Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1763
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: 38499
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Found at i:11049 original size:42 final size:42
Alignment explanation
Indices: 10944--11145 Score: 114
Period size: 42 Copynumber: 4.8 Consensus size: 42
10934 AATTTACCTG
10944 GGACTAAGCCGACAGGTAATA-AAA-GATAAAAAGGTTGA-TCA
1 GGACTAAGCCGACAGGTAA-ACAAAGGAT-AAAAGGTTGACTCA
* * *
10985 GG-CTTGAA-CTGACAAGTCAACAAAGGATAAAAGGATT-ACTCA
1 GGAC-T-AAGCCGACAGGTAAACAAAGGATAAAAGG-TTGACTCA
* * *
11027 GGACTAAGCCGACAGGTAAACAAAGGGTACAAAAGTTGAC-CG
1 GGACTAAGCCGACAGGTAAACAAAGGATA-AAAGGTTGACTCA
** * * * ** * *
11069 GGGTTAAACCGATAAGCCAACAAAGGATAAAAAGGATTTACT-T
1 GGACTAAGCCGACAGGTAAACAAAGGAT-AAAAGG-TTGACTCA
*
11112 GAGACTAAGCCAACAGGTAAAGCAAAGGATAAAA
1 G-GACTAAGCCGACAGGTAAA-CAAAGGATAAAA
11146 AAGTCGATCG
Statistics
Matches: 118, Mismatches: 28, Indels: 27
0.68 0.16 0.16
Matches are distributed among these distances:
40 2 0.02
41 23 0.19
42 57 0.48
43 13 0.11
44 15 0.13
45 8 0.07
ACGTcount: A:0.45, C:0.15, G:0.24, T:0.16
Consensus pattern (42 bp):
GGACTAAGCCGACAGGTAAACAAAGGATAAAAGGTTGACTCA
Found at i:11065 original size:84 final size:85
Alignment explanation
Indices: 10832--11188 Score: 322
Period size: 84 Copynumber: 4.2 Consensus size: 85
10822 TAGCAATCAG
** * *
10832 GTCAAC-AAGGATAAAAAAGG--TTACTCGGGACTAAGTTGACAAGTAAACAAAGGAGATAAAAG
1 GTCAACAAAGGAT-AAAAAGGATTTACTCGGGACTAAGCCGACAGGTAAACAAAGGATA-AAAAG
*
10894 TTGATCGGGATTGAATTGACAA
64 TTGATCGGGATTGAACTGACAA
*
10916 GTACAA-AAAGGATAAAAA-AATTTAC-CTGGGACTAAGCCGACAGGTAATA-AAA-GATAAAAA
1 GT-CAACAAAGGATAAAAAGGATTTACTC-GGGACTAAGCCGACAGGTAA-ACAAAGGATAAAAA
* *
10976 GGTTGATCAGGCTTGAACTGACAA
63 -GTTGATCGGGATTGAACTGACAA
* *
11000 GTCAACAAAGGAT-AAAAGGA-TTACTCAGGACTAAGCCGACAGGTAAACAAAGGGTACAAAAGT
1 GTCAACAAAGGATAAAAAGGATTTACTCGGGACTAAGCCGACAGGTAAACAAAGGATA-AAAAGT
* * * * *
11063 TGACCGGGGTTAAACCGATAA
65 TGATCGGGATTGAACTGACAA
* * * *
11084 GCCAACAAAGGATAAAAAGGATTTACTTGAGACTAAGCCAACAGGTAAAGCAAAGGATAAAAAAG
1 GTCAACAAAGGATAAAAAGGATTTACTCGGGACTAAGCCGACAGGTAAA-CAAAGGAT-AAAAAG
* ** * **
11149 TCGATCGAAATTGAACCGTTAA
64 TTGATCGGGATTGAACTGACAA
11171 GT-AATCAAAGGATAAAAA
1 GTCAA-CAAAGGATAAAAA
11189 ACAATACCTA
Statistics
Matches: 224, Mismatches: 31, Indels: 33
0.78 0.11 0.11
Matches are distributed among these distances:
82 1 0.00
83 37 0.17
84 74 0.33
85 44 0.20
86 26 0.12
87 41 0.18
88 1 0.00
ACGTcount: A:0.46, C:0.13, G:0.23, T:0.18
Consensus pattern (85 bp):
GTCAACAAAGGATAAAAAGGATTTACTCGGGACTAAGCCGACAGGTAAACAAAGGATAAAAAGTT
GATCGGGATTGAACTGACAA
Found at i:11181 original size:87 final size:85
Alignment explanation
Indices: 11002--11188 Score: 209
Period size: 87 Copynumber: 2.2 Consensus size: 85
10992 ACTGACAAGT
* * * *
11002 CAACAAAGGAT-AAAAGGATTACTCAGGACTAAGCCGACAGGTAAACAAAGGGTACAAAAGTTGA
1 CAACAAAGGATAAAAAGGATTACTCAGGACTAAGCCAACAGGTAAACAAAGGATAAAAAAGTCGA
***
11066 CCGGGGTTAAACCGATAAGC
66 CCGAAATTAAACCGATAAGC
*
11086 CAACAAAGGATAAAAAGGATTTACT-TGAGACTAAGCCAACAGGTAAAGCAAAGGATAAAAAAGT
1 CAACAAAGGATAAAAAGGA-TTACTCAG-GACTAAGCCAACAGGTAAA-CAAAGGATAAAAAAGT
* * *
11150 CGATCGAAATTGAACCGTTAAG-
63 CGACCGAAATTAAACCGATAAGC
*
11172 TAATCAAAGGATAAAAA
1 CAA-CAAAGGATAAAAA
11189 ACAATACCTA
Statistics
Matches: 86, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
84 11 0.13
85 8 0.09
86 25 0.29
87 42 0.49
ACGTcount: A:0.47, C:0.15, G:0.22, T:0.16
Consensus pattern (85 bp):
CAACAAAGGATAAAAAGGATTACTCAGGACTAAGCCAACAGGTAAACAAAGGATAAAAAAGTCGA
CCGAAATTAAACCGATAAGC
Found at i:11333 original size:46 final size:45
Alignment explanation
Indices: 11248--11397 Score: 183
Period size: 46 Copynumber: 3.2 Consensus size: 45
11238 AACGAGGATT
* * * *
11248 AAAAGAGTTCGACCAAGGTGTTAACCGATACAGTAAAATAAGAATG
1 AAAAG-GTTTGACCAAGGTGGTAACTGATACAGTCAAATAAGAATG
* * *
11294 AAAAGTGTTTGACTAGGGTGGTAACTGATACAATCAAATAAGAATG
1 AAAAG-GTTTGACCAAGGTGGTAACTGATACAGTCAAATAAGAATG
* *
11340 AAAAGGGGTTTGACCAAGGTGGTAACTAATATAGTCAAATAAGAATG
1 AAAA--GGTTTGACCAAGGTGGTAACTGATACAGTCAAATAAGAATG
11387 AAAAGGTTTGA
1 AAAAGGTTTGA
11398 GGGTGGTAAG
Statistics
Matches: 89, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
45 7 0.08
46 42 0.47
47 39 0.44
48 1 0.01
ACGTcount: A:0.43, C:0.09, G:0.24, T:0.23
Consensus pattern (45 bp):
AAAAGGTTTGACCAAGGTGGTAACTGATACAGTCAAATAAGAATG
Found at i:11378 original size:47 final size:47
Alignment explanation
Indices: 11258--11392 Score: 182
Period size: 47 Copynumber: 2.9 Consensus size: 47
11248 AAAAGAGTTC
* * * *
11258 GACCAAGGTGTTAACCGATACAGTAAAATAAGAATGAAAA-GTGTTT
1 GACCAAGGTGGTAACTGATACAGTCAAATAAGAATGAAAAGGGGTTT
* * *
11304 GACTAGGGTGGTAACTGATACAATCAAATAAGAATGAAAAGGGGTTT
1 GACCAAGGTGGTAACTGATACAGTCAAATAAGAATGAAAAGGGGTTT
* *
11351 GACCAAGGTGGTAACTAATATAGTCAAATAAGAATGAAAAGG
1 GACCAAGGTGGTAACTGATACAGTCAAATAAGAATGAAAAGG
11393 TTTGAGGGTG
Statistics
Matches: 76, Mismatches: 12, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
46 34 0.45
47 42 0.55
ACGTcount: A:0.44, C:0.10, G:0.24, T:0.22
Consensus pattern (47 bp):
GACCAAGGTGGTAACTGATACAGTCAAATAAGAATGAAAAGGGGTTT
Found at i:11499 original size:28 final size:28
Alignment explanation
Indices: 11467--11520 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
11457 ATGGTTCGAA
*
11467 GGGTTGAATAAGATGAAACTGATAAAAT
1 GGGTTGAATAAGATGAAACCGATAAAAT
*
11495 GGGTTGAATAAGGTGAAACCGATAAA
1 GGGTTGAATAAGATGAAACCGATAAA
11521 GTCAATCAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.44, C:0.06, G:0.28, T:0.22
Consensus pattern (28 bp):
GGGTTGAATAAGATGAAACCGATAAAAT
Found at i:11552 original size:39 final size:40
Alignment explanation
Indices: 11504--11581 Score: 122
Period size: 39 Copynumber: 2.0 Consensus size: 40
11494 TGGGTTGAAT
*
11504 AAGGTGAAACCGATAAAGTCAATCAATTAAAAGGTTGGCC
1 AAGGTGAAACCGATAAAGTCAACCAATTAAAAGGTTGGCC
* *
11544 AAGG-GAAACTGATAAAGTCAACCAGTTAAAAGGTTGGC
1 AAGGTGAAACCGATAAAGTCAACCAATTAAAAGGTTGGC
11582 TAGGGCAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 31 0.89
40 4 0.11
ACGTcount: A:0.42, C:0.14, G:0.24, T:0.19
Consensus pattern (40 bp):
AAGGTGAAACCGATAAAGTCAACCAATTAAAAGGTTGGCC
Found at i:11678 original size:40 final size:40
Alignment explanation
Indices: 11510--11681 Score: 179
Period size: 40 Copynumber: 4.3 Consensus size: 40
11500 GAATAAGGTG
*
11510 AAACCGATAAAGTCAATC-AATTAAAAGGTTGGCCAAGGG--
1 AAACTGATAAAGTCAA-CGAATTAAAAGGTTGGCC-AGGGCA
* * *
11549 AAACTGATAAAGTCAACCAGTTAAAAGGTTGGCTAGGGCA
1 AAACTGATAAAGTCAACGAATTAAAAGGTTGGCCAGGGCA
* ** * * **
11589 AAACTGATAAAGCCAACGGGTTGAGAGGGTTAACCAGGGCA
1 AAACTGATAAAGTCAACGAATT-AAAAGGTTGGCCAGGGCA
* *
11630 AAATTGATAAAGTCAACGAATTAAAAGATTGGCCAGGGCA
1 AAACTGATAAAGTCAACGAATTAAAAGGTTGGCCAGGGCA
11670 AAACTGATAAAG
1 AAACTGATAAAG
11682 CTAACAGGTG
Statistics
Matches: 108, Mismatches: 21, Indels: 7
0.79 0.15 0.05
Matches are distributed among these distances:
38 5 0.05
39 29 0.27
40 43 0.40
41 31 0.29
ACGTcount: A:0.42, C:0.15, G:0.25, T:0.18
Consensus pattern (40 bp):
AAACTGATAAAGTCAACGAATTAAAAGGTTGGCCAGGGCA
Found at i:11709 original size:120 final size:118
Alignment explanation
Indices: 11510--11773 Score: 283
Period size: 120 Copynumber: 2.2 Consensus size: 118
11500 GAATAAGGTG
* *
11510 AAACC-GATAAAGTCAATCAATTAAAAGGTTGGCCAAGGGAAACTGATAAAGTCAACCAGTTAAA
1 AAACCTGATAAAGTCAA-CAATTAAAAGATTGGCCAAGGGAAACTGATAAAGTCAACCAGGTAAA
* * *
11574 AGGTTGGCTAGGGCAAAA-CTGATAAAGCCAACGGGTT-GAGAGGGTTAACCAGGGCA
65 AGGTTGGCCAAGGCAAAACCT-AT--AGCCAACGGGTTAGA-AAGGTTAACCAGGGCA
*
11630 AAA-TTGATAAAGTCAACGAATTAAAAGATTGGCC-AGGGCAAAACTGATAAAG-CTAA-CAGGT
1 AAACCTGATAAAGTCAAC-AATTAAAAGATTGGCCAAGGG--AAACTGATAAAGTC-AACCAGGT
* * * *
11691 GAAGGGTTGGCCAAGGCAAAACCTATAGCCAACGGGTTAGAAAGGTTGACTAGGGCA
62 AAAAGGTTGGCCAAGGCAAAACCTATAGCCAACGGGTTAGAAAGGTTAACCAGGGCA
*
11748 AAACCT-ATAAAGTGAACCAATTAAAA
1 AAACCTGATAAAGTCAA-CAATTAAAA
11774 AGTAATATCT
Statistics
Matches: 123, Mismatches: 12, Indels: 20
0.79 0.08 0.13
Matches are distributed among these distances:
118 45 0.37
119 9 0.07
120 53 0.43
121 16 0.13
ACGTcount: A:0.42, C:0.16, G:0.25, T:0.18
Consensus pattern (118 bp):
AAACCTGATAAAGTCAACAATTAAAAGATTGGCCAAGGGAAACTGATAAAGTCAACCAGGTAAAA
GGTTGGCCAAGGCAAAACCTATAGCCAACGGGTTAGAAAGGTTAACCAGGGCA
Found at i:12298 original size:88 final size:86
Alignment explanation
Indices: 12153--12503 Score: 386
Period size: 88 Copynumber: 4.0 Consensus size: 86
12143 GTCGTGATTA
* ** *
12153 CTTGCCCCAGGGAAACCAGGCTTGTGATGCATCAATACCATCTAGTGGTTGAGTAAAAGAGATAT
1 CTTGCCCCAAGGAAATTAGGCTTGTGATGCATCAATACCATCTAGTGGTGGA-TAAAAGAGATAT
12218 GATTAGGAATGTGTGGGCTACAC
65 GATT-GGAATGTGTGGGCTACAC
* *
12241 CTTGCCCCAAGGAAATTAGGCTGTTGTGATGCAT-AATACCATCCAATGGTGGATAAAAGAGATA
1 CTTGCCCCAAGGAAATTAGGC--TTGTGATGCATCAATACCATCTAGTGGTGGATAAAAGAGATA
*
12305 TCATTGGCAATGTGTGGGCTACAC
64 TGATTGG-AATGTGTGGGCTACAC
* * * * * * *
12329 CCTGCCCTAAGGAAATTAGACTTATGATACATCAATACCATCTAGTGGTTGGATAAAGGGGATAT
1 CTTGCCCCAAGGAAATTAGGCTTGTGATGCATCAATACCATCTAGTGG-TGGATAAAAGAGATAT
* *
12394 GATTGGGAATGTGTGGGTTGCAC
65 GATT-GGAATGTGTGGGCTACAC
* * * * *
12417 CTTG-CCCAAGGAAATTAGGCTTGTGAAGCATCAAT-GCATCTAGTGGTTGGATGAAGGGGATAT
1 CTTGCCCCAAGGAAATTAGGCTTGTGATGCATCAATACCATCTAGTGG-TGGATAAAAGAGATAT
* * *
12480 -TTTGGAGTGTGTGGGTTACAC
65 GATTGGAATGTGTGGGCTACAC
12501 CTT
1 CTT
12504 TTTGTGGTCA
Statistics
Matches: 227, Mismatches: 30, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
84 19 0.08
85 2 0.01
86 35 0.15
87 41 0.18
88 101 0.44
89 18 0.08
90 11 0.05
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (86 bp):
CTTGCCCCAAGGAAATTAGGCTTGTGATGCATCAATACCATCTAGTGGTGGATAAAAGAGATATG
ATTGGAATGTGTGGGCTACAC
Found at i:14678 original size:58 final size:59
Alignment explanation
Indices: 14581--14697 Score: 211
Period size: 58 Copynumber: 2.0 Consensus size: 59
14571 AAGTGGGGAA
14581 ATCAGTAGATGAATCACCCATCGTAATCGATCCTCACAGTCA-CACGAAGTAATAGAAG
1 ATCAGTAGATGAATCACCCATCGTAATCGATCCTCACAGTCACCACGAAGTAATAGAAG
14639 ATCAGTAGATGAATCACCCATC-TAATCGATCCTCAACAGTCACCACGAAGTAATAGAAG
1 ATCAGTAGATGAATCACCCATCGTAATCGATCCTC-ACAGTCACCACGAAGTAATAGAAG
14698 TTTTGGAGTC
Statistics
Matches: 57, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
57 12 0.21
58 29 0.51
59 16 0.28
ACGTcount: A:0.38, C:0.25, G:0.16, T:0.21
Consensus pattern (59 bp):
ATCAGTAGATGAATCACCCATCGTAATCGATCCTCACAGTCACCACGAAGTAATAGAAG
Found at i:18092 original size:21 final size:20
Alignment explanation
Indices: 18045--18098 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
18035 CATTTGAGAC
* * *
18045 ATGTATCGATGCATTCATTT
1 ATGTATCGATACATTCACTA
18065 ATGTATCGATACATTCACTA
1 ATGTATCGATACATTCACTA
18085 ATTGTATCGATACA
1 A-TGTATCGATACA
18099 AATCGTAGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 18 0.60
21 12 0.40
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTCACTA
Found at i:24235 original size:28 final size:27
Alignment explanation
Indices: 24203--24272 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 27
24193 ATAAAGCCAA
24203 GGGTTGGAGTATCCCC-TCGAAAGTAACG
1 GGGTTGGAGTATCCCCAT-GAAA-TAACG
24231 GGGTTGGAGTATCCCCGATGAAATAACG
1 GGGTTGGAGTATCCCC-ATGAAATAACG
*
24259 AGGTTGGAGTATCC
1 GGGTTGGAGTATCC
24273 TCGATTGTAA
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 34 0.87
29 4 0.10
30 1 0.03
ACGTcount: A:0.26, C:0.19, G:0.33, T:0.23
Consensus pattern (27 bp):
GGGTTGGAGTATCCCCATGAAATAACG
Found at i:24319 original size:50 final size:51
Alignment explanation
Indices: 24260--24478 Score: 214
Period size: 51 Copynumber: 4.3 Consensus size: 51
24250 GAAATAACGA
* * * *
24260 GGTTGGAGTATCCTCGATTGT-AAAAAATTGGTATTTTGGAAATAAAATCG
1 GGTTGGAGTATCCCCGATTATGAAAAAATTAGTATTTTGGAAATAAAACCG
* * *
24310 AGTTGGAGTATCCCCGATTA--AAGGAAAATTAGTGTTTTGAAAATAAAACCG
1 GGTTGGAGTATCCCCGATTATGAA--AAAATTAGTATTTTGGAAATAAAACCG
* * * *
24361 GGTTGGAGTATCCCCGATTATGGAAAAATTAGTGTTTTAGCAAT-AAACCGG
1 GGTTGGAGTATCCCCGATTATGAAAAAATTAGTATTTTGGAAATAAAACC-G
* * * **
24412 GGTTGGAGTAT-CCCGATTATGAAAAACTCAATATTTTGGGAAATAAAGTCG
1 GGTTGGAGTATCCCCGATTATGAAAAAATTAGTATTTT-GGAAATAAAACCG
24463 GGTTTGGAGTATCCCC
1 GG-TTGGAGTATCCCC
24479 AATGATTAAC
Statistics
Matches: 139, Mismatches: 21, Indels: 15
0.79 0.12 0.09
Matches are distributed among these distances:
49 2 0.01
50 43 0.31
51 78 0.56
52 12 0.09
53 4 0.03
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.30
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAAATTAGTATTTTGGAAATAAAACCG
Found at i:27017 original size:33 final size:33
Alignment explanation
Indices: 26959--27025 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
26949 AAAATTCTCA
*** *
26959 AATGTATCGATACAAAGATCCATGTATTGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
26992 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
27025 A
1 A
