Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015180.1 Kokia drynarioides strain JFW-HI SEQ_130224, 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: 162323
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 84 characters in sequence are not A, C, G, or T
Found at i:5122 original size:31 final size:31
Alignment explanation
Indices: 5087--5160 Score: 139
Period size: 31 Copynumber: 2.4 Consensus size: 31
5077 TCTATTTTTT
5087 TAGTATAGGGGCCAAAATGCCATCCGACTTC
1 TAGTATAGGGGCCAAAATGCCATCCGACTTC
5118 TAGTATAGGGGCCAAAATGCCATCCGACTTC
1 TAGTATAGGGGCCAAAATGCCATCCGACTTC
*
5149 TAGTACAGGGGC
1 TAGTATAGGGGC
5161 TTCCATGATA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.28, C:0.24, G:0.26, T:0.22
Consensus pattern (31 bp):
TAGTATAGGGGCCAAAATGCCATCCGACTTC
Found at i:17340 original size:10 final size:10
Alignment explanation
Indices: 17316--17401 Score: 51
Period size: 9 Copynumber: 8.8 Consensus size: 10
17306 AGAGTTAATT
17316 TTATTT-TT-
1 TTATTTATTA
17324 TTATATTATTTA
1 TTAT-TTA-TTA
17336 TTATTTATT-
1 TTATTTATTA
17345 TTATTT-TTA
1 TTATTTATTA
*
17354 TAATTTAATTA
1 TTATTT-ATTA
*
17365 TT-TTTAATA
1 TTATTTATTA
*
17374 ATATTTAATTA
1 TTATTT-ATTA
17385 TT-TTATATTA
1 TTATT-TATTA
17395 TT-TTTAT
1 TTATTTAT
17402 AATTTAATTA
Statistics
Matches: 62, Mismatches: 6, Indels: 19
0.71 0.07 0.22
Matches are distributed among these distances:
8 6 0.10
9 20 0.32
10 18 0.29
11 14 0.23
12 4 0.06
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
TTATTTATTA
Found at i:17348 original size:16 final size:15
Alignment explanation
Indices: 17319--17401 Score: 55
Period size: 15 Copynumber: 5.4 Consensus size: 15
17309 GTTAATTTTA
17319 TTTT-TTTATATTAT
1 TTTTATTTATATTAT
*
17333 TTATTATTTATTTTAT
1 TT-TTATTTATATTAT
17349 TTTTATAATT-TAATTAT
1 TTTTAT--TTAT-ATTAT
* *
17366 TTTTAATAATATT-T
1 TTTTATTTATATTAT
**
17380 AATTATTTTATATTAT
1 TTTTA-TTTATATTAT
17396 TTTTAT
1 TTTTAT
17402 AATTTAATTA
Statistics
Matches: 51, Mismatches: 10, Indels: 15
0.67 0.13 0.20
Matches are distributed among these distances:
14 6 0.12
15 17 0.33
16 17 0.33
17 11 0.22
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTATTTATATTAT
Found at i:17365 original size:29 final size:28
Alignment explanation
Indices: 17313--17370 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 28
17303 ATAAGAGTTA
* *
17313 ATTTTATTTTTTTATATTATTTATTATTT
1 ATTTTATTTTTTAATATTAATTATT-TTT
17342 ATTTTATTTTTATAAT-TTAATTATTTTT
1 ATTTTATTTTT-TAATATTAATTATTTTT
17370 A
1 A
17371 ATAATATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 4 0.15
29 19 0.73
30 3 0.12
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (28 bp):
ATTTTATTTTTTAATATTAATTATTTTT
Found at i:17367 original size:17 final size:20
Alignment explanation
Indices: 17345--17388 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
17335 ATTATTTATT
17345 TTATTTTT-AT-A-ATTTAA
1 TTATTTTTAATAATATTTAA
17362 TTATTTTTAATAATATTTAA
1 TTATTTTTAATAATATTTAA
17382 TTATTTT
1 TTATTTT
17389 ATATTATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.33
18 2 0.08
19 1 0.04
20 13 0.54
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TTATTTTTAATAATATTTAA
Found at i:17397 original size:30 final size:32
Alignment explanation
Indices: 17357--17430 Score: 86
Period size: 30 Copynumber: 2.4 Consensus size: 32
17347 ATTTTTATAA
*
17357 TTTA-ATTATTTTTAATAA-TATTTAAT-TA-T
1 TTTATATTATTTTT-ATAATTAATTAATATATT
17386 TTTATATTATTTTTATAATTTAATTAATATATT
1 TTTATATTATTTTTATAA-TTAATTAATATATT
17419 TTTATATT-TTTT
1 TTTATATTATTTT
17431 ATGTGAATAG
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
29 8 0.21
30 9 0.23
31 7 0.18
32 6 0.15
33 9 0.23
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (32 bp):
TTTATATTATTTTTATAATTAATTAATATATT
Found at i:17401 original size:47 final size:44
Alignment explanation
Indices: 17311--17411 Score: 141
Period size: 47 Copynumber: 2.2 Consensus size: 44
17301 TGATAAGAGT
* * *
17311 TAATTTTATT-TTTTTATATTATTTATTATTTATTTTATTTTTA
1 TAATTTAATTATTTTTATAATATTTATTATTTATATTATTTTTA
17354 TAATTTAATTATTTTTAATAATATTTAATTATTTTATATTATTTTTA
