Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012744.1 Kokia drynarioides strain JFW-HI SEQ_127755, 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: 99215
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 452 characters in sequence are not A, C, G, or T
Found at i:316 original size:37 final size:37
Alignment explanation
Indices: 275--353 Score: 149
Period size: 37 Copynumber: 2.1 Consensus size: 37
265 TTCTCTAAAT
*
275 CTATGGTCACCATTGGGTTTTACAGCATTACATATTA
1 CTATGGTCACCATTGGGTTTTAAAGCATTACATATTA
312 CTATGGTCACCATTGGGTTTTAAAGCATTACATATTA
1 CTATGGTCACCATTGGGTTTTAAAGCATTACATATTA
349 CTATG
1 CTATG
354 CTGTCGAGGT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.38
Consensus pattern (37 bp):
CTATGGTCACCATTGGGTTTTAAAGCATTACATATTA
Found at i:3351 original size:43 final size:43
Alignment explanation
Indices: 3233--3494 Score: 285
Period size: 43 Copynumber: 6.1 Consensus size: 43
3223 TTTATTAATA
* * * *
3233 TTAGCGGTGTTTGTGGGAAAAGTGCCGCTAAAGACCATGTTCT
1 TTAGCGGCGTTTGTGGGGAAAGCGTCGCTAAAGACCATGTTCT
* * * * * *
3276 TTAG-GGTGTTTGAGGGTAAAGCGCCGTTAAAGACCATGATCT
1 TTAGCGGCGTTTGTGGGGAAAGCGTCGCTAAAGACCATGTTCT
* *
3318 TTAGTGGCGTTTGTGGGGAAAGTGTCGCTAAAGACCATGTTCT
1 TTAGCGGCGTTTGTGGGGAAAGCGTCGCTAAAGACCATGTTCT
* * *
3361 TTAGTGGCGTTTGTGGGAAAAGTGTCGCTAAAGACCATGTTCT
1 TTAGCGGCGTTTGTGGGGAAAGCGTCGCTAAAGACCATGTTCT
* * * * *
3404 TTTGCGGGGTTTAT-GGGAAAGCGTTGCTAAAGATCATGTTCT
1 TTAGCGGCGTTTGTGGGGAAAGCGTCGCTAAAGACCATGTTCT
** * * *
3446 TTAGCGGTATTTGTGGGGAAAACGTTGCTAAAGATCATGTTCT
1 TTAGCGGCGTTTGTGGGGAAAGCGTCGCTAAAGACCATGTTCT
3489 TTAGCG
1 TTAGCG
3495 AAGTTTTCTC
Statistics
Matches: 191, Mismatches: 26, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
42 71 0.37
43 120 0.63
ACGTcount: A:0.23, C:0.14, G:0.31, T:0.32
Consensus pattern (43 bp):
TTAGCGGCGTTTGTGGGGAAAGCGTCGCTAAAGACCATGTTCT
Found at i:3422 original size:85 final size:84
Alignment explanation
Indices: 3233--3494 Score: 294
Period size: 85 Copynumber: 3.1 Consensus size: 84
3223 TTTATTAATA
* * * * *
3233 TTAGCGGTGTTTGTGGGAAAAGTGCCGCTAAAGACCATGTTCTTTAGGGTGTTTGAGGGTAAAGC
1 TTAGCGGCGTTTGTGGG-AAAGTGTCGCTAAAGACCATGTTCTTTAGGGTGTTTGTGGGAAAAGT
* * *
3298 GCCGTTAAAGACCATGATCT
65 GTCGCTAAAGACCATGTTCT
* *
3318 TTAGTGGCGTTTGTGGGGAAAGTGTCGCTAAAGACCATGTTCTTTAGTGGCGTTTGTGGGAAAAG
1 TTAGCGGCGTTTGT-GGGAAAGTGTCGCTAAAGACCATGTTCTTTAG-GGTGTTTGTGGGAAAAG
3383 TGTCGCTAAAGACCATGTTCT
64 TGTCGCTAAAGACCATGTTCT
* * * * * * *
3404 TTTGCGGGGTTTATGGGAAAGCGTTGCTAAAGATCATGTTCTTTAGCGGTATTTGTGGGGAAAAC
1 TTAGCGGCGTTTGTGGGAAAGTGTCGCTAAAGACCATGTTCTTTAG-GGTGTTTGT-GGGAAAA-
*
3469 GT-T-GCTAAAGATCATGTTCT
63 GTGTCGCTAAAGACCATGTTCT
3489 TTAGCG
1 TTAGCG
3495 AAGTTTTCTC
Statistics
Matches: 151, Mismatches: 22, Indels: 8
0.83 0.12 0.04
Matches are distributed among these distances:
85 97 0.64
86 52 0.34
87 2 0.01
ACGTcount: A:0.23, C:0.14, G:0.31, T:0.32
Consensus pattern (84 bp):
TTAGCGGCGTTTGTGGGAAAGTGTCGCTAAAGACCATGTTCTTTAGGGTGTTTGTGGGAAAAGTG
TCGCTAAAGACCATGTTCT
Found at i:3476 original size:128 final size:128
Alignment explanation
Indices: 3241--3492 Score: 337
Period size: 128 Copynumber: 2.0 Consensus size: 128
3231 TATTAGCGGT
* *
3241 GTTTGTGGGAAAAGTGCCGCTAAAGACCATGTTCTTTAGGGTGTTTGAGGGTAAAGCGCCGTTAA
1 GTTTGTGGGAAAAGTGCCGCTAAAGACCATGTTCTTTAGGGGGTTTGAGGGTAAAGCGCCGCTAA
* * **
3306 AGACCATGATCTTTAGTGGCGTTTGTGGGGAAAGTGTCGCTAAAGACCATGTTCTTTAGTGGC
66 AGACCATGATCTTTAGCGGCATTTGTGGGGAAAACGTCGCTAAAGACCATGTTCTTTAGTGGC
* * **
3369 GTTTGTGGGAAAAGTGTCGCTAAAGACCATGTTCTTTTGCGGGGTTT-ATGGG-AAAGCGTTGCT
1 GTTTGTGGGAAAAGTGCCGCTAAAGACCATGTTCTTTAG-GGGGTTTGA-GGGTAAAGCGCCGCT
* * * * *
3432 AAAGATCATGTTCTTTAGCGGTATTTGTGGGGAAAACGTTGCTAAAGATCATGTTCTTTAG
64 AAAGACCATGATCTTTAGCGGCATTTGTGGGGAAAACGTCGCTAAAGACCATGTTCTTTAG
3493 CGAAGTTTTC
Statistics
Matches: 107, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
128 98 0.92
129 9 0.08
ACGTcount: A:0.24, C:0.13, G:0.30, T:0.33
Consensus pattern (128 bp):
GTTTGTGGGAAAAGTGCCGCTAAAGACCATGTTCTTTAGGGGGTTTGAGGGTAAAGCGCCGCTAA
AGACCATGATCTTTAGCGGCATTTGTGGGGAAAACGTCGCTAAAGACCATGTTCTTTAGTGGC
Found at i:10155 original size:19 final size:18
Alignment explanation
Indices: 10128--10167 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
10118 TCACATCAGC
*
10128 AAATGAATTTAAACTTAAA
1 AAATGAA-TTAAAATTAAA
*
10147 AAATTAATTAAAATTAAA
1 AAATGAATTAAAATTAAA
10165 AAA
1 AAA
10168 ATTTAAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.30
Consensus pattern (18 bp):
AAATGAATTAAAATTAAA
Found at i:10222 original size:8 final size:9
Alignment explanation
Indices: 10189--10233 Score: 65
Period size: 9 Copynumber: 5.0 Consensus size: 9
10179 TTTGAGACCC
*
10189 ACAATTAAC
1 ACAATTAAA
10198 ACAATTAAA
1 ACAATTAAA
10207 ACAATTAAA
1 ACAATTAAA
10216 A-AATTAAA
1 ACAATTAAA
10224 ACAAATTAAA
1 AC-AATTAAA
10234 CACTAACAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
8 8 0.24
9 18 0.55
10 7 0.21
ACGTcount: A:0.67, C:0.11, G:0.00, T:0.22
Consensus pattern (9 bp):
ACAATTAAA
Found at i:11837 original size:54 final size:54
Alignment explanation
Indices: 11778--11885 Score: 207
Period size: 54 Copynumber: 2.0 Consensus size: 54
11768 TATATAATTA
11778 CCACAGAGTGTCATACTTAGCGTACAATTTGTGTTCTTTGTGTGCAGGTTAGAT
1 CCACAGAGTGTCATACTTAGCGTACAATTTGTGTTCTTTGTGTGCAGGTTAGAT
*
11832 CCACAGAGTGTCGTACTTAGCGTACAATTTGTGTTCTTTGTGTGCAGGTTAGAT
1 CCACAGAGTGTCATACTTAGCGTACAATTTGTGTTCTTTGTGTGCAGGTTAGAT
11886 TTAATTCGAG
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.21, C:0.17, G:0.25, T:0.37
Consensus pattern (54 bp):
CCACAGAGTGTCATACTTAGCGTACAATTTGTGTTCTTTGTGTGCAGGTTAGAT
Found at i:17876 original size:18 final size:19
Alignment explanation
Indices: 17855--17895 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
17845 TTATCAAAAG
*
17855 ATATATTAATTA-CTAATA
1 ATATATTAATTATATAATA
*
17873 ATAT-TTTATTATATAATA
1 ATATATTAATTATATAATA
17891 ATATA
1 ATATA
17896 AAATATAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (19 bp):
ATATATTAATTATATAATA
Found at i:35793 original size:34 final size:34
Alignment explanation
Indices: 35709--35867 Score: 156
Period size: 34 Copynumber: 4.6 Consensus size: 34
35699 ATTAAATTAC
* *
35709 AATGACAAATGGAAATGTAATGACAATGCAAATGG
1 AATGAC-AATGGAAATGTAATGACAATGAAAATGT
* * **
35744 AGTGATAATTAAAATGTAATGACAATGAAAATGT
1 AATGACAATGGAAATGTAATGACAATGAAAATGT
* * * * * *
35778 AATGACAATGCAAATGGAGTGATAATTACAATGT
1 AATGACAATGGAAATGTAATGACAATGAAAATGT
* * *
35812 AATGACAATGGAAATGTGATGACAGTTAAAATGT
1 AATGACAATGGAAATGTAATGACAATGAAAATGT
* *
35846 AATGACAATGGGAATGTGATGA
1 AATGACAATGGAAATGTAATGA
35868 AAAAAGAGAT
Statistics
Matches: 101, Mismatches: 23, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
34 97 0.96
35 4 0.04
ACGTcount: A:0.46, C:0.06, G:0.23, T:0.25
Consensus pattern (34 bp):
AATGACAATGGAAATGTAATGACAATGAAAATGT
Found at i:35844 original size:51 final size:51
Alignment explanation
Indices: 35709--35835 Score: 218
Period size: 51 Copynumber: 2.5 Consensus size: 51
35699 ATTAAATTAC
35709 AATGACAAATGGAAATGTAATGACAATGCAAATGGAGTGATAATTAAAATGT
1 AATGAC-AATGGAAATGTAATGACAATGCAAATGGAGTGATAATTAAAATGT
* *
35761 AATGACAATGAAAATGTAATGACAATGCAAATGGAGTGATAATTACAATGT
1 AATGACAATGGAAATGTAATGACAATGCAAATGGAGTGATAATTAAAATGT
*
35812 AATGACAATGGAAATGTGATGACA
1 AATGACAATGGAAATGTAATGACA
35836 GTTAAAATGT
Statistics
Matches: 71, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
51 65 0.92
52 6 0.08
ACGTcount: A:0.47, C:0.07, G:0.21, T:0.24
Consensus pattern (51 bp):
AATGACAATGGAAATGTAATGACAATGCAAATGGAGTGATAATTAAAATGT
Found at i:35862 original size:17 final size:17
Alignment explanation
Indices: 35709--35855 Score: 141
Period size: 17 Copynumber: 8.6 Consensus size: 17
35699 ATTAAATTAC
*
35709 AATGACAAATGGAAATGT
1 AATGAC-AATGAAAATGT
* *
35727 AATGACAATGCAAATGG
1 AATGACAATGAAAATGT
* * *
35744 AGTGATAATTAAAATGT
1 AATGACAATGAAAATGT
35761 AATGACAATGAAAATGT
1 AATGACAATGAAAATGT
* *
35778 AATGACAATGCAAATGG
1 AATGACAATGAAAATGT
* * * *
35795 AGTGATAATTACAATGT
1 AATGACAATGAAAATGT
*
35812 AATGACAATGGAAATGT
1 AATGACAATGAAAATGT
* * *
35829 GATGACAGTTAAAATGT
1 AATGACAATGAAAATGT
35846 AATGACAATG
1 AATGACAATG
35856 GGAATGTGAT
Statistics
Matches: 99, Mismatches: 30, Indels: 1
0.76 0.23 0.01
Matches are distributed among these distances:
17 93 0.94
18 6 0.06
ACGTcount: A:0.47, C:0.07, G:0.21, T:0.25
Consensus pattern (17 bp):
AATGACAATGAAAATGT
