Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014892.1 Kokia drynarioides strain JFW-HI SEQ_129935, 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: 189546
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 337 characters in sequence are not A, C, G, or T
Found at i:4077 original size:33 final size:33
Alignment explanation
Indices: 4037--4146 Score: 220
Period size: 33 Copynumber: 3.3 Consensus size: 33
4027 AAAATTTAAA
4037 AATTATTAACCGACCTCTGATCGAACTAAATTT
1 AATTATTAACCGACCTCTGATCGAACTAAATTT
4070 AATTATTAACCGACCTCTGATCGAACTAAATTT
1 AATTATTAACCGACCTCTGATCGAACTAAATTT
4103 AATTATTAACCGACCTCTGATCGAACTAAATTT
1 AATTATTAACCGACCTCTGATCGAACTAAATTT
4136 AATTATTAACC
1 AATTATTAACC
4147 AATTAACTGA
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 77 1.00
ACGTcount: A:0.37, C:0.21, G:0.08, T:0.34
Consensus pattern (33 bp):
AATTATTAACCGACCTCTGATCGAACTAAATTT
Found at i:8716 original size:53 final size:54
Alignment explanation
Indices: 8638--8749 Score: 190
Period size: 53 Copynumber: 2.1 Consensus size: 54
8628 TCCTGAGAGT
* *
8638 ATCGCTGTAATGAATAAATCCTTAACGTTGTGGGTTAAATCAATAGAGAGTGAC
1 ATCGCTGTAATGAATAAATCCTTAACGTTGCGGCTTAAATCAATAGAGAGTGAC
*
8692 ATCGCTGTAATG-TTAAATCCTTAACGTTGCGGCTTAAATCAATAGAGAGTGAC
1 ATCGCTGTAATGAATAAATCCTTAACGTTGCGGCTTAAATCAATAGAGAGTGAC
8745 ATCGC
1 ATCGC
8750 AACCTCAAGC
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
53 43 0.78
54 12 0.22
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.29
Consensus pattern (54 bp):
ATCGCTGTAATGAATAAATCCTTAACGTTGCGGCTTAAATCAATAGAGAGTGAC
Found at i:9502 original size:28 final size:27
Alignment explanation
Indices: 9449--9503 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
9439 TTAAATGCAT
* *
9449 TCAAATTAATAACTTTTTATGATCAAA
1 TCAAATTAATAAATTTTTATAATCAAA
9476 TCAAATTAAGTAAAATTTTT-TAATCAAA
1 TCAAATTAA-T-AAATTTTTATAATCAAA
9504 ATTGAATCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 9 0.38
28 8 0.33
29 7 0.29
ACGTcount: A:0.47, C:0.09, G:0.04, T:0.40
Consensus pattern (27 bp):
TCAAATTAATAAATTTTTATAATCAAA
Found at i:14349 original size:32 final size:34
Alignment explanation
Indices: 14294--14361 Score: 88
Period size: 32 Copynumber: 2.0 Consensus size: 34
14284 GTAAAATTAT
*
14294 TAAAATACATTTAAAAGATTTAAAATT-TATAAA
1 TAAAATACATTAAAAAGATTTAAAATTATATAAA
14327 TAAAAT-CATTAAAAAG-TATTAAAATTGATATAAA
1 TAAAATACATTAAAAAGAT-TTAAAATT-ATATAAA
14361 T
1 T
14362 TTATAAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
31 1 0.03
32 17 0.55
33 6 0.19
34 7 0.23
ACGTcount: A:0.57, C:0.03, G:0.04, T:0.35
Consensus pattern (34 bp):
TAAAATACATTAAAAAGATTTAAAATTATATAAA
Found at i:17982 original size:12 final size:12
Alignment explanation
Indices: 17965--17996 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
17955 TGAGGGAAGA
17965 GAGTCCGAGAAT
1 GAGTCCGAGAAT
17977 GAGTCCGAGAAT
1 GAGTCCGAGAAT
*
17989 GAGCCCGA
1 GAGTCCGA
17997 CTATGAGCCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.31, C:0.22, G:0.34, T:0.12
Consensus pattern (12 bp):
GAGTCCGAGAAT
Found at i:35269 original size:24 final size:22
Alignment explanation
Indices: 35215--35271 Score: 60
Period size: 24 Copynumber: 2.5 Consensus size: 22
35205 TAAAATTTAT
*
35215 TTTTATTATAAAAGTATTAAAA
1 TTTTATTAAAAAAGTATTAAAA
* *
35237 TATTAATTAAAATAAGTATTTAATA
1 T-TTTATTAAAA-AAGTA-TTAAAA
35262 TTTTATTAAA
1 TTTTATTAAA
35272 TTTTAAATAG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
22 1 0.04
23 8 0.29
24 13 0.46
25 6 0.21
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (22 bp):
TTTTATTAAAAAAGTATTAAAA
Found at i:35272 original size:23 final size:22
Alignment explanation
Indices: 35215--35272 Score: 55
Period size: 23 Copynumber: 2.5 Consensus size: 22
35205 TAAAATTTAT
35215 TTTTATTATAA-AAGTATTAAAA
1 TTTTATTA-AATAAGTATTAAAA
* *
35237 TATTAATTAAAATAAGTATTTAATA
1 T-TTTATT-AAATAAGTA-TTAAAA
35262 TTTTATTAAAT
1 TTTTATTAAAT
35273 TTTAAATAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
22 1 0.03
23 11 0.38
24 11 0.38
25 6 0.21
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (22 bp):
TTTTATTAAATAAGTATTAAAA
Found at i:61279 original size:2 final size:2
Alignment explanation
Indices: 61267--61306 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
61257 TCAAATGCAG
61267 TA TA T- TA TA TA TA TA 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 TA TA TA T
61307 TAGAGCTAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:75050 original size:115 final size:115
Alignment explanation
Indices: 74848--75078 Score: 453
Period size: 115 Copynumber: 2.0 Consensus size: 115
74838 GGTGCGAAGG
74848 TAAAATTAAGTTTTAACGAGACCTAAATTGAAATATAAATTTTTTAGGAGTAAAAGATGATTTTA
1 TAAAATTAAGTTTTAACGAGACCTAAATTGAAATATAAATTTTTTAGGAGTAAAAGATGATTTTA
74913 CTATTGTACTAATTTATAATTTCATAGTTTTCAAAATGATTTAAAAGCAA
66 CTATTGTACTAATTTATAATTTCATAGTTTTCAAAATGATTTAAAAGCAA
*
74963 TAAAATTAAGTTTTAACGAGACTTAAATTGAAATATAAATTTTTTAGGAGTAAAAGATGATTTTA
1 TAAAATTAAGTTTTAACGAGACCTAAATTGAAATATAAATTTTTTAGGAGTAAAAGATGATTTTA
75028 CTATTGTACTAATTTATAATTTCATAGTTTTCAAAATGATTTAAAAGCAA
66 CTATTGTACTAATTTATAATTTCATAGTTTTCAAAATGATTTAAAAGCAA
75078 T
1 T
75079 TTTACCATTT
Statistics
Matches: 115, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
115 115 1.00
ACGTcount: A:0.42, C:0.06, G:0.11, T:0.40
Consensus pattern (115 bp):
TAAAATTAAGTTTTAACGAGACCTAAATTGAAATATAAATTTTTTAGGAGTAAAAGATGATTTTA
CTATTGTACTAATTTATAATTTCATAGTTTTCAAAATGATTTAAAAGCAA
Found at i:75217 original size:29 final size:29
Alignment explanation
Indices: 75171--75231 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
75161 GGAGCCTTTG
*
75171 CCTCAAAATTTGTAAA-TTACATTTTAGAT
1 CCTCAAAATTTATAAATTTA-ATTTTAGAT
*
75200 CCTCAAAAGTTTAT-AATTTAATTTTAGCT
1 CCTCAAAA-TTTATAAATTTAATTTTAGAT
75229 CCT
1 CCT
75232 TTAAAAAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 21 0.75
30 7 0.25
ACGTcount: A:0.34, C:0.16, G:0.07, T:0.43
Consensus pattern (29 bp):
CCTCAAAATTTATAAATTTAATTTTAGAT
Found at i:76072 original size:17 final size:16
Alignment explanation
Indices: 76046--76079 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
76036 ATTAGTTAAC
*
76046 TTTGGTTTTTATATTT
1 TTTGGTTTTTAAATTT
76062 TTTGAGTTTTTAAATTT
1 TTTG-GTTTTTAAATTT
76079 T
1 T
76080 AGCTCAGACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.18, C:0.00, G:0.12, T:0.71
Consensus pattern (16 bp):
TTTGGTTTTTAAATTT
Found at i:81051 original size:38 final size:38
Alignment explanation
Indices: 81006--81084 Score: 149
Period size: 38 Copynumber: 2.1 Consensus size: 38
80996 AATATTTAGG
*
81006 ATTATTATTGTTATATTGTTTATATTTAATTTTAATTT
1 ATTATTATTATTATATTGTTTATATTTAATTTTAATTT
81044 ATTATTATTATTATATTGTTTATATTTAATTTTAATTT
1 ATTATTATTATTATATTGTTTATATTTAATTTTAATTT
81082 ATT
1 ATT
81085 TTTTAAGCTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (38 bp):
ATTATTATTATTATATTGTTTATATTTAATTTTAATTT
Found at i:81164 original size:25 final size:23
Alignment explanation
Indices: 81123--81168 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
81113 CCAATTAGGG
81123 AATTATTATTTAGATTTAATTCT
1 AATTATTATTTAGATTTAATTCT
*
81146 AATTATCTTTTTAGAATTTAATT
1 AATTAT-TATTTAG-ATTTAATT
81169 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (23 bp):
AATTATTATTTAGATTTAATTCT
Found at i:84574 original size:31 final size:31
Alignment explanation
Indices: 84539--84649 Score: 90
Period size: 31 Copynumber: 3.7 Consensus size: 31
84529 CAAAAGAAAG
* *
84539 TGTCAAGTTTAGGTACTAAATTAAGAAAAAA
1 TGTCAAATTTAGGTACCAAATTAAGAAAAAA
* *
84570 TGTCAAATTT-GAGTACCAAATT-GGACCCAAAA
1 TGTCAAATTTAG-GTACCAAATTAAGA--AAAAA
* *
84602 ----AAATTTAGGTACTAAATTAAGAAAATA
1 TGTCAAATTTAGGTACCAAATTAAGAAAAAA
*
84629 TGTCAAATTCAGGTACCAAAT
1 TGTCAAATTTAGGTACCAAAT
84650 ATTATATTAA
Statistics
Matches: 61, Mismatches: 10, Indels: 18
0.69 0.11 0.20
Matches are distributed among these distances:
27 3 0.05
28 15 0.25
29 3 0.05
30 3 0.05
31 33 0.54
32 4 0.07
ACGTcount: A:0.46, C:0.12, G:0.14, T:0.28
Consensus pattern (31 bp):
TGTCAAATTTAGGTACCAAATTAAGAAAAAA
Found at i:84633 original size:90 final size:90
Alignment explanation
Indices: 84462--84649 Score: 202
Period size: 90 Copynumber: 2.1 Consensus size: 90
84452 AAAAATTACA
* * * * *
84462 TACTAAATTAGGAAAAATAGTCAAGTTCAAGTACTAAATTGGACCCCAAAAAGTTTAAGTACCAA
1 TACTAAATTAGAAAAAATAGTCAAATTCAAGTACCAAATTGGACCCAAAAAAATTTAAGTACCAA
* * *
84527 CTCAAAAGAAAGTGTCAAGTTTAGG
66 ATCAAAAGAAAGTGTCAAATTCAGG
** * *
84552 TACTAAATTAAGAAAAAAT-GTCAAATTTGAGTACCAAATTGGACCCAAAAAAATTTAGGTACTA
1 TACTAAATT-AGAAAAAATAGTCAAATTCAAGTACCAAATTGGACCCAAAAAAATTTAAGTACCA
*
84616 AATTAAGAA-AATA-TGTCAAATTCAGG
65 AATCAA-AAGAA-AGTGTCAAATTCAGG
*
84642 TACCAAAT
1 TACTAAAT
84650 ATTATATTAA
Statistics
Matches: 81, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
90 70 0.86
91 11 0.14
ACGTcount: A:0.47, C:0.13, G:0.14, T:0.26
Consensus pattern (90 bp):
TACTAAATTAGAAAAAATAGTCAAATTCAAGTACCAAATTGGACCCAAAAAAATTTAAGTACCAA
ATCAAAAGAAAGTGTCAAATTCAGG
Found at i:86025 original size:17 final size:17
Alignment explanation
Indices: 86000--86034 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
85990 AACATAATTT
* *
86000 AAAATAAAAAAATTAAA
1 AAAAAAAAAAAAGTAAA
86017 AAAAAAAAAAAAGTAAA
1 AAAAAAAAAAAAGTAAA
86034 A
1 A
86035 TGTTTCTGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.86, C:0.00, G:0.03, T:0.11
Consensus pattern (17 bp):
AAAAAAAAAAAAGTAAA
Found at i:88653 original size:6 final size:6
Alignment explanation
Indices: 88644--88669 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
88634 CATATTCAAT
88644 CACAAA CACAAA CACAAA CACAAA CA
1 CACAAA CACAAA CACAAA CACAAA CA
88670 TGGTTACCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.65, C:0.35, G:0.00, T:0.00
Consensus pattern (6 bp):
CACAAA
Found at i:94819 original size:21 final size:22
Alignment explanation
Indices: 94794--94835 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
94784 TTTTAAATAT
*
94794 TTTTTAATAATCT-TATTATAA
1 TTTTTAATAATATATATTATAA
*
94815 TTTTTGATAATATATATTATA
1 TTTTTAATAATATATATTATA
94836 CAATACTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (22 bp):
TTTTTAATAATATATATTATAA
Found at i:95281 original size:109 final size:109
Alignment explanation
Indices: 95090--95314 Score: 450
Period size: 109 Copynumber: 2.1 Consensus size: 109
95080 AACAATAATG
95090 GCCACAAACCAGAATTAATGGAAAACTATTAGGATGATAATAGGTACTAAAAAAATTAAAATAAA
1 GCCACAAACCAGAATTAATGGAAAACTATTAGGATGATAATAGGTACTAAAAAAATTAAAATAAA
95155 ATTCCAACGTAATACAGATGAGTTTTTTTTTAAGGTTAAAATAT
66 ATTCCAACGTAATACAGATGAGTTTTTTTTTAAGGTTAAAATAT
95199 GCCACAAACCAGAATTAATGGAAAACTATTAGGATGATAATAGGTACTAAAAAAATTAAAATAAA
1 GCCACAAACCAGAATTAATGGAAAACTATTAGGATGATAATAGGTACTAAAAAAATTAAAATAAA
95264 ATTCCAACGTAATACAGATGAGTTTTTTTTTAAGGTTAAAATAT
66 ATTCCAACGTAATACAGATGAGTTTTTTTTTAAGGTTAAAATAT
95308 GCCACAA
1 GCCACAA
95315 GTCTTTGTAT
Statistics
Matches: 116, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
109 116 1.00
ACGTcount: A:0.47, C:0.11, G:0.14, T:0.28
Consensus pattern (109 bp):
GCCACAAACCAGAATTAATGGAAAACTATTAGGATGATAATAGGTACTAAAAAAATTAAAATAAA
ATTCCAACGTAATACAGATGAGTTTTTTTTTAAGGTTAAAATAT
Found at i:96912 original size:26 final size:27
Alignment explanation
Indices: 96868--96919 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
96858 TTTTGAACAA
96868 CTTTTAAAGGGTCTCAATTTCTTTTTAG
1 CTTTTAAAGGGTCTCAATTT-TTTTTAG
96896 CTTTT-AAGGG-CTCAATTTTTTTTA
1 CTTTTAAAGGGTCTCAATTTTTTTTA
96920 ACCAATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 6 0.25
26 8 0.33
27 5 0.21
28 5 0.21
ACGTcount: A:0.21, C:0.13, G:0.13, T:0.52
Consensus pattern (27 bp):
CTTTTAAAGGGTCTCAATTTTTTTTAG
Found at i:96928 original size:28 final size:29
Alignment explanation
Indices: 96853--96928 Score: 79
Period size: 26 Copynumber: 2.7 Consensus size: 29
96843 TAAAGACCAA
*
96853 AATTTTTTTGAACAACTTTTAAAGGGTCTC
1 AATTTTTTTTAACAA-TTTTAAAGGGTCTC
*
96883 AATTTCTTTTTAGC--TTTT-AAGGG-CTC
1 AATTT-TTTTTAACAATTTTAAAGGGTCTC
96909 AATTTTTTTTAACCAATTTT
1 AATTTTTTTTAA-CAATTTT
96929 TAAGAGATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
25 6 0.15
26 9 0.23
27 5 0.13
28 8 0.21
30 5 0.13
31 6 0.15
ACGTcount: A:0.26, C:0.13, G:0.11, T:0.50
Consensus pattern (29 bp):
AATTTTTTTTAACAATTTTAAAGGGTCTC
Found at i:99373 original size:16 final size:16
Alignment explanation
Indices: 99354--99384 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
99344 AATTTAAAAA
99354 TAAAAAACTAAATTAG
1 TAAAAAACTAAATTAG
99370 TAAAAAACTAAATTA
1 TAAAAAACTAAATTA
99385 CTAATTTACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (16 bp):
TAAAAAACTAAATTAG
Found at i:100938 original size:101 final size:101
Alignment explanation
Indices: 100763--100950 Score: 331
Period size: 101 Copynumber: 1.9 Consensus size: 101
100753 CNNNNNNCCC
* * *
100763 TTTGTAGATGATTGAATTAGAGTGAAATCAACGTTTTATGGTGGATTATATTATGTTATGTTCCT
1 TTTGTAGATGACTGAATTAGAGTGAAATCAACCTTGTATGGTGGATTATATTATGTTATGTTCCT
100828 CCTTTCTCAGTATGGTTACCATCTCTCCCCCCCCTT
66 CCTTTCTCAGTATGGTTACCATCTCTCCCCCCCCTT
* *
100864 TTTGTAGATGACTGAATTAGAGTGAAATCAACCTTGTATGGTGGATTATATTATGTTATTTTCGT
1 TTTGTAGATGACTGAATTAGAGTGAAATCAACCTTGTATGGTGGATTATATTATGTTATGTTCCT
100929 CCTTTCTCAGTATGGTTACCAT
66 CCTTTCTCAGTATGGTTACCAT
100951 GATGATGGTA
Statistics
Matches: 82, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
101 82 1.00
ACGTcount: A:0.23, C:0.16, G:0.18, T:0.42
Consensus pattern (101 bp):
TTTGTAGATGACTGAATTAGAGTGAAATCAACCTTGTATGGTGGATTATATTATGTTATGTTCCT
CCTTTCTCAGTATGGTTACCATCTCTCCCCCCCCTT
Found at i:105762 original size:76 final size:76
Alignment explanation
Indices: 105636--105788 Score: 297
Period size: 76 Copynumber: 2.0 Consensus size: 76
105626 TGAAAATTGG
*
105636 TTAATGTAATAAACTAGATAGGTTGTTTTAAATGGATAAAATTTTATGGATCAATGGTCTAAGCC
1 TTAATGTAATAAACTAGATAGGTTGTTTCAAATGGATAAAATTTTATGGATCAATGGTCTAAGCC
105701 ATTTGTTTGAT
66 ATTTGTTTGAT
105712 TTAATGTAATAAACTAGATAGGTTGTTTCAAATGGATAAAATTTTATGGATCAATGGTCTAAGCC
1 TTAATGTAATAAACTAGATAGGTTGTTTCAAATGGATAAAATTTTATGGATCAATGGTCTAAGCC
105777 ATTTGTTTGAT
66 ATTTGTTTGAT
105788 T
1 T
105789 AAGTTGATTC
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 76 1.00
ACGTcount: A:0.34, C:0.07, G:0.18, T:0.41
Consensus pattern (76 bp):
TTAATGTAATAAACTAGATAGGTTGTTTCAAATGGATAAAATTTTATGGATCAATGGTCTAAGCC
ATTTGTTTGAT
Found at i:106453 original size:39 final size:38
Alignment explanation
Indices: 106384--106463 Score: 108
Period size: 39 Copynumber: 2.1 Consensus size: 38
106374 GTAATTACGC
*
106384 AATTACACAAATTATTACTTCTTCCATAATGTTTTGTGT
1 AATTACACAAATTATTACATCTT-CATAATGTTTTGTGT
*
106423 AATTACACAAATTATTACAAATCTT-GTAATGTTTTGTGT
1 AATTACACAAATTATTAC--ATCTTCATAATGTTTTGTGT
106462 AA
1 AA
106464 CATGGATCAC
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
39 33 0.89
41 4 0.11
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.44
Consensus pattern (38 bp):
AATTACACAAATTATTACATCTTCATAATGTTTTGTGT
Found at i:108476 original size:65 final size:65
Alignment explanation
Indices: 108372--108511 Score: 262
Period size: 65 Copynumber: 2.2 Consensus size: 65
108362 AGTCCATTCT
* *
108372 TGAAAACCTTGAGTTTGTGTTGTGTGTGTTTATATGGTTAACCAAGAAAAAATTATGAAATTTTA
1 TGAAAACCATGAGTTTGTGTTGTGTGTGTTTATATGGTTAACCAAGAAAAAATTATGAAAATTTA
108437 TGAAAACCATGAGTTTGTGTTGTGTGTGTTTATATGGTTAACCAAGAAAAAATTATGAAAATTTA
1 TGAAAACCATGAGTTTGTGTTGTGTGTGTTTATATGGTTAACCAAGAAAAAATTATGAAAATTTA
108502 TGAAAACCAT
1 TGAAAACCAT
108512 AATATAGGGG
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 73 1.00
ACGTcount: A:0.36, C:0.07, G:0.19, T:0.37
Consensus pattern (65 bp):
TGAAAACCATGAGTTTGTGTTGTGTGTGTTTATATGGTTAACCAAGAAAAAATTATGAAAATTTA
Found at i:108580 original size:28 final size:30
Alignment explanation
Indices: 108533--108596 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 30
108523 GAAGAATTGG
108533 TTTTTTGGGGGTTAGAAATTAAATAGT-AT
1 TTTTTTGGGGGTTAGAAATTAAATAGTAAT
* * *
108562 TTTTTTGGGTGTTAG-AATTGAATGGTAAT
1 TTTTTTGGGGGTTAGAAATTAAATAGTAAT
108591 TTTTTT
1 TTTTTT
108597 AGGTCAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
28 9 0.29
29 22 0.71
ACGTcount: A:0.25, C:0.00, G:0.23, T:0.52
Consensus pattern (30 bp):
TTTTTTGGGGGTTAGAAATTAAATAGTAAT
Found at i:113228 original size:3 final size:3
Alignment explanation
Indices: 113220--113273 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
113210 TGTTACATTT
113220 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
113268 TTC TTC
1 TTC TTC
113274 AACATATTAG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:113954 original size:2 final size:2
Alignment explanation
Indices: 113947--113979 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
113937 TACATACACA
113947 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
113980 GTTATATACC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:118597 original size:26 final size:26
Alignment explanation
Indices: 118564--118615 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
118554 TATCGATTGG
118564 GTCTTAATTCAGTTGGTATTGTCATT
1 GTCTTAATTCAGTTGGTATTGTCATT
118590 GTCTTAATTCAGTTGGTATTGTCATT
1 GTCTTAATTCAGTTGGTATTGTCATT
118616 ACTGTTAGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.19, C:0.12, G:0.19, T:0.50
Consensus pattern (26 bp):
GTCTTAATTCAGTTGGTATTGTCATT
Found at i:119637 original size:4 final size:4
Alignment explanation
Indices: 119628--119652 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
119618 CGACTCAATT
119628 ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA A
119653 AACATTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:120367 original size:20 final size:21
Alignment explanation
Indices: 120344--120383 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
120334 TAATGTTACA
120344 TTCA-TATTTTTATTTTGAAT
1 TTCAGTATTTTTATTTTGAAT
120364 TTCAGTATTTTTATTTTGAA
1 TTCAGTATTTTTATTTTGAA
120384 AAAAAATCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.25, C:0.05, G:0.07, T:0.62
Consensus pattern (21 bp):
TTCAGTATTTTTATTTTGAAT
Found at i:120768 original size:23 final size:21
Alignment explanation
Indices: 120729--120772 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 21
120719 TATACACGAT
* *
120729 AAAATTATATTTTAATTCTTAA
1 AAAATTATAATTCAATT-TTAA
120751 AAAATTTATAATTCAATTTTAA
1 AAAA-TTATAATTCAATTTTAA
120773 CCTCATTTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (21 bp):
AAAATTATAATTCAATTTTAA
Found at i:123244 original size:144 final size:143
Alignment explanation
Indices: 123089--123377 Score: 542
Period size: 144 Copynumber: 2.0 Consensus size: 143
123079 AACTTAATAA
123089 ATAATATTATAAATATATAAGTATTAGTCCACTTAATAAATCGATCGGTTCAAAATTGTTCTGTT
1 ATAATATTATAAATATATAAGTATTAGTCCACTTAATAAATCGATCGGTTCAAAATTGTTCTGTT
* *
123154 AATTTGATTAATTTTTATATGTTTTATATTTGTTTCAACAAAAAATAAAAAATATATAAATTTCG
66 AATTCGATTAATTTTTATATGTTTTATATTTGTTTCAACAAAAAAT-AAAAACATATAAATTTCG
*
123219 GTTAATTTGGTTCG
130 GTTAATTCGGTTCG
123233 ATAATATTATAAATATATAAGTATTAGTCCACTTAATAAATCGATCGGTTCAAAATTGTTCTGTT
1 ATAATATTATAAATATATAAGTATTAGTCCACTTAATAAATCGATCGGTTCAAAATTGTTCTGTT
123298 AATTCGATTAATTTTTATATGTTTTATATTTGTTTCAACAAAAAATAAAAACATATAAATTTCGG
66 AATTCGATTAATTTTTATATGTTTTATATTTGTTTCAACAAAAAATAAAAACATATAAATTTCGG
123363 TTAATTCGGTTCG
131 TTAATTCGGTTCG
123376 AT
1 AT
123378 TAATGTTTTT
Statistics
Matches: 142, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
143 32 0.23
144 110 0.77
ACGTcount: A:0.38, C:0.09, G:0.10, T:0.43
Consensus pattern (143 bp):
ATAATATTATAAATATATAAGTATTAGTCCACTTAATAAATCGATCGGTTCAAAATTGTTCTGTT
AATTCGATTAATTTTTATATGTTTTATATTTGTTTCAACAAAAAATAAAAACATATAAATTTCGG
TTAATTCGGTTCG
Found at i:126839 original size:24 final size:23
Alignment explanation
Indices: 126804--126871 Score: 75
Period size: 24 Copynumber: 2.9 Consensus size: 23
126794 AATCAATTAT
*
126804 ATTCAACT-AATACTAAATTTAC
1 ATTCAATTAAATACTAAATTTAC
* **
126826 ATTGCAATTAAATACTTAAAATTGT
1 ATT-CAATTAAATAC-TAAATTTAC
126851 ATTCAATTAAATACTAAATTT
1 ATTCAATTAAATACTAAATTT
126872 GGAGTTACTA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
22 3 0.08
23 10 0.26
24 16 0.42
25 9 0.24
ACGTcount: A:0.46, C:0.12, G:0.03, T:0.40
Consensus pattern (23 bp):
ATTCAATTAAATACTAAATTTAC
Found at i:130216 original size:29 final size:30
Alignment explanation
Indices: 130162--130226 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
130152 TTTAATATAC
* * *
130162 AATTATATATATGAATTTTGATTTTG-TTT
1 AATTTTATACATGAATTTTGATTTTGATCT
130191 AATTTTATACATGATATTTTGA-TTTGATCT
1 AATTTTATACATGA-ATTTTGATTTTGATCT
130221 AATTTT
1 AATTTT
130227 TGTAAATTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 16 0.52
30 15 0.48
ACGTcount: A:0.31, C:0.03, G:0.09, T:0.57
Consensus pattern (30 bp):
AATTTTATACATGAATTTTGATTTTGATCT
Found at i:134177 original size:25 final size:25
Alignment explanation
Indices: 134126--134183 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
134116 TTTTAATTTA
**
134126 ATATGTAATAATTTAATATATTTTTAT
1 ATAT-TAA-AATTTAATATATAATTAT
* *
134153 TTATTAAAATTTTATATATAATTAT
1 ATATTAAAATTTAATATATAATTAT
134178 ATATTA
1 ATATTA
134184 GTATAGATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
25 20 0.77
26 3 0.12
27 3 0.12
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (25 bp):
ATATTAAAATTTAATATATAATTAT
Found at i:139649 original size:19 final size:19
Alignment explanation
Indices: 139625--139663 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
139615 AGTAACGAAT
139625 GCCTGTTTATACCAAAGGA
1 GCCTGTTTATACCAAAGGA
139644 GCCTGTTTATACCAAAGGA
1 GCCTGTTTATACCAAAGGA
139663 G
1 G
139664 GTAGCAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.26
Consensus pattern (19 bp):
GCCTGTTTATACCAAAGGA
Found at i:142616 original size:12 final size:12
Alignment explanation
Indices: 142601--142626 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
142591 ATACATTTAA
142601 AAATATTAAAAC
1 AAATATTAAAAC
142613 AAATATTAAAAC
1 AAATATTAAAAC
142625 AA
1 AA
142627 CAAACAAATT
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:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (12 bp):
AAATATTAAAAC
Found at i:142664 original size:41 final size:41
Alignment explanation
Indices: 142603--142682 Score: 124
Period size: 41 Copynumber: 2.0 Consensus size: 41
142593 ACATTTAAAA
*
142603 ATATTAAAACAAATATTAAAACAACAAACAAATTAAAAACG
1 ATATTAAAACAAATAGTAAAACAACAAACAAATTAAAAACG
* * *
142644 ATATTAAAACAATTCGTAAAACAACAAACAAATTGAAAA
1 ATATTAAAACAAATAGTAAAACAACAAACAAATTAAAAA
142683 TACAATAAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.64, C:0.12, G:0.04, T:0.20
Consensus pattern (41 bp):
ATATTAAAACAAATAGTAAAACAACAAACAAATTAAAAACG
Found at i:143376 original size:24 final size:23
Alignment explanation
Indices: 143337--143382 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
143327 TATTACAAGC
143337 AAAAAAAATTAGTATTAAAAATA
1 AAAAAAAATTAGTATTAAAAATA
* *
143360 AAAATAAAATTATTATTATAAAT
1 AAAA-AAAATTAGTATTAAAAAT
143383 CTGGGCGGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (23 bp):
AAAAAAAATTAGTATTAAAAATA
Found at i:147861 original size:21 final size:23
Alignment explanation
Indices: 147812--147855 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
147802 ATAGTAAGCA
147812 CACATAGCGCAAATCAGTAGGAG
1 CACATAGCGCAAATCAGTAGGAG
147835 CACATAGCGCAAATCAGTAGG
1 CACATAGCGCAAATCAGTAGG
147856 CACATAAGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.39, C:0.23, G:0.25, T:0.14
Consensus pattern (23 bp):
CACATAGCGCAAATCAGTAGGAG
Found at i:147869 original size:23 final size:21
Alignment explanation
Indices: 147812--147861 Score: 82
Period size: 23 Copynumber: 2.3 Consensus size: 21
147802 ATAGTAAGCA
147812 CACATAGCGCAAATCAGTAGGAG
1 CACATAGCGCAAATCAGTA-G-G
147835 CACATAGCGCAAATCAGTAGG
1 CACATAGCGCAAATCAGTAGG
147856 CACATA
1 CACATA
147862 AGGTGCAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 7 0.26
22 1 0.04
23 19 0.70
ACGTcount: A:0.40, C:0.24, G:0.22, T:0.14
Consensus pattern (21 bp):
CACATAGCGCAAATCAGTAGG
Found at i:152089 original size:2 final size:2
Alignment explanation
Indices: 152082--152106 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
152072 TCTTTTTCTG
152082 GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT G
152107 GAGGTATTTG
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:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:152175 original size:72 final size:72
Alignment explanation
Indices: 152034--152178 Score: 184
Period size: 72 Copynumber: 2.0 Consensus size: 72
152024 GTATACATTG
* * * * * * **
152034 GGAGGTATTTGTGTTCAAACTAGTTCAAGCGAGTTTCTTCTTTTTCTGGTGTGTGTGTGTGTGTG
1 GGAGGTATTTGTGTTCAAACTAATCCAAGCGAGTTCCTTCTTTTTCAGGTGTATGTATGTGTGCC
152099 TGTGTGT
66 TGTGTGT
* *
152106 GGAGGTATTTGTGTTCAAACTAATCCAAGCGAGTTCCTTCTTTTTTCAGG-GTATTTATGTTTGC
1 GGAGGTATTTGTGTTCAAACTAATCCAAGCGAGTTCCTTC-TTTTTCAGGTGTATGTATGTGTGC
152170 CTGTGTGT
65 CTGTGTGT
152178 G
1 G
152179 TTGTTCACCA
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
72 54 0.87
73 8 0.13
ACGTcount: A:0.15, C:0.12, G:0.28, T:0.44
Consensus pattern (72 bp):
GGAGGTATTTGTGTTCAAACTAATCCAAGCGAGTTCCTTCTTTTTCAGGTGTATGTATGTGTGCC
TGTGTGT
Found at i:152953 original size:30 final size:30
Alignment explanation
Indices: 152917--152989 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
152907 AATTTAGACG
152917 GTCTTAATTTTTACTATAGAGATAATATTA
1 GTCTTAATTTTTACTATAGAGATAATATTA
152947 GTCTTAATTTTTACTATAGAGATAATATTA
1 GTCTTAATTTTTACTATAGAGATAATATTA
* *
152977 GTTTTAAATTTTA
1 GTCTTAATTTTTA
152990 GTGTTTTCGT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.36, C:0.05, G:0.10, T:0.49
Consensus pattern (30 bp):
GTCTTAATTTTTACTATAGAGATAATATTA
Found at i:158285 original size:55 final size:55
Alignment explanation
Indices: 158219--158329 Score: 213
Period size: 55 Copynumber: 2.0 Consensus size: 55
158209 ATGGGTTAAA
158219 GTTAGTTTTTGCAAATATAGATAAGTTTGAACAAAATTTTAGGCCTACATTTTCG
1 GTTAGTTTTTGCAAATATAGATAAGTTTGAACAAAATTTTAGGCCTACATTTTCG
*
158274 GTTAGTTTTTGCAAATATAGATACGTTTGAACAAAATTTTAGGCCTACATTTTCG
1 GTTAGTTTTTGCAAATATAGATAAGTTTGAACAAAATTTTAGGCCTACATTTTCG
158329 G
1 G
158330 GTCGAGTTAG
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.40
Consensus pattern (55 bp):
GTTAGTTTTTGCAAATATAGATAAGTTTGAACAAAATTTTAGGCCTACATTTTCG
Found at i:162266 original size:364 final size:364
Alignment explanation
Indices: 161597--162539 Score: 1663
Period size: 364 Copynumber: 2.6 Consensus size: 364
161587 AAAAGCTTCT
* * *
161597 TCTGTCAGGTAATGGCTGCAAGTTGATATTCTATTATGTTAATTTAAAGTTATAATTTGGTCTCT
1 TCTGTCAGGTAATGGCTGCAAGTTGATATTCTATTATGTTAATCTACAGTTATAATTTGGTGTCT
*
161662 ACATTCTTAAATTGTCAGTATAACAATCTTACTTGTAAAAATTAATTATGTTTTCTAGACAACAA
66 ACATTCTTAAACTGTCAGTATAACAATCTTACTTGTAAAAATTAATTATGTTTTCTAGACAACAA
* *
161727 GATACCGGATGATTTGGGTGAAGGCACCAGTGATGCTAGAGCAAATCAACACAATATGGAACTGT
131 GATACCCGATGATTTGGGTGAAGGCACCAGTGATGCTAGAGCAAATCAACACAATATGAAACTGT
* **
161792 CACAAGAGAACATCTTTACTGTTGATACTGTAAGTTTTGGCTTGTATATATATTTTAAATTCAAT
196 CACAAGAGAACAACTTTACTGTTGATACTGTAAGTTTTGGCGAGTATATATATTTTAAATTCAAT
* *
161857 TTGCTTAGTTTTGGATCAGATCTGATTCTCTTTTGCATATAGGTTCTTCCGTCACCGCTGTGTTT
261 TTGCTTAGTTTTGGATCAGATCCGATTCTCTTCTGCATATAGGTTCTTCCGTCACCGCTGTGTTT
161922 TCCTGATATGGAAAACTTTGGTGATTTCAGACTCTGTGA
326 TCCTGATATGGAAAACTTTGGTGATTTCAGACTCTGTGA
* *
161961 TCTGTCAGGTAATGGCTGCAAGTTGATATTCTATTATGTTAATCTACAGTTTTAATTTGTTGTCT
1 TCTGTCAGGTAATGGCTGCAAGTTGATATTCTATTATGTTAATCTACAGTTATAATTTGGTGTCT
*
162026 ACATTTTTAAACTGTCAGTATAACAATCTTACTTGTAAAAATTAATTATGTTTTCTAGACAACAA
66 ACATTCTTAAACTGTCAGTATAACAATCTTACTTGTAAAAATTAATTATGTTTTCTAGACAACAA
*
162091 GATACCCGATGATTTGGGTGAAGGTACCAGTGATGCTAGAGCAAATCAACACAATATGAAACTGT
131 GATACCCGATGATTTGGGTGAAGGCACCAGTGATGCTAGAGCAAATCAACACAATATGAAACTGT
* *
162156 CACAAGAGAACACCTTTACTGTTGATCCTGTAAGTTTTGGCGAGTATATATATTTTAAATTCAAT
196 CACAAGAGAACAACTTTACTGTTGATACTGTAAGTTTTGGCGAGTATATATATTTTAAATTCAAT
162221 TTGCTTAGTTTTGGATCAGATCCGATTCTCTTCTGCATATAGGTTCTTCCGTCACCGCTGTGTTT
261 TTGCTTAGTTTTGGATCAGATCCGATTCTCTTCTGCATATAGGTTCTTCCGTCACCGCTGTGTTT
* *
162286 TTCTGATATGGAAAACTTTGGTGATTTCGGACTCTGTGA
326 TCCTGATATGGAAAACTTTGGTGATTTCAGACTCTGTGA
162325 TCTGTCAGGTAATGGCTGCAAGTTGATATTCTATTATGTTAATCTACAGTTATAATTTGGTGTCT
1 TCTGTCAGGTAATGGCTGCAAGTTGATATTCTATTATGTTAATCTACAGTTATAATTTGGTGTCT
* * * *
162390 ACATTCTTAAACTGTCAGTATAAGAATCTCACTTGT-TATATTAATTATGTTTTCTAGACAACAA
66 ACATTCTTAAACTGTCAGTATAACAATCTTACTTGTAAAAATTAATTATGTTTTCTAGACAACAA
*
162454 GATACCCGATGGTTTGGGTGAAGGCACCAGTGATGCTAGAGCAAATCAACACAATATGAAACTGT
131 GATACCCGATGATTTGGGTGAAGGCACCAGTGATGCTAGAGCAAATCAACACAATATGAAACTGT
162519 CACAAGAGAACAACTTTACTG
196 CACAAGAGAACAACTTTACTG
162540 CTGAAGGGTA
Statistics
Matches: 551, Mismatches: 28, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
363 109 0.20
364 442 0.80
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (364 bp):
TCTGTCAGGTAATGGCTGCAAGTTGATATTCTATTATGTTAATCTACAGTTATAATTTGGTGTCT
ACATTCTTAAACTGTCAGTATAACAATCTTACTTGTAAAAATTAATTATGTTTTCTAGACAACAA
GATACCCGATGATTTGGGTGAAGGCACCAGTGATGCTAGAGCAAATCAACACAATATGAAACTGT
CACAAGAGAACAACTTTACTGTTGATACTGTAAGTTTTGGCGAGTATATATATTTTAAATTCAAT
TTGCTTAGTTTTGGATCAGATCCGATTCTCTTCTGCATATAGGTTCTTCCGTCACCGCTGTGTTT
TCCTGATATGGAAAACTTTGGTGATTTCAGACTCTGTGA
Found at i:168296 original size:18 final size:16
Alignment explanation
Indices: 168249--168299 Score: 50
Period size: 18 Copynumber: 3.0 Consensus size: 16
168239 AATTAATAAG
168249 TTGG-AATTTTTTATT
1 TTGGTAATTTTTTATT
*
168264 TTGGTTATTAATTTTATAT
1 TTGGTAATT--TTTTAT-T
168283 TTGAGTAATTTTTTATT
1 TTG-GTAATTTTTTATT
168300 CTATATTGGG
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
15 4 0.14
16 3 0.10
17 1 0.03
18 12 0.41
19 4 0.14
20 5 0.17
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.65
Consensus pattern (16 bp):
TTGGTAATTTTTTATT
Found at i:169904 original size:2 final size:2
Alignment explanation
Indices: 169897--169927 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
169887 AGAATTTTAA
169897 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
169928 ATCTAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:170876 original size:6 final size:6
Alignment explanation
Indices: 170864--170900 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
170854 AGAGGATAAG
*
170864 GATGAA GAAGAA GATGAA GATGAA GATGAA GATGAA G
1 GATGAA GATGAA GATGAA GATGAA GATGAA GATGAA G
170901 GGAGTATTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.51, C:0.00, G:0.35, T:0.14
Consensus pattern (6 bp):
GATGAA
Found at i:177143 original size:18 final size:20
Alignment explanation
Indices: 177108--177149 Score: 52
Period size: 18 Copynumber: 2.2 Consensus size: 20
177098 CTATAGTGTA
*
177108 TATATATTTGAAATACATGG
1 TATATATTTGAAAGACATGG
*
177128 TATATA-TTG-AAGACATGT
1 TATATATTTGAAAGACATGG
177146 TATA
1 TATA
177150 CATATATTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 11 0.55
19 3 0.15
20 6 0.30
ACGTcount: A:0.40, C:0.05, G:0.14, T:0.40
Consensus pattern (20 bp):
TATATATTTGAAAGACATGG
Found at i:177786 original size:22 final size:24
Alignment explanation
Indices: 177742--177787 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 24
177732 AAAAAAATTA
*
177742 CCACTATTTTCTTTTATTATTTTG
1 CCACTATTTTCTTTCATTATTTTG
*
177766 CCACT-TTTT-TTTCATTGTTTTG
1 CCACTATTTTCTTTCATTATTTTG
177788 TCAGCATTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 11 0.55
23 4 0.20
24 5 0.25
ACGTcount: A:0.13, C:0.17, G:0.07, T:0.63
Consensus pattern (24 bp):
CCACTATTTTCTTTCATTATTTTG
Found at i:180871 original size:4 final size:4
Alignment explanation
Indices: 180855--180892 Score: 69
Period size: 4 Copynumber: 9.8 Consensus size: 4
180845 CAAACATCAT
180855 CATA CAT- CATA CATA CATA CATA CATA CATA CATA CAT
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CAT
180893 TGATTTGCTA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.09
4 30 0.91
ACGTcount: A:0.47, C:0.26, G:0.00, T:0.26
Consensus pattern (4 bp):
CATA
Found at i:183127 original size:2 final size:2
Alignment explanation
Indices: 183120--183151 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
183110 TCAAATTAAA
183120 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
183152 GAAAATGTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:187585 original size:210 final size:210
Alignment explanation
Indices: 187216--189130 Score: 2977
Period size: 210 Copynumber: 9.1 Consensus size: 210
187206 CGTCCATGGA
*
187216 AGAACAAGACCTTAGTTCTAATTCTTTGAGACAAGTGGAGGTAGATAATCCGTCTCTAATCTTGC
1 AGAACAAGACCTTAGTTCTAATTCTTTGAGACAAGTGGAGGTAGATAATCCGTCTCCAATCTTGC
* *
187281 TTAATTTTTCGCAACCGTCAATCTGAAGCTTTTCAAGAGATAAACATCCTCCTGTCAATGGAAGA
66 TTAATTTTTCGCAACCGTAAATCTGAAGCTTTTCAAGAGATGAACATCCTCCTGTCAATGGAAGA
*
187346 ACTTCCAATTTGTCAAAACCACAAATTGATAGATTTCGAAGAGAGGAAAATCCTTTCAAATCTGG
131 ACTTCCAATTTGTCACAACCACAAATTGATAGATTTCGAAGAGAGGAAAATCCTTTCAAATCTGG
187411 AATGGAAGTTAAATT
196 AATGGAAGTTAAATT
* *
187426 AGAACAATATCTTAGTTCTAATTCTTTGAGACAAGTGGAGGTAGATAATCCGTCTCCAATCTTGC
1 AGAACAAGACCTTAGTTCTAATTCTTTGAGACAAGTGGAGGTAGATAATCCGTCTCCAATCTTGC
* *
187491 TTAATTTTGCGCAACCGTCAATCTGAAGCTTTTCAAGAGATGAACATCCTCCTGTCAATGGAAGA
66 TTAATTTTTCGCAACCGTAAATCTGAAGCTTTTCAAGAGATGAACATCCTCCTGTCAATGGAAGA
** * * *
187556 ACTTCCAATTCCTCACAATCTCCAATTGATAGATTTCGAAGAGAGGAAAATCCTTTCAAATCTGG
131 ACTTCCAATTTGTCACAACCACAAATTGATAGATTTCGAAGAGAGGAAAATCCTTTCAAATCTGG
187621 AATGGAAGTTAAATT
196 AATGGAAGTTAAATT
*
187636 AGAACAAGACCTTAGTTCTAATTCTTTGAGACAAGTGGAGGGAGATAATCCGTCTCCAATCTTGC
1 AGAACAAGACCTTAGTTCTAATTCTTTGAGACAAGTGGAGGTAGATAATCCGTCTCCAATCTTGC
* * *
187701 TTAATTTTTCGCAACGGAAAATCCGAAGCTTTTCAAGAGATGAACATCCTCCAT-TCAATGGAAG
66 TTAATTTTTCGCAACCGTAAATCTGAAGCTTTTCAAGAGATGAACATCCTCC-TGTCAATGGAAG
187765 AACTTCCAATTTGTCACAACCACAAATTGATAGATTTCGAAGAGAGGAAAATCCTTTCAAATCTG
130 AACTTCCAATTTGTCACAACCACAAATTGATAGATTTCGAAGAGAGGAAAATCCTTTCAAATCTG
187830 GAATGGAAGTTAAATT
195 GAATGGAAGTTAAATT
187846 AGAACAAGACCTTAGTTCTAATTCTTTGAGACAAGTGGAGGTAGATAATCCGTCTCCAATCTTGC
1 AGAACAAGACCTTAGTTCTAATTCTTTGAGACAAGTGGAGGTAGATAATCCGTCTCCAATCTTGC
** *
187911 TTAATTTTTCGCAAGAGAAAATCTGAAGCTTTTCAAGAGATGAACATCCTCCTGTCAATGGAAGA
66 TTAATTTTTCGCAACCGTAAATCTGAAGCTTTTCAAGAGATGAACATCCTCCTGTCAATGGAAGA
* * *
187976 A-TTCCAATTGGTCACAGCCACCAATTGATAGATTTCGAAGAGAGGAAAATCCTTTCAAATCTGG
131 ACTTCCAATTTGTCACAACCACAAATTGATAGATTTCGAAGAGAGGAAAATCCTTTCAAATCTGG
188040 AATGGAAGTTAAATT
196 AATGGAAGTTAAATT
*
188055 AGAACAAGAGCTTAGTTCTAATTCTTTGAGACAAGTGGAGGTAGATAATCCGTCTCCAATCTTGC
1 AGAACAAGACCTTAGTTCTAATTCTTTGAGACAAGTGGAGGTAGATAATCCGTCTCCAATCTTGC
* * * * *
188120 TTAATTTGTGGCAACTGAAAATCTCAAGCTTTTCAAGAGATGAACATCCTCCTGTCAATGGAAGA
66 TTAATTTTTCGCAACCGTAAATCTGAAGCTTTTCAAGAGATGAACATCCTCCTGTCAATGGAAGA
** * * *
188185 ACTTCCAATTTGTTGCAGCCAGAAA-TAATCAGATTTCGAAGAGAGGAAAATCCTTTCAAATCTG
131 ACTTCCAATTTGTCACAACCACAAATTGAT-AGATTTCGAAGAGAGGAAAATCCTTTCAAATCTG
188249 GAATGGAAGTTAAATT
195 GAATGGAAGTTAAATT
* ** *
188265 AGAACAACATATTAGTGCTAATTCTTTGAGACAAGTGGAGGTAGATAATCCGTCTCCAATCTTGC
1 AGAACAAGACCTTAGTTCTAATTCTTTGAGACAAGTGGAGGTAGATAATCCGTCTCCAATCTTGC
* * *
188330 TTAATTTTTCGCAACGGAAAATCCGAAGCTTTTCAAGAGATGAACATCCTCCTGTCAATGGAAGA
66 TTAATTTTTCGCAACCGTAAATCTGAAGCTTTTCAAGAGATGAACATCCTCCTGTCAATGGAAGA
* *
188395 ACTTCCAATTTGCCACAGCCATC-AATTGATAGATTTCGAAGAGAGGAAAATCCTTTCAAATCTG
131 ACTTCCAATTTGTCACAACCA-CAAATTGATAGATTTCGAAGAGAGGAAAATCCTTTCAAATCTG
188459 GAATGGAAGTTAAATT
195 GAATGGAAGTTAAATT
188475 AGAACAAGACCTTAGTTCTAATTCTTTGAGACAAGTGGAGGTAGATAATCCGTCTCCAATCTTGC
1 AGAACAAGACCTTAGTTCTAATTCTTTGAGACAAGTGGAGGTAGATAATCCGTCTCCAATCTTGC
* * * * * *
188540 TTAATTTTGCGCAACCGTCAATCTCAAGCTCTTCAAGAGTTGAACATCCTCCTTTCAATGGAAGA
66 TTAATTTTTCGCAACCGTAAATCTGAAGCTTTTCAAGAGATGAACATCCTCCTGTCAATGGAAGA
* ** ** ** *
188605 ACGTCCAATTTGTTGCAGGCATGAATT-ATCAGATTTCGAACAGAGGAAAATCCTTTCAAATCTG
131 ACTTCCAATTTGTCACAACCACAAATTGAT-AGATTTCGAAGAGAGGAAAATCCTTTCAAATCTG
188669 GAATGGAAGTTAAATT
195 GAATGGAAGTTAAATT
* *
188685 AGAACAAGAGCTTAGTGCTAATTCTTTGAGACAAGTGGAGGTAGATAATCCGTCTCCAATCTTGC
1 AGAACAAGACCTTAGTTCTAATTCTTTGAGACAAGTGGAGGTAGATAATCCGTCTCCAATCTTGC
* * *
188750 TTAATTTTGCGCAACCGTAAATCTCAAGCTTTTCAAGAGACGAACATCCTCCTGTCAATGGAAGA
66 TTAATTTTTCGCAACCGTAAATCTGAAGCTTTTCAAGAGATGAACATCCTCCTGTCAATGGAAGA
* ** * *
188815 ACTGCCAATTTGTTGCAGA-CATAAATT-ATCAGGTTTCGAAGAGAGGAAAATCCTTTCAAATCT
131 ACTTCCAATTTGTCACA-ACCACAAATTGAT-AGATTTCGAAGAGAGGAAAATCCTTTCAAATCT
188878 GGAATGGAAGTTAAATT
194 GGAATGGAAGTTAAATT
*
188895 AGAACAATG-TCTTAGTTCTAATTCTTTGAGACAAGTGGAGGTAGATAATCCGTCTCCAATCTTG
1 AGAACAA-GACCTTAGTTCTAATTCTTTGAGACAAGTGGAGGTAGATAATCCGTCTCCAATCTTG
*
188959 CTTAATTTTTCGCAACCGTCAATCTGAAGCTTTTCAAGAGATGAACATCCTCCTGTCAATGGAAG
65 CTTAATTTTTCGCAACCGTAAATCTGAAGCTTTTCAAGAGATGAACATCCTCCTGTCAATGGAAG
** ** *
189024 AACTTCCAATTTGTTGCAGGCA-AGAATT-CTCAGATTTCGAAGAGAGGAAAATCCTTTCAAATC
130 AACTTCCAATTTGTCACAACCACA-AATTGAT-AGATTTCGAAGAGAGGAAAATCCTTTCAAATC
189087 TGGAATGGAAGTTAAATT
193 TGGAATGGAAGTTAAATT
** * *
189105 AGCGCAAGACCTTTGTTTTAATTCTT
1 AGAACAAGACCTTAGTTCTAATTCTT
189131 CCAAGCAAGG
Statistics
Matches: 1587, Mismatches: 105, Indels: 26
0.92 0.06 0.02
Matches are distributed among these distances:
209 208 0.13
210 1374 0.87
211 5 0.00
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.30
Consensus pattern (210 bp):
AGAACAAGACCTTAGTTCTAATTCTTTGAGACAAGTGGAGGTAGATAATCCGTCTCCAATCTTGC
TTAATTTTTCGCAACCGTAAATCTGAAGCTTTTCAAGAGATGAACATCCTCCTGTCAATGGAAGA
ACTTCCAATTTGTCACAACCACAAATTGATAGATTTCGAAGAGAGGAAAATCCTTTCAAATCTGG
AATGGAAGTTAAATT
Done.