1 TAATTTAATTATTTTT-ATAATATTT-ATTA-TTTATATTATTTTTA
17401 TAATTTAATTA
1 TAATTTAATTA
17412 ATATATTTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
43 9 0.18
44 5 0.10
45 8 0.16
46 4 0.08
47 25 0.49
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (44 bp):
TAATTTAATTATTTTTATAATATTTATTATTTATATTATTTTTA
Found at i:17406 original size:27 final size:29
Alignment explanation
Indices: 17357--17411 Score: 80
Period size: 27 Copynumber: 2.0 Consensus size: 29
17347 ATTTTTATAA
17357 TTTAATTATTTTTAATAATATTTAATTAT
1 TTTAATTATTTTTAATAATATTTAATTAT
17386 TTTATATTATTTTT-AT-A-ATTTAATTA
1 TTTA-ATTATTTTTAATAATATTTAATTA
17412 ATATATTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 9 0.36
28 1 0.04
29 6 0.24
30 9 0.36
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (29 bp):
TTTAATTATTTTTAATAATATTTAATTAT
Found at i:17407 original size:18 final size:18
Alignment explanation
Indices: 17323--17411 Score: 65
Period size: 18 Copynumber: 5.5 Consensus size: 18
17313 ATTTTATTTT
*
17323 TTTATATTA--TTTATTA
1 TTTATATTATTTTTATAA
*
17339 TTTATTTTATTTTTATAA
1 TTTATATTATTTTTATAA
17357 TTTA-ATTATTTTTAATAA
1 TTTATATTATTTTT-ATAA
*
17375 --TAT-TTA--ATTAT--
1 TTTATATTATTTTTATAA
17386 TTTATATTATTTTTATAA
1 TTTATATTATTTTTATAA
17404 TTTA-ATTA
1 TTTATATTA
17412 ATATATTTTT
Statistics
Matches: 57, Mismatches: 5, Indels: 21
0.69 0.06 0.25
Matches are distributed among these distances:
13 5 0.09
14 5 0.09
16 17 0.30
17 12 0.21
18 18 0.32
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTATATTATTTTTATAA
Found at i:17431 original size:42 final size:43
Alignment explanation
Indices: 17325--17432 Score: 105
Period size: 47 Copynumber: 2.5 Consensus size: 43
17315 TTTATTTTTT
* * * *
17325 TATATTATT-TATTATTTATTTTATTTTTATAATTTAATTATTTT
1 TATATTTTTATATTTTTTATATTATTTTTATAATTTAATTA--TA
*
17369 TAATAATATTTA-ATTATTTTATATTATTTTTATAATTTAATTA-A
1 T-AT-ATTTTTATATT-TTTTATATTATTTTTATAATTTAATTATA
17413 TATATTTTTATATTTTTTAT
1 TATATTTTTATATTTTTTAT
17433 GTGAATAGCT
Statistics
Matches: 53, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
42 12 0.23
43 5 0.09
44 2 0.04
45 2 0.04
46 7 0.13
47 25 0.47
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (43 bp):
TATATTTTTATATTTTTTATATTATTTTTATAATTTAATTATA
Found at i:18994 original size:17 final size:17
Alignment explanation
Indices: 18972--19004 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
18962 TACGTATCAA
18972 AACCCTTATATGTTTCT
1 AACCCTTATATGTTTCT
18989 AACCCTTATATGTTTC
1 AACCCTTATATGTTTC
19005 CATTTTCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.24, G:0.06, T:0.45
Consensus pattern (17 bp):
AACCCTTATATGTTTCT
Found at i:19539 original size:62 final size:62
Alignment explanation
Indices: 19467--19627 Score: 268
Period size: 62 Copynumber: 2.6 Consensus size: 62
19457 ATAATTTTTT
* *
19467 ATATTATTTCATTTAACAAAATCGAAGTTCATTTGAATATATTTGTACAAATTAGTTTTAGC
1 ATATTGTTTCATTTAATAAAATCGAAGTTCATTTGAATATATTTGTACAAATTAGTTTTAGC
* *
19529 ATATTGTTTCATTTAATAAAATCGAAGTTCATTTGAATATTTTTGTATAAATTAGTTTTAGC
1 ATATTGTTTCATTTAATAAAATCGAAGTTCATTTGAATATATTTGTACAAATTAGTTTTAGC
* *
19591 ATATTGTTTCATTTCATAAAATCGAAATTCATTTGAA
1 ATATTGTTTCATTTAATAAAATCGAAGTTCATTTGAA
19628 AAAGAGCTTT
Statistics
Matches: 93, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 93 1.00
ACGTcount: A:0.36, C:0.09, G:0.10, T:0.45
Consensus pattern (62 bp):
ATATTGTTTCATTTAATAAAATCGAAGTTCATTTGAATATATTTGTACAAATTAGTTTTAGC
Found at i:35311 original size:14 final size:14
Alignment explanation
Indices: 35294--35323 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
35284 TTTTGCGTTC
*
35294 TTTTTTTGTGTTTT
1 TTTTTTTGTATTTT
35308 TTTTTTTGTATTTT
1 TTTTTTTGTATTTT
35322 TT
1 TT
35324 ATAAACTAAA
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:0.03, C:0.00, G:0.10, T:0.87
Consensus pattern (14 bp):
TTTTTTTGTATTTT
Found at i:35383 original size:16 final size:17
Alignment explanation
Indices: 35364--35396 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
35354 AAAATCAAAG
*
35364 TTTAAAT-TTTTTTTGT
1 TTTAAATCTGTTTTTGT
35380 TTTAAATCTGTTTTTGT
1 TTTAAATCTGTTTTTGT
35397 ATTTTCGTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.18, C:0.03, G:0.09, T:0.70
Consensus pattern (17 bp):
TTTAAATCTGTTTTTGT
Found at i:35427 original size:13 final size:13
Alignment explanation
Indices: 35389--35425 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
35379 TTTTAAATCT
35389 GTTTTTGTATTTTC
1 GTTTTT-TATTTTC
35403 GTTTTTTATTTTC
1 GTTTTTTATTTTC
35416 -TTTTTT-TTTT
1 GTTTTTTATTTT
35426 TTAAATATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 4 0.17
12 6 0.26
13 7 0.30
14 6 0.26
ACGTcount: A:0.05, C:0.05, G:0.08, T:0.81
Consensus pattern (13 bp):
GTTTTTTATTTTC
Found at i:36277 original size:21 final size:21
Alignment explanation
Indices: 36252--36298 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
36242 ATTAAAATTA
36252 ATTTTAATTTT-AATTTATTTT
1 ATTTTAATTTTGAATTTA-TTT
* *
36273 ATTTTATTTTTGGATTTATTT
1 ATTTTAATTTTGAATTTATTT
36294 ATTTT
1 ATTTT
36299 TTTGGGTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.72
Consensus pattern (21 bp):
ATTTTAATTTTGAATTTATTT
Found at i:43548 original size:52 final size:53
Alignment explanation
Indices: 43486--43608 Score: 169
Period size: 52 Copynumber: 2.4 Consensus size: 53
43476 ACCAACTTGC
* * *
43486 ACATATGCGTTTACGCTCAT-CAATTTGCACACATTTACGCTCGCCAGCTTAT
1 ACATATGCGTTTACGCTCATCCAACTTGCAAACATGTACGCTCGCCAGCTTAT
* * * *
43538 ACATATGCGTTTACGCTC-TCCAGCTTGCAAACGTGTACTCTCGTCAGCTTAT
1 ACATATGCGTTTACGCTCATCCAACTTGCAAACATGTACGCTCGCCAGCTTAT
43590 ACATATGCGTTTACGCTCA
1 ACATATGCGTTTACGCTCA
43609 CAGCTTGTAC
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
51 1 0.02
52 61 0.98
ACGTcount: A:0.24, C:0.28, G:0.15, T:0.33
Consensus pattern (53 bp):
ACATATGCGTTTACGCTCATCCAACTTGCAAACATGTACGCTCGCCAGCTTAT
Found at i:43560 original size:28 final size:28
Alignment explanation
Indices: 43519--43642 Score: 141
Period size: 28 Copynumber: 4.6 Consensus size: 28
43509 TTTGCACACA
43519 TTTACGCTCGCCAGCTTATACATATGCG
1 TTTACGCTCGCCAGCTTATACATATGCG
* * *
43547 TTTACGCTCTCCAGC-T-TGCA-A-ACG
1 TTTACGCTCGCCAGCTTATACATATGCG
* * *
43571 TGTACTCTCGTCAGCTTATACATATGCG
1 TTTACGCTCGCCAGCTTATACATATGCG
* *
43599 TTTACGCTC-ACAGCTTGTACATATGCG
1 TTTACGCTCGCCAGCTTATACATATGCG
43626 TTTACGCTCGCCAGCTT
1 TTTACGCTCGCCAGCTT
43643 GCACGCGTTT
Statistics
Matches: 77, Mismatches: 14, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
24 13 0.17
25 2 0.03
26 6 0.08
27 27 0.35
28 29 0.38
ACGTcount: A:0.20, C:0.29, G:0.18, T:0.33
Consensus pattern (28 bp):
TTTACGCTCGCCAGCTTATACATATGCG
Found at i:43852 original size:63 final size:63
Alignment explanation
Indices: 43744--43864 Score: 224
Period size: 63 Copynumber: 1.9 Consensus size: 63
43734 TTACCCATTG
43744 CACCACAATTAAACACATTAATTAAAATTAAAACGAGATAAGTCATAGGTGTACTTACTGGAA
1 CACCACAATTAAACACATTAATTAAAATTAAAACGAGATAAGTCATAGGTGTACTTACTGGAA
* *
43807 CACCTCAATTAAACACATTAATTAAAATTAAAACGAGATAGGTCATAGGTGTACTTAC
1 CACCACAATTAAACACATTAATTAAAATTAAAACGAGATAAGTCATAGGTGTACTTAC
43865 CGGATAAGAA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 56 1.00
ACGTcount: A:0.45, C:0.17, G:0.12, T:0.26
Consensus pattern (63 bp):
CACCACAATTAAACACATTAATTAAAATTAAAACGAGATAAGTCATAGGTGTACTTACTGGAA
Found at i:45670 original size:24 final size:24
Alignment explanation
Indices: 45635--45695 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 24
45625 ACTGACCCCT
*
45635 TTAATTTTATAATTTAAATTTTAAT-
1 TTAATTTAATAATTTAAA--TTAATA
*
45660 TT-ATTTAATAATTTTAATTAATA
1 TTAATTTAATAATTTAAATTAATA
45683 TTAATTTAATAAT
1 TTAATTTAATAAT
45696 CCAAATTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 5 0.16
23 2 0.06
24 23 0.72
25 2 0.06
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
TTAATTTAATAATTTAAATTAATA
Found at i:46498 original size:3 final size:3
Alignment explanation
Indices: 46490--46518 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
46480 ATTTTTTAGG
46490 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
46519 ATTGTTTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:60024 original size:31 final size:27
Alignment explanation
Indices: 59977--60047 Score: 79
Period size: 31 Copynumber: 2.5 Consensus size: 27
59967 ATTATTTAGG
*
59977 AGTTCTTATTTAAGTCACTAAACTATTCAAA
1 AGTTTTTATTTAAGTCA-TAAACTATT---A
* *
60008 AGTTTTTATTTTAGTCATTAACTATTA
1 AGTTTTTATTTAAGTCATAAACTATTA
60035 AGTTTTTATTTAA
1 AGTTTTTATTTAA
60048 AAAAGGTCTG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
27 13 0.36
30 8 0.22
31 15 0.42
ACGTcount: A:0.34, C:0.10, G:0.07, T:0.49
Consensus pattern (27 bp):
AGTTTTTATTTAAGTCATAAACTATTA
Found at i:65390 original size:7 final size:7
Alignment explanation
Indices: 65378--65451 Score: 103
Period size: 7 Copynumber: 10.1 Consensus size: 7
65368 AAAAAAGAAT
65378 TATAAAA
1 TATAAAA
65385 TATAAAA
1 TATAAAA
65392 TATAAAA
1 TATAAAA
65399 TATAAAA
1 TATAAAA
65406 TATAAAA
1 TATAAAA
65413 TATAAAA
1 TATAAAA
*
65420 TAAAAACA
1 TATAAA-A
65428 TATACAAA
1 TATA-AAA
65436 TAATAAAA
1 T-ATAAAA
*
65444 TAAAAAA
1 TATAAAA
65451 T
1 T
65452 TAGGTCCCCT
Statistics
Matches: 61, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
7 46 0.75
8 10 0.16
9 5 0.08
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (7 bp):
TATAAAA
Found at i:67393 original size:23 final size:24
Alignment explanation
Indices: 67340--67398 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
67330 ACATTGTTTG
* *
67340 TGAACATGTTCAATTATATGTTCA
1 TGAACATGTTCGATTATATGTTAA
67364 TGAACATGTTCGATTA-A-GTTAAA
1 TGAACATGTTCGATTATATGTT-AA
67387 TGAACATGTTCG
1 TGAACATGTTCG
67399 TGAACATTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
22 3 0.09
23 14 0.44
24 15 0.47
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (24 bp):
TGAACATGTTCGATTATATGTTAA
Found at i:67408 original size:23 final size:23
Alignment explanation
Indices: 67363--67409 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
67353 TTATATGTTC
* *
67363 ATGAACATGTTCGATTAAGTTAA
1 ATGAACATGTTCGATGAAATTAA
67386 ATGAACATGTTCG-TGAACATTAA
1 ATGAACATGTTCGATGAA-ATTAA
67409 A
1 A
67410 CAAATGAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 3 0.14
23 18 0.86
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.32
Consensus pattern (23 bp):
ATGAACATGTTCGATGAAATTAA
Found at i:73059 original size:483 final size:479
Alignment explanation
Indices: 72147--73111 Score: 1383
Period size: 483 Copynumber: 2.0 Consensus size: 479
72137 ACGGGTAAAA
* * *
72147 ATAATTTCATTAATTTGACAAAAAAAGAGAGTACAAAGATGGAGATAAAAACTAAACTCAAAAAC
1 ATAATTTCATTAAATTGACAAAAAAAGAGAGTACAAAGATGGAGATAAAAACTAAAATAAAAAAC
* * *
72212 ACAAAAATAAAAATCCTCAAAACTTAAACACAAAATTCACTAAAAGCTTGTAAAAGCTGATATTT
66 ACAAAAATAAAAATCCTAAAAACTTAAACACAAAATTCACTAAAAGCTTGTAAAAGCTAATACTT
*
72277 AAATGTGTTATGGGTTAATCTTTCTAAGGTAAAAAATGACCTATTTATAAACTAAATTCGTAGGT
131 AAATGTGTTATGGATTAATCTTTCTAAGGTAAAAAATGACCTATTTATAAACTAAATTCGT--GT
*
72342 CAAATAATCTTAAAATAATACAATAATCAGAGTTTGGGACGAATAATCAAAATTTGACGAGAAGA
194 AAAATAA--TTAAAATAATACAATAATCAGAGTTTGGGACGAATAATCAAAATTTGACGAGAAGA
* * *
72407 AGAAAACCAAGAAAATTGCATGACAGGTCGTCACGTCGTTTCTACATCTCCCTTGTTTCGTTGTC
257 AGAAAACCAAGAAAATTGCATGACAGGCCGTCACGTCATTTCTACATCTCCCTTGTTTCGTTATC
* * *
72472 ATGACATCGCTTTTTGTTTGTATCTTACTTTGACCGAAATGAGAGGCATAGTCCACATTCAAATA
322 ATGACATCACTCTTTGTTTGTATCTTACTTTGACCGAAATGAGAGGCATACTCCACATTCAAATA
* *
72537 AAGACCAGACATTTCAAAATGTTCAAATAAAGACCAAATCTTTTCGAAAGTACTTAAATAAATAC
387 AAGACCAAACATTTCAAAATGTTCAAATAAAGACCAAATCTTTTCGAAAGTACTTAAATAAAGAC
72602 TTATCAAATATTATATATCAAGTTTTAG
452 TTATCAAATATTATATATCAAGTTTTAG
*
72630 ATAATTTCATTAAATTGAC-AAAAAA-A-AGTACAAAGATGGAGATAAAAATTAAAATAAAAAAC
1 ATAATTTCATTAAATTGACAAAAAAAGAGAGTACAAAGATGGAGATAAAAACTAAAATAAAAAAC
* * *
72692 CCAAAAATAAGAA-CCATAAAAACTTAAACACAAAATTCACTAAAAGCTTGTAAAAGGTAATACT
66 ACAAAAATAAAAATCC-TAAAAACTTAAACACAAAATTCACTAAAAGCTTGTAAAAGCTAATACT
* **
72756 TAAATGTGTTATGGATTAATCTTTCTAAGGTAGAAAATGACCTATTTAT-AGGTCAAATAATC-T
130 TAAATGTGTTATGGATTAATCTTTCTAAGGTAAAAAATGACCTATTTATAAACT-AAAT--TCGT
* * * *
72819 -TAAAATAA-TAATAAT-CTACACTAATCGGAGTTTGGGACGAATAATCAAAATTTGACTAGAAG
192 GTAAAATAATTAA-AATAATACAATAATCAGAGTTTGGGACGAATAATCAAAATTTGACGAGAAG
*
72881 AAGAAAACCAAGAAAATTGCATGACACGTGGCCATGTCTCAACGTCATTTCTACTTCTCCCTTGT
256 AAGAAAACCAAGAAAATTGCATGACA---GGCC--G--TC-ACGTCATTTCTACATCTCCCTTGT
* * * *
72946 TTC-TTCATCGTGACGTCACTCTTTGTTTGTATCTTACTTTGACGGAAATGCGAGGCATACTCCA
313 TTCGTT-ATCATGACATCACTCTTTGTTTGTATCTTACTTTGACCGAAATGAGAGGCATACTCCA
*
73010 CATTCAAATAAAGACCAAACATTTCAAAATGTTCAAATAAAGTCCAAATCTTTTCGAAAGTACTT
377 CATTCAAATAAAGACCAAACATTTCAAAATGTTCAAATAAAGACCAAATCTTTTCGAAAGTACTT
* *
73075 AAATAAAGACTTCTTAAATATTATATATCAAGTTTTA
442 AAATAAAGACTTATCAAATATTATATATCAAGTTTTA
73112 AATTATGTCT
Statistics
Matches: 433, Mismatches: 35, Indels: 28
0.87 0.07 0.06
Matches are distributed among these distances:
475 72 0.17
476 3 0.01
478 10 0.02
479 4 0.01
480 140 0.32
481 2 0.00
482 12 0.03
483 190 0.44
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.30
Consensus pattern (479 bp):
ATAATTTCATTAAATTGACAAAAAAAGAGAGTACAAAGATGGAGATAAAAACTAAAATAAAAAAC
ACAAAAATAAAAATCCTAAAAACTTAAACACAAAATTCACTAAAAGCTTGTAAAAGCTAATACTT
AAATGTGTTATGGATTAATCTTTCTAAGGTAAAAAATGACCTATTTATAAACTAAATTCGTGTAA
AATAATTAAAATAATACAATAATCAGAGTTTGGGACGAATAATCAAAATTTGACGAGAAGAAGAA
AACCAAGAAAATTGCATGACAGGCCGTCACGTCATTTCTACATCTCCCTTGTTTCGTTATCATGA
CATCACTCTTTGTTTGTATCTTACTTTGACCGAAATGAGAGGCATACTCCACATTCAAATAAAGA
CCAAACATTTCAAAATGTTCAAATAAAGACCAAATCTTTTCGAAAGTACTTAAATAAAGACTTAT
CAAATATTATATATCAAGTTTTAG
Found at i:76528 original size:2 final size:2
Alignment explanation
Indices: 76521--76545 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
76511 ATTCATACAT
76521 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
76546 TAAGTATAAT
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:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:77972 original size:16 final size:17
Alignment explanation
Indices: 77946--77983 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
77936 AATCCTTTAA
*
77946 AAATT-ATAAAATTAT-
1 AAATTAATAAAATGATG
77961 AAATTAATAAAATGATG
1 AAATTAATAAAATGATG
77978 AAATTA
1 AAATTA
77984 TATATTTACT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 5 0.25
16 9 0.45
17 6 0.30
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (17 bp):
AAATTAATAAAATGATG
Found at i:79947 original size:21 final size:22
Alignment explanation
Indices: 79912--79952 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
79902 TATAAATTAT
79912 ATTTCATAATATAATTTTTAGG
1 ATTTCATAATATAATTTTTAGG
*
79934 ATTT-ATAATTTAATTTTTA
1 ATTTCATAATATAATTTTTA
79953 TTTTGTTGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (22 bp):
ATTTCATAATATAATTTTTAGG
Found at i:98421 original size:13 final size:13
Alignment explanation
Indices: 98404--98447 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
98394 ATTTCAATTT
98404 TATTTTAATAATAA
1 TATTTTAA-AATAA
98418 -ATTTTAAAAATAA
1 TATTTT-AAAATAA
*
98431 TAATTTAAAATAA
1 TATTTTAAAATAA
98444 TATT
1 TATT
98448 CTTCACATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
13 20 0.77
14 6 0.23
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
TATTTTAAAATAA
Found at i:98668 original size:15 final size:15
Alignment explanation
Indices: 98634--98704 Score: 65
Period size: 15 Copynumber: 4.6 Consensus size: 15
98624 CTATTATTAA
98634 AAATA-TTTAAT-AT
1 AAATATTTTAATAAT
*
98647 TAATATTTTAATAAT
1 AAATATTTTAATAAT
*
98662 AAATATTTATAACAATTAT
1 AAATATTT-T---AATAAT
*
98681 AAATATATTAATAAT
1 AAATATTTTAATAAT
98696 AAATATTTT
1 AAATATTTT
98705 GTAGTATAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
13 4 0.09
14 6 0.13
15 22 0.48
16 1 0.02
18 1 0.02
19 12 0.26
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (15 bp):
AAATATTTTAATAAT
Found at i:99308 original size:27 final size:27
Alignment explanation
Indices: 99249--99317 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 27
99239 AAAAGTTTCA
* **
99249 AAAAAATATTAAAAATTTATTTTTGAAT
1 AAAAAATA-TAAAAATTAATTTTAAAAT
99277 AAAAAATATAAAAA-TAATTTTAAAAT
1 AAAAAATATAAAAATTAATTTTAAAAT
*
99303 ATAAAAGTATAAAAA
1 A-AAAAATATAAAAA
99318 AAAAATCAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
26 10 0.28
27 18 0.50
28 8 0.22
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (27 bp):
AAAAAATATAAAAATTAATTTTAAAAT
Found at i:100914 original size:6 final size:6
Alignment explanation
Indices: 100905--100935 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
100895 AACGTGGTAG
100905 AGACCA AGACCA AGACCA AGACCA AGACCA A
1 AGACCA AGACCA AGACCA AGACCA AGACCA A
100936 AACCCCATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.52, C:0.32, G:0.16, T:0.00
Consensus pattern (6 bp):
AGACCA
Found at i:104056 original size:32 final size:32
Alignment explanation
Indices: 103988--104056 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
103978 AAAAAAATGA
*
103988 TAAAATTTTATTTAAAGTATTTAAATTATATC
1 TAAAATTTTATTTAAAGTATATAAATTATATC
*
104020 TAAAATTTTATTTTAAA-TATATATATATATAT-
1 TAAAATTTTA-TTTAAAGTATATAAAT-TATATC
104052 TAAAA
1 TAAAA
104057 AATACCCGCT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
32 22 0.67
33 11 0.33
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (32 bp):
TAAAATTTTATTTAAAGTATATAAATTATATC
Found at i:108151 original size:103 final size:103
Alignment explanation
Indices: 108027--108233 Score: 389
Period size: 103 Copynumber: 2.0 Consensus size: 103
108017 GTTAAGTAAA
*
108027 ACTAGAGCTCCCAATTGGCAGTGGTTACACGATCACAAATTCAAGTATAACTCGGGCCC-CTAGT
1 ACTAGAGCTCCCAATTGGCAGTGGTTACACGATCACAAATTCAACTATAACTCGGGCCCTC-AGT
108091 TGATGGTGGTTATGCGGTAACGGGTTCAAGTTTCATGCC
65 TGATGGTGGTTATGCGGTAACGGGTTCAAGTTTCATGCC
108130 ACTAGAGCTCCCAATTGGCAGTGGTTACACGATCACAAATTCAACTATAACTCGGGCCCTCAGTT
1 ACTAGAGCTCCCAATTGGCAGTGGTTACACGATCACAAATTCAACTATAACTCGGGCCCTCAGTT
108195 GATGGTGGTTATGCGGTAACGGGTTCAAGTTTCATGCC
66 GATGGTGGTTATGCGGTAACGGGTTCAAGTTTCATGCC
108233 A
1 A
108234 TCTTAATAGG
Statistics
Matches: 102, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
103 101 0.99
104 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.25, T:0.27
Consensus pattern (103 bp):
ACTAGAGCTCCCAATTGGCAGTGGTTACACGATCACAAATTCAACTATAACTCGGGCCCTCAGTT
GATGGTGGTTATGCGGTAACGGGTTCAAGTTTCATGCC
Found at i:110209 original size:21 final size:22
Alignment explanation
Indices: 110163--110214 Score: 70
Period size: 25 Copynumber: 2.3 Consensus size: 22
110153 ACCATCCAAT
110163 AAAAATGTATCACTTCATATATTAA
1 AAAAATGTATCACTTC--A-ATTAA
110188 AAAAATGTATCACTTC-ATTAA
1 AAAAATGTATCACTTCAATTAA
110209 AAAAAT
1 AAAAAT
110215 TAAATATGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
21 11 0.41
25 16 0.59
ACGTcount: A:0.52, C:0.12, G:0.04, T:0.33
Consensus pattern (22 bp):
AAAAATGTATCACTTCAATTAA
Found at i:110704 original size:18 final size:18
Alignment explanation
Indices: 110667--110718 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
110657 TTTTTAGTTG
*
110667 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAATTTATT
110685 TAATTAATTAAATTTATT
1 TAATTAATTAAATTTATT
*
110703 TAGTTAA--AAATTTATT
1 TAATTAATTAAATTTATT
110719 CTCAATCTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 9 0.29
17 7 0.23
18 15 0.48
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (18 bp):
TAATTAATTAAATTTATT
Found at i:119055 original size:13 final size:13
Alignment explanation
Indices: 119037--119061 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
119027 ATTTTTGGAA
119037 AGGGAAGGGAAGT
1 AGGGAAGGGAAGT
119050 AGGGAAGGGAAG
1 AGGGAAGGGAAG
119062 GAGGAAATGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.56, T:0.04
Consensus pattern (13 bp):
AGGGAAGGGAAGT
Found at i:120761 original size:46 final size:46
Alignment explanation
Indices: 120676--120785 Score: 159
Period size: 46 Copynumber: 2.4 Consensus size: 46
120666 ATTATTCCAG
*** *
120676 CTATGGTCTTACTCA-TTTTTATAATGATGTTATAGCATCTTTCAA
1 CTATGGTCTTACTCATTTTTTATAATGATCCCATAACATCTTTCAA
* *
120721 CTATGGTCTTACTCATTTTTTATCATGATCCCATAACATCTTTCAG
1 CTATGGTCTTACTCATTTTTTATAATGATCCCATAACATCTTTCAA
120767 CTATGGTCTTACTCATTTT
1 CTATGGTCTTACTCATTTT
120786 AGGCATATAG
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 15 0.26
46 43 0.74
ACGTcount: A:0.24, C:0.20, G:0.10, T:0.46
Consensus pattern (46 bp):
CTATGGTCTTACTCATTTTTTATAATGATCCCATAACATCTTTCAA
Found at i:124270 original size:23 final size:24
Alignment explanation
Indices: 124237--124282 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
124227 CGAAAAATAA
*
124237 ATCAAATTATATT-TTTACAAAAT
1 ATCAAAGTATATTATTTACAAAAT
*
124260 ATCAAAGTATATTATTTATAAAA
1 ATCAAAGTATATTATTTACAAAA
124283 AAAAGGCTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.41
Consensus pattern (24 bp):
ATCAAAGTATATTATTTACAAAAT
Found at i:125508 original size:16 final size:17
Alignment explanation
Indices: 125476--125529 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 17
125466 ATATTAATTA
*
125476 AATACTAATTAACGTGAT
1 AATA-TAATTAATGTGAT
125494 AATAT-ATTAATGTGA-
1 AATATAATTAATGTGAT
*
125509 AAT-TAATTAATTTGAT
1 AATATAATTAATGTGAT
*
125525 TATAT
1 AATAT
125530 TTTTTTAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
14 1 0.03
15 12 0.40
16 11 0.37
17 2 0.07
18 4 0.13
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.43
Consensus pattern (17 bp):
AATATAATTAATGTGAT
Found at i:130189 original size:29 final size:28
Alignment explanation
Indices: 130154--130235 Score: 87
Period size: 28 Copynumber: 2.9 Consensus size: 28
130144 AAAATTGAGA
*
130154 AAAAAAAAATAGCTTAGGTACCAATT-G
1 AAAAAAAAATAGTTTAGGTACCAATTAG
* * * *
130181 TGACAAAAAA-AGTTTAGGTACTAAAATAG
1 -AAAAAAAAATAGTTTAGGTAC-CAATTAG
130210 AAAAAAAAATAGTTTAGGTACCAATT
1 AAAAAAAAATAGTTTAGGTACCAATT
130236 TGTAAGTTAA
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
27 10 0.24
28 20 0.48
29 12 0.29
ACGTcount: A:0.52, C:0.09, G:0.15, T:0.24
Consensus pattern (28 bp):
AAAAAAAAATAGTTTAGGTACCAATTAG
Found at i:130596 original size:20 final size:20
Alignment explanation
Indices: 130571--130615 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 20
130561 ATATAAAATT
130571 ATATATTTAAATTTA-TAATA
1 ATATATTTAAATTTATTAA-A
130591 ATATATTTAAATTTATTAAA
1 ATATATTTAAATTTATTAAA
130611 ATATA
1 ATATA
130616 GATTATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 21 0.88
21 3 0.12
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
ATATATTTAAATTTATTAAA
Found at i:132417 original size:7 final size:7
Alignment explanation
Indices: 132405--132435 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
132395 ACACATGCAA
132405 CACTCCC
1 CACTCCC
132412 CACTCCC
1 CACTCCC
132419 CACTCCC
1 CACTCCC
132426 CACTCCC
1 CACTCCC
132433 CAC
1 CAC
132436 ACTCAAACAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.71, G:0.00, T:0.13
Consensus pattern (7 bp):
CACTCCC
Found at i:140644 original size:15 final size:15
Alignment explanation
Indices: 140606--140642 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
140596 TAAAAAATTC
140606 TTAAAAAATATTTTA
1 TTAAAAAATATTTTA
*
140621 TTAGAAAATATTTT-
1 TTAAAAAATATTTTA
140635 TTAAAAAA
1 TTAAAAAA
140643 ATTAAAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (15 bp):
TTAAAAAATATTTTA
Found at i:144626 original size:31 final size:31
Alignment explanation
Indices: 144582--144699 Score: 89
Period size: 31 Copynumber: 3.8 Consensus size: 31
144572 TACCAGCTTA
*
144582 AAAAAATGTCAAGTTTAGGTACCAAAATAGG
1 AAAAAATGACAAGTTTAGGTACCAAAATAGG
* * *
144613 AAAAAGTGACAAGTTT-GAGTATC-AAAT-CG
1 AAAAAATGACAAGTTTAG-GTACCAAAATAGG
** * * *
144642 AACAAAAAAAAAAGTTTAAGTACCAAATTAGG
1 AA-AAAATGACAAGTTTAGGTACCAAAATAGG
* * *
144674 AAAAAGTGTCAAGTTCAGGTACCAAA
1 AAAAAATGACAAGTTTAGGTACCAAA
144700 TATTATATTA
Statistics
Matches: 63, Mismatches: 19, Indels: 10
0.68 0.21 0.11
Matches are distributed among these distances:
29 3 0.05
30 19 0.30
31 38 0.60
32 3 0.05
ACGTcount: A:0.50, C:0.11, G:0.18, T:0.21
Consensus pattern (31 bp):
AAAAAATGACAAGTTTAGGTACCAAAATAGG
Found at i:146905 original size:202 final size:202
Alignment explanation
Indices: 146559--146965 Score: 706
Period size: 202 Copynumber: 2.0 Consensus size: 202
146549 GTGTAAATAA
* * *
146559 GAGTAAAAAGGTATATGATGATATATATGTGATGAACAATGTCTATGTGAAATATTATGTGTTTA
1 GAGTAAAAAGGTATATGATGATATATATGTGATGAAAAATGTATATGTGAAATATTATATGTTTA
*
146624 ATTATAAATATTGATTATATAATAAAATGGTGATATTATGGAAGCCTTTGAGAAAATAAAGGTGA
66 ATTATAAATATTGATTATATAATAAAATGGTGATATTATGGAAGCCTTTGAGAAAATAAAAGTGA
*
146689 GAAATACGTGATTATGTATATGTGAAGAAAAATGTATATATGATGTATAAGTTGTGGATAATGAG
131 GAAATACATGATTATGTATATGTGAAGAAAAATGTATATATGATGTATAAGTTGTGGATAATGAG
146754 ATTAAAT
196 ATTAAAT
* *
146761 GAGTAAAGAGGTATATGATGATATATATGTGATGAAAAATGTATATGTGAAATATTTTATGTTTA
1 GAGTAAAAAGGTATATGATGATATATATGTGATGAAAAATGTATATGTGAAATATTATATGTTTA
* ** *
146826 ATTATAAATATTTATTATATGGTAAAATGGTGATATTGTGGAAGCCTTTGAGAAAATAAAAGTGA
66 ATTATAAATATTGATTATATAATAAAATGGTGATATTATGGAAGCCTTTGAGAAAATAAAAGTGA
146891 GAAATACATGATTATGTATATGTGAAGAAAAATGTATATATGATGTATAAGTTGTGGATAATGAG
131 GAAATACATGATTATGTATATGTGAAGAAAAATGTATATATGATGTATAAGTTGTGGATAATGAG
*
146956 GTTAAAT
196 ATTAAAT
146963 GAG
1 GAG
146966 ATTATGCCCA
Statistics
Matches: 193, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
202 193 1.00
ACGTcount: A:0.41, C:0.02, G:0.21, T:0.35
Consensus pattern (202 bp):
GAGTAAAAAGGTATATGATGATATATATGTGATGAAAAATGTATATGTGAAATATTATATGTTTA
ATTATAAATATTGATTATATAATAAAATGGTGATATTATGGAAGCCTTTGAGAAAATAAAAGTGA
GAAATACATGATTATGTATATGTGAAGAAAAATGTATATATGATGTATAAGTTGTGGATAATGAG
ATTAAAT
Found at i:147060 original size:23 final size:23
Alignment explanation
Indices: 147025--147201 Score: 205
Period size: 23 Copynumber: 7.6 Consensus size: 23
147015 CATTAAGGAA
*
147025 CACTGTGTGTGCTCTTTGATTAG
1 CACTGTGTGTGCTCTCTGATTAG
* *
147048 CACTATGTATGCTCTCTGATTAG
1 CACTGTGTGTGCTCTCTGATTAG
*
147071 CACTGTGTGTGCTCTCTGATTAA
1 CACTGTGTGTGCTCTCTGATTAG
* *
147094 CACTGTGTATGCTTTCTGATTAG
1 CACTGTGTGTGCTCTCTGATTAG
*
147117 CACTGTGTGTGCTCTCTGTTTAG
1 CACTGTGTGTGCTCTCTGATTAG
* *
147140 CAC-GTCTCGTACTCTCTGTTATTAG
1 CACTGTGT-GTGCTCTCTG--ATTAG
147165 CACT-TCGTGTGCTCTCTGATTAG
1 CACTGT-GTGTGCTCTCTGATTAG
* *
147188 CACTTTGTGCGCTC
1 CACTGTGTGTGCTC
147202 AGTACTTTAT
Statistics
Matches: 130, Mismatches: 18, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
22 3 0.02
23 108 0.83
24 1 0.01
25 17 0.13
26 1 0.01
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.41
Consensus pattern (23 bp):
CACTGTGTGTGCTCTCTGATTAG
Found at i:148877 original size:27 final size:27
Alignment explanation
Indices: 148847--148899 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
148837 ACCAAGGTGG
* *
148847 TTATCCAATCGGATAGCTTGAAGGCAA
1 TTATCCAACCGAATAGCTTGAAGGCAA
148874 TTATCCAACCGAATAGCTTGAAGGCA
1 TTATCCAACCGAATAGCTTGAAGGCA
148900 GTTAAAACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.25
Consensus pattern (27 bp):
TTATCCAACCGAATAGCTTGAAGGCAA
Found at i:156015 original size:27 final size:25
Alignment explanation
Indices: 155956--156014 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 25
155946 AATTCTTTTA
*
155956 TTTCTCTCTTTGTTTTTTTTTTCTAT
1 TTTCT-TCTCTGTTTTTTTTTTCTAT
155982 TTGTCTTCTCTG-TTTTTTTTTCT-T
1 TT-TCTTCTCTGTTTTTTTTTTCTAT
156006 TATTCTTCT
1 T-TTCTTCT
156015 TTTATAATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
24 8 0.27
25 12 0.40
26 7 0.23
27 3 0.10
ACGTcount: A:0.03, C:0.17, G:0.05, T:0.75
Consensus pattern (25 bp):
TTTCTTCTCTGTTTTTTTTTTCTAT
Found at i:156701 original size:30 final size:29
Alignment explanation
Indices: 156665--156729 Score: 73
Period size: 28 Copynumber: 2.3 Consensus size: 29
156655 ACTAACGGAA
156665 GTATCAAATTGGGGA-AAAAAAATAGTCTAG
1 GTATCAAATT-GGGACAAAAAAA-AGTCTAG
* *
156695 GTATC-AATTGTGACAAAAAAAAGTTTAG
1 GTATCAAATTGGGACAAAAAAAAGTCTAG
156723 GTA-CAAA
1 GTATCAAA
156730 AATAGAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
27 1 0.03
28 14 0.45
29 11 0.35
30 5 0.16
ACGTcount: A:0.48, C:0.08, G:0.20, T:0.25
Consensus pattern (29 bp):
GTATCAAATTGGGACAAAAAAAAGTCTAG
Found at i:157129 original size:35 final size:33
Alignment explanation
Indices: 157072--157164 Score: 100
Period size: 35 Copynumber: 2.7 Consensus size: 33
157062 TATTATACTC
* *
157072 TAATATATTTTATGTAATATTTATATCAAGTATA
1 TAATATATTTTATTTAA-ATTTATATCAAATATA
*
157106 TAATTATATTTCTATTTAAATTTATTTCAAATATA
1 TAA-TATATTT-TATTTAAATTTATATCAAATATA
157141 TAA-A-ATTATATATTTAAATTTATA
1 TAATATATT-T-TATTTAAATTTATA
157165 ATGGATATAT
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
32 3 0.06
33 15 0.29
34 3 0.06
35 24 0.47
36 6 0.12
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (33 bp):
TAATATATTTTATTTAAATTTATATCAAATATA
Done.