Found at i:52933 original size:6 final size:6
Alignment explanation
Indices: 52904--52942 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
52894 GACAATTCAG
*
52904 TTAGTT TTA-TT TCAGTT CTTAGTT TTAGTT TTAGTT TTA
1 TTAGTT TTAGTT TTAGTT -TTAGTT TTAGTT TTAGTT TTA
52943 TTTGAGTTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 4 0.14
6 20 0.69
7 5 0.17
ACGTcount: A:0.18, C:0.05, G:0.13, T:0.64
Consensus pattern (6 bp):
TTAGTT
Found at i:56379 original size:20 final size:19
Alignment explanation
Indices: 56351--56406 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 19
56341 TCACATTAGC
*
56351 AAATGATTTTAAAATTATAA
1 AAATTATTTTAAAATTAT-A
56371 AAATTATTTTTTAAAA-TATA
1 AAATTA--TTTTAAAATTATA
56391 AAATTA--TTAAAATTAT
1 AAATTATTTTAAAATTAT
56407 TTTTTAAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
16 6 0.19
17 3 0.09
20 12 0.38
21 3 0.09
22 8 0.25
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.45
Consensus pattern (19 bp):
AAATTATTTTAAAATTATA
Found at i:56390 original size:21 final size:21
Alignment explanation
Indices: 56357--56398 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
56347 TAGCAAATGA
56357 TTTTAAAATTATAAAAATTATT
1 TTTTAAAATTAT-AAAATTATT
56379 TTTTAAAA-TATAAAATTATT
1 TTTTAAAATTATAAAATTATT
56399 AAAATTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 9 0.45
21 3 0.15
22 8 0.40
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TTTTAAAATTATAAAATTATT
Found at i:56402 original size:16 final size:16
Alignment explanation
Indices: 56381--56431 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
56371 AAATTATTTT
56381 TTAAAATATAAAATTA
1 TTAAAATATAAAATTA
*
56397 TTAAAAT-T---ATTT
1 TTAAAATATAAAATTA
*
56409 TTTAAATATAAAATTA
1 TTAAAATATAAAATTA
56425 TTAAAAT
1 TTAAAAT
56432 CATCATCATC
Statistics
Matches: 27, Mismatches: 4, Indels: 8
0.69 0.10 0.21
Matches are distributed among these distances:
12 9 0.33
13 1 0.04
15 1 0.04
16 16 0.59
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATAAAATTA
Found at i:56418 original size:28 final size:29
Alignment explanation
Indices: 56360--56431 Score: 128
Period size: 29 Copynumber: 2.5 Consensus size: 29
56350 CAAATGATTT
*
56360 TAAAATTATAAAAATTATTTTTTAAAATA
1 TAAAATTATTAAAATTATTTTTTAAAATA
56389 TAAAATTATTAAAATTATTTTTT-AAATA
1 TAAAATTATTAAAATTATTTTTTAAAATA
56417 TAAAATTATTAAAAT
1 TAAAATTATTAAAAT
56432 CATCATCATC
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
28 20 0.48
29 22 0.52
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (29 bp):
TAAAATTATTAAAATTATTTTTTAAAATA
Found at i:57239 original size:38 final size:39
Alignment explanation
Indices: 57146--57227 Score: 107
Period size: 39 Copynumber: 2.2 Consensus size: 39
57136 TAGAAATTAG
* *
57146 AAATTAAAATT-A-TTTAATAATTTTATTATTTTAAAAA
1 AAATTTAAATTAATTTTAATAATTTAATTATTTTAAAAA
57183 AAATTTAAATTAATTTTAATAATTTAA-TATTTTTAAAAA
1 AAATTTAAATTAATTTTAATAATTTAATTA-TTTTAAAAA
*
57222 TAATTT
1 AAATTT
57228 TTATAATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
37 10 0.26
38 3 0.08
39 26 0.67
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (39 bp):
AAATTTAAATTAATTTTAATAATTTAATTATTTTAAAAA
Found at i:57242 original size:20 final size:21
Alignment explanation
Indices: 57161--57241 Score: 73
Period size: 21 Copynumber: 4.0 Consensus size: 21
57151 AAAATTATTT
*
57161 AATAATTTT-ATTATTTTAAA
1 AATAATTTTAATAATTTTAAA
* *
57181 AAAAATTTAAATTAATTTT---
1 AATAATTTTAA-TAATTTTAAA
*
57200 AATAA-TTTAATATTTTTAAA
1 AATAATTTTAATAATTTTAAA
*
57220 AATAATTTTTATAATTTTAAA
1 AATAATTTTAATAATTTTAAA
57241 A
1 A
57242 TCATTTGCTA
Statistics
Matches: 47, Mismatches: 8, Indels: 11
0.71 0.12 0.17
Matches are distributed among these distances:
17 6 0.13
18 4 0.09
19 4 0.09
20 12 0.26
21 15 0.32
22 6 0.13
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
AATAATTTTAATAATTTTAAA
Found at i:58902 original size:30 final size:30
Alignment explanation
Indices: 58868--58937 Score: 140
Period size: 30 Copynumber: 2.3 Consensus size: 30
58858 AATTTTGGTT
58868 TCTTGATTTTATTGAAAACAAGAAAGTGAA
1 TCTTGATTTTATTGAAAACAAGAAAGTGAA
58898 TCTTGATTTTATTGAAAACAAGAAAGTGAA
1 TCTTGATTTTATTGAAAACAAGAAAGTGAA
58928 TCTTGATTTT
1 TCTTGATTTT
58938 CTTTTTCGGC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.39, C:0.07, G:0.16, T:0.39
Consensus pattern (30 bp):
TCTTGATTTTATTGAAAACAAGAAAGTGAA
Found at i:68138 original size:79 final size:79
Alignment explanation
Indices: 68007--68207 Score: 278
Period size: 79 Copynumber: 2.5 Consensus size: 79
67997 ACGAAAATTG
* * * * *
68007 AATAATTTTGTTTCAAGATTTATTCTTACTGTTCAACAGAATTCATTCGAGTTTCTG-TTCATAA
1 AATAATTCTGTTTCAAGATTTATTCCTACCGTTCAACAGAATTCACTCGAGTTTCTGTTTC-CAA
*
68071 ATAGAAATAAATTAA
65 ACAGAAATAAATTAA
*
68086 AATAATTCTGTTTTAAGATTTATTCCTACCGTTCAACAGAATTCACTCGAGTTTCTGTTTCCAAA
1 AATAATTCTGTTTCAAGATTTATTCCTACCGTTCAACAGAATTCACTCGAGTTTCTGTTTCCAAA
*
68151 CATAAATAAATTAA
66 CAGAAATAAATTAA
* ** *
68165 AATAATTCTGTTTCAGGATTTATTCCTGTCATTCAACAGAATT
1 AATAATTCTGTTTCAAGATTTATTCCTACCGTTCAACAGAATT
68208 TATTTGATTT
Statistics
Matches: 108, Mismatches: 13, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
79 105 0.97
80 3 0.03
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (79 bp):
AATAATTCTGTTTCAAGATTTATTCCTACCGTTCAACAGAATTCACTCGAGTTTCTGTTTCCAAA
CAGAAATAAATTAA
Found at i:72495 original size:22 final size:23
Alignment explanation
Indices: 72450--72499 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 23
72440 GTATTTGATA
*
72450 TGTAATCTTTAGAAGATGTGATTT
1 TGTAATCTTTAGAAGATGT-AATT
*
72474 TGTAATC-TTAG-AGATTTAATT
1 TGTAATCTTTAGAAGATGTAATT
72495 TGTAA
1 TGTAA
72500 ATAGCTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 8 0.33
22 5 0.21
23 4 0.17
24 7 0.29
ACGTcount: A:0.32, C:0.04, G:0.18, T:0.46
Consensus pattern (23 bp):
TGTAATCTTTAGAAGATGTAATT
Found at i:75384 original size:33 final size:33
Alignment explanation
Indices: 75342--75408 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
75332 AGGGAAGAAA
75342 TGACACATCATCATCTTCTTTATTTTTCTCCCT
1 TGACACATCATCATCTTCTTTATTTTTCTCCCT
*
75375 TGACACATCATCATCTTCTTTATTTTTCTTCCT
1 TGACACATCATCATCTTCTTTATTTTTCTCCCT
75408 T
1 T
75409 CCTTTGATCG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.18, C:0.28, G:0.03, T:0.51
Consensus pattern (33 bp):
TGACACATCATCATCTTCTTTATTTTTCTCCCT
Found at i:76261 original size:37 final size:37
Alignment explanation
Indices: 76211--76352 Score: 196
Period size: 37 Copynumber: 3.8 Consensus size: 37
76201 ATCTAAAAAG
*
76211 TCAGGCTTTGTGCCTAGTAGTCTTCATGCCGGTGTTT
1 TCAGGCTTTGTGCCTAGTAGGCTTCATGCCGGTGTTT
*
76248 TCAGGCTTTGTGCCTAGTAGGCTTCATGCCGGTGATT
1 TCAGGCTTTGTGCCTAGTAGGCTTCATGCCGGTGTTT
* *
76285 TCAGGCTATGTGCCTAGTAGGCTTCATGCCGGTGTAT
1 TCAGGCTTTGTGCCTAGTAGGCTTCATGCCGGTGTTT
* * * *
76322 TC-GAGATATGTGCTTAGTAGGCTTTATGCCG
1 TCAG-GCTTTGTGCCTAGTAGGCTTCATGCCG
76353 ATGATCCAAG
Statistics
Matches: 96, Mismatches: 8, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
36 1 0.01
37 95 0.99
ACGTcount: A:0.15, C:0.20, G:0.29, T:0.36
Consensus pattern (37 bp):
TCAGGCTTTGTGCCTAGTAGGCTTCATGCCGGTGTTT
Found at i:83731 original size:17 final size:19
Alignment explanation
Indices: 83709--83752 Score: 58
Period size: 17 Copynumber: 2.5 Consensus size: 19
83699 TGTTGTTGAG
83709 TTTTTAATA-TTTTT-ATT
1 TTTTTAATATTTTTTAATT
83726 TTTTTAA-ATTTTTTAATT
1 TTTTTAATATTTTTTAATT
*
83744 TTTATAATA
1 TTTTTAATA
83753 CCTATACAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 1 0.04
17 12 0.52
18 9 0.39
19 1 0.04
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTTTAATATTTTTTAATT
Found at i:97364 original size:2 final size:2
Alignment explanation
Indices: 97357--97381 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
97347 ATGTCATTAT
97357 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 T
97382 GAAATTAAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:98090 original size:28 final size:28
Alignment explanation
Indices: 98050--98118 Score: 77
Period size: 28 Copynumber: 2.4 Consensus size: 28
98040 TTTAAAAAAA
*
98050 AATTTATATTATATTATTTTA-TTATTTAAT
1 AATTT-TA-TATATT-TTTTATTTATTAAAT
98080 AATTTTATATATTTTTTATTTATTAAAT
1 AATTTTATATATTTTTTATTTATTAAAT
**
98108 TTTTTTATATA
1 AATTTTATATA
98119 GTAATCTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
27 5 0.14
28 23 0.66
29 2 0.06
30 5 0.14
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (28 bp):
AATTTTATATATTTTTTATTTATTAAAT
Done.