Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012628.1 Kokia drynarioides strain JFW-HI SEQ_127637, 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: 183682
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Warning! 61 characters in sequence are not A, C, G, or T
Found at i:2137 original size:4 final size:4
Alignment explanation
Indices: 2128--2184 Score: 69
Period size: 4 Copynumber: 13.8 Consensus size: 4
2118 TCTGTCCTTC
* * *
2128 TTCT TTCT TTCCT CTCC TTCT TCCT TTCT TTCT TTCT TTCTT TTCT TTCT
1 TTCT TTCT TT-CT TTCT TTCT TTCT TTCT TTCT TTCT TTC-T TTCT TTCT
2178 TTCT TTC
1 TTCT TTC
2185 CCGTTTATTT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
4 38 0.84
5 7 0.16
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (4 bp):
TTCT
Found at i:2161 original size:25 final size:22
Alignment explanation
Indices: 2128--2185 Score: 73
Period size: 21 Copynumber: 2.5 Consensus size: 22
2118 TCTGTCCTTC
2128 TTCTTTCTTTCCTCTCCTTCTTCCT
1 TTCTTTCTTTCCT-TCCTT-TT-CT
*
2153 TTCTTTCTTT-CTTTCTTTTCT
1 TTCTTTCTTTCCTTCCTTTTCT
2174 TTCTTTCTTTCC
1 TTCTTTCTTTCC
2186 CGTTTATTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
21 12 0.39
22 3 0.10
23 4 0.13
24 2 0.06
25 10 0.32
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (22 bp):
TTCTTTCTTTCCTTCCTTTTCT
Found at i:3091 original size:1 final size:1
Alignment explanation
Indices: 3085--3111 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
3075 NNNNNNNNNN
3085 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
3112 ATGAACATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:8153 original size:4 final size:4
Alignment explanation
Indices: 8144--8170 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
8134 TCAAAATACA
8144 TAAT TAAT TAAT TAAT TAAT TAAT TAA
1 TAAT TAAT TAAT TAAT TAAT TAAT TAA
8171 AATTTTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
TAAT
Found at i:19512 original size:16 final size:17
Alignment explanation
Indices: 19493--19528 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
19483 ATTTTCAAAA
19493 TTTCACTTT-TTTTTAG
1 TTTCACTTTATTTTTAG
19509 TTTCACTTTATTTTTAG
1 TTTCACTTTATTTTTAG
19526 TTT
1 TTT
19529 TCATTTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.14, C:0.11, G:0.06, T:0.69
Consensus pattern (17 bp):
TTTCACTTTATTTTTAG
Found at i:25799 original size:9 final size:9
Alignment explanation
Indices: 25785--25814 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
25775 ACACCAATTT
25785 ATTATTTAA
1 ATTATTTAA
*
25794 ATTATTTGA
1 ATTATTTAA
25803 ATTATTTAA
1 ATTATTTAA
25812 ATT
1 ATT
25815 GTAAGATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (9 bp):
ATTATTTAA
Found at i:33400 original size:29 final size:30
Alignment explanation
Indices: 33367--33425 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
33357 TATAGTTTAA
*
33367 TGTGTAATTGTATATATG-AATTTTGATTT
1 TGTGTAATTGTATACATGAAATTTTGATTT
*
33396 TGTGTAATTTTATACATGAAATTTTGATTT
1 TGTGTAATTGTATACATGAAATTTTGATTT
33426 AATCCAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 16 0.59
30 11 0.41