27026 TTTTCTTGGC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.27
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:27069 original size:19 final size:19
Alignment explanation
Indices: 27045--27098 Score: 108
Period size: 19 Copynumber: 2.8 Consensus size: 19
27035 CAGTAGCTAA
27045 TTATGTATCGATACAATAC
1 TTATGTATCGATACAATAC
27064 TTATGTATCGATACAATAC
1 TTATGTATCGATACAATAC
27083 TTATGTATCGATACAA
1 TTATGTATCGATACAA
27099 ATCACTGAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (19 bp):
TTATGTATCGATACAATAC
Found at i:28008 original size:59 final size:59
Alignment explanation
Indices: 27912--29274 Score: 1914
Period size: 59 Copynumber: 23.3 Consensus size: 59
27902 ATAAAGTGTA
* *
27912 TCCTGCTCTTTGAGGACTAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
27971 T-CTCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
1 TCCT-GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* * *
28030 TCCCGTTCTTTAAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAG-AAAGGCG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* * * *
28088 TCCCGCTCTTTAAGGACTGAAGGTGCCACCAACTTGTGTAGGCTTTAAAAGAAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
** * *
28147 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGTGCTTT-----AAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* * ** *
28202 TCCTTCTCTTTGAGGATTGGAAAATGCCACCAACTTGTGTGGGCTTT----G-AAAGGAG
1 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* * * *
28257 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTATGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGGCG
*
28318 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTCAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* *
28377 TCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGAG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
28436 TCAC-GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
1 TC-CTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* *
28495 TCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
**
28554 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-AAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
** * *
28613 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGTGCTTT-----AAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* ** *
28668 TCCTGCTCTTTGAGGATTGGAAAATGCCACCAACTTGTGTGGGCTTT----G-AAAGGAG
1 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* * * *
28723 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTATGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGGCG
28784 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
*
28843 TCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
28902 TCAC-GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
1 TC-CTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
*
28961 TCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
29020 TCAC-GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
1 TC-CTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* *
29079 TCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
**
29138 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
** * * *
29198 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGGGGGCTTTTTAAAGGAAAAGGCA
1 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGC--TTTAAAAGAAAAGGCG
*
29260 TCCTACTCTTTGAGG
1 TCCTGCTCTTTGAGG
29275 GCTAAAAAGT
Statistics
Matches: 1206, Mismatches: 68, Indels: 57
0.91 0.05 0.04
Matches are distributed among these distances:
54 2 0.00
55 195 0.16
58 61 0.05
59 687 0.57
60 189 0.16
61 44 0.04
62 28 0.02
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (59 bp):
TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
Found at i:28786 original size:466 final size:465
Alignment explanation
Indices: 27916--29274 Score: 2294
Period size: 466 Copynumber: 2.9 Consensus size: 465
27906 AGTGTATCCT
* * *
27916 GCTCTTTGAGGACTAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCTCGCTCTT
1 GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCACGCTCTT
* *
27981 TGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGTTCTTTAAGGA
66 TGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGA
*
28046 CTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAG-AAAGGCGTCCCGCTCTTTAAGGACTGAAG
131 CTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGT-CCGCTCTTTGAGGACTGAAG
* *
28110 GTGCCACCAACTTGTGTAGGCTTTAAAAGAAAAGGTGTCCTGCTCTTTGAGGACTGGAAAATGCC
195 GTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCTGCTCTTTGAGGACTGGAAAATGCC
*
28175 ACCAACTTGTGTGTGCTTTAAAAGGTGTCCTTCTCTTTGAGGATTGGAAAATGCCACCAACTTGT
260 ACCAACTTGTGTGTGCTTTAAAAGGTGTCCTGCTCTTTGAGGATTGGAAAATGCCACCAACTTGT
28240 GTGGGCTTTGAAAGGAGTCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTATGTGGGCTTTG
325 GTGGGCTTTGAAAGGAGTCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTATGTGGGCTTTG
*
28305 AAAAGAAAAAGCATCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTCAAAGA
390 AAAAGAAAAAGCATCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGA
28370 AAAGGCGTCCC
455 AAAGGCGTCCC
*
28381 GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGAGTCACGCTCTT
1 GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCACGCTCTT
28446 TGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGA
66 TGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGA
*
28511 CTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGTGTCCTGCTCTTTGAGGACTGGAA
131 CTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCC-GCTCTTTGAGGACT-GAA
**
28576 AATGCCACCAACTTGTGTGGGCTTT-AAAGAAAAGGCGTCCTGCTCTTTGAGGACTGGAAAATGC
194 GGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCTGCTCTTTGAGGACTGGAAAATGC
28640 CACCAACTTGTGTGTGCTTTAAAAGGTGTCCTGCTCTTTGAGGATTGGAAAATGCCACCAACTTG
259 CACCAACTTGTGTGTGCTTTAAAAGGTGTCCTGCTCTTTGAGGATTGGAAAATGCCACCAACTTG
28705 TGTGGGCTTTGAAAGGAGTCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTATGTGGGCTTT
324 TGTGGGCTTTGAAAGGAGTCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTATGTGGGCTTT
28770 GAAAAGAAAAAGCATCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAG
389 GAAAAGAAAAAGCATCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAG
28835 AAAAGGCGTCCC
454 AAAAGGCGTCCC
28847 GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCACGCTCTT
1 GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCACGCTCTT
28912 TGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGA
66 TGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGA
28977 CTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCACGCTCTTTGAGGACTGAAG
131 CTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTC-CGCTCTTTGAGGACTGAAG
* **
29042 GTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACT-GAAGGTGCC
195 GTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCTGCTCTTTGAGGACTGGAAAATGCC
* *
29106 ACCAACTTGTGTGGGCTTTAAAAGAAAAGGTGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAA
260 ACCAACTTGTGTGTGCTTT-----AAAAGGTGTCCTGCTCTTTGAGGATTGGAAAATGCCACCAA
* * * *
29171 CTTGTGTGGGCTTTAAAAGAAAAGGCGTCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTG
320 CTTGTGTGGGCTTT----G-AAAGGAGTCCTGCTCTTTGGGGACT-GAAAGGTGCCACCAACTTA
* * * * *
29235 TGGGGGCTTTTTAAAGGAAAAGGCATCCTACTCTTTGAGG
379 TGTGGGC-TTTGAAAAGAAAAAGCATCCTGCTCTTTGAGG
29275 GCTAAAAAGT
Statistics
Matches: 845, Mismatches: 32, Indels: 23
0.94 0.04 0.03
Matches are distributed among these distances:
465 212 0.25
466 479 0.57
467 26 0.03
470 54 0.06
474 1 0.00
475 41 0.05
476 32 0.04
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (465 bp):
GCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCACGCTCTT
TGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGA
CTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCGCTCTTTGAGGACTGAAGG
TGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCTGCTCTTTGAGGACTGGAAAATGCCA
CCAACTTGTGTGTGCTTTAAAAGGTGTCCTGCTCTTTGAGGATTGGAAAATGCCACCAACTTGTG
TGGGCTTTGAAAGGAGTCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTATGTGGGCTTTGA
AAAGAAAAAGCATCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAA
AAGGCGTCCC
Found at i:30281 original size:8 final size:8
Alignment explanation
Indices: 30270--30313 Score: 56
Period size: 8 Copynumber: 5.5 Consensus size: 8
30260 TTTTCTCTTG
30270 TTTTGTTT
1 TTTTGTTT
30278 TTTTGTTT
1 TTTTGTTT
30286 TGTTT-TTT
1 T-TTTGTTT
30294 TTTT-TTT
1 TTTTGTTT
30301 TTTTGCTTT
1 TTTTG-TTT
30310 TTTT
1 TTTT
30314 TAAGAGAATG
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
7 10 0.30
8 13 0.39
9 10 0.30
ACGTcount: A:0.00, C:0.02, G:0.09, T:0.89
Consensus pattern (8 bp):
TTTTGTTT
Found at i:30288 original size:18 final size:17
Alignment explanation
Indices: 30267--30314 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 17
30257 TCTTTTTCTC
30267 TTGTTTTGTTTTTTTGTT
1 TTGTTTT-TTTTTTTGTT
*
30285 TTGTTTTTTTTTTTTTTT
1 TTG-TTTTTTTTTTTGTT
30303 TTGCTTTTTTTT
1 TTG-TTTTTTTT
30315 AAGAGAATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 23 0.85
19 4 0.15
ACGTcount: A:0.00, C:0.02, G:0.10, T:0.88
Consensus pattern (17 bp):
TTGTTTTTTTTTTTGTT
Found at i:30310 original size:13 final size:12
Alignment explanation
Indices: 30267--30314 Score: 62
Period size: 13 Copynumber: 3.9 Consensus size: 12
30257 TCTTTTTCTC
30267 TTGTTTTGTTTTT
1 TTGTTTT-TTTTT
*
30280 TTGTTTTGTTTT
1 TTGTTTTTTTTT
30292 TT-TTTTTTTTT
1 TTGTTTTTTTTT
30303 TTGCTTTTTTTT
1 TTG-TTTTTTTT
30315 AAGAGAATGT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
11 10 0.32
12 6 0.19
13 15 0.48
ACGTcount: A:0.00, C:0.02, G:0.10, T:0.88
Consensus pattern (12 bp):
TTGTTTTTTTTT
Done.