Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015294.1 Kokia drynarioides strain JFW-HI SEQ_130339, 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: 417562
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 148 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:328123 original size:29 final size:29
Alignment explanation
Indices: 328063--328138 Score: 82
Period size: 29 Copynumber: 2.7 Consensus size: 29
328053 AACGGAGTCA
* *
328063 AAAAT-ATGATTTTTGGATGCCCGGGGGT
1 AAAATGATGATTTTTGGATGCCCGGAGGC
**
328091 AAAATGATGATTTTTGGATGTTCGGAGGC
1 AAAATGATGATTTTTGGATGCCCGGAGGC
* * *
328120 AAAAGGGTAATTTTTGGAT
1 AAAATGATGATTTTTGGAT
328139 ACTTGGGGGT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
28 5 0.12
29 35 0.88
ACGTcount: A:0.29, C:0.07, G:0.30, T:0.34
Consensus pattern (29 bp):
AAAATGATGATTTTTGGATGCCCGGAGGC
Found at i:328220 original size:88 final size:87
Alignment explanation
Indices: 328150--328310 Score: 211
Period size: 88 Copynumber: 1.8 Consensus size: 87
328140 CTTGGGGGTG
* * *
328150 AAAATGGTAATTTTT-GAACACTCAAGG-GAAAATGTGAC-TTTTGGAAGTTTGGGGGGGTAAAA
1 AAAATGGTAATTTTTGGAAAACTCAAGGTGAAAA-ATGACATTTTGGAAGTTT--AGGGGTAAAA
*
328212 TGGTAATTTTTAGAAGTTCGAGAGC
63 TGGTAATTTTTAGAACTTCGAGAGC
* *
328237 AAAATGGTAATTTTTGGAAAACTCGAGGTTAAAAATGACATTTTTGGAAGTTTAGGGGTAAAATG
1 AAAATGGTAATTTTTGGAAAACTCAAGGTGAAAAATGACA-TTTTGGAAGTTTAGGGGTAAAATG
328302 GTAATTTTT
65 GTAATTTTT
328311 TAAGGTTTAG
Statistics
Matches: 65, Mismatches: 5, Indels: 7
0.84 0.06 0.09
Matches are distributed among these distances:
87 15 0.23
88 34 0.52
89 4 0.06
90 12 0.18
ACGTcount: A:0.35, C:0.06, G:0.26, T:0.34
Consensus pattern (87 bp):
AAAATGGTAATTTTTGGAAAACTCAAGGTGAAAAATGACATTTTGGAAGTTTAGGGGTAAAATGG
TAATTTTTAGAACTTCGAGAGC
Found at i:328311 original size:30 final size:29
Alignment explanation
Indices: 328276--328589 Score: 165
Period size: 29 Copynumber: 10.8 Consensus size: 29
328266 TAAAAATGAC
*
328276 ATTTTTGGAAGTTTAGGGGTAAAATGGTA
1 ATTTTTGAAAGTTTAGGGGTAAAATGGTA
* * **
328305 ATTTTTTAAGGTTTA-GGG-AAAAAAGT-
1 ATTTTTGAAAGTTTAGGGGTAAAATGGTA
*
328331 ATTTTTGAAAG-TTCGAGGGTAAAATGGTA
1 ATTTTTGAAAGTTTAG-GGGTAAAATGGTA
*
328360 ATTTTT-AGAAG-TTCGAGGGTAAAAAT-GTGA
1 ATTTTTGA-AAGTTTAG-GGGT-AAAATGGT-A
* * * *
328390 TTTTTTGCAAGTTCTA-GGGAAAAATGGCA
1 ATTTTTGAAAGTT-TAGGGGTAAAATGGTA
* *
328419 ATTTTTGAAAGTTT-GGGGTAAAAAT-ATG
1 ATTTTTGAAAGTTTAGGGGT-AAAATGGTA
** * *
328447 ATTTTTAGAAAGTTCGGGGGCAAAATGATA
1 ATTTTT-GAAAGTTTAGGGGTAAAATGGTA
* * *
328477 ATTTTTGAAAG-TTCGAGAGTAAAAAT-GCA
1 ATTTTTGAAAGTTTAG-GGGT-AAAATGGTA
*
328506 ATTTTTGGAAAGTTCTA-GGGTAAAAT-ATA
1 ATTTTT-GAAAGTT-TAGGGGTAAAATGGTA
*
328535 ATTTTTGTAAAGTTTA-GGGTCAAAAT-ATA
1 ATTTTTG-AAAGTTTAGGGGT-AAAATGGTA
*
328564 ATTTTTGGAAAGATTAGGGGTCAAAA
1 ATTTTT-GAAAGTTTAGGGGT-AAAA
328590 CGTGATTTTT
Statistics
Matches: 225, Mismatches: 35, Indels: 49
0.73 0.11 0.16
Matches are distributed among these distances:
25 2 0.01
26 9 0.04
27 9 0.04
28 29 0.13
29 119 0.53
30 53 0.24
31 2 0.01
32 2 0.01
ACGTcount: A:0.36, C:0.04, G:0.25, T:0.35
Consensus pattern (29 bp):
ATTTTTGAAAGTTTAGGGGTAAAATGGTA
Found at i:328416 original size:59 final size:59
Alignment explanation
Indices: 328237--328575 Score: 293
Period size: 59 Copynumber: 5.8 Consensus size: 59
328227 GTTCGAGAGC
** * ** *
328237 AAAATGGTAATTTTTGGAAAACTCGAGGTTAAAAATGACA-TTTTTGGAAGTT-TAGGGGT
1 AAAATGGTAATTTTT-GAAAGTTCGAGGGTAAAAATGTGATTTTTTGAAAGTTCTA-GGGT
* * * * *
328296 AAAATGGTAATTTTTTAAGGTT-TAGGG-AAAAAAGT-A-TTTTTGAAAGTTCGAGGGT
1 AAAATGGTAATTTTTGAAAGTTCGAGGGTAAAAATGTGATTTTTTGAAAGTTCTAGGGT
* *
328351 AAAATGGTAATTTTT-AGAAGTTCGAGGGTAAAAATGTGATTTTTTGCAAGTTCTAGGGA
1 AAAATGGTAATTTTTGA-AAGTTCGAGGGTAAAAATGTGATTTTTTGAAAGTTCTAGGGT
* * * * ** *
328410 AAAATGGCAATTTTTGAAAGTTTG-GGGTAAAAATATGATTTTTAGAAAGTTCGGGGGC
1 AAAATGGTAATTTTTGAAAGTTCGAGGGTAAAAATGTGATTTTTTGAAAGTTCTAGGGT
* * ** *
328468 AAAATGATAATTTTTGAAAGTTCGAGAGTAAAAATGCAATTTTTGGAAAGTTCTAGGGT
1 AAAATGGTAATTTTTGAAAGTTCGAGGGTAAAAATGTGATTTTTTGAAAGTTCTAGGGT
* * * * * *
328527 AAAAT-ATAATTTTTGTAAAGTT-TAGGGTCAAAATATAATTTTTGGAAAG
1 AAAATGGTAATTTTTG-AAAGTTCGAGGGTAAAAATGTGATTTTTTGAAAG
328576 ATTAGGGGTC
Statistics
Matches: 231, Mismatches: 40, Indels: 19
0.80 0.14 0.07
Matches are distributed among these distances:
54 1 0.00
55 35 0.15
56 11 0.05
57 10 0.04
58 85 0.37
59 88 0.38
60 1 0.00
ACGTcount: A:0.37, C:0.04, G:0.24, T:0.35
Consensus pattern (59 bp):
AAAATGGTAATTTTTGAAAGTTCGAGGGTAAAAATGTGATTTTTTGAAAGTTCTAGGGT
Found at i:328598 original size:30 final size:29
Alignment explanation
Indices: 328505--328599 Score: 102
Period size: 29 Copynumber: 3.2 Consensus size: 29
328495 GTAAAAATGC
* *
328505 AATTTTTGGAAAGTTCTAGGGT-AAAATAT
1 AATTTTTGGAAAGAT-TAGGGTCAAAACAT
* * *
328534 AATTTTTGTAAAGTTTAGGGTCAAAATAT
1 AATTTTTGGAAAGATTAGGGTCAAAACAT
*
328563 AATTTTTGGAAAGATTAGGGGTCAAAACGT
1 AATTTTTGGAAAGATTA-GGGTCAAAACAT
*
328593 GATTTTT
1 AATTTTT
328600 TAATAGTTTA
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
28 6 0.10
29 36 0.62
30 16 0.28
ACGTcount: A:0.36, C:0.04, G:0.21, T:0.39
Consensus pattern (29 bp):
AATTTTTGGAAAGATTAGGGTCAAAACAT
Found at i:328598 original size:117 final size:112
Alignment explanation
Indices: 328266--328599 Score: 331
Period size: 117 Copynumber: 2.9 Consensus size: 112
328256 AACTCGAGGT
* *
328266 TAAAAATGACATTTTTGGAAGTT-TAGGGGTAAAATGGTAATTTTT-TAAGGTTTAGGG-AAAAA
1 TAAAAATGA-ATTTTTGGAAGTTCTA-GGGTAAAATGGTAATTTTTGTAAAGTTTAGGGTAAAAT
* *
328328 AGTATTTTTGAAAGTTCGAGGGT-AAAATGGTAATTTTTAGAAGTTCGAGGG
64 A-TATTTTTGAAAGTTCG-GGGTCAAAA-CGTAATTTTTAGAAGTTCGAGAG
* * * * *
328379 TAAAAATGTGATTTTTTGCAAGTTCTAGGGAAAAATGGCAATTTTTG-AAAGTTTGGGGTAAAAA
1 TAAAAA--TGAATTTTTGGAAGTTCTAGGGTAAAATGGTAATTTTTGTAAAGTTTAGGGT-AAAA
* *
328443 TATGATTTTTAGAAAGTTCGGGGGCAAAATGATAATTTTT-GAAAGTTCGAGAG
63 TAT-ATTTTT-GAAAGTTCGGGGTCAAAACG-TAATTTTTAG-AAGTTCGAGAG
*
328496 TAAAAATGCAATTTTTGGAAAGTTCTAGGGTAAAAT-ATAATTTTTGTAAAGTTTAGGGTCAAAA
1 TAAAAATG-AATTTTTGG-AAGTTCTAGGGTAAAATGGTAATTTTTGTAAAGTTTAGGGT-AAAA
* *
328560 TATAATTTTTGGAAAGATTAGGGGTCAAAACGTGATTTTT
63 TAT-ATTTTT-GAAAG-TTCGGGGTCAAAACGTAATTTTT
328600 TAATAGTTTA
Statistics
Matches: 183, Mismatches: 23, Indels: 26
0.79 0.10 0.11
Matches are distributed among these distances:
113 6 0.03
114 37 0.20
115 8 0.04
116 31 0.17
117 89 0.49
118 12 0.07
ACGTcount: A:0.36, C:0.04, G:0.24, T:0.36
Consensus pattern (112 bp):
TAAAAATGAATTTTTGGAAGTTCTAGGGTAAAATGGTAATTTTTGTAAAGTTTAGGGTAAAATAT
ATTTTTGAAAGTTCGGGGTCAAAACGTAATTTTTAGAAGTTCGAGAG
Found at i:330459 original size:6 final size:6
Alignment explanation
Indices: 330448--330508 Score: 56
Period size: 6 Copynumber: 10.7 Consensus size: 6
330438 AAATTGAAAA
* * * *
330448 TAAATT TAAATT TAAA-A TAAATT TAAATT TAAA-A TAATTT TAAACT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
*
330494 TAAA-A TAAATT TAAA
1 TAAATT TAAATT TAAA
330509 AATTGAGTTT
Statistics
Matches: 43, Mismatches: 9, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
5 11 0.26
6 32 0.74
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (6 bp):
TAAATT
Found at i:330464 original size:17 final size:17
Alignment explanation
Indices: 330438--330508 Score: 115
Period size: 17 Copynumber: 4.2 Consensus size: 17
330428 TTCAAATTGA
*
330438 AAATTGAAAATAAATTT
1 AAATTTAAAATAAATTT
330455 AAATTTAAAATAAATTT
1 AAATTTAAAATAAATTT
*
330472 AAATTTAAAATAATTTT
1 AAATTTAAAATAAATTT
*
330489 AAACTTAAAATAAATTT
1 AAATTTAAAATAAATTT
330506 AAA
1 AAA
330509 AATTGAGTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 50 1.00
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (17 bp):
AAATTTAAAATAAATTT
Found at i:341738 original size:16 final size:16
Alignment explanation
Indices: 341698--341731 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
341688 GGATTGAGAT
341698 AGCAAAGTGTTCAACA
1 AGCAAAGTGTTCAACA
341714 AGCAAAGTGTTCAACA
1 AGCAAAGTGTTCAACA
341730 AG
1 AG
341732 TTAAGTGAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.44, C:0.18, G:0.21, T:0.18
Consensus pattern (16 bp):
AGCAAAGTGTTCAACA
Found at i:347981 original size:49 final size:48
Alignment explanation
Indices: 347917--348010 Score: 145
Period size: 49 Copynumber: 1.9 Consensus size: 48
347907 TTATGAAAAC
347917 AATTTTGAAAACAAACATGCGACTTTAATA-TGAATTTTGGATTTTTAGT
1 AATTTTGAAAACAAACATGCGACTTT-ATAGT-AATTTTGGATTTTTAGT
* *
347966 AATTTTGAAAACAAACATGCGAGTTTTTAGTAATTTTGGATTTTT
1 AATTTTGAAAACAAACATGCGACTTTATAGTAATTTTGGATTTTT
348011 GGGGGTAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
48 16 0.38
49 26 0.62
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.43
Consensus pattern (48 bp):
AATTTTGAAAACAAACATGCGACTTTATAGTAATTTTGGATTTTTAGT
Found at i:348113 original size:29 final size:29
Alignment explanation
Indices: 348072--348384 Score: 332
Period size: 29 Copynumber: 10.8 Consensus size: 29
348062 AGACATTCTA
* *
348072 GGGT-AAAAGGGAATTTTTGGAAGTTTTG
1 GGGTAAAAATGGAATTTTTGGAAGTTTCG
*
348100 GGGTCAAAATGGAATTTTTGGAAG-TTCGG
1 GGGTAAAAATGGAATTTTTGGAAGTTTC-G
*
348129 GGGTAAAAATGGAATTTTTGGAAGTTTAG
1 GGGTAAAAATGGAATTTTTGGAAGTTTCG
* * * * *
348158 AGGTCAAAATGGAATTTTTAGATGTTTTG
1 GGGTAAAAATGGAATTTTTGGAAGTTTCG
* *
348187 AGGTCGAAAATGGAATTTTTGGAAG-TTCAG
1 GGGT-AAAAATGGAATTTTTGGAAGTTTC-G
* * * *
348217 AGGTAAAAATGAAATTTTTGAAAGTTTCA
1 GGGTAAAAATGGAATTTTTGGAAGTTTCG
* *
348246 GGGTCAAATATGAAATTTTTGGAAG-TTCG
1 GGGT-AAAAATGGAATTTTTGGAAGTTTCG
348275 AGGGT-AAAATGGAATTTTTGGAAGTTTCG
1 -GGGTAAAAATGGAATTTTTGGAAGTTTCG
* **
348304 AGGTTAAAAATGGAATTTTTTAAAGTTTCG
1 -GGGTAAAAATGGAATTTTTGGAAGTTTCG
*
348334 GGATAAAAATGGAATTTTTGGAAG-TTCGG
1 GGGTAAAAATGGAATTTTTGGAAGTTTC-G
348363 GGGTAAAAATGGAATTTTTGGA
1 GGGTAAAAATGGAATTTTTGGA
348385 CAGATTAGGG
Statistics
Matches: 244, Mismatches: 30, Indels: 21
0.83 0.10 0.07
Matches are distributed among these distances:
28 26 0.11
29 147 0.60
30 71 0.29
ACGTcount: A:0.34, C:0.04, G:0.28, T:0.35
Consensus pattern (29 bp):
GGGTAAAAATGGAATTTTTGGAAGTTTCG
Found at i:349533 original size:3 final size:3
Alignment explanation
Indices: 349525--349567 Score: 50
Period size: 3 Copynumber: 13.7 Consensus size: 3
349515 ACCTTTCGGC
* *
349525 TTA TTA TTA TTA TTA TTAA TTA TTA ATA ATA TTA TTAA TTA TT
1 TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TT-A TTA TT
349568 TAATAAATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
3 30 0.83
4 6 0.17
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:349549 original size:19 final size:19
Alignment explanation
Indices: 349525--349580 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 19
349515 ACCTTTCGGC
* *
349525 TTATTATTATTATTATTAA
1 TTATTAATAATATTATTAA
349544 TTATTAATAATATTATTAA
1 TTATTAATAATATTATTAA
349563 TTATTTAATAAATATTAT
1 TTA-TTAAT-AATATTAT
349581 CTTTAATAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 20 0.61
20 5 0.15
21 8 0.24
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TTATTAATAATATTATTAA
Found at i:350363 original size:6 final size:6
Alignment explanation
Indices: 350335--350415 Score: 82
Period size: 6 Copynumber: 14.0 Consensus size: 6
350325 CTTTATTTAT
* *
350335 TTTAAA TTTGAAA -ATAAA TTTAAA CTTAAA -TTAAA TTTAAA TTTAAA
1 TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
350382 -ATAAA TTTAAA TTTAGAA --TAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTA-AA TTTAAA TTTAAA TTTAAA
350416 AAAAAATTAA
Statistics
Matches: 63, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
4 2 0.03
5 14 0.22
6 42 0.67
7 5 0.08
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.42
Consensus pattern (6 bp):
TTTAAA
Found at i:350371 original size:17 final size:17
Alignment explanation
Indices: 350335--350443 Score: 148
Period size: 17 Copynumber: 6.4 Consensus size: 17
350325 CTTTATTTAT
350335 TTTAAATTTGAAAATAAA
1 TTTAAATTT-AAAATAAA
* *
350353 TTTAAACTTAAATTAAA
1 TTTAAATTTAAAATAAA
350370 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
*
350387 TTTAAATTTAGAATAAA
1 TTTAAATTTAAAATAAA
*
350404 TTTAAATTTAAAAAAAA
1 TTTAAATTTAAAATAAA
*
350421 ATT-AATCTTAAAATAAA
1 TTTAAAT-TTAAAATAAA
350438 TTTAAA
1 TTTAAA
350444 ATGAGTTTGG
Statistics
Matches: 79, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
16 3 0.04
17 66 0.84
18 10 0.13
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:350442 original size:11 final size:11
Alignment explanation
Indices: 350337--350445 Score: 61
Period size: 11 Copynumber: 10.1 Consensus size: 11
350327 TTATTTATTT
350337 TAAATTTGAAAA
1 TAAATTT-AAAA
*
350349 TAAATTTAAACT
1 TAAATTTAAA-A
*
350361 TAAA-TTAAATT
1 TAAATTTAAA-A
350372 TAAATTTAAAA
1 TAAATTTAAAA
350383 TAAA-TT----
1 TAAATTTAAAA
*
350389 TAAATTTAGAA
1 TAAATTTAAAA
*
350400 TAAATTTAAATT
1 TAAATTTAAA-A
**
350412 TAAA-AAAAAA
1 TAAATTTAAAA
*
350422 TTAATCTTAAAA
1 TAAAT-TTAAAA
350434 TAAATTTAAAA
1 TAAATTTAAAA
350445 T
1 T
350446 GAGTTTGGGC
Statistics
Matches: 75, Mismatches: 12, Indels: 21
0.69 0.11 0.19
Matches are distributed among these distances:
6 4 0.05
7 2 0.03
10 5 0.07
11 36 0.48
12 28 0.37
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:351157 original size:205 final size:205
Alignment explanation
Indices: 350848--351829 Score: 1320
Period size: 205 Copynumber: 4.8 Consensus size: 205
350838 GGAAGATGGT
* * * * * * * * *
350848 TTTGGTTCACTTCCCCGTATTTCGTCA-GAAAGCTAACCATTTAATTACTTTGACTTGCTTCTCA
1 TTTGGTCCACTTCTCAGTATCTCATCAGGAAA-CTAACC-TTTTATTGCTTCGACCTGCTTCTCA
* *
350912 GTATCTCATCAGGAAGCTGGGGTTCGAGGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTT
64 GTATCTCATCAGGAAGCTGGGGTTCGAAGATTTACTCACATCGAGCGTGGGTTTGATTTGGTCTT
* * * *
350977 CTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGCTTCAATTCGCTTCTTTGTATCTCAT
129 CTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTCGCTTCAATCCGCTTCTCTGTACCTCAT
* *
351042 CAAGAAGATGAA
194 CAGGAAGACGAA
* *** * * *
351054 TTTGGTCCACTTCTCAGTACCTCATCAGGAAACTAACCTTTTATTGCTAAAACTTGCTGCTTAG-
1 TTTGGTCCACTTCTCAGTATCTCATCAGGAAACTAACCTTTTATTGCTTCGACCTGCTTCTCAGT
* *
351118 AGTCTCATCAGGAAGCTGGGGTTCGAAGGTTTACTCACATCGAGCATGGGTTTGATTTGGTCTTC
66 A-TCTCATCAGGAAGCTGGGGTTCGAAGATTTACTCACATCGAGCGTGGGTTTGATTTGGTCTTC
* *
351183 TTCTCAGTATCTCATCAGGAAGATGGCCGCGTCGTTCGCTTCAATCCGTTTCTCTGTACCTCATC
130 TTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTCGCTTCAATCCGCTTCTCTGTACCTCATC
351248 AGGAAGACGAA
195 AGGAAGACGAA
* *
351259 TTTGGTCCACTTCTCAGTATCTCATCAAGAAACTAACCTTTTATTGCTTCGACTTGCTTCTCAGT
1 TTTGGTCCACTTCTCAGTATCTCATCAGGAAACTAACCTTTTATTGCTTCGACCTGCTTCTCAGT
* * *
351324 ATCTCATCAAGAAGCTGGGATTCGAAGATTTACTCACATCAAGCGTGGGTTTGATTTGGTCTTCT
66 ATCTCATCAGGAAGCTGGGGTTCGAAGATTTACTCACATCGAGCGTGGGTTTGATTTGGTCTTCT
* * * *
351389 TCTCAGTATCTCATCAGGAAGATGATCGCGTCATTCGCTTTAATTCGCTTCTCTGTACCTCATCA
131 TCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTCGCTTCAATCCGCTTCTCTGTACCTCATCA
*
351454 GGAAGACGAT
196 GGAAGACGAA
* *
351464 TTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAAT
1 TTTGGTCCACTTCTCAGTATCTCATCAGGAAACTAACCTTTTATTGCTTCGACCTGCTTCTCAGT
* * ** *
351529 ATCTCATCAGGAAGCTGGGATTCGAAGATTTACTCACATCAAGCGTAAGTTTGATTTGGTCATCT
66 ATCTCATCAGGAAGCTGGGGTTCGAAGATTTACTCACATCGAGCGTGGGTTTGATTTGGTCTTCT
* * * * * *
351594 TCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCCGCTTCTTTATATCTCATCA
131 TCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTCGCTTCAATCCGCTTCTCTGTACCTCATCA
351659 GGAAGACGAA
196 GGAAGACGAA
* *
351669 TTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTGACCATTTTATTGCTTCGACCTGCTTCTCAG
1 TTTGGTCCACTTCTCAGTATCTCATCAGGAAACTAACC-TTTTATTGCTTCGACCTGCTTCTCAG
* ** * * * * * **
351734 TATCTCATCAGGAAGCTAGGGTTTAAAGATTTGCTCGCTTTGAGCCTCGTTTCATTGATTTGGTC
65 TATCTCATCAGGAAGCTGGGGTTCGAAGATTTACTCACATCGAGCGT-GGGT--TTGATTTGGTC
351799 TTCTTCTCAGTATCTCATCAGGAAGATGACC
127 TTCTTCTCAGTATCTCATCAGGAAGATGACC
351830 ACATCGCTAT
Statistics
Matches: 690, Mismatches: 79, Indels: 11
0.88 0.10 0.01
Matches are distributed among these distances:
204 1 0.00
205 553 0.80
206 90 0.13
207 5 0.01
209 41 0.06
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (205 bp):
TTTGGTCCACTTCTCAGTATCTCATCAGGAAACTAACCTTTTATTGCTTCGACCTGCTTCTCAGT
ATCTCATCAGGAAGCTGGGGTTCGAAGATTTACTCACATCGAGCGTGGGTTTGATTTGGTCTTCT
TCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTCGCTTCAATCCGCTTCTCTGTACCTCATCA
GGAAGACGAA
Found at i:361039 original size:29 final size:29
Alignment explanation
Indices: 360997--361055 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
360987 CTTAAAACCG
360997 ACAAAGGTGCATATCCGGTTGCTCCCCAT
1 ACAAAGGTGCATATCCGGTTGCTCCCCAT
361026 ACAAAGGTGCATATCCGGTTGCTCCCCAT
1 ACAAAGGTGCATATCCGGTTGCTCCCCAT
361055 A
1 A
361056 TTCCTGCCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.24
Consensus pattern (29 bp):
ACAAAGGTGCATATCCGGTTGCTCCCCAT
Found at i:363645 original size:30 final size:30
Alignment explanation
Indices: 363611--363908 Score: 204
Period size: 29 Copynumber: 10.2 Consensus size: 30
363601 GGAAAATGGT
* * *
363611 AATTTTGGGAAAATTCGAGGTTAAAAAGGG
1 AATTTTTGGAAGATTCGAGGTCAAAAAGGG
* * *
363641 AATTTTTAG-ACATTCAAGGGT--AAAAGGG
1 AATTTTTGGAAGATTCGA-GGTCAAAAAGGG
* *
363669 AATTTTTGGAAGTTTCGAGGTCAAAAATGG
1 AATTTTTGGAAGATTCGAGGTCAAAAAGGG
* * *
363699 AATTTTTGGAAGTTTCGGGGTCAAAAATGG
1 AATTTTTGGAAGATTCGAGGTCAAAAAGGