Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold155
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: 399999
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
File 2 of 2
Found at i:332888 original size:47 final size:48
Alignment explanation
Indices: 332724--332910 Score: 281
Period size: 47 Copynumber: 3.9 Consensus size: 48
332714 AATATTTGAA
* *
332724 ACAAGTTCATGCAAATATACATGCCCATCAAGTTCATTCAAA-ATTTT
1 ACAAGTTCATGCAAATATACATGACAATCAAGTTCATTCAAATATTTT
* *
332771 ACAAGTTCATGCAAATATACAT-ACCCATCAAGTTTATTCAAATATTTT
1 ACAAGTTCATGCAAATATACATGA-CAATCAAGTTCATTCAAATATTTT
*
332819 ACAAGTTCATGCAAATATACATGACAATCAAGTTCGTTCAAATA-TTT
1 ACAAGTTCATGCAAATATACATGACAATCAAGTTCATTCAAATATTTT
* *
332866 ACAAGTTCATGCAAATATACATGACAATAAAGTTCATACAAATAT
1 ACAAGTTCATGCAAATATACATGACAATCAAGTTCATTCAAATAT
332911 ATGTAAATAA
Statistics
Matches: 128, Mismatches: 8, Indels: 7
0.90 0.06 0.05
Matches are distributed among these distances:
47 83 0.65
48 44 0.34
49 1 0.01
ACGTcount: A:0.42, C:0.18, G:0.09, T:0.32
Consensus pattern (48 bp):
ACAAGTTCATGCAAATATACATGACAATCAAGTTCATTCAAATATTTT
Found at i:332899 original size:95 final size:95
Alignment explanation
Indices: 332724--332910 Score: 279
Period size: 95 Copynumber: 2.0 Consensus size: 95
332714 AATATTTGAA
* *
332724 ACAAGTTCATGCAAATATACATGCCCATCAAGTTCATTCAAAATTTTACAAGTTCATGCAAATAT
1 ACAAGTTCATGCAAATATACATGACAATCAAGTTCATTCAAAATTTTACAAGTTCATGCAAATAT
* * * *
332789 ACATACCCATCAAGTTTATTCAAATATTTT
66 ACATACCAATAAAGTTCATACAAATATTTT
*
332819 ACAAGTTCATGCAAATATACATGACAATCAAGTTCGTTC-AAATATTTACAAGTTCATGCAAATA
1 ACAAGTTCATGCAAATATACATGACAATCAAGTTCATTCAAAAT-TTTACAAGTTCATGCAAATA
332883 TACATGA-CAATAAAGTTCATACAAATAT
65 TACAT-ACCAATAAAGTTCATACAAATAT
332911 ATGTAAATAA
Statistics
Matches: 83, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
94 4 0.05
95 78 0.94
96 1 0.01
ACGTcount: A:0.42, C:0.18, G:0.09, T:0.32
Consensus pattern (95 bp):
ACAAGTTCATGCAAATATACATGACAATCAAGTTCATTCAAAATTTTACAAGTTCATGCAAATAT
ACATACCAATAAAGTTCATACAAATATTTT
Found at i:336363 original size:21 final size:20
Alignment explanation
Indices: 336337--336404 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 20
336327 TCTCATATGA
336337 GTTTCAGTTTAACCTTTCTGG
1 GTTTCAGTTTAACCTTT-TGG
* * *
336358 GTTTCAGTTCAGCTCTTTTGA
1 GTTTCAGTTTAAC-CTTTTGG
* *
336379 GCTTCAGTTTAACCCTTATGG
1 GTTTCAGTTTAA-CCTTTTGG
336400 GTTTC
1 GTTTC
336405 CATTCAACTC
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
21 31 0.86
22 5 0.14
ACGTcount: A:0.15, C:0.21, G:0.19, T:0.46
Consensus pattern (20 bp):
GTTTCAGTTTAACCTTTTGG
Found at i:336387 original size:42 final size:42
Alignment explanation
Indices: 336332--336424 Score: 125
Period size: 42 Copynumber: 2.2 Consensus size: 42
336322 AGTTATCTCA
* * * *
336332 TATGAGTTTCAGTTTAACCTTTCTGGGTTT-CAGTTCAGCTCT
1 TATGAGCTTCAGTTTAACCCTTATGGGTTTCCA-TTCAACTCT
*
336374 TTTGAGCTTCAGTTTAACCCTTATGGGTTTCCATTCAACTCT
1 TATGAGCTTCAGTTTAACCCTTATGGGTTTCCATTCAACTCT
336416 TATGAGCTT
1 TATGAGCTT
336425 TCGTTCAATT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
42 42 0.95
43 2 0.05
ACGTcount: A:0.18, C:0.20, G:0.17, T:0.44
Consensus pattern (42 bp):
TATGAGCTTCAGTTTAACCCTTATGGGTTTCCATTCAACTCT
Found at i:336419 original size:21 final size:20
Alignment explanation
Indices: 336355--336445 Score: 56
Period size: 21 Copynumber: 4.3 Consensus size: 20
336345 TTAACCTTTC
* *
336355 TGGGTTTCAGTTCAGCTCTTT
1 TGGGTTTCA-TTCAACTCTTA
* * * *
336376 TGAGCTTCAGTTTAACCCTTA
1 TGGGTTTCA-TTCAACTCTTA
336397 TGGGTTTCCATTCAACTCTTA
1 TGGGTTT-CATTCAACTCTTA
* * *
336418 TGAGCTTTCGTTCAATTCTTA
1 TG-GGTTTCATTCAACTCTTA
*
336439 CGGGTTT
1 TGGGTTT
336446 TCTTTAGCAC
Statistics
Matches: 53, Mismatches: 15, Indels: 5
0.73 0.21 0.07
Matches are distributed among these distances:
20 4 0.08
21 43 0.81
22 6 0.11
ACGTcount: A:0.16, C:0.21, G:0.19, T:0.44
Consensus pattern (20 bp):
TGGGTTTCATTCAACTCTTA
Found at i:341289 original size:14 final size:14
Alignment explanation
Indices: 341270--341299 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
341260 ATATTGGGGT
341270 CACTAAAATTTTCA
1 CACTAAAATTTTCA
341284 CACTAAAATTTTCA
1 CACTAAAATTTTCA
341298 CA
1 CA
341300 TTCGTGATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.23, G:0.00, T:0.33
Consensus pattern (14 bp):
CACTAAAATTTTCA
Found at i:345010 original size:25 final size:26
Alignment explanation
Indices: 344968--345019 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 26
344958 AGTTATAAAT
* *
344968 TAGAAAAATTTCTCTAGA-AATTTTC
1 TAGAAAAATCTCTCTAGAGAATATTC
* *
344993 TAGAATAATCTCTTTAGAGAATATTC
1 TAGAAAAATCTCTCTAGAGAATATTC
345019 T
1 T
345020 CTCTACAACT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (26 bp):
TAGAAAAATCTCTCTAGAGAATATTC
Found at i:345163 original size:32 final size:31
Alignment explanation
Indices: 345126--345306 Score: 88
Period size: 32 Copynumber: 5.7 Consensus size: 31
345116 TAATCACTTT
345126 AATATTAAATTAATATAATATTTATCAAGATA
1 AATATTAAATTAATATAATA-TTATCAAGATA
* *
345158 AATATTAGATTATATTTAATA-T-T-AA-AT-
1 AATATTAAATTA-ATATAATATTATCAAGATA
** * * *
345185 CTTATTAAAATAATAAAATATTTATCTTGTAGATA
1 AATATTAAATTAATATAATA-TTATC---AAGATA
* * *
345220 AATATTAAATTAA-AT-TTAATATCCAGATA
1 AATATTAAATTAATATAATATTATCAAGATA
* * *
345249 ATCACTATTAAATTAATAAAATACTATTAAGATA
1 A--A-TATTAAATTAATATAATATTATCAAGATA
* *
345283 AGTATTAAATATAATTTAATATTA
1 AATATTAAAT-TAATATAATATTA
345307 AACTATTAAA
Statistics
Matches: 108, Mismatches: 25, Indels: 32
0.65 0.15 0.19
Matches are distributed among these distances:
26 6 0.06
27 8 0.07
28 3 0.03
29 9 0.08
30 1 0.01
31 10 0.09
32 36 0.33
33 11 0.10
34 14 0.13
35 10 0.09
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.41
Consensus pattern (31 bp):
AATATTAAATTAATATAATATTATCAAGATA
Found at i:349480 original size:2 final size:2
Alignment explanation
Indices: 349475--349508 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
349465 TGGTGAATGA
349475 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
349509 GTGTGTGTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:351259 original size:22 final size:22
Alignment explanation
Indices: 351213--351265 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
351203 TTTTGAGCAA
*
351213 TTTAATTTTTTCTTTTATGTTC
1 TTTAATTTTTTCTTTTATGTCC
351235 TTTAACTTTCTTTCTTTT-T-TCC
1 TTTAA-TTT-TTTCTTTTATGTCC
351257 TTT-ATTTTT
1 TTTAATTTTT
351266 CATTCTCTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
19 2 0.07
20 3 0.11
21 1 0.04
22 10 0.36
23 4 0.14
24 8 0.29
ACGTcount: A:0.11, C:0.13, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTAATTTTTTCTTTTATGTCC
Found at i:360306 original size:30 final size:30
Alignment explanation
Indices: 360272--360463 Score: 154
Period size: 30 Copynumber: 6.4 Consensus size: 30
360262 CTTCATCCAA
*
360272 AACCCTAGATGTGTGAACCCTATATATGCG
1 AACCCTATATGTGTGAACCCTATATATGCG
* ***** * ** *
360302 AACCCTAGATACACAAACCCTAGATACACA
1 AACCCTATATGTGTGAACCCTATATATGCG
* *
360332 AACCCTATATGTGTAAACCC-ATAGATGCG
1 AACCCTATATGTGTGAACCCTATATATGCG
*
360361 AACCCTATATGTGTGAACCCTTTATATGCG
1 AACCCTATATGTGTGAACCCTATATATGCG
** * *
360391 AACCCTATATACGTGAACCCTATATGTG-T
1 AACCCTATATGTGTGAACCCTATATATGCG
* * * *
360420 AGATCCTATACGTGCGAACCCTATACATGCG
1 A-ACCCTATATGTGTGAACCCTATATATGCG
*
360451 AACCCTATGTGTG
1 AACCCTATATGTG
360464 CAAATCTTAT
Statistics
Matches: 121, Mismatches: 38, Indels: 6
0.73 0.23 0.04
Matches are distributed among these distances:
29 24 0.20
30 96 0.79
31 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (30 bp):
AACCCTATATGTGTGAACCCTATATATGCG
Found at i:360413 original size:15 final size:15
Alignment explanation
Indices: 360272--360505 Score: 121
Period size: 15 Copynumber: 15.7 Consensus size: 15
360262 CTTCATCCAA
* * *
360272 AACCCTAGATGTGTG
1 AACCCTATATATGCG
360287 AACCCTATATATGCG
1 AACCCTATATATGCG
* ** *
360302 AACCCTAGATACACA
1 AACCCTATATATGCG
* ** *
360317 AACCCTAGATACACA
1 AACCCTATATATGCG
* **
360332 AACCCTATATGTGTA
1 AACCCTATATATGCG
*
360347 AACCC-ATAGATGCG
1 AACCCTATATATGCG
* *
360361 AACCCTATATGTGTG
1 AACCCTATATATGCG
*
360376 AACCCTTTATATGCG
1 AACCCTATATATGCG
* *
360391 AACCCTATATACGTG
1 AACCCTATATATGCG
* *
360406 AACCCTATATGTG-T
1 AACCCTATATATGCG
* **
360420 AGATCCTATACGTGCG
1 A-ACCCTATATATGCG
*
360436 AACCCTATACATGCG
1 AACCCTATATATGCG
* * *
360451 AACCCTATGTGTGCA
1 AACCCTATATATGCG
* * ** *
360466 AATCTTATACGTGCA
1 AACCCTATATATGCG
* *
360481 AACCCTAAATATGCA
1 AACCCTATATATGCG
360496 AACCCTATAT
1 AACCCTATAT
360506 GCGTGAACCC
Statistics
Matches: 169, Mismatches: 47, Indels: 6
0.76 0.21 0.03
Matches are distributed among these distances:
14 11 0.07
15 157 0.93
16 1 0.01
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.26
Consensus pattern (15 bp):
AACCCTATATATGCG
Found at i:360475 original size:45 final size:45
Alignment explanation
Indices: 360347--360506 Score: 160
Period size: 45 Copynumber: 3.6 Consensus size: 45
360337 TATATGTGTA
* ** * * **
360347 AACCC-ATAGATGCGAACCCTATATGTGTGAACCCTTTATATGCG
1 AACCCTATATATGCGAACCCTATATGTGCAAATCCTATACGTGCG
* * * *
360391 AACCCTATATACGTGAACCCTATATGTGTAGATCCTATACGTGCG
1 AACCCTATATATGCGAACCCTATATGTGCAAATCCTATACGTGCG
* * * *
360436 AACCCTATACATGCGAACCCTATGTGTGCAAATCTTATACGTGCA
1 AACCCTATATATGCGAACCCTATATGTGCAAATCCTATACGTGCG
* *
360481 AACCCTAAATATGCAAACCCTATATG
1 AACCCTATATATGCGAACCCTATATG
360507 CGTGAACCCT
Statistics
Matches: 94, Mismatches: 21, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
44 5 0.05
45 89 0.95
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.27
Consensus pattern (45 bp):
AACCCTATATATGCGAACCCTATATGTGCAAATCCTATACGTGCG
Found at i:366023 original size:17 final size:17
Alignment explanation
Indices: 365993--366032 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
365983 AAAAGAAAAA
365993 AAAATAAGTATCAAGTT
1 AAAATAAGTATCAAGTT
* *
366010 AAAATTAGTGTCAAGTT
1 AAAATAAGTATCAAGTT
*
366027 CAAATA
1 AAAATA
366033 CCAAACAAGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.50, C:0.07, G:0.12, T:0.30
Consensus pattern (17 bp):
AAAATAAGTATCAAGTT
Found at i:370544 original size:31 final size:31
Alignment explanation
Indices: 370482--370545 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
370472 ATGAACTTAT
* *
370482 ATAAAATTTTGATTGTAATTTAAATATGTAC
1 ATAAAATTTTAATTGTAATTTAAATAAGTAC
* *
370513 ATAAAATTTTAATTTTGATTT-AATCAAGTAC
1 ATAAAATTTTAATTGTAATTTAAAT-AAGTAC
370544 AT
1 AT
370546 TTAAACAAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 3 0.11
31 25 0.89
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (31 bp):
ATAAAATTTTAATTGTAATTTAAATAAGTAC
Found at i:377848 original size:120 final size:120
Alignment explanation
Indices: 377711--378213 Score: 855
Period size: 120 Copynumber: 4.2 Consensus size: 120
377701 TTTTCAAGTT
* *
377711 ATATATTTAATAATAATTATGTTAATTTATATTTTGCAGTATCATGTATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
*
377776 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATAGTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATCATATAGTTTAATTAAA
*
377831 ATATTTTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
* *
377896 TAATATAAGAATATTAATTATTAAAAATTTTATTAAATTATATAGTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATCATATAGTTTAATTAAA
*
377951 ATATATTTAATAATAATTATGTTAATTTATATTTTACAATATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
* * *
378016 TAATATAAGAATATTAATTATTAATAATTTTATTAAATCAAATATTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATCATATAGTTTAATTAAA
* *
378071 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAATT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
* * *
378136 TAATATAAGAATATTAATTATTAAGAATTTTA-CAGTATCATATATTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTA-AATCATATAGTTTAATTAAA
378191 ATATATTTAATAATAATTATGTT
1 ATATATTTAATAATAATTATGTT
378214 TAAATATGAT
Statistics
Matches: 365, Mismatches: 17, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
119 1 0.00
120 364 1.00
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (120 bp):
ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
TAATATAAGAATATTAATTATTAAGAATTTTATTAAATCATATAGTTTAATTAAA
Found at i:377999 original size:43 final size:42
Alignment explanation
Indices: 377951--378120 Score: 99
Period size: 43 Copynumber: 4.2 Consensus size: 42
377941 TTTAATTAAA
377951 ATATATTTAATAATAATTATGTTAATTTATATTTTACAATATC
1 ATATATTTAATAAT-ATTATGTTAATTTATATTTTACAATATC
* * * * * *
377994 ATATA-TT-ATGAT-TTGA-G-TAAATTA-ATATAAGAATATT
1 ATATATTTAATAATATT-ATGTTAATTTATATTTTACAATATC
* * ** * **
378031 A-AT-TATTAATAATTTTAT-TAAATCAAATATTTTA-ATTAAA
1 ATATAT-TTAATAATATTATGTTAAT-TTATATTTTACAATATC
*
378071 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATC
1 ATATATTTAATAAT-ATTATGTTAATTTATATTTTACAATATC
378114 ATATATT
1 ATATATT
378121 ATGATTTCAG
Statistics
Matches: 90, Mismatches: 23, Indels: 28
0.64 0.16 0.20
Matches are distributed among these distances:
36 2 0.02
37 12 0.13
38 11 0.12
39 7 0.08
40 6 0.07
41 18 0.20
42 15 0.17
43 19 0.21
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.49
Consensus pattern (42 bp):
ATATATTTAATAATATTATGTTAATTTATATTTTACAATATC
Found at i:378440 original size:45 final size:43
Alignment explanation
Indices: 378344--378451 Score: 109
Period size: 45 Copynumber: 2.5 Consensus size: 43
378334 TTCCATTATG
378344 CTATTACACCTCTATT-C-T--ATTCAACCAAACACAAGATTA
1 CTATTACACCTCTATTCCATACATTCAACCAAACACAAGATTA
* **
378383 CTATTACGCCTCTATTCCATTACATTCAACCAAACA-GTGAATTAA
1 CTATTACACCTCTATTCCA-TACATTCAACCAAACACAAG-ATT-A
*
378428 CTATTACACCTCTAATCCAATACA
1 CTATTACACCTCTATTCC-ATACA
378452 CCTCTAATCC
Statistics
Matches: 56, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
39 15 0.27
40 1 0.02
42 1 0.02
43 1 0.02
44 16 0.29
45 21 0.38
46 1 0.02
ACGTcount: A:0.37, C:0.29, G:0.04, T:0.31
Consensus pattern (43 bp):
CTATTACACCTCTATTCCATACATTCAACCAAACACAAGATTA
Found at i:378453 original size:16 final size:16
Alignment explanation
Indices: 378432--378467 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
378422 AATTAACTAT
378432 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
378448 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
378464 TACA
1 TACA
378468 GCGAACCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:389354 original size:18 final size:18
Alignment explanation
Indices: 389331--389372 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
389321 TAAACGGATT
* *
389331 AATTATTTATTTGTATTA
1 AATTATTAATTTATATTA
*
389349 AATTATTAATTTATGTTA
1 AATTATTAATTTATATTA
389367 AATTAT
1 AATTAT
389373 AAAGTACAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (18 bp):
AATTATTAATTTATATTA
Found at i:390135 original size:106 final size:106
Alignment explanation
Indices: 389930--390142 Score: 240
Period size: 106 Copynumber: 2.0 Consensus size: 106
389920 GTACGAGCTT
* * * *
389930 TGAGGTATATTAAGATTAGTGGTGCTTATGCAAAAACGCCGCTAAAGCACAGTATTAGCGGCGCA
1 TGAGGTATATTAAGATTAGTGGCGCTTATGAAAAAACACCGCTAAAGCACAGTATTAGCGGCGAA
*
389995 TCATACAGACTGCCGCAAACTATCTTAACCAAAACGCAGCG
66 TCATACAGACTGCCGCAAACTATCTTAACAAAAACGCAGCG
* * * *
390036 TGAGGTGTATT-AGAATTAGTGGCGCTTATGAAAAAACACCGCTAGA-CACAGTATTTGCGGTGT
1 TGAGGTATATTAAG-ATTAGTGGCGCTTATGAAAAAACACCGCTAAAGCACAGTATTAGCGGCG-
*
390099 AAT-ATA-AGAAGC-GCCGCCAAA-TATCTTAACAAAAAACGTAGCG
64 AATCATACAG-A-CTGCCG-CAAACTATCTTAAC-AAAAACGCAGCG
390142 T
1 T
390143 TTTGGTATTG
Statistics
Matches: 91, Mismatches: 10, Indels: 12
0.81 0.09 0.11
Matches are distributed among these distances:
104 2 0.02
105 33 0.36
106 56 0.62
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.23
Consensus pattern (106 bp):
TGAGGTATATTAAGATTAGTGGCGCTTATGAAAAAACACCGCTAAAGCACAGTATTAGCGGCGAA
TCATACAGACTGCCGCAAACTATCTTAACAAAAACGCAGCG
Found at i:390241 original size:115 final size:112
Alignment explanation
Indices: 390036--390385 Score: 373
Period size: 113 Copynumber: 3.1 Consensus size: 112
390026 AAACGCAGCG
* * * * * *
390036 TGAGGTGTATTAGAATTAGTGGCGCTTATGAAAAAACACCGCTAGA-CACAGTATTTGCGGTGTA
1 TGAGGTATATTAGAATTAGTGGCGCTTAT-AGAAAACGCCGCTAAAGCACAGTATTAGCGGCGTA
* * * *
390100 ATATAAGAAGCGCCGCCAAATATCTTAACAAAAAACGTAGCGTTTTGGTAT
65 AT-TAAAAAACGCCGCAAAATATCTTAAC-AAAAACGCAGCG-TTTGGTAT
* * *
390151 TGAGGTATATCAGAATTAGTGGCGCTTATAGAAAACGCCACTAAAGCATAGTATTAGCGGCGCT-
1 TGAGGTATATTAGAATTAGTGGCGCTTATAGAAAACGCCGCTAAAGCACAGTATTAGCGGCG-TA
* * * *
390215 ATGTAAAAAACGCCGCAAAATTTCTTAACTAAAACGCAGTGTTTGGTCT
65 AT-TAAAAAACGCCGCAAAATATCTTAACAAAAACGCAGCGTTTGGTAT
* * * *
390264 TCAGGCATATTAAAATTAGTGGCACTTAT-GAAAATCGCCGCTAAAGCACAGTATTAGCGGCGTA
1 TGAGGTATATTAGAATTAGTGGCGCTTATAGAAAA-CGCCGCTAAAGCACAGTATTAGCGGCGTA
* ** *
390328 ATAAAAAAAGCGCCGCAAAATATCTTAACCGAAACGCAGCGTTTGGTCT
65 ATTAAAAAA-CGCCGCAAAATATCTTAACAAAAACGCAGCGTTTGGTAT
*
390377 TTAGGTATA
1 TGAGGTATA
390386 GAGCCAATAG
Statistics
Matches: 198, Mismatches: 32, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
112 12 0.06
113 100 0.51
114 21 0.11
115 64 0.32
116 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.26
Consensus pattern (112 bp):
TGAGGTATATTAGAATTAGTGGCGCTTATAGAAAACGCCGCTAAAGCACAGTATTAGCGGCGTAA
TTAAAAAACGCCGCAAAATATCTTAACAAAAACGCAGCGTTTGGTAT
Found at i:391160 original size:22 final size:21
Alignment explanation
Indices: 391126--391168 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
391116 TGGTGGTTGT
* *
391126 TGTTTGTGGTTTACGAGTTTAA
1 TGTTTATGATTTA-GAGTTTAA
*
391148 TGTTTATGATTTAGGGTTTAA
1 TGTTTATGATTTAGAGTTTAA
391169 GATTTACGGT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.21, C:0.02, G:0.26, T:0.51
Consensus pattern (21 bp):
TGTTTATGATTTAGAGTTTAA
Found at i:391281 original size:14 final size:14
Alignment explanation
Indices: 391264--391312 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 14
391254 CAGGGGTTAA
* *
391264 GGTTTACAGTTTGG
1 GGTTTATAGTTTAG
* *
391278 GGTTTGTGGTTTAG
1 GGTTTATAGTTTAG
391292 GGTTTATAGTTTAG
1 GGTTTATAGTTTAG
391306 GGTTTAT
1 GGTTTAT
391313 GATTTACGGT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.14, C:0.02, G:0.35, T:0.49
Consensus pattern (14 bp):
GGTTTATAGTTTAG
Found at i:391318 original size:14 final size:14
Alignment explanation
Indices: 391277--391323 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
391267 TTACAGTTTG
* *
391277 GGGTTTGTGGTTTA
1 GGGTTTATGATTTA
391291 GGGTTTAT-AGTTTA
1 GGGTTTATGA-TTTA
391305 GGGTTTATGATTTA
1 GGGTTTATGATTTA
*
391319 CGGTT
1 GGGTT
391324 AAGGCTTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
14 27 0.96
15 1 0.04
ACGTcount: A:0.15, C:0.02, G:0.34, T:0.49
Consensus pattern (14 bp):
GGGTTTATGATTTA
Found at i:391318 original size:28 final size:28
Alignment explanation
Indices: 391264--391323 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
391254 CAGGGGTTAA
* * * *
391264 GGTTTACAGTTTGGGGTTTGTGGTTTAG
1 GGTTTACAGTTTAGGGTTTATGATTTAC
*
391292 GGTTTATAGTTTAGGGTTTATGATTTAC
1 GGTTTACAGTTTAGGGTTTATGATTTAC
391320 GGTT
1 GGTT
