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
*
120701 -ATTTT CAAATTT AAA
1 AAATTT -AAATTT AAA
120716 ATTATCATAA
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
5 12 0.28
6 27 0.63
7 4 0.09
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (6 bp):
AAATTT
Found at i:120674 original size:11 final size:11
Alignment explanation
Indices: 120658--120713 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
120648 TGTTTAAAAA
120658 TTTAAATTTAT
1 TTTAAATTTAT
*
120669 TTTAAATTTAAA
1 TTTAAATTT-AT
*
120681 TTT-AATTTAAG
1 TTTAAATTT-AT
*
120692 TTTAAAATTAT
1 TTTAAATTTAT
120703 TTTCAAATTTA
1 TTT-AAATTTA
120714 AAATTATCAT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
11 23 0.62
12 14 0.38
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:120684 original size:52 final size:52
Alignment explanation
Indices: 120623--120732 Score: 130
Period size: 52 Copynumber: 2.1 Consensus size: 52
120613 CCAAACTCCC
* * * * **
120623 TTTAAATTTATTTTAAAATTAAATTTGTTTAAAAATTTAAATTTATTTTAAA
1 TTTAAATTTAATTTAAAATTAAAATTATTTAAAAATTTAAAATTATCATAAA
** **
120675 TTTAAATTTAATTTAAGTTTAAAATTATTTTCAAATTTAAAATTATCATAAA
1 TTTAAATTTAATTTAAAATTAAAATTATTTAAAAATTTAAAATTATCATAAA
120727 TTTAAA
1 TTTAAA
120733 ATAAATAAAG
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (52 bp):
TTTAAATTTAATTTAAAATTAAAATTATTTAAAAATTTAAAATTATCATAAA
Found at i:120700 original size:35 final size:34
Alignment explanation
Indices: 120623--120720 Score: 117
Period size: 35 Copynumber: 2.8 Consensus size: 34
120613 CCAAACTCCC
* *
120623 TTTAAATTTATTTTAAAATTAAATTTGTTTAAAAA
1 TTTAAATTTATTTTAAATTTAAATTTATTT-AAAA
*
120658 TTTAAATTTATTTTAAATTTAAATTTAATTT-AAG
1 TTTAAATTTATTTTAAATTTAAATTT-ATTTAAAA
* *
120692 TTTAAAATTATTTTCAAATTTAAAATTAT
1 TTTAAATTTATTTT-AAATTTAAATTTAT
120721 CATAAATTTA
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
34 17 0.30
35 36 0.64
36 3 0.05
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (34 bp):
TTTAAATTTATTTTAAATTTAAATTTATTTAAAA
Found at i:120729 original size:17 final size:17
Alignment explanation
Indices: 120623--120734 Score: 107
Period size: 17 Copynumber: 6.5 Consensus size: 17
120613 CCAAACTCCC
*
120623 TTTAAATTTATTTTAAA
1 TTTAAAATTATTTTAAA
* * * *
120640 ATTAAATTTGTTTAAAAA
1 TTTAAAATTATTT-TAAA
*
120658 TTTAAATTTATTTTAAA
1 TTTAAAATTATTTTAAA
* * *
120675 TTTAAATTTAATTTAAG
1 TTTAAAATTATTTTAAA
120692 TTTAAAATTATTTTCAAA
1 TTTAAAATTATTTT-AAA
**
120710 TTTAAAATTATCATAAA
1 TTTAAAATTATTTTAAA
120727 TTTAAAAT
1 TTTAAAAT
120735 AAATAAAGCC
Statistics
Matches: 80, Mismatches: 13, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
17 52 0.65
18 28 0.35
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (17 bp):
TTTAAAATTATTTTAAA
Found at i:122736 original size:30 final size:29
Alignment explanation
Indices: 122643--122842 Score: 260
Period size: 29 Copynumber: 6.8 Consensus size: 29
122633 GAGGGTCCCT
122643 AAACTATCCAAAAATTCCATTTTTACCCCC
1 AAACT-TCCAAAAATTCCATTTTTACCCCC
* * *
122673 GAACTTCCAAAAATTCTAATTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTTACCCCC
* *
122702 AAACTTCCAAAAATCCCATTTTTGACCCCA
1 AAACTTCCAAAAATTCCATTTTT-ACCCCC
*
122732 AAACTTCCAAAAATTCCATTTTTACCCCT
1 AAACTTCCAAAAATTCCATTTTTACCCCC
*
122761 AAACTTCC-AAAATTCCTATTTTTGACCCCG
1 AAACTTCCAAAAATTCC-ATTTTT-ACCCCC
*
122791 AAACTTCCAAAAATTCCATTTTTACCCTCG
1 AAACTTCCAAAAATTCCATTTTTACCC-CC
*
122821 AAA-TTCCAAAAATCCCATTTTT
1 AAACTTCCAAAAATTCCATTTTT
122843 GAAACAAACA
Statistics
Matches: 153, Mismatches: 12, Indels: 11
0.87 0.07 0.06
Matches are distributed among these distances:
28 8 0.05
29 82 0.54
30 55 0.36
31 8 0.05
ACGTcount: A:0.35, C:0.30, G:0.03, T:0.32
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTACCCCC
Found at i:122739 original size:59 final size:59
Alignment explanation
Indices: 122643--122844 Score: 282
Period size: 59 Copynumber: 3.4 Consensus size: 59
122633 GAGGGTCCCT
* ** * *
122643 AAACTATCCAAAAATTCCATTTTT-ACCCCCGAACTTCCAAAAATTCTAATTTTACCCCC
1 AAACT-TCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTACCCCC
*
122702 AAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTACCCCT
1 AAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTACCCCC
* * * *
122761 AAACTTCCAAAATTCCTATTTTTGACCCCGAAACTTCCAAAAATTCCATTTTTACCCTCG
1 AAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTACCC-CC
122821 AAA-TTCCAAAAATCCCATTTTTGA
1 AAACTTCCAAAAATCCCATTTTTGA
122845 AACAAACAGG
Statistics
Matches: 129, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
58 17 0.13
59 108 0.84
60 4 0.03
ACGTcount: A:0.35, C:0.30, G:0.03, T:0.32
Consensus pattern (59 bp):
AAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTACCCCC
Found at i:123440 original size:196 final size:199
Alignment explanation
Indices: 122851--123477 Score: 835
Period size: 196 Copynumber: 3.1 Consensus size: 199
122841 TTGAAACAAA
*
122851 CAGGTCGAAGCAATAAAAGGTTAGCTTCCTGATGAGGTACTGAGAAGTGAACCAAATTCATCTTC
1 CAGGTCGAAGCAATAAAAGGTTAGCTTCC--AT--GGTACTGAGAAGTGAACCAAATTCGTCTTC
*
122916 CAGATGAGATACGGAGGAGCGAATTGAAACAAACAGTGATGTAATCATCTTCCTGATGAGGCACT
62 CAGATGAGATACGGAGGAGCGAATTGAAACAAACAGCGATGTAATCATCTTCCTGATGAGGCACT
* * * *
122981 GAGAAGAAGACCCAAACGAGACTCAAAATGAGCAAATCTTCGAACCCTAGCTTCCTGA-GAAGAT
127 GAGAAGAAGACCCAAACGAGGCTCAAAATGAGCAAATCTTTGAACCCCAGCTTCCTGATG-AGAC
*
123045 ATTGAGAAG
191 ACTGAGAAG
* *
123054 CAGGTCGAAGCAATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTAAACCAAATTCGCCTTC
1 CAGGTCGAAGCAATAAAAGGTTAGCTTCC--ATG-G-TACTGAGAAGTGAACCAAATTCGTCTTC
* * * * * * *
123119 CTGATAAGATACAGAGAAACGAGTTGAAACAAACGACGCG--G---TCATCTTCCTGATGAGACA
62 CAGATGAGATACGGAGGAGCGAATTGAAACAAAC-A-GCGATGTAATCATCTTCCTGATGAGGCA
* * *
123179 CTGAGAAGAAGACCCAAACGAGGCTCAAAGTGAGCAAAATCTTTGAACCTCAGCTTCCGGATGAG
125 CTGAGAAGAAGACCCAAACGAGGCTCAAAATGAGC-AAATCTTTGAACCCCAGCTTCCTGATGAG
123244 ACACTGAGAAG
189 ACACTGAGAAG
*
123255 CAGGTCGAAGCAATAAAAGGTTAGCTTCC-T-G-A-TGAGAAGTGAACCAAATTCGTCTTCCGGA
1 CAGGTCGAAGCAATAAAAGGTTAGCTTCCATGGTACTGAGAAGTGAACCAAATTCGTCTTCCAGA
123316 TGAGATACGGAGGAGCGAATTGAAACAAACAGCGATGTAATCATCTTCCTGATGAGGCACTGAGA
66 TGAGATACGGAGGAGCGAATTGAAACAAACAGCGATGTAATCATCTTCCTGATGAGGCACTGAGA
* *
123381 AGAAGACCCAAACGAGGCTCAAAACGAGCAAATCTTTGAACCCCAGCTTTCCTGATGAGACGCTG
131 AGAAGACCCAAACGAGGCTCAAAATGAGCAAATCTTTGAACCCCAGC-TTCCTGATGAGACACTG
123446 AGAAG
195 AGAAG
*
123451 CAGGTCGAAGTC-ATAAAGTGGTTAGCT
1 CAGGTCGAAG-CAATAAA-AGGTTAGCT
123478 CCCTGATGAG
Statistics
Matches: 376, Mismatches: 34, Indels: 34
0.85 0.08 0.08
Matches are distributed among these distances:
191 3 0.01
192 1 0.00
193 52 0.14
194 1 0.00
195 17 0.05
196 87 0.23
197 9 0.02
198 1 0.00
200 51 0.14
201 62 0.16
202 2 0.01
203 87 0.23
204 1 0.00
205 2 0.01
ACGTcount: A:0.36, C:0.20, G:0.24, T:0.20
Consensus pattern (199 bp):
CAGGTCGAAGCAATAAAAGGTTAGCTTCCATGGTACTGAGAAGTGAACCAAATTCGTCTTCCAGA
TGAGATACGGAGGAGCGAATTGAAACAAACAGCGATGTAATCATCTTCCTGATGAGGCACTGAGA
AGAAGACCCAAACGAGGCTCAAAATGAGCAAATCTTTGAACCCCAGCTTCCTGATGAGACACTGA
GAAG
Found at i:123942 original size:17 final size:17
Alignment explanation
Indices: 123919--124027 Score: 119
Period size: 17 Copynumber: 6.4 Consensus size: 17
123909 CCAAACTCCC
123919 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* * *
123936 ATTAAATTTGTTTAAAAA
1 TTTAAATTTATTT-TAAA
123954 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* *
123971 TTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
* *
123988 TTTAAAATTATTTCAAA
1 TTTAAATTTATTTTAAA
* **
124005 TTTAAAATTATCATAAA
1 TTTAAATTTATTTTAAA
124022 TTTAAA
1 TTTAAA
124028 ATAAATAAAG
Statistics
Matches: 76, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
17 62 0.82
18 14 0.18
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:123960 original size:6 final size:6
Alignment explanation
Indices: 123951--124010 Score: 56
Period size: 6 Copynumber: 10.5 Consensus size: 6
123941 ATTTGTTTAA
* * *
123951 AAATTT AAATTT -ATTTT AAATTT AAATTT -AATTT AAGTTT AAAATT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
123997 --ATTT CAAATTT AAA
1 AAATTT -AAATTT AAA
124011 ATTATCATAA
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
4 3 0.07
5 9 0.21
6 27 0.63
7 4 0.09
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (6 bp):
AAATTT
Found at i:125939 original size:30 final size:29
Alignment explanation
Indices: 125903--126317 Score: 396
Period size: 29 Copynumber: 14.1 Consensus size: 29
125893 CCTCGAGGGT
*
125903 CCCTAAACTGTCAAAAAATTCCATTTTTAC
1 CCCTAAACT-TCCAAAAATTCCATTTTTAC
* *
125933 CCCTAAACTTCCAAAAATTCTATTTTTGC
1 CCCTAAACTTCCAAAAATTCCATTTTTAC
* *
125962 CCCTAAACTTCCAAAAATACTATTTTTTAAC
1 CCCTAAACTTCCAAAAATTCCA-TTTTT-AC
* * *
125993 CCCAAAACTTCCAAAAATTACAATTTTAC
1 CCCTAAACTTCCAAAAATTCCATTTTTAC
*
126022 CCATAAACTTCCAAAAA-TCCTATTTTTAAC
1 CCCTAAACTTCCAAAAATTCC-ATTTTT-AC
* * *
126052 CTCGAAACTTCCAAAAATTTCATTTTTA-
1 CCCTAAACTTCCAAAAATTCCATTTTTAC
* *
126080 CCCGATAACTTACAAAAA-TCCTATTTTTGAC
1 CCCTA-AACTTCCAAAAATTCC-ATTTTT-AC
* *
126111 CCCAAAACTTCTAAAAATTCCA-TTTTAC
1 CCCTAAACTTCCAAAAATTCCATTTTTAC
126139 CCCTAAACTTCCAAAAA-TCTCATTTTTGAC
1 CCCTAAACTTCCAAAAATTC-CATTTTT-AC
* *
126169 CCCGAAACTTCCAAAAATTCCATTTTTGC
1 CCCTAAACTTCCAAAAATTCCATTTTTAC
* *
126198 CCCTAAACATCCAAAAA-TCCTATTTTAAC
1 CCCTAAACTTCCAAAAATTCC-ATTTTTAC
* * *
126227 CCCAAAACTTCCAAAACTTCCATTTTTAG
1 CCCTAAACTTCCAAAAATTCCATTTTTAC
* *
126256 CCTTGAACTTCCAAAAATTCCATTTTTGA-
1 CCCTAAACTTCCAAAAATTCCATTTTT-AC
* *
126285 CACTGAAACTTTCAAAAAATTACCA-TTTTAC
1 CCCT-AAAC-TTCCAAAAATT-CCATTTTTAC
126316 CC
1 CC
126318 ACGGATGTCC
Statistics
Matches: 318, Mismatches: 46, Indels: 41
0.79 0.11 0.10
Matches are distributed among these distances:
27 2 0.01
28 30 0.09
29 153 0.48
30 85 0.27
31 45 0.14
32 3 0.01
ACGTcount: A:0.37, C:0.27, G:0.03, T:0.33
Consensus pattern (29 bp):
CCCTAAACTTCCAAAAATTCCATTTTTAC
Found at i:126079 original size:59 final size:59
Alignment explanation
Indices: 125906--126318 Score: 437
Period size: 59 Copynumber: 7.0 Consensus size: 59
125896 CGAGGGTCCC
* * * * *
125906 TAAACTGTCAAAAAATTCC-ATTTTT-ACCCCTAAACTTCCAAAAATTCTATTTTTGCCCC
1 TAAACT-TCCAAAAA-TCCTATTTTTAACCCCGAAACTTCCAAAAATTCCATTTTTACCCA
* * * *
125965 TAAACTTCCAAAAATACTATTTTTTAACCCCAAAACTTCCAAAAATTACAATTTTACCCA
1 TAAACTTCCAAAAATCCTA-TTTTTAACCCCGAAACTTCCAAAAATTCCATTTTTACCCA
* *
126025 TAAACTTCCAAAAATCCTATTTTTAACCTCGAAACTTCCAAAAATTTCATTTTTACCCGA
1 TAAACTTCCAAAAATCCTATTTTTAACCCCGAAACTTCCAAAAATTCCATTTTTACCC-A
* * * * *
126085 T-AACTTACAAAAATCCTATTTTTGACCCCAAAACTTCTAAAAATTCCA-TTTTACCCC
1 TAAACTTCCAAAAATCCTATTTTTAACCCCGAAACTTCCAAAAATTCCATTTTTACCCA
* * *
126142 TAAACTTCCAAAAAT-CTCATTTTTGACCCCGAAACTTCCAAAAATTCCATTTTTGCCCC
1 TAAACTTCCAAAAATCCT-ATTTTTAACCCCGAAACTTCCAAAAATTCCATTTTTACCCA
* * * * *
126201 TAAACATCCAAAAATCCTA-TTTTAACCCCAAAACTTCCAAAACTTCCATTTTTAGCCT
1 TAAACTTCCAAAAATCCTATTTTTAACCCCGAAACTTCCAAAAATTCCATTTTTACCCA
* * * * *
126259 TGAACTTCCAAAAATTCC-ATTTTTGACACTGAAACTTTCAAAAAATTACCA-TTTTACCCA
1 TAAACTTCCAAAAA-TCCTATTTTTAACCCCGAAAC-TTCCAAAAATT-CCATTTTTACCCA
126319 CGGATGTCCA
Statistics
Matches: 301, Mismatches: 41, Indels: 23
0.82 0.11 0.06
Matches are distributed among these distances:
57 5 0.02
58 103 0.34
59 124 0.41
60 66 0.22
61 3 0.01
ACGTcount: A:0.37, C:0.27, G:0.03, T:0.33
Consensus pattern (59 bp):
TAAACTTCCAAAAATCCTATTTTTAACCCCGAAACTTCCAAAAATTCCATTTTTACCCA
Found at i:126411 original size:29 final size:29
Alignment explanation
Indices: 126334--126411 Score: 70
Period size: 29 Copynumber: 2.7 Consensus size: 29
126324 GTCCAAAAAC
*
126334 TCCATTTTCAACCTCGAAACTCTTAAAATT
1 TCCATTTTTAACCTCGAAA-TCTTAAAATT
* * * * *
126364 ACCCTTTTT-ACCCCTAAATGTTTAAAATT
1 TCCATTTTTAACCTCGAAAT-CTTAAAATT
126393 TCCATTTTTAACCTC-AAAT
1 TCCATTTTTAACCTCGAAAT
126412 TTTTCCAAAA
Statistics
Matches: 37, Mismatches: 9, Indels: 5
0.73 0.18 0.10
Matches are distributed among these distances:
28 1 0.03
29 26 0.70
30 10 0.27
ACGTcount: A:0.32, C:0.26, G:0.03, T:0.40
Consensus pattern (29 bp):
TCCATTTTTAACCTCGAAATCTTAAAATT
Done.