Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001703.1 Kokia drynarioides strain JFW-HI SEQ_113392, 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: 232222
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 24 characters in sequence are not A, C, G, or T
Found at i:719 original size:2 final size:2
Alignment explanation
Indices: 712--741 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
702 TGACTTTTTC
712 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
742 TATTCCAGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7449 original size:26 final size:26
Alignment explanation
Indices: 7416--7466 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
7406 TTTAATTCGA
7416 TATTAAA-TCAAAATAA-TTTTTTATG
1 TATTAAATTC-AAATAACTTTTTTATG
7441 TATTCAAATTCAAATAACTTTTTTAT
1 TATT-AAATTCAAATAACTTTTTTAT
7467 TAGTATGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 4 0.17
26 9 0.39
27 10 0.43
ACGTcount: A:0.41, C:0.08, G:0.02, T:0.49
Consensus pattern (26 bp):
TATTAAATTCAAATAACTTTTTTATG
Found at i:8821 original size:16 final size:15
Alignment explanation
Indices: 8775--8822 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 15
8765 AGAGAATTAT
8775 TTAAAATTATTAAGAA
1 TTAAAATTATTAA-AA
* *
8791 TTATAAAATAATAAAA
1 TTA-AAATTATTAAAA
8807 TTAAAATTTATTAAAA
1 TTAAAA-TTATTAAAA
8823 ACAACATCTA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 3 0.12
16 15 0.58
17 8 0.31
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (15 bp):
TTAAAATTATTAAAA
Found at i:13274 original size:12 final size:12
Alignment explanation
Indices: 13211--13321 Score: 80
Period size: 12 Copynumber: 9.3 Consensus size: 12
13201 GTTTTGATGC
13211 TGTTATTTTTGT
1 TGTTATTTTTGT
** * *
13223 TACTGTTTTTGC
1 TGTTATTTTTGT
13235 TGTTATTTTTGT
1 TGTTATTTTTGT
** *
13247 TACTATTTTTGC
1 TGTTATTTTTGT
13259 TGTTATTTTTGT
1 TGTTATTTTTGT
* *
13271 TGTT-GTTTTGC
1 TGTTATTTTTGT
*
13282 TGCTATTTTTGT
1 TGTTATTTTTGT
* * *
13294 TATTGTTTTGGT
1 TGTTATTTTTGT
* *
13306 TATTATTTTGGT
1 TGTTATTTTTGT
13318 TGTT
1 TGTT
13322 TGAATGTTAT
Statistics
Matches: 73, Mismatches: 25, Indels: 2
0.73 0.25 0.02
Matches are distributed among these distances:
11 8 0.11
12 65 0.89
ACGTcount: A:0.09, C:0.05, G:0.18, T:0.68
Consensus pattern (12 bp):
TGTTATTTTTGT
Found at i:13312 original size:47 final size:48
Alignment explanation
Indices: 13213--13321 Score: 130
Period size: 47 Copynumber: 2.3 Consensus size: 48
13203 TTTGATGCTG
** * * *
13213 TTATTTTTGTTACTGTTTTTGCTGTTATTTTTGTTACTATTTTTGCTG
1 TTATTTTTGTTGTTGTTTTTGCTGCTATTTTTGTTACTATTTTGGCTA
* * *
13261 TTATTTTTGTTGTTG-TTTTGCTGCTATTTTTGTTATTGTTTTGGTTA
1 TTATTTTTGTTGTTGTTTTTGCTGCTATTTTTGTTACTATTTTGGCTA
*
13308 TTATTTTGGTTGTT
1 TTATTTTTGTTGTT
13322 TGAATGTTAT
Statistics
Matches: 52, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
47 39 0.75
48 13 0.25
ACGTcount: A:0.09, C:0.06, G:0.17, T:0.68
Consensus pattern (48 bp):
TTATTTTTGTTGTTGTTTTTGCTGCTATTTTTGTTACTATTTTGGCTA
Found at i:13314 original size:24 final size:24
Alignment explanation
Indices: 13208--13302 Score: 138
Period size: 24 Copynumber: 4.0 Consensus size: 24
13198 GGTGTTTTGA
13208 TGCTGTTATTTTTGTTACTGTTTT
1 TGCTGTTATTTTTGTTACTGTTTT
*
13232 TGCTGTTATTTTTGTTACTATTTT
1 TGCTGTTATTTTTGTTACTGTTTT
**
13256 TGCTGTTATTTTTGTTGTTG-TTT
1 TGCTGTTATTTTTGTTACTGTTTT
* *
13279 TGCTGCTATTTTTGTTATTGTTTT
1 TGCTGTTATTTTTGTTACTGTTTT
13303 GGTTATTATT
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
23 21 0.33
24 43 0.67
ACGTcount: A:0.08, C:0.07, G:0.17, T:0.67
Consensus pattern (24 bp):
TGCTGTTATTTTTGTTACTGTTTT
Found at i:13516 original size:21 final size:21
Alignment explanation
Indices: 13472--13517 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
13462 TAAATTTATT
* *
13472 TATTTTTAATGTTTGTTTTAA
1 TATTTTTAATGTTTATTTGAA
13493 TATTTTTAA-GTTTATTTGATA
1 TATTTTTAATGTTTATTTGA-A
13514 TATT
1 TATT
13518 ATATATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.65
Consensus pattern (21 bp):
TATTTTTAATGTTTATTTGAA
Found at i:16001 original size:16 final size:16
Alignment explanation
Indices: 15971--16031 Score: 52
Period size: 16 Copynumber: 3.7 Consensus size: 16
15961 TTATTCAAAA
* *
15971 AAATAATATACAAATCT
1 AAAT-ATATATAAATAT
15988 AAATATATATAAATAT
1 AAATATATATAAATAT
* *
16004 AAA-ATATTAGAAATTT
1 AAATATA-TATAAATAT
16020 ATAATATATATA
1 A-AATATATATA
16032 TTTGCTGAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
15 3 0.08
16 21 0.58
17 9 0.25
18 3 0.08
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (16 bp):
AAATATATATAAATAT
Found at i:25235 original size:40 final size:40
Alignment explanation
Indices: 25180--25260 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
25170 ATCTAAACAC
25180 GCGGTTAGTATTAATTATATTGTAGAAGAATCCAACAAGT
1 GCGGTTAGTATTAATTATATTGTAGAAGAATCCAACAAGT
*
25220 GCGGTTAGTATTAATTATCTTGTAGAAGAATCCAACAAGT
1 GCGGTTAGTATTAATTATATTGTAGAAGAATCCAACAAGT
25260 G
1 G
25261 GCTCTAGTGA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.32
Consensus pattern (40 bp):
GCGGTTAGTATTAATTATATTGTAGAAGAATCCAACAAGT
Found at i:31767 original size:52 final size:53
Alignment explanation
Indices: 31711--31814 Score: 201
Period size: 52 Copynumber: 2.0 Consensus size: 53
31701 AGTAAGGATG
31711 ATAGTTTCCATACTAGAAATTTAAGCAAATCATTTTAAATTGAAAAG-AAAAT
1 ATAGTTTCCATACTAGAAATTTAAGCAAATCATTTTAAATTGAAAAGTAAAAT
31763 ATAGTTTCCATACTAGAAATTTAAGCAAATCATTTTAAATTGAAAAGTAAAA
1 ATAGTTTCCATACTAGAAATTTAAGCAAATCATTTTAAATTGAAAAGTAAAA
31815 AGAAAGGAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 47 0.92
53 4 0.08
ACGTcount: A:0.48, C:0.10, G:0.10, T:0.33
Consensus pattern (53 bp):
ATAGTTTCCATACTAGAAATTTAAGCAAATCATTTTAAATTGAAAAGTAAAAT
Found at i:34068 original size:19 final size:20
Alignment explanation
Indices: 34044--34083 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
34034 AGTTATTTGA
*
34044 TTAGTGGAATT-TAATATTT
1 TTAGTGGAATTATAAAATTT
*
34063 TTAGTGGTATTATAAAATTT
1 TTAGTGGAATTATAAAATTT
34083 T
1 T
34084 GAAATATGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.53
Consensus pattern (20 bp):
TTAGTGGAATTATAAAATTT
Found at i:34166 original size:140 final size:139
Alignment explanation
Indices: 34014--34274 Score: 389
Period size: 140 Copynumber: 1.9 Consensus size: 139
34004 TAAGATTACT
* * * *
34014 AAAATGTAAAATTACTTGAG-AGTTATTTGATTAGTGGAATTTAATATTTTTAGTGGTATTATAA
1 AAAATGTAAAATTACTTAAGTA-TTATTTGATTAGAGAAATTTAATATTTTTAGTGGTATTACAA
* *
34078 AATTTTGAAATATGATTATTTTGTTTAGATTTCAAAATTTCCTTGAAGTGTTAATCTCGTATTCT
65 AATTTTGAAATATAATTATCTTGTTTAGATTTCAAAATTT-CTTGAAGTGTTAATCTCGTATTCT
34143 CATAAATGTCA
129 CATAAATGTCA
* * *
34154 AAAATGTAAAATTACTTAAGTATTATTTGATTTGAGAAATTTTATATTTTTAGTGGTATTGCAAA
1 AAAATGTAAAATTACTTAAGTATTATTTGATTAGAGAAATTTAATATTTTTAGTGGTATTACAAA
* **
34219 ATTTTGAAATATAATTATCTTGTTTAGATTTCAAAATTTTTTGTGGTGTTAATCTC
66 ATTTTGAAATATAATTATCTTGTTTAGATTTCAAAATTTCTTGAAGTGTTAATCTC
34275 ATGTAATGTT
Statistics
Matches: 108, Mismatches: 12, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
139 14 0.13
140 93 0.86
141 1 0.01
ACGTcount: A:0.34, C:0.06, G:0.14, T:0.46
Consensus pattern (139 bp):
AAAATGTAAAATTACTTAAGTATTATTTGATTAGAGAAATTTAATATTTTTAGTGGTATTACAAA
ATTTTGAAATATAATTATCTTGTTTAGATTTCAAAATTTCTTGAAGTGTTAATCTCGTATTCTCA
TAAATGTCA
Found at i:35454 original size:24 final size:24
Alignment explanation
Indices: 35427--35512 Score: 93
Period size: 24 Copynumber: 3.5 Consensus size: 24
35417 TAAAAATAAT
*
35427 TATATTAATAATGTTATTAAATTA
1 TATATTAATAATTTTATTAAATTA
* * *
35451 TATATTATTATTTTTATTAGATTA
1 TATATTAATAATTTTATTAAATTA
*
35475 TATTTAATAATAATTTTTATTAAATTA
1 TA--TATTAATAA-TTTTATTAAATTA
35502 TAT-TTAATAAT
1 TATATTAATAAT
35513 AATCTTATTA
Statistics
Matches: 50, Mismatches: 9, Indels: 7
0.76 0.14 0.11
Matches are distributed among these distances:
23 1 0.02
24 28 0.56
25 1 0.02
26 6 0.12
27 14 0.28
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (24 bp):
TATATTAATAATTTTATTAAATTA
Found at i:35459 original size:27 final size:26
Alignment explanation
Indices: 35432--35522 Score: 107
Period size: 27 Copynumber: 3.5 Consensus size: 26
35422 ATAATTATAT
*
35432 TAATAATGTTATTAAATTATATATT-A
1 TAATAATTTTATTAAATTATAT-TTAA
* *
35458 T--TATTTTTATTAGATTATATTTAA
1 TAATAATTTTATTAAATTATATTTAA
35482 TAATAATTTTTATTAAATTATATTTAA
1 TAATAA-TTTTATTAAATTATATTTAA
*
35509 TAATAATCTTATTA
1 TAATAATTTTATTA
35523 TATTTAAAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
23 2 0.04
24 18 0.33
26 10 0.18
27 25 0.45
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (26 bp):
TAATAATTTTATTAAATTATATTTAA
Found at i:35480 original size:14 final size:13
Alignment explanation
Indices: 35440--35512 Score: 53
Period size: 14 Copynumber: 5.6 Consensus size: 13
35430 ATTAATAATG
35440 TTATTAAATTATA-
1 TTATT-AATTATAT
*
35453 -TATT-ATTATTT
1 TTATTAATTATAT
35464 TTATTAGATTATAT
1 TTATTA-ATTATAT
* * *
35478 TTAATAATAATTT
1 TTATTAATTATAT
35491 TTATTAAATTATAT
1 TTATT-AATTATAT
*
35505 TTAATAAT
1 TTATTAAT
35513 AATCTTATTA
Statistics
Matches: 46, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
10 5 0.11
12 8 0.17
13 12 0.26
14 21 0.46
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (13 bp):
TTATTAATTATAT
Found at i:40606 original size:21 final size:23
Alignment explanation
Indices: 40576--40637 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 23
40566 TTTAAAATTA
40576 AAAAATTTTAACTTAATAAAA-AT
1 AAAAA-TTTAACTTAATAAAAGAT
40599 -AAAATTTAACTTACA-AAAATGAT
1 AAAAATTTAACTTA-ATAAAA-GAT
*
40622 AAAAATTTAATTTAAT
1 AAAAATTTAACTTAAT
40638 TATTTAAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
21 13 0.39
22 5 0.15
23 3 0.09
24 12 0.36
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (23 bp):
AAAAATTTAACTTAATAAAAGAT
Found at i:41272 original size:6 final size:6
Alignment explanation
Indices: 41261--41287 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
41251 TCTTATTTTA
41261 TTTATT TTTATT TTTATT TTTATT TTT
1 TTTATT TTTATT TTTATT TTTATT TTT
41288 GTTTGATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTATT
Found at i:56446 original size:19 final size:19
Alignment explanation
Indices: 56418--56462 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
56408 CAATTTTCTC
*
56418 TATTTT-TAAATATTTTT-T
1 TATTTTATAAA-ATTTTTAA
56436 TATTTTATAAAATTTTTAA
1 TATTTTATAAAATTTTTAA
56455 TATTTTAT
1 TATTTTAT
56463 TTGATCAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 12 0.50
19 12 0.50
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TATTTTATAAAATTTTTAA
Found at i:75925 original size:58 final size:58
Alignment explanation
Indices: 75863--75982 Score: 222
Period size: 58 Copynumber: 2.1 Consensus size: 58
75853 ACCCATCAAC
*
75863 AAACTAAACTCAAATATTTTTAAACCCAAATATAATTTTATTCTTAAAAAACACTCAT
1 AAACTAAACTCAAATATTTTTAAACCCAAATATAATTTTATTCCTAAAAAACACTCAT
*
75921 AAACTAAACTCAAATATTTTTAAACCCAAATATAATTTTATTCCTAAATAACACTCAT
1 AAACTAAACTCAAATATTTTTAAACCCAAATATAATTTTATTCCTAAAAAACACTCAT
75979 AAAC
1 AAAC
75983 AACTTTTTTT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 60 1.00
ACGTcount: A:0.48, C:0.18, G:0.00, T:0.33
Consensus pattern (58 bp):
AAACTAAACTCAAATATTTTTAAACCCAAATATAATTTTATTCCTAAAAAACACTCAT
Found at i:76606 original size:21 final size:22
Alignment explanation
Indices: 76566--76607 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
76556 TTGTTGTGTT
* *
76566 TTATTTACTTTGATTTTTTCAC
1 TTATTTACTTTCAATTTTTCAC
76588 TTATTTA-TTTCAATTTTTCA
1 TTATTTACTTTCAATTTTTCA
76608 TTGTATAATC
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:0.21, C:0.12, G:0.02, T:0.64
Consensus pattern (22 bp):
TTATTTACTTTCAATTTTTCAC
Found at i:85270 original size:16 final size:15
Alignment explanation
Indices: 85243--85279 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
85233 CTATTTTTTA
*
85243 TTATTTAAAATAT-T
1 TTATTTAAAAAATAT
85257 TTATTTAAAAAATAT
1 TTATTTAAAAAATAT
85272 TTATTTAA
1 TTATTTAA
85280 TTTTGACTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TTATTTAAAAAATAT
Found at i:88003 original size:56 final size:59
Alignment explanation
Indices: 87838--88042 Score: 170
Period size: 61 Copynumber: 3.4 Consensus size: 59
87828 AAAATTATCA
* * ** * *
87838 GATAAAAAAATTTCAATTTTTTTTGGTGTTGGCCATGCAATGGTTGACACC-CCTGTTCTCG
1 GATAAAAAAATTAC-A--TTTTTGGGTGTTGGCCATGCAATGGCCGACACCTCATTTTCTCG
* * ** * *
87899 AATAAAAAAATTTCAAACTTTTTTTGTGTTGGCCATGCAATGGTCGACACCTCCTTTT-T-G
1 GATAAAAAAA-TT-ACA-TTTTTGGGTGTTGGCCATGCAATGGCCGACACCTCATTTTCTCG
* *
87959 AGA-AAAAAAA-TGCATTTTTGGGTGTTGGTCATTGC-ATGGCCGACACCTCATTTTCTCG
1 -GATAAAAAAATTACATTTTTGGGTGTTGGCCA-TGCAATGGCCGACACCTCATTTTCTCG
88017 GATAAAAAAATTACATTTTTGGGTGT
1 GATAAAAAAATTACATTTTTGGGTGT
88043 CGGCTTTTAG
Statistics
Matches: 119, Mismatches: 16, Indels: 20
0.77 0.10 0.13
Matches are distributed among these distances:
56 31 0.26
57 7 0.06
58 9 0.08
59 14 0.12
60 8 0.07
61 42 0.35
62 8 0.07
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.37
Consensus pattern (59 bp):
GATAAAAAAATTACATTTTTGGGTGTTGGCCATGCAATGGCCGACACCTCATTTTCTCG
Found at i:88042 original size:59 final size:56
Alignment explanation
Indices: 87924--88042 Score: 143
Period size: 56 Copynumber: 2.1 Consensus size: 56
87914 AACTTTTTTT
* * *
87924 GTGTTGGCCATGCAATGGTCGACACCTCCTTTTTGAGAAAAAAAATGCATTTTTGG
1 GTGTTGGCCATGCAATGGCCGACACCTCATTTTTGAGAAAAAAAATACATTTTTGG
*
87980 GTGTTGGTCATTGC-ATGGCCGACACCTCATTTTCTCG-GATAAAAAAATTACATTTTTGG
1 GTGTTGGCCA-TGCAATGGCCGACACCTCATTTT-T-GAGA-AAAAAAA-TACATTTTTGG
88039 GTGT
1 GTGT
88043 CGGCTTTTAG
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
56 26 0.48
57 6 0.11
58 8 0.15
59 14 0.26
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (56 bp):
GTGTTGGCCATGCAATGGCCGACACCTCATTTTTGAGAAAAAAAATACATTTTTGG
Found at i:92332 original size:86 final size:86
Alignment explanation
Indices: 92097--92494 Score: 610
Period size: 86 Copynumber: 4.6 Consensus size: 86
92087 TACATTTAAA
** * * *
92097 ATTAA-TTTAACATTATTTAAATAAAAAAGATTATTATTATATTATAATTTATAT-AAACTATTG
1 ATTAATTTTAA-A-TATTTAAATAAAAATTATTATTATTATATTACAATTTTTATCAAA-TAATG
92160 TGTTAATTTGACAATACATTATTT
63 TGTTAATTTGACAATACATTATTT
* * *
92184 ATCAAATTTT-TATATTTAAAGT-ACAA--ATTATTATTATATTACAATTTTTATCAAATAATGT
1 AT-TAATTTTAAATATTTAAA-TAAAAATTATTATTATTATATTACAATTTTTATCAAATAATGT
92245 GTTAATTTGACAATACATTATTT
64 GTTAATTTGACAATACATTATTT
92268 ATTAATTTTAAATATTTAAATAAAAATTATTATTATTATATTACAATTTTTATCAAATAATGTGT
1 ATTAATTTTAAATATTTAAATAAAAATTATTATTATTATATTACAATTTTTATCAAATAATGTGT
*
92333 TGATTTGACAATACATTATTT
66 TAATTTGACAATACATTATTT
92354 ATTAATTTTAAATATTTAAATAAAAATTATTATTATTATATTACAATTTTTATCAAATAATGTGT
1 ATTAATTTTAAATATTTAAATAAAAATTATTATTATTATATTACAATTTTTATCAAATAATGTGT
*
92419 TGATTTGACAATACATTATTT
66 TAATTTGACAATACATTATTT
*
92440 ATTAATTTTAAATATTTAAATAAAAATTATTATTTTTATATTACAATTTTTATCA
1 ATTAATTTTAAATATTTAAATAAAAATTATTATTATTATATTACAATTTTTATCA
92495 TATTTTAAAT
Statistics
Matches: 292, Mismatches: 11, Indels: 17
0.91 0.03 0.05
Matches are distributed among these distances:
83 7 0.02
84 65 0.22
85 3 0.01
86 208 0.71
87 4 0.01
88 2 0.01
89 3 0.01
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.49
Consensus pattern (86 bp):
ATTAATTTTAAATATTTAAATAAAAATTATTATTATTATATTACAATTTTTATCAAATAATGTGT
TAATTTGACAATACATTATTT
Found at i:93517 original size:14 final size:15
Alignment explanation
Indices: 93500--93532 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
93490 ATTTTTTAAA
93500 TTTTAT-TAATTATT
1 TTTTATCTAATTATT
93514 TTTT-TCTAATTATT
1 TTTTATCTAATTATT
93528 TTTTA
1 TTTTA
93533 ATTTTTCAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 1 0.06
14 16 0.94
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTTATCTAATTATT
Found at i:94942 original size:30 final size:30
Alignment explanation
Indices: 94908--94968 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
94898 ATTTTTTTTC
*
94908 CGTTTACT-TTTTAAATTTAATTTGTAATTT
1 CGTTT-CTATTTTAAATTTAATTTCTAATTT
*
94938 CGTTTTTATTTTAAATTTAATTTCTAATTT
1 CGTTTCTATTTTAAATTTAATTTCTAATTT
94968 C
1 C
94969 CTGTATTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 1 0.04
30 27 0.96
ACGTcount: A:0.26, C:0.08, G:0.05, T:0.61
Consensus pattern (30 bp):
CGTTTCTATTTTAAATTTAATTTCTAATTT
Found at i:95973 original size:60 final size:59
Alignment explanation
Indices: 95837--96014 Score: 214
Period size: 61 Copynumber: 2.9 Consensus size: 59
95827 CAGCCATTAT
* * * * * *
95837 ATGGCCAACACTAAAAAAATTTGAAATTTTTTATTCAAGAAAAGGAGGTATCGGCCATTGC
1 ATGGCCAACAC-AAAAAAATTTGAATTTTTTTATCCGAGAAAAGG-GATGTCGACCATTGC
*
95898 ATGGCCAACACCAAAAAAATTTGAATTTTTTTATCCGAGAACACGGGATGTCGACCATTGC
1 ATGGCCAACA-CAAAAAAATTTGAATTTTTTTATCCGAGAA-AAGGGATGTCGACCATTGC
* *
95959 ATGGCCAACACAAAAAATTTTTGAATTTTTTTTATCTGA-AAAAGGGATGTCGACCA
1 ATGGCCAACACAAAAAA-ATTTGAA-TTTTTTTATCCGAGAAAAGGGATGTCGACCA
96015 AAAATACAAT
Statistics
Matches: 103, Mismatches: 10, Indels: 9
0.84 0.08 0.07
Matches are distributed among these distances:
60 21 0.20
61 66 0.64
62 16 0.16
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (59 bp):
ATGGCCAACACAAAAAAATTTGAATTTTTTTATCCGAGAAAAGGGATGTCGACCATTGC
Found at i:104545 original size:33 final size:31
Alignment explanation
Indices: 104501--104562 Score: 97
Period size: 33 Copynumber: 1.9 Consensus size: 31
104491 GACTTATGCA
*
104501 CCCCTTTCCCTTTCTTCTTCTTCTTTTTTTTT
1 CCCCTTCCCCTTTCTTCTTCTT-TTTTTTTTT
104533 NCCCCTTCCCCTTTCTTCTTCTTTTTTTTT
1 -CCCCTTCCCCTTTCTTCTTCTTTTTTTTT
104563 ATTTATTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
32 7 0.25
33 21 0.75
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.63
Consensus pattern (31 bp):
CCCCTTCCCCTTTCTTCTTCTTTTTTTTTTT
Found at i:105246 original size:14 final size:15
Alignment explanation
Indices: 105227--105259 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
105217 GGGCAATTCC
*
105227 TTTGGAATT-TGGAA
1 TTTGGAATTGGGGAA
105241 TTTGGAATTGGGGAA
1 TTTGGAATTGGGGAA
105256 TTTG
1 TTTG
105260 CTTGCAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.24, C:0.00, G:0.33, T:0.42
Consensus pattern (15 bp):
TTTGGAATTGGGGAA
Found at i:109876 original size:36 final size:35
Alignment explanation
Indices: 109836--109906 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 35
109826 GGGTGGCAGC
109836 AATGAAGTTATGATTTGATGATGTATGA-ATGTAATG
1 AATGAAGTTATGATTTGATGATG-ATGATAT-TAATG
* *
109872 AATGAAGTTGTGGTTTGATGATGATGATATTAATG
1 AATGAAGTTATGATTTGATGATGATGATATTAATG
109907 TAATCAATGG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
35 9 0.28
36 23 0.72
ACGTcount: A:0.34, C:0.00, G:0.27, T:0.39
Consensus pattern (35 bp):
AATGAAGTTATGATTTGATGATGATGATATTAATG
Found at i:111086 original size:42 final size:39
Alignment explanation
Indices: 111034--111131 Score: 101
Period size: 42 Copynumber: 2.4 Consensus size: 39
111024 ATTATAAAGG
* * *
111034 ATATTATATAATAATTAATATATAATGTATTACTATTATATT
1 ATATAATATAATAATTAACATAT-A-GTATTAC-ATGATATT
111076 ATATAATATAATAA--AACATATAGTATTACATGATATT
1 ATATAATATAATAATTAACATATAGTATTACATGATATT
*
111113 ATAATATATATAAAAATTA
1 AT-ATA-ATATAATAATTA
111132 TTAATATATT
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
37 9 0.19
38 10 0.21
39 9 0.19
40 6 0.12
41 1 0.02
42 13 0.27
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (39 bp):
ATATAATATAATAATTAACATATAGTATTACATGATATT
Found at i:111112 original size:37 final size:38
Alignment explanation
Indices: 111033--111125 Score: 102
Period size: 37 Copynumber: 2.4 Consensus size: 38
111023 AATTATAAAG
* * *
111033 GATATTATATAATA-ATTAATATATAATGTATTACTAT
1 GATATTATATAATATAATAAAACATAATGTATTACTAT
*
111070 TATATTATATAATATAATAAAACAT-ATAGTATTAC-AT
1 GATATTATATAATATAATAAAACATAAT-GTATTACTAT
111107 GATATTATAATATATATAA
1 GATATTAT-ATA-ATATAA
111126 AAATTATTAA
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
37 24 0.51
38 17 0.36
39 6 0.13
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.43
Consensus pattern (38 bp):
GATATTATATAATATAATAAAACATAATGTATTACTAT
Found at i:111479 original size:18 final size:19
Alignment explanation
Indices: 111458--111494 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
111448 AATACAAAAA
*
111458 ATATTATTAAAAT-TTAAT
1 ATATTAATAAAATATTAAT
111476 ATATTAATAAAATATTAAT
1 ATATTAATAAAATATTAAT
111495 TTTTAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
ATATTAATAAAATATTAAT
Found at i:123479 original size:11 final size:11
Alignment explanation
Indices: 123464--123494 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
123454 AGACTGTCAA
123464 AAAGGAAAAGG
1 AAAGGAAAAGG
*
123475 GAAGGAAAAGG
1 AAAGGAAAAGG
123486 AAAGGAAAA
1 AAAGGAAAA
123495 TGTAAACATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (11 bp):
AAAGGAAAAGG
Found at i:124102 original size:2 final size:2
Alignment explanation
Indices: 124095--124140 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
124085 AACCGCCTCC
*
124095 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT TT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
124137 CT CT
1 CT CT
124141 AGAACCAAAG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
CT
Found at i:126620 original size:15 final size:14
Alignment explanation
Indices: 126574--126619 Score: 58
Period size: 14 Copynumber: 3.2 Consensus size: 14
126564 AAGTTACAGA
126574 TTTAATTTTTATAT
1 TTTAATTTTTATAT
*
126588 ATTAATTTTGT-TAAT
1 TTTAATTTT-TAT-AT
126603 TTTAATTTTTATAT
1 TTTAATTTTTATAT
126617 TTT
1 TTT
126620 TTTTAATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
14 15 0.56
15 12 0.44
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (14 bp):
TTTAATTTTTATAT
Found at i:126625 original size:24 final size:26
Alignment explanation
Indices: 126574--126636 Score: 76
Period size: 24 Copynumber: 2.4 Consensus size: 26
126564 AAGTTACAGA
126574 TTTAATTTTTATATATTAATTTTGTTAAT
1 TTTAA-TTTT-TATATT-ATTTTGTTAAT
126603 TTTAATTTTTATATT-TTTT-TTAAT
1 TTTAATTTTTATATTATTTTGTTAAT
*
126627 TTTAAATTTT
1 TTTAATTTTT
126637 CAATCACGAC
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
24 14 0.42
25 4 0.12
27 6 0.18
28 4 0.12
29 5 0.15
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.70
Consensus pattern (26 bp):
TTTAATTTTTATATTATTTTGTTAAT
Found at i:126629 original size:17 final size:18
Alignment explanation
Indices: 126602--126636 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
126592 ATTTTGTTAA
*
126602 TTTTAATTTTTATATTTT
1 TTTTAATTTTTAAATTTT
126620 TTTTAA-TTTTAAATTTT
1 TTTTAATTTTTAAATTTT
126637 CAATCACGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTAATTTTTAAATTTT
Found at i:126992 original size:16 final size:16
Alignment explanation
Indices: 126963--126997 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
126953 GAATGGAATT
*
126963 AAAATTTAAAAATTAA
1 AAAATATAAAAATTAA
*
126979 AAAATATAATAATTAA
1 AAAATATAAAAATTAA
126995 AAA
1 AAA
126998 TGATCAAATT
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:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAATATAAAAATTAA
Found at i:131586 original size:143 final size:143
Alignment explanation
Indices: 131414--131703 Score: 535
Period size: 143 Copynumber: 2.0 Consensus size: 143
131404 GTTAAAACCA
*
131414 ATTGATCCAACCAATTTTAATTTTTCGATTAATCGAGTTGGATTTTGGGCTGTTTATAAGCCATA
1 ATTGATCCAACCAATTTTAATTTTTCGATTAATCGAGTTGAATTTTGGGCTGTTTATAAGCCATA
131479 ATTTGCCTACTACTTTAAATTATAAGGGGAACCGAAGGTAGAAAAAGAGATAAGAAAGAAAAACA
66 ATTTGCCTACTACTTTAAATTATAAGGGGAACCGAAGGTAGAAAAAGAGATAAGAAAGAAAAACA
131544 CAATATTGAAATT
131 CAATATTGAAATT
* *
131557 ATTGATCCAACCATTTTTAATTTTTCGATTAATCGAGTTGAATTTTGGGCTGTTTTTAAGCCATA
1 ATTGATCCAACCAATTTTAATTTTTCGATTAATCGAGTTGAATTTTGGGCTGTTTATAAGCCATA
* *
131622 ATTTGCCTACTACTTTAAATTATAAGGGGAACCGAAGGTAGAGAGAGAGATAAGAAAGAAAAACA
66 ATTTGCCTACTACTTTAAATTATAAGGGGAACCGAAGGTAGAAAAAGAGATAAGAAAGAAAAACA
131687 CAATATTGAAATT
131 CAATATTGAAATT
131700 ATTG
1 ATTG
131704 CACAGCATCG
Statistics
Matches: 142, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
143 142 1.00
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (143 bp):
ATTGATCCAACCAATTTTAATTTTTCGATTAATCGAGTTGAATTTTGGGCTGTTTATAAGCCATA
ATTTGCCTACTACTTTAAATTATAAGGGGAACCGAAGGTAGAAAAAGAGATAAGAAAGAAAAACA
CAATATTGAAATT
Found at i:131853 original size:7 final size:7
Alignment explanation
Indices: 131841--131886 Score: 92
Period size: 7 Copynumber: 6.6 Consensus size: 7
131831 TATATAGCAA
131841 CACACGT
1 CACACGT
131848 CACACGT
1 CACACGT
131855 CACACGT
1 CACACGT
131862 CACACGT
1 CACACGT
131869 CACACGT
1 CACACGT
131876 CACACGT
1 CACACGT
131883 CACA
1 CACA
131887 AGCCCACTAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 39 1.00
ACGTcount: A:0.30, C:0.43, G:0.13, T:0.13
Consensus pattern (7 bp):
CACACGT
Found at i:138519 original size:158 final size:158
Alignment explanation
Indices: 138231--138539 Score: 476
Period size: 158 Copynumber: 2.0 Consensus size: 158
138221 ATACCTTGTA
** * * * *
138231 TTTTGGTACTTATACTTGGCCCTTGTTTTGCTTAAAATCACTTTCAAACGTAAACGATTGATCGA
1 TTTTGGTACCAATACTTGGCCCCTGTTTTGCTTAAAATCACTTTCAAACATAAACGACTGACCGA
*
138296 TAATGACCCCAAACATTTAAGATAATAACTAATGAGTTAAATAAATTAAAATGATATAGTTAATG
66 CAATGACCCCAAACATTTAAGATAATAACTAATGAGTTAAATAAATTAAAATGATATAGTTAATG
* *
138361 TTCGAAATTACTTTGTGTTTACCCTATG
131 TTCGAAATAACTTAGTGTTTACCCTATG
138389 TTTTGGTACCAATACTT-GCCCCTGTTTTGCTTAGAAATCACTTTCAAACATAAACGACTGACCG
1 TTTTGGTACCAATACTTGGCCCCTGTTTTGCTTA-AAATCACTTTCAAACATAAACGACTGACCG
* ** * *
138453 ACAATGACCCCAAATATTTAAGATAATAGTTAATGAGTTAAATAAGTTAAAATGCTATAGTTAAT
65 ACAATGACCCCAAACATTTAAGATAATAACTAATGAGTTAAATAAATTAAAATGATATAGTTAAT
138518 GTTCGAAATAACTTAGTGTTTA
130 GTTCGAAATAACTTAGTGTTTA
138540 GCCAATATCA
Statistics
Matches: 136, Mismatches: 14, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
157 15 0.11
158 121 0.89
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.36
Consensus pattern (158 bp):
TTTTGGTACCAATACTTGGCCCCTGTTTTGCTTAAAATCACTTTCAAACATAAACGACTGACCGA
CAATGACCCCAAACATTTAAGATAATAACTAATGAGTTAAATAAATTAAAATGATATAGTTAATG
TTCGAAATAACTTAGTGTTTACCCTATG
Found at i:140496 original size:21 final size:21
Alignment explanation
Indices: 140472--140515 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
140462 TTCTAATGAC
*
140472 TAAGGTCAGGTTTCTTAGTGG
1 TAAGGTCAAGTTTCTTAGTGG
140493 TAAGGTCAAGTTTCTTAGTGG
1 TAAGGTCAAGTTTCTTAGTGG
140514 TA
1 TA
140516 TTTATTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.09, G:0.30, T:0.39
Consensus pattern (21 bp):
TAAGGTCAAGTTTCTTAGTGG
Found at i:143424 original size:47 final size:47
Alignment explanation
Indices: 143373--143468 Score: 183
Period size: 47 Copynumber: 2.0 Consensus size: 47
143363 TGGGATGTTA
143373 GTTTTACTGAATCGGATCCCTAGTGTTCATGATTGGAAACATGCTTT
1 GTTTTACTGAATCGGATCCCTAGTGTTCATGATTGGAAACATGCTTT
*
143420 GTTTTACTGAATCGGGTCCCTAGTGTTCATGATTGGAAACATGCTTT
1 GTTTTACTGAATCGGATCCCTAGTGTTCATGATTGGAAACATGCTTT
143467 GT
1 GT
143469 CATCATGATC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.39
Consensus pattern (47 bp):
GTTTTACTGAATCGGATCCCTAGTGTTCATGATTGGAAACATGCTTT
Found at i:146607 original size:58 final size:58
Alignment explanation
Indices: 146545--146659 Score: 185
Period size: 58 Copynumber: 2.0 Consensus size: 58
146535 ATCAACAAAC
*
146545 TAAACCCAAATATTTTTAAACCCAAATATAATTTAATTATTAAAAAACACTCATAAAT
1 TAAACCCAAATATTTTTAAACCCAAATATAATTTAATTACTAAAAAACACTCATAAAT
* * * *
146603 TAAACTCAAATATTTTTAAACCCAAATATAATTTTATTCCTAAATAACACTCATAAA
1 TAAACCCAAATATTTTTAAACCCAAATATAATTTAATTACTAAAAAACACTCATAAA
146660 CAACTCTTTT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
58 52 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.34
Consensus pattern (58 bp):
TAAACCCAAATATTTTTAAACCCAAATATAATTTAATTACTAAAAAACACTCATAAAT
Found at i:179552 original size:22 final size:21
Alignment explanation
Indices: 179525--179565 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
179515 AGAATCAGCT
179525 TTTTGCAATACAACAATACTGC
1 TTTTGCAATACAAC-ATACTGC
*
179547 TTTTGCAATGCAACATACT
1 TTTTGCAATACAACATACT
179566 TAAATTTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.34, C:0.22, G:0.10, T:0.34
Consensus pattern (21 bp):
TTTTGCAATACAACATACTGC
Found at i:183217 original size:19 final size:19
Alignment explanation
Indices: 183193--183242 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
183183 ATCTTCAAAA
*
183193 AAAAATATTCTCTCTCTTC
1 AAAAATATTATCTCTCTTC
*
183212 AAAAATATTATCTTTCTTC
1 AAAAATATTATCTCTCTTC
*
183231 AATAATAATTAT
1 AAAAAT-ATTAT
183243 AATATTAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 22 0.81
20 5 0.19
ACGTcount: A:0.40, C:0.16, G:0.00, T:0.44
Consensus pattern (19 bp):
AAAAATATTATCTCTCTTC
Found at i:185942 original size:29 final size:29
Alignment explanation
Indices: 185828--185958 Score: 95
Period size: 28 Copynumber: 4.5 Consensus size: 29
185818 TGAAATGAGT
* * **
185828 CCAAAATATTATTTTTCAATTTTTAAAGGGT
1 CCAAAAT-TT-TTTTTTAACTTTTAAAGGAC
* * *
185859 TCAAAATTGTTTTTAAACTTTTAAAGG-C
1 CCAAAATTTTTTTTTAACTTTTAAAGGAC
* ** ***
185887 CAAAAAAATTTTACCAACTTTTAAAGGATC
1 CCAAAATTTTTTTTTAACTTTTAAAGGA-C
185917 CCAAAATTTTTTTTTAACTTTT-AAGGAC
1 CCAAAATTTTTTTTTAACTTTTAAAGGAC
*
185945 CGAAAATTTTTTTT
1 CCAAAATTTTTTTT
185959 ACTAACATTT
Statistics
Matches: 78, Mismatches: 20, Indels: 7
0.74 0.19 0.07
Matches are distributed among these distances:
28 33 0.42
29 21 0.27
30 18 0.23
31 6 0.08
ACGTcount: A:0.37, C:0.12, G:0.08, T:0.43
Consensus pattern (29 bp):
CCAAAATTTTTTTTTAACTTTTAAAGGAC
Found at i:185970 original size:30 final size:31
Alignment explanation
Indices: 185895--185970 Score: 95
Period size: 30 Copynumber: 2.5 Consensus size: 31
185885 GCCAAAAAAA
*
185895 TTTTACCAACTTTTAAAGGATCCCAAAATTTT
1 TTTTACTAACTTTT-AAGGATCCCAAAATTTT
*
185927 TTTT--TAACTTTTAAGGA-CCGAAAATTTT
1 TTTTACTAACTTTTAAGGATCCCAAAATTTT
*
185955 TTTTACTAACATTTAA
1 TTTTACTAACTTTTAA
185971 AAAATCTAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
28 14 0.36
29 5 0.13
30 16 0.41
32 4 0.10
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.45
Consensus pattern (31 bp):
TTTTACTAACTTTTAAGGATCCCAAAATTTT
Found at i:187784 original size:9 final size:9
Alignment explanation
Indices: 187765--187798 Score: 50
Period size: 10 Copynumber: 3.6 Consensus size: 9
187755 GAAAAAAGTA
187765 TAAAATATTT
1 TAAAAT-TTT
187775 TAAAATTTT
1 TAAAATTTT
187784 TAAAATTTTT
1 TAAAA-TTTT
187794 TAAAA
1 TAAAA
187799 ATTAATTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (9 bp):
TAAAATTTT
Found at i:195950 original size:24 final size:24
Alignment explanation
Indices: 195923--195995 Score: 128
Period size: 24 Copynumber: 3.0 Consensus size: 24
195913 AGCACTAGCA
195923 CTGTTGTATTAGCATCAGTAACAC
1 CTGTTGTATTAGCATCAGTAACAC
195947 CTGTTGTATTAGCATCAGTAACAC
1 CTGTTGTATTAGCATCAGTAACAC
* *
195971 CTGTTGTAATAGCATCAGTAGCAC
1 CTGTTGTATTAGCATCAGTAACAC
195995 C
1 C
195996 AATACCTGCT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.32
Consensus pattern (24 bp):
CTGTTGTATTAGCATCAGTAACAC
Found at i:200365 original size:11 final size:11
Alignment explanation
Indices: 200349--200373 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
200339 TAATATCATA
200349 ATTTAATAATT
1 ATTTAATAATT
200360 ATTTAATAATT
1 ATTTAATAATT
200371 ATT
1 ATT
200374 ATTTAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
ATTTAATAATT
Found at i:200374 original size:14 final size:14
Alignment explanation
Indices: 200352--200401 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
200342 TATCATAATT
*
200352 TAATAATTATTTAA
1 TAATTATTATTTAA
200366 TAATTATTATTTAA
1 TAATTATTATTTAA
* * *
200380 AAAATAAT-TTTAA
1 TAATTATTATTTAA
200393 TAATT-TTAT
1 TAATTATTAT
200402 ATTTTAAAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
12 1 0.04
13 9 0.32
14 18 0.64
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TAATTATTATTTAA
Found at i:200414 original size:30 final size:28
Alignment explanation
Indices: 200361--200430 Score: 106
Period size: 30 Copynumber: 2.5 Consensus size: 28
200351 TTAATAATTA
*
200361 TTTAATAATTAT-TATTTAAAAAATAAT