ACGTcount: A:0.29, C:0.02, G:0.15, T:0.54
Consensus pattern (30 bp):
TGTGTAATTGTATACATGAAATTTTGATTT
Found at i:34312 original size:23 final size:23
Alignment explanation
Indices: 34286--34337 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
34276 ATAAAATTAT
34286 TAAATAT-TATATTAAAATAAATA
1 TAAATATATATATTAAAA-AAATA
* *
34309 TAAACATATATTTTAAAAAAATA
1 TAAATATATATATTAAAAAAATA
*
34332 AAAATA
1 TAAATA
34338 ATAATATGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
23 15 0.62
24 9 0.38
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (23 bp):
TAAATATATATATTAAAAAAATA
Found at i:38166 original size:225 final size:225
Alignment explanation
Indices: 37900--38309 Score: 513
Period size: 225 Copynumber: 1.8 Consensus size: 225
37890 TGATAATAGG
*
37900 TCATAAGTTAAATGTTAACATGATAATTAATGAAACTATGAACAAT-GTTCGTTCGAATAAA-AA
1 TCATAAGTTAAATGTTAACATGATAATTAATGAAACTATGAACAATGGTT-GTTC-AAAAAAGAA
** * *
37963 ATCGTTTGTTATTTTCAAAATCTAAAAAGTTCGGATTTAGAATAAAATTGTTAATTGTTAAGC-G
64 ATCACTTGTTATTTTCAAAATCTAAAAAGTTCGGATTTAGAA-AAAATTGTCAAATGTTAA-CAG
* *
38027 CTTTCTTAAAGAAACATACAAATGATTTTTGGTGATA-TTTTTAGGGTTTAAGATTTAAGAGTTA
127 CTTTCTTAAAGAAACATACAAATGATTTTTGGTGATATTTTTTAAGGTTTAAGAGTTAAGAGTTA
38091 ACATAACGATATTTAATGACAGGTTGATATTAAA
192 ACATAACGATATTTAATGACAGGTTGATATTAAA
* * * * *
38125 TCATATGTTAAATGTTAACTTGGTGATTAATGAATCTATGAACAATGGTTGTTCAAAAAAGAAAT
1 TCATAAGTTAAATGTTAACATGATAATTAATGAAACTATGAACAATGGTTGTTCAAAAAAGAAAT
* * * ** * * *
38190 CACTTGTTATTTTGAAATTTTGTAATGTTCGGATTTAGAAAAAATTGTCAAATGTTGACAGTTTT
66 CACTTGTTATTTTCAAAATCTAAAAAGTTCGGATTTAGAAAAAATTGTCAAATGTTAACAGCTTT
* ** * * * *
38255 TTTAGGGGAACGTATAAGTGATTTTTGGTGATATTTTTTAAGGTTTAAGAGTTAA
131 CTTAAAGAAACATACAAATGATTTTTGGTGATATTTTTTAAGGTTTAAGAGTTAA
38310 CATGATATTA
Statistics
Matches: 154, Mismatches: 27, Indels: 8
0.81 0.14 0.04
Matches are distributed among these distances:
223 1 0.01
224 50 0.32
225 100 0.65
226 3 0.02
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.39
Consensus pattern (225 bp):
TCATAAGTTAAATGTTAACATGATAATTAATGAAACTATGAACAATGGTTGTTCAAAAAAGAAAT
CACTTGTTATTTTCAAAATCTAAAAAGTTCGGATTTAGAAAAAATTGTCAAATGTTAACAGCTTT
CTTAAAGAAACATACAAATGATTTTTGGTGATATTTTTTAAGGTTTAAGAGTTAAGAGTTAACAT
AACGATATTTAATGACAGGTTGATATTAAA
Found at i:39614 original size:24 final size:26
Alignment explanation
Indices: 39587--39634 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
39577 TCTCTTCTTT
*
39587 ATTCAA-ATGGGTTTT-TGAGTTTAA
1 ATTCAAGATAGGTTTTCTGAGTTTAA
*
39611 ATTCAAGGTAGGTTTTCTGAGTTT
1 ATTCAAGATAGGTTTTCTGAGTTT
39635 TTTTTCTCGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 6 0.30
25 7 0.35
26 7 0.35
ACGTcount: A:0.25, C:0.06, G:0.23, T:0.46
Consensus pattern (26 bp):
ATTCAAGATAGGTTTTCTGAGTTTAA
Found at i:44654 original size:26 final size:26
Alignment explanation
Indices: 44618--44670 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
44608 GTTGTACATG
44618 GTTAGAATGGATATGATCGTGAAAAT
1 GTTAGAATGGATATGATCGTGAAAAT
*
44644 GTTAGAATGGATATGATCTTGAAAAT
1 GTTAGAATGGATATGATCGTGAAAAT
44670 G
1 G
44671 GGCTTACTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.04, G:0.26, T:0.32
Consensus pattern (26 bp):
GTTAGAATGGATATGATCGTGAAAAT
Found at i:50128 original size:20 final size:20
Alignment explanation
Indices: 50103--50141 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
50093 TTTTTTTTGC
* *
50103 AATAATTTATTTAATTTAAT
1 AATAATTAATTTAAATTAAT
50123 AATAATTAATTTAAATTAA
1 AATAATTAATTTAAATTAA
50142 AAATTTAGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AATAATTAATTTAAATTAAT
Found at i:50444 original size:27 final size:27
Alignment explanation
Indices: 50396--50453 Score: 73
Period size: 26 Copynumber: 2.1 Consensus size: 27
50386 ATATTAAGCC
*
50396 ATTACAAAAAGATTAAAGTTTAATTA-
1 ATTACAAAAAAATTAAAGTTTAATTAT
* *
50422 ATTACAAAAAAATTATCATTTTAATTAT
1 ATTACAAAAAAATTA-AAGTTTAATTAT
50450 ATTA
1 ATTA
50454 AATAAATGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 14 0.52
27 9 0.33
28 4 0.15
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.40
Consensus pattern (27 bp):
ATTACAAAAAAATTAAAGTTTAATTAT
Found at i:51539 original size:44 final size:44
Alignment explanation
Indices: 51450--51537 Score: 106
Period size: 44 Copynumber: 2.0 Consensus size: 44
51440 TAGTGTCGAG
* * *
51450 TTAAGAGTTAGAATATGTGGTTAAAATAAGAAGATTAGGAAAAA
1 TTAAGAATTAGAATATGTAGTTAAAATAAGAAGATTAAGAAAAA
* *
51494 TTAAGAATTAGAATGTGTAGTCT-AAATAAGAAAGGTTAAGAAAA
1 TTAAGAATTAGAATATGTAGT-TAAAATAAG-AAGATTAAGAAAA
51538 TTCAAGGATT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
44 25 0.68
45 12 0.32
ACGTcount: A:0.50, C:0.01, G:0.22, T:0.27
Consensus pattern (44 bp):
TTAAGAATTAGAATATGTAGTTAAAATAAGAAGATTAAGAAAAA
Found at i:58927 original size:24 final size:24
Alignment explanation
Indices: 58870--58929 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
58860 CCTTACTACA
**
58870 ATATTAAAAGCTAGTCATATTTAT
1 ATATTAAAAAATAGTCATATTTAT
*
58894 TTATTAAAAAATAGTCATATTTAAT
1 ATATTAAAAAATAGTCATATTT-AT
*
58919 ATATCAAAAAA
1 ATATTAAAAAA
58930 CTAAAAAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 19 0.63
25 11 0.37
ACGTcount: A:0.50, C:0.07, G:0.05, T:0.38
Consensus pattern (24 bp):
ATATTAAAAAATAGTCATATTTAT
Found at i:60097 original size:22 final size:23
Alignment explanation
Indices: 60053--60098 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
60043 GAGTTCGACA
* **
60053 TTTTTTTATGTGATATTTGTATT
1 TTTTTTTATCTGATATTCATATT
60076 TTTTTTTATCTGAT-TTCATATT
1 TTTTTTTATCTGATATTCATATT
60098 T
1 T
60099 GTATTTAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.17, C:0.04, G:0.09, T:0.70
Consensus pattern (23 bp):
TTTTTTTATCTGATATTCATATT
Found at i:63029 original size:25 final size:23
Alignment explanation
Indices: 62970--63035 Score: 60
Period size: 24 Copynumber: 2.7 Consensus size: 23
62960 GAAAAAGGGG
* *
62970 AAAAAGGAAAATGCAAAGAGAAA
1 AAAAAGGAAAAGGGAAAGAGAAA
* *
62993 ATAAAAGAAAAAGGGAAAGATACTAA
1 A-AAAAGGAAAAGGGAAAGAGA--AA
*
63019 AAAAAGGAAAAGAGAAA
1 AAAAAGGAAAAGGGAAA
63036 AAAAAATTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
23 1 0.03
24 16 0.47
25 14 0.41
26 3 0.09
ACGTcount: A:0.70, C:0.03, G:0.21, T:0.06
Consensus pattern (23 bp):
AAAAAGGAAAAGGGAAAGAGAAA
Found at i:64709 original size:15 final size:15
Alignment explanation
Indices: 64664--64710 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
64654 AAATAAATTA
64664 AAAAATTAAGTGTT-
1 AAAAATTAAGTGTTG
*
64678 AAAAATATAAGTATTG
1 AAAAAT-TAAGTGTTG
*
64694 AAAAATTAAATGTTG
1 AAAAATTAAGTGTTG
64709 AA
1 AA
64711 TTTAAGTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 6 0.21
15 16 0.57
16 6 0.21
ACGTcount: A:0.55, C:0.00, G:0.13, T:0.32
Consensus pattern (15 bp):
AAAAATTAAGTGTTG
Found at i:64896 original size:13 final size:14
Alignment explanation
Indices: 64870--64898 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
64860 TCTTTTATAG
64870 TAAATTTCAATATT
1 TAAATTTCAATATT
64884 TAAATTT-AATATT
1 TAAATTTCAATATT
64897 TA
1 TA
64899 CATCATATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (14 bp):
TAAATTTCAATATT
Found at i:72713 original size:16 final size:16
Alignment explanation
Indices: 72689--72723 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
72679 CATTAAACAC
* *
72689 AACATCTACATTCGTT
1 AACACCTACATACGTT
72705 AACACCTACATACGTT
1 AACACCTACATACGTT
72721 AAC
1 AAC
72724 GAAAACGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.37, C:0.29, G:0.06, T:0.29
Consensus pattern (16 bp):
AACACCTACATACGTT
Found at i:75179 original size:95 final size:97
Alignment explanation
Indices: 75079--75275 Score: 217
Period size: 95 Copynumber: 2.0 Consensus size: 97
75069 ACTCAAAAGA
* * *
75079 TTTTTTTTGATGTATTTTG-ACAGTTCAAGTAAT-CAATTAAGTGCAATAAAAAAAA-CA-ATGG
1 TTTTTTTTGATGCA-TTTGAACAGTTCAAGT-ATCCAATCAAGTGCAA-AAAAAAAATCATA-AG
*
75140 CTTATTTG-C-TTCTTTTTTTTTAAGTTTGAAGGCT
62 CTTAATTGTCTTTCTTTTTTTTTAAGTTTGAAGGCT
* * * *
75174 TTTTTTTTTATGCATTTGAACAGTTTAAGTATCCAATCGAGTGTAAAAAAAAAATTCATAAGCTT
1 TTTTTTTTGATGCATTTGAACAGTTCAAGTATCCAATCAAGTGCAAAAAAAAAA-TCATAAGCTT
* *
75239 AATTGTCTTTTTTTTTTTTTAAGTTTGAGGGCT
65 AATTGTCTTTCTTTTTTTTTAAGTTTGAAGGCT
75272 TTTT
1 TTTT
75276 ACATCTTTAA
Statistics
Matches: 85, Mismatches: 10, Indels: 11
0.80 0.09 0.10
Matches are distributed among these distances:
94 14 0.16
95 32 0.38
96 10 0.12
97 2 0.02
98 27 0.32
ACGTcount: A:0.29, C:0.09, G:0.14, T:0.47
Consensus pattern (97 bp):
TTTTTTTTGATGCATTTGAACAGTTCAAGTATCCAATCAAGTGCAAAAAAAAAATCATAAGCTTA
ATTGTCTTTCTTTTTTTTTAAGTTTGAAGGCT
Found at i:75959 original size:24 final size:25
Alignment explanation
Indices: 75932--75983 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
75922 TGAATTAATA
* *
75932 AATTTAAGTAGAAAAA-ATCAAAAC
1 AATTTAAGAAGAAAAATAACAAAAC
**
75956 AATTTTTGAAGAAAAATAACAAAAC
1 AATTTAAGAAGAAAAATAACAAAAC
75981 AAT
1 AAT
75984 CTGATAATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 13 0.57
25 10 0.43
ACGTcount: A:0.62, C:0.08, G:0.08, T:0.23
Consensus pattern (25 bp):
AATTTAAGAAGAAAAATAACAAAAC
Found at i:90660 original size:21 final size:20
Alignment explanation
Indices: 90636--90720 Score: 65
Period size: 21 Copynumber: 4.5 Consensus size: 20
90626 CTTCTTTTGG
90636 ATCGATTGTTTTTATGTTTAA
1 ATCGATTG-TTTTATGTTTAA
* **
90657 ATCGATTG--TCATGTTGGA
1 ATCGATTGTTTTATGTTTAA
* *
90675 A-C-ATTG-TTTCT-TTTGA
1 ATCGATTGTTTTATGTTTAA
90691 ATCGATTGTTTATATGTTTAA
1 ATCGATTGTTT-TATGTTTAA
90712 ATCGATTGT
1 ATCGATTGT
90721 CGTGTTGGAA
Statistics
Matches: 50, Mismatches: 8, Indels: 12
0.71 0.11 0.17
Matches are distributed among these distances:
16 9 0.18
17 4 0.08
18 12 0.24
19 2 0.04
20 2 0.04
21 21 0.42
ACGTcount: A:0.24, C:0.08, G:0.18, T:0.51
Consensus pattern (20 bp):
ATCGATTGTTTTATGTTTAA
Found at i:90695 original size:55 final size:55
Alignment explanation
Indices: 90619--91003 Score: 477
Period size: 55 Copynumber: 6.9 Consensus size: 55
90609 ATTTCCCAAA
* * *
90619 AATATTGCTTCTTTTGGATCGATTGTTTTTATGTTTAAATCGATTGTCATGTTGG
1 AATATTGCTTCTTTTGAATCGATTGTTTATATGTTTAAATCGATTGTTATGTTGG
* * **
90674 AACATTGTTTCTTTTGAATCGATTGTTTATATGTTTAAATCGATTGTCGTGTTGG
1 AATATTGCTTCTTTTGAATCGATTGTTTATATGTTTAAATCGATTGTTATGTTGG
* * *
90729 AATACTGCTTCTTTTGAATCGATT-TTTAATATGTTTAAATCGATTGTTATGGTGA
1 AATATTGCTTCTTTTGAATCGATTGTTT-ATATGTTTAAATCGATTGTTATGTTGG
*
90784 AATATTGTTTCTTCTTCTTTTGAATCGATTGTTTATATGTTTAAATCAATTGTTATGTTGG
1 AATATTG------CTTCTTTTGAATCGATTGTTTATATGTTTAAATCGATTGTTATGTTGG
* * * *
90845 AATACTGCTTCTTTTGAATTGATTATTTATAGGTTTAAATCGATTGTTAT-TGTGG
1 AATATTGCTTCTTTTGAATCGATTGTTTATATGTTTAAATCGATTGTTATGT-TGG
* * * *
90900 AATATTACTTCTTTTGAATCGATTATTTATATGTTTAAATCAATTGTTTTGTTGG
1 AATATTGCTTCTTTTGAATCGATTGTTTATATGTTTAAATCGATTGTTATGTTGG
* ** *
90955 AATACTGCTTCTTTTGAATATATTGTTTATATGTTTAAATTGATTGTTA
1 AATATTGCTTCTTTTGAATCGATTGTTTATATGTTTAAATCGATTGTTA
91004 CGTAACACAA
Statistics
Matches: 285, Mismatches: 35, Indels: 20
0.84 0.10 0.06
Matches are distributed among these distances:
54 4 0.01
55 230 0.81
56 1 0.00
61 47 0.16
62 3 0.01
ACGTcount: A:0.25, C:0.08, G:0.16, T:0.51
Consensus pattern (55 bp):
AATATTGCTTCTTTTGAATCGATTGTTTATATGTTTAAATCGATTGTTATGTTGG
Found at i:90884 original size:171 final size:171
Alignment explanation
Indices: 90626--90947 Score: 477
Period size: 171 Copynumber: 1.9 Consensus size: 171
90616 AAAAATATTG
* * * * *
90626 CTTCTTTTGGATCGATTGTTTTTATGTTTAAATCGATTGTCATGTTGGAACATTGTTTCTTTTGA
1 CTTCTTTTGAATCGATTGTTTATATGTTTAAATCAATTGTCATGTTGGAACACTGCTTCTTTTGA
* * * *
90691 ATCGATTGTTTATATGTTTAAATCGATTGTC-GTGTTGGAATACTGCTTCTTTTGAATCGATT-T
66 ATCGATTATTTATAGGTTTAAATCGATTGTCATTG-TGGAATACTACTTCTTTTGAATCGATTAT
*
90754 TTAATATGTTTAAATCGATTGTTATGGTGAAATATTGTTTCTT
130 TT-ATATGTTTAAATCAATTGTTATGGTGAAATATTGTTTCTT
* *
90797 CTTCTTTTGAATCGATTGTTTATATGTTTAAATCAATTGTTATGTTGGAATACTGCTTCTTTTGA
1 CTTCTTTTGAATCGATTGTTTATATGTTTAAATCAATTGTCATGTTGGAACACTGCTTCTTTTGA
* * *
90862 ATTGATTATTTATAGGTTTAAATCGATTGTTATTGTGGAATATTACTTCTTTTGAATCGATTATT
66 ATCGATTATTTATAGGTTTAAATCGATTGTCATTGTGGAATACTACTTCTTTTGAATCGATTATT
90927 TATATGTTTAAATCAATTGTT
131 TATATGTTTAAATCAATTGTT
90948 TTGTTGGAAT
Statistics
Matches: 134, Mismatches: 15, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
171 129 0.96
172 5 0.04
ACGTcount: A:0.24, C:0.09, G:0.16, T:0.51
Consensus pattern (171 bp):
CTTCTTTTGAATCGATTGTTTATATGTTTAAATCAATTGTCATGTTGGAACACTGCTTCTTTTGA
ATCGATTATTTATAGGTTTAAATCGATTGTCATTGTGGAATACTACTTCTTTTGAATCGATTATT
TATATGTTTAAATCAATTGTTATGGTGAAATATTGTTTCTT
Found at i:91214 original size:24 final size:24
Alignment explanation
Indices: 91187--91234 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
91177 AAAACGTGTT
91187 TTCAAATTAATTTATTTTAAAACA
1 TTCAAATTAATTTATTTTAAAACA
91211 TTCAAATTAATTTATTTTAAAACA
1 TTCAAATTAATTTATTTTAAAACA
91235 ACTTACGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (24 bp):
TTCAAATTAATTTATTTTAAAACA
Found at i:96744 original size:202 final size:194
Alignment explanation
Indices: 96427--96818 Score: 497
Period size: 197 Copynumber: 2.0 Consensus size: 194
96417 GAAGAAGGGC
*
96427 ACAACTATCAAAACTTGTTTAAAATAATTTCCGAGACAAGAAAAATTTCCTCCAAACAAAAAAAA
1 ACAACTATCAAAACTTGTTTAAAATAATTTCCAAGACAAGAAAAATTTCCTCCAAAC--AAAAAA
*
96492 AAAAAAGCAGAAAATTTCAATATTCACTTCTTGTTATTAGTATAAAAATAAATATAATATAATTC
64 AAAAAA-CAGAAAATTTCAATAATCACTTCTTGTTATTAGTATAAAAAT-AATAT-A-AT--TT-
* *
96557 CTAATCCACTACA-CTTTTTTCAAAAGCTACTTTTACTATTTTTGAATTCTCACCTCATTGGAGA
122 CAAATCCACTACACCTTTTTTCAAAAGCTACTTTTACTATTTTTGAATTCTCACCTCATTGAAGA
96621 ACAAATGT
187 ACAAATGT
* *
96629 ACAATTATCAAAACTTGTTTAAAATAAATTT-TAAGACAAGAAAAATTT-CTCCAAAC-AAAAAA
1 ACAACTATCAAAACTTGTTTAAAAT-AATTTCCAAGACAAGAAAAATTTCCTCCAAACAAAAAAA
*
96691 AAAAA-AGAAAATTTCAATAATGACTTCTTGTTATTAGTATAAAAATTAAAATAATATAATTTCA
65 AAAAACAGAAAATTTCAATAATCACTTCTTGTTATTAGTAT----A--AAAATAATATAATTTCA
* * * * *
96755 AATTCACTACACCTTTTTTCTAAAGTTACTTTTGCTATTTTTGAATTGTCACCTCATTGAAGAA
124 AATCCACTACACCTTTTTTCAAAAGCTACTTTTACTATTTTTGAATTCTCACCTCATTGAAGAA
96819 TAAAGACACA
Statistics
Matches: 170, Mismatches: 12, Indels: 21
0.84 0.06 0.10
Matches are distributed among these distances:
196 44 0.26
197 49 0.29
198 11 0.06
199 2 0.01
200 2 0.01
201 13 0.08
202 44 0.26
203 5 0.03
ACGTcount: A:0.44, C:0.15, G:0.07, T:0.34
Consensus pattern (194 bp):
ACAACTATCAAAACTTGTTTAAAATAATTTCCAAGACAAGAAAAATTTCCTCCAAACAAAAAAAA
AAAACAGAAAATTTCAATAATCACTTCTTGTTATTAGTATAAAAATAATATAATTTCAAATCCAC
TACACCTTTTTTCAAAAGCTACTTTTACTATTTTTGAATTCTCACCTCATTGAAGAACAAATGT
Found at i:104314 original size:20 final size:22
Alignment explanation
Indices: 104281--104328 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 22
104271 TAAAATAAAT
*
104281 AAATAATACATTAAATTGAA-A
1 AAATAATACATTAAATTAAAGA
* *
104302 AAATAATTC-TTAATTTAAAGA
1 AAATAATACATTAAATTAAAGA
104323 AAATAA
1 AAATAA
104329 ATGTAATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.31
Consensus pattern (22 bp):
AAATAATACATTAAATTAAAGA
Found at i:110637 original size:22 final size:21
Alignment explanation
Indices: 110590--110637 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
110580 TTGAATTTTC
*
110590 AAAAATTATAGTTAAAAAGTA
1 AAAAATTATAGTTAAAAAGCA
110611 AAAAATATATAGTTAAAAA-CA
1 AAAAAT-TATAGTTAAAAAGCA
110632 ATAAAA
1 A-AAAA
110638 ATGTTATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 8 0.33
22 16 0.67
ACGTcount: A:0.67, C:0.02, G:0.06, T:0.25
Consensus pattern (21 bp):
AAAAATTATAGTTAAAAAGCA
Found at i:110645 original size:24 final size:22
Alignment explanation
Indices: 110590--110645 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
110580 TTGAATTTTC
**
110590 AAAAA-TTATAGTTAAAAAGTA
1 AAAAATTTATAGTTAAAAACAA
*
110611 AAAAATATATAGTTAAAAACAA
1 AAAAATTTATAGTTAAAAACAA
110633 TAAAAATGTTATA
1 -AAAAAT-TTATA
110646 AATAAATAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
21 5 0.18
22 13 0.46
23 6 0.21
24 4 0.14
ACGTcount: A:0.62, C:0.02, G:0.07, T:0.29
Consensus pattern (22 bp):
AAAAATTTATAGTTAAAAACAA
Found at i:120886 original size:3 final size:3
Alignment explanation
Indices: 120878--120904 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
120868 CTCTCTCTTT
120878 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
120905 AAGGGTAGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:128153 original size:22 final size:24
Alignment explanation
Indices: 128128--128188 Score: 63
Period size: 22 Copynumber: 2.6 Consensus size: 24
128118 AAATTAAATT
128128 ATATATTTTTATAATAGTAA-A-A
1 ATATATTTTTATAATAGTAATAGA
* * * *
128150 ATATAATTTTATCATATTAATAGT
1 ATATATTTTTATAATAGTAATAGA
*
128174 CTATATTTTTATAAT
1 ATATATTTTTATAAT
128189 TTTTAAAAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
22 17 0.57
23 1 0.03
24 12 0.40
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (24 bp):
ATATATTTTTATAATAGTAATAGA
Found at i:161661 original size:3 final size:3
Alignment explanation
Indices: 161653--161688 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
161643 TTCAACGGTA
161653 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
161689 GTTTTTGTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:163329 original size:65 final size:65
Alignment explanation
Indices: 163246--163378 Score: 248
Period size: 65 Copynumber: 2.0 Consensus size: 65
163236 CATCAAGTCA
163246 ATACACAAAATTTTTATATATATAATTATTGAACGGTGGGTAGTAAGCTTTGGTTCAATTTATTT
1 ATACACAAAATTTTTATATATATAATTATTGAACGGTGGGTAGTAAGCTTTGGTTCAATTTATTT
* *
163311 ATACACGAGATTTTTATATATATAATTATTGAACGGTGGGTAGTAAGCTTTGGTTCAATTTATTT
1 ATACACAAAATTTTTATATATATAATTATTGAACGGTGGGTAGTAAGCTTTGGTTCAATTTATTT
163376 ATA
1 ATA
163379 TATAAAAATA
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 66 1.00
ACGTcount: A:0.33, C:0.08, G:0.17, T:0.43
Consensus pattern (65 bp):
ATACACAAAATTTTTATATATATAATTATTGAACGGTGGGTAGTAAGCTTTGGTTCAATTTATTT
Found at i:167528 original size:16 final size:15
Alignment explanation
Indices: 167489--167531 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
167479 CTTTAAAATA
167489 ATAAAATTTTAATTT
1 ATAAAATTTTAATTT
* **
167504 ACATTATTTATAATTT
1 ATAAAATTT-TAATTT
167520 ATAAAATTTTAA
1 ATAAAATTTTAA
167532 ATTAATAATA
Statistics
Matches: 21, Mismatches: 6, Indels: 2
0.72 0.21 0.07
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (15 bp):
ATAAAATTTTAATTT
Found at i:168811 original size:18 final size:17
Alignment explanation
Indices: 168771--168813 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
168761 TTTTCAGTTG
* *
168771 TAATTAATTTAAAATTT
1 TAATTAATTGAAAAATT
168788 TCAATTAATTGAATAAATT
1 T-AATTAATTGAA-AAATT
168807 TAATTAA
1 TAATTAA
168814 AAAATTATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 1 0.05
18 16 0.73
19 5 0.23
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (17 bp):
TAATTAATTGAAAAATT
Found at i:169213 original size:43 final size:43
Alignment explanation
Indices: 169147--169230 Score: 141
Period size: 43 Copynumber: 2.0 Consensus size: 43
169137 AGATAAAAAG
*
169147 TTATTCAATTGTGAATTGTTAATATAACAACAGCAAATAATAT
1 TTATTCAATTGTGAATTGCTAATATAACAACAGCAAATAATAT
* *
169190 TTATTCAATTGTGAATTGCTAATATAATAGCAGCAAATAAT
1 TTATTCAATTGTGAATTGCTAATATAACAACAGCAAATAAT
169231 GTCTTGCTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.43, C:0.10, G:0.11, T:0.37
Consensus pattern (43 bp):
TTATTCAATTGTGAATTGCTAATATAACAACAGCAAATAATAT
Found at i:169615 original size:15 final size:16
Alignment explanation
Indices: 169582--169628 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
169572 CTCGAATCCT
169582 AAAAATCTGAGCTCGA
1 AAAAATCTGAGCTCGA
* *
169598 AAAAATTTGAG-TCTA
1 AAAAATCTGAGCTCGA
*
169613 AAAAGACCTGAGCTCG
1 AAAA-ATCTGAGCTCG
169629 TTACAGATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
15 7 0.29
16 15 0.62
17 2 0.08
ACGTcount: A:0.43, C:0.17, G:0.19, T:0.21
Consensus pattern (16 bp):
AAAAATCTGAGCTCGA
Found at i:173138 original size:20 final size:18
Alignment explanation
Indices: 173103--173144 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 18
173093 TTAGATTTTT
173103 TTTTTTAACATATTGATAA
1 TTTTTTAACATATTGAT-A
173122 TTTTTTATA-ATAGTTGATA
1 TTTTTTA-ACATA-TTGATA
173141 TTTT
1 TTTT
173145 AAAATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.31, C:0.02, G:0.07, T:0.60
Consensus pattern (18 bp):
TTTTTTAACATATTGATA
Found at i:174131 original size:2 final size:2
Alignment explanation
Indices: 174124--174157 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
174114 GTTTAGTCCC
174124 TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
174158 GAAGTACTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:174870 original size:18 final size:17
Alignment explanation
Indices: 174817--174870 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 17
174807 TGCAGCAAAT
*
174817 ATAAAATTTTATTATATT
1 ATAAAATTTTATTATA-C
* *
174835 ATTAAATTTTA-AATAC
1 ATAAAATTTTATTATAC
174851 ATAAAATTATTATTATAC
1 ATAAAATT-TTATTATAC
174869 AT
1 AT
174871 TCATCCATAG
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
16 7 0.24
17 6 0.21
18 16 0.55
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (17 bp):
ATAAAATTTTATTATAC
Found at i:176274 original size:18 final size:16
Alignment explanation
Indices: 176216--176261 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
176206 CGAGTGTATA
176216 ATAAAATTTTATGTGT
1 ATAAAATTTTATGTGT
* *
176232 TTAAAATTTAATGATGT
1 ATAAAATTTTATG-TGT
176249 GATAAAATTTTAT
1 -ATAAAATTTTAT
176262 TGTTGTCTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
16 11 0.46
17 3 0.12
18 10 0.42
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (16 bp):
ATAAAATTTTATGTGT
Done.