391324 AAGGCTTATA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.15, C:0.03, G:0.33, T:0.48
Consensus pattern (28 bp):
GGTTTACAGTTTAGGGTTTATGATTTAC
Found at i:391469 original size:15 final size:16
Alignment explanation
Indices: 391449--391484 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
391439 TATTTAAAAG
*
391449 AATATAAATGTAAA-T
1 AATATAAATATAAATT
391464 AATATAAATATAAATT
1 AATATAAATATAAATT
391480 AATAT
1 AATAT
391485 TTAAAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (16 bp):
AATATAAATATAAATT
Found at i:392513 original size:18 final size:18
Alignment explanation
Indices: 392490--392524 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
392480 TTTCTAGGGT
*
392490 TTGCCTCTGTCGATTACG
1 TTGCCTCTGCCGATTACG
392508 TTGCCTCTGCCGATTAC
1 TTGCCTCTGCCGATTAC
392525 TAAGGGCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.11, C:0.31, G:0.20, T:0.37
Consensus pattern (18 bp):
TTGCCTCTGCCGATTACG
Found at i:392791 original size:12 final size:13
Alignment explanation
Indices: 392759--392805 Score: 87
Period size: 13 Copynumber: 3.7 Consensus size: 13
392749 ATACAAATTG
392759 CTGAATGAATTTT
1 CTGAATGAATTTT
392772 CTGAATGAATTTT
1 CTGAATGAATTTT
392785 C-GAATGAATTTT
1 CTGAATGAATTTT
392797 CTGAATGAA
1 CTGAATGAA
392806 GTTTATTTAG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.36
13 21 0.64
ACGTcount: A:0.34, C:0.09, G:0.17, T:0.40
Consensus pattern (13 bp):
CTGAATGAATTTT
Found at i:396861 original size:21 final size:21
Alignment explanation
Indices: 396837--396887 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
396827 CTACAACTTA
*
396837 AAGCAGAGGCAGCAACGAGGG
1 AAGCAGAGGCAGCAACGAGAG
* *
396858 AAGCAGAGGCTGCAGCGAGAG
1 AAGCAGAGGCAGCAACGAGAG
396879 AAGCAGAGG
1 AAGCAGAGG
396888 TTCAAAAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.37, C:0.18, G:0.43, T:0.02
Consensus pattern (21 bp):
AAGCAGAGGCAGCAACGAGAG
Found at i:397381 original size:41 final size:41
Alignment explanation
Indices: 397254--397426 Score: 204
Period size: 42 Copynumber: 4.2 Consensus size: 41
397244 AATCCCAAAA
* *
397254 TTAGTGGCGTTTTTATAAAAGCGCCGCTAAAGAACATGACCT
1 TTAGCGGCGTTTTTAT-TAAGCGCCGCTAAAGAACATGACCT
* ** ** *
397296 TTAACGGCGTTTCCAAGAAAGCGCTGCTAAAGAACATGACCT
1 TTAGCGGCGTTT-TTATTAAGCGCCGCTAAAGAACATGACCT
* * *
397338 TTAGCGGCGTTTTTTTTATGCGCCGCTAAAGAACATGATCT
1 TTAGCGGCGTTTTTATTAAGCGCCGCTAAAGAACATGACCT
* *
397379 TTAGCGGTG-TTTTCTTAAGCGCCGCTAAAGAACATGACCT
1 TTAGCGGCGTTTTTATTAAGCGCCGCTAAAGAACATGACCT
397419 TTAGCGGC
1 TTAGCGGC
397427 ATTTATTTCT
Statistics
Matches: 110, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
40 35 0.32
41 29 0.26
42 45 0.41
43 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (41 bp):
TTAGCGGCGTTTTTATTAAGCGCCGCTAAAGAACATGACCT
Found at i:397412 original size:40 final size:40
Alignment explanation
Indices: 397272--397426 Score: 202
Period size: 40 Copynumber: 3.8 Consensus size: 40
397262 GTTTTTATAA
* * **
397272 AAGCGCCGCTAAAGAACATGACCTTTAACGGCGTTTCCAAGA
1 AAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTC--TT
* *
397314 AAGCGCTGCTAAAGAACATGACCTTTAGCGGCGTTTTTTTT
1 AAGCGCCGCTAAAGAACATGACCTTTAGCGGCG-TTTTCTT
* * *
397355 ATGCGCCGCTAAAGAACATGATCTTTAGCGGTGTTTTCTT
1 AAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTCTT
397395 AAGCGCCGCTAAAGAACATGACCTTTAGCGGC
1 AAGCGCCGCTAAAGAACATGACCTTTAGCGGC
397427 ATTTATTTCT
Statistics
Matches: 98, Mismatches: 14, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
40 35 0.36
41 29 0.30
42 31 0.32
43 3 0.03
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (40 bp):
AAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTCTT
Found at i:398088 original size:28 final size:28
Alignment explanation
Indices: 398048--398105 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
398038 TTTGCATCAC
398048 CTATTCCAGGTAATTTGTTCATTATTTT
1 CTATTCCAGGTAATTTGTTCATTATTTT
398076 CTATTCCAGGTAATTTGTTCATTATTTT
1 CTATTCCAGGTAATTTGTTCATTATTTT
398104 CT
1 CT
398106 CTTATTTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.21, C:0.16, G:0.10, T:0.53
Consensus pattern (28 bp):
CTATTCCAGGTAATTTGTTCATTATTTT
Found at i:399025 original size:122 final size:121
Alignment explanation
Indices: 398753--399044 Score: 505
Period size: 122 Copynumber: 2.4 Consensus size: 121
398743 TAATCATATC
398753 TTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTA
1 TTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTA
*
398818 GATATTCTTAATATTAAATTACTAAAACCATAATATATAATACTATAAAATATAAT
66 GATATTCTTAATATGAAATTACTAAAACCATAATATATAATACTATAAAATATAAT
398874 TTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTA
1 TTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT-
* * *
398939 AATATATTCTT-ATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAAT
65 -AGATATTCTTAATATGAAATTACTAAAACCATAATATATAATACTATAAAATATAAT
* *
398996 TTAAAATAATTTTTATTAAATATAATTTAATAAAAATATATAATTTAAT
1 TTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAAT
399045 CTAAAGTTTT
Statistics
Matches: 163, Mismatches: 6, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
121 64 0.39
122 90 0.55
123 9 0.06
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (121 bp):
TTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTA
GATATTCTTAATATGAAATTACTAAAACCATAATATATAATACTATAAAATATAAT
Found at i:399198 original size:27 final size:28
Alignment explanation
Indices: 399168--399226 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 28
399158 TAAATATAGT
*
399168 AATG-AAGAATTTATAGTATACGATTAA
1 AATGCAAGAATTTATAGTATACAATTAA
*
399195 AATGCTAATAATTTATAGTATACAATTAA
1 AATGC-AAGAATTTATAGTATACAATTAA
399224 AAT
1 AAT
399227 ATTATAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 4 0.14
29 24 0.86
ACGTcount: A:0.49, C:0.05, G:0.10, T:0.36
Consensus pattern (28 bp):
AATGCAAGAATTTATAGTATACAATTAA
Found at i:399279 original size:21 final size:20
Alignment explanation
Indices: 399229--399279 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
399219 ATTAAAATAT
*
399229 TATAAATAAAATATATTAAA
1 TATAAATAAAATAAATTAAA
* *
399249 TGATATATAAGATAAATTAACA
1 T-ATAAATAAAATAAATTAA-A
399271 TATAAATAA
1 TATAAATAA
399280 TTCATATATT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 1 0.04
21 22 0.88
22 2 0.08
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (20 bp):
TATAAATAAAATAAATTAAA
Done.