1 TTTAATAATTTTATATTTAAAAAATAAT
200388 TTTAATAATTTTATATTTTAAAAAAATAAT
1 TTTAATAATTTTATA-TTT-AAAAAATAAT
200418 TTTAATAATTTTA
1 TTTAATAATTTTA
200431 AAATCATTTA
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
27 11 0.28
28 2 0.05
29 3 0.08
30 23 0.59
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (28 bp):
TTTAATAATTTTATATTTAAAAAATAAT
Found at i:200415 original size:21 final size:23
Alignment explanation
Indices: 200391--200433 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 23
200381 AAATAATTTT
200391 AATAATTTT-AT-ATTTTAAAAA
1 AATAATTTTAATAATTTTAAAAA
200412 AATAATTTTAATAATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
200434 TCATTTACTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 9 0.45
22 2 0.10
23 9 0.45
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
AATAATTTTAATAATTTTAAAAA
Found at i:201172 original size:29 final size:30
Alignment explanation
Indices: 201140--201198 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 30
201130 AAAATAAATA
201140 AATATAATTATT-A-TT-TAACATATATAATT
1 AATATAA-TATTAATTTATAACATA-ATAATT
201169 AATATAATATTAATTTATAACATAATAATT
1 AATATAATATTAATTTATAACATAATAATT
201199 GGGTCTAGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
28 4 0.15
29 8 0.30
30 8 0.30
31 7 0.26
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (30 bp):
AATATAATATTAATTTATAACATAATAATT
Found at i:204631 original size:2 final size:2
Alignment explanation
Indices: 204624--204650 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
204614 TACTGCAAAT
204624 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 T
204651 GCGTGCATGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:207345 original size:14 final size:14
Alignment explanation
Indices: 207322--207351 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
207312 CTAGTAAATG
*
207322 AAAGATAAAAAAAA
1 AAAGAAAAAAAAAA
207336 AAAGAAAAAAAAAA
1 AAAGAAAAAAAAAA
207350 AA
1 AA
207352 GATATGCGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.90, C:0.00, G:0.07, T:0.03
Consensus pattern (14 bp):
AAAGAAAAAAAAAA
Found at i:207346 original size:13 final size:14
Alignment explanation
Indices: 207322--207355 Score: 61
Period size: 13 Copynumber: 2.5 Consensus size: 14
207312 CTAGTAAATG
207322 AAAGATAAAAAAAA
1 AAAGATAAAAAAAA
207336 AAAGA-AAAAAAAA
1 AAAGATAAAAAAAA
207349 AAAGATA
1 AAAGATA
207356 TGCGGATGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.85, C:0.00, G:0.09, T:0.06
Consensus pattern (14 bp):
AAAGATAAAAAAAA
Found at i:209394 original size:25 final size:24
Alignment explanation
Indices: 209343--209391 Score: 73
Period size: 23 Copynumber: 2.0 Consensus size: 24
209333 TGTTCTTTAA
*
209343 TTTTTTTTTTAATTTTTACTCTTTC
1 TTTTTTTTTT-ATTCTTACTCTTTC
209368 TTTTTTTTTT-TTCTTACTCTTTC
1 TTTTTTTTTTATTCTTACTCTTTC
209391 T
1 T
209392 CTTGCTTATC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 13 0.57
25 10 0.43
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.78
Consensus pattern (24 bp):
TTTTTTTTTTATTCTTACTCTTTC
Found at i:210423 original size:46 final size:44
Alignment explanation
Indices: 210338--210423 Score: 102
Period size: 46 Copynumber: 1.9 Consensus size: 44
210328 ATATTATAAA
* *
210338 TAAATAATAATATTGATTAAAATGTAATAATTTAAAATATAATT
1 TAAATAATAATAATGATTAAAATGTAATAATATAAAATATAATT
* *
210382 TAAATAATATATAAATGATTAAAATATTAA-AATATATAATAT
1 TAAATAATA-AT-AATGATTAAAAT-GTAATAATATAAAATAT
210424 TAATAATTGA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
44 9 0.26
45 2 0.06
46 21 0.60
47 3 0.09
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (44 bp):
TAAATAATAATAATGATTAAAATGTAATAATATAAAATATAATT
Found at i:211347 original size:14 final size:14
Alignment explanation
Indices: 211330--211357 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
211320 AATTTAATGG
211330 TTTTTATTTTATTT
1 TTTTTATTTTATTT
211344 TTTTTATTTTATTT
1 TTTTTATTTTATTT
211358 AAGCTCTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTTTATTTTATTT
Found at i:216376 original size:20 final size:21
Alignment explanation
Indices: 216351--216395 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
216341 TTTAAAATTA
**
216351 TAAAAATAAAAGTTATTTTC-
1 TAAAAATAAAAAATATTTTCG
216371 TAAAAATAAAAAATATTTTCG
1 TAAAAATAAAAAATATTTTCG
216392 TAAA
1 TAAA
216396 CTAAACGGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.36
Consensus pattern (21 bp):
TAAAAATAAAAAATATTTTCG
Found at i:217900 original size:10 final size:10
Alignment explanation
Indices: 217885--217911 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
217875 TTTATATAAA
217885 AAAAAAAAAT
1 AAAAAAAAAT
217895 AAAAAAAAAT
1 AAAAAAAAAT
217905 AAAAAAA
1 AAAAAAA
217912 GAAGAAGAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.93, C:0.00, G:0.00, T:0.07
Consensus pattern (10 bp):
AAAAAAAAAT
Found at i:219457 original size:19 final size:19
Alignment explanation
Indices: 219418--219454 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
219408 ATGAGCTCTA
219418 TATTGTATTTATTAGTTTT
1 TATTGTATTTATTAGTTTT
219437 TATTGT-TTTATTA-TTTT
1 TATTGTATTTATTAGTTTT
219454 T
1 T
219455 TTACATTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.28
18 7 0.39
19 6 0.33
ACGTcount: A:0.19, C:0.00, G:0.08, T:0.73
Consensus pattern (19 bp):
TATTGTATTTATTAGTTTT
Found at i:222506 original size:12 final size:13
Alignment explanation
Indices: 222489--222518 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
222479 TATTTAATTT
222489 TTTTAA-ATTGAA
1 TTTTAATATTGAA
222501 TTTTAATATTGAA
1 TTTTAATATTGAA
222514 TTTTA
1 TTTTA
222519 TTTTCACTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.57
Consensus pattern (13 bp):
TTTTAATATTGAA
Found at i:225377 original size:6 final size:6
Alignment explanation
Indices: 225366--225403 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
225356 AAATTAGGAG
*
225366 GGGATT GGGATT GGGATT GGGATT GGGATT GAGATT GG
1 GGGATT GGGATT GGGATT GGGATT GGGATT GGGATT GG
225404 AGACTGAGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.18, C:0.00, G:0.50, T:0.32
Consensus pattern (6 bp):
GGGATT
Found at i:227926 original size:19 final size:17
Alignment explanation
Indices: 227897--228116 Score: 87
Period size: 18 Copynumber: 12.5 Consensus size: 17
227887 TTTTTTTTTC
227897 TTTTTAATTAAAATATAT
1 TTTTTAATT-AAATATAT
227915 TTTTTAATTTAAATATAT
1 TTTTTAA-TTAAATATAT
* * *
227933 TACTTTAAATT-GATTTAT
1 T--TTTTAATTAAATATAT
* * *
227951 TCTTTAATT--ATTTTT
1 TTTTTAATTAAATATAT
*
227966 TCTTTTAATTAAATTCTAT
1 T-TTTTAATTAAA-TATAT
*
227985 TTTTTGATTTAAATATAT
1 TTTTT-AATTAAATATAT
* * *
228003 TGCTTTAAATT-GATTTAT
1 T--TTTTAATTAAATATAT
*
228021 TTTTTAATT--ATTTAT
1 TTTTTAATTAAATATAT
* *
228036 TCTTTTGATTAAATTTTAT
1 T-TTTTAATTAAA-TATAT
228055 TTTTTAATTTAAATATAT
1 TTTTTAA-TTAAATATAT
* * *
228073 TGCTTTAAATT-GATTTAT
1 T--TTTTAATTAAATATAT
*
228091 TTTTTAATTAAAT-TGT
1 TTTTTAATTAAATATAT
228107 ATTTTTAATT
1 -TTTTTAATT
228117 TTTAATGAAG
Statistics
Matches: 158, Mismatches: 25, Indels: 39
0.71 0.11 0.18
Matches are distributed among these distances:
15 13 0.08
16 36 0.23
17 11 0.07
18 55 0.35
19 30 0.19
20 13 0.08
ACGTcount: A:0.32, C:0.03, G:0.04, T:0.61
Consensus pattern (17 bp):
TTTTTAATTAAATATAT
Found at i:227977 original size:70 final size:70
Alignment explanation
Indices: 227890--228100 Score: 341
Period size: 70 Copynumber: 3.0 Consensus size: 70
227880 TATTTAGTTT
* * *
227890 TTTTTTCTTTTTAATTAAAATATATTTTTTAATTTAAATATATTACTTTAAATTGATTTATTCTT
1 TTTTTTC-TTTTAATTAAATTATATTTTTTAATTTAAATATATTGCTTTAAATTGATTTATTTTT
227955 TAATTA
65 TAATTA
* *
227961 TTTTTTCTTTTAATTAAATTCTATTTTTTGATTTAAATATATTGCTTTAAATTGATTTATTTTTT
1 TTTTTTCTTTTAATTAAATTATATTTTTTAATTTAAATATATTGCTTTAAATTGATTTATTTTTT
228026 AATTA
66 AATTA
* * *
228031 TTTATTCTTTTGATTAAATTTTATTTTTTAATTTAAATATATTGCTTTAAATTGATTTATTTTTT
1 TTTTTTCTTTTAATTAAATTATATTTTTTAATTTAAATATATTGCTTTAAATTGATTTATTTTTT
228096 AATTA
66 AATTA
228101 AATTGTATTT
Statistics
Matches: 131, Mismatches: 9, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
70 124 0.95
71 7 0.05
ACGTcount: A:0.31, C:0.04, G:0.03, T:0.62
Consensus pattern (70 bp):
TTTTTTCTTTTAATTAAATTATATTTTTTAATTTAAATATATTGCTTTAAATTGATTTATTTTTT
AATTA
Found at i:228021 original size:18 final size:17
Alignment explanation
Indices: 227930--228114 Score: 85
Period size: 19 Copynumber: 10.6 Consensus size: 17
227920 AATTTAAATA
*
227930 TATTACTTTAAATTGATT
1 TATT-CTTTAAATTAATT
227948 TATTCTTT-AATT-ATT
1 TATTCTTTAAATTAATT
* *
227963 TTTTCTTTTAATTAAATT
1 TATTCTTTAAATT-AATT
* * * *
227981 CTATTTTTTGATTTAAATA
1 -TATTCTTTAAATT-AATT
*
228000 TATTGCTTTAAATTGATT
1 TATT-CTTTAAATTAATT
*
228018 TATT-TTTTAATT-ATT
1 TATTCTTTAAATTAATT
**
228033 TATTCTTTTGATTAAATTT
1 TATTCTTTAAATT-AA-TT
* * *
228052 TATTTTTTAATTTAAATA
1 TATTCTTTAAATT-AATT
*
228070 TATTGCTTTAAATTGATT
1 TATT-CTTTAAATTAATT
*
228088 TATT-TTTTAATTAAATT
1 TATTCTTTAAATT-AATT
228105 GTATT-TTTAA
1 -TATTCTTTAA
228115 TTTTTAATGA
Statistics
Matches: 130, Mismatches: 25, Indels: 24
0.73 0.14 0.13
Matches are distributed among these distances:
15 17 0.13
16 29 0.22
17 7 0.05
18 37 0.28
19 40 0.31
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.62
Consensus pattern (17 bp):
TATTCTTTAAATTAATT
Found at i:228081 original size:33 final size:35
Alignment explanation
Indices: 227912--228103 Score: 159
Period size: 36 Copynumber: 5.5 Consensus size: 35
227902 AATTAAAATA
*
227912 TATTTTTTAATTTAAATATATTACTTTAAATTGATT
1 TATTTTTTAATTTAAATATATTGCTTTAAATT-ATT
* * * *
227948 TATTCTTTAA-TT--AT-TTTTTCTTTTAATTAAATT
1 TATTTTTTAATTTAAATATATTGCTTTAAATT--ATT
*
227981 CTATTTTTTGATTTAAATATATTGCTTTAAATTGATT
1 -TATTTTTTAATTTAAATATATTGCTTTAAATT-ATT
* **
228018 TATTTTTTAA-TT--ATTTATT-CTTTTGATTAAATTT
1 TATTTTTTAATTTAAATATATTGCTTTAAATT--A-TT
228052 TATTTTTTAATTTAAATATATTGCTTTAAATTGATT
1 TATTTTTTAATTTAAATATATTGCTTTAAATT-ATT
228088 TATTTTTTAA-TTAAAT
1 TATTTTTTAATTTAAAT
228104 TGTATTTTTA
Statistics
Matches: 124, Mismatches: 20, Indels: 25
0.73 0.12 0.15
Matches are distributed among these distances:
32 18 0.15
33 12 0.10
34 20 0.16
35 14 0.11
36 30 0.24
37 12 0.10
38 18 0.15
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.61
Consensus pattern (35 bp):
TATTTTTTAATTTAAATATATTGCTTTAAATTATT
Found at i:231938 original size:6 final size:6
Alignment explanation
Indices: 231927--231954 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
231917 ATGTTGTGGT
231927 ATCACC ATCACC ATCACC ATCACC ATCA
1 ATCACC ATCACC ATCACC ATCACC ATCA
231955 GGGCTGGGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.36, C:0.46, G:0.00, T:0.18
Consensus pattern (6 bp):
ATCACC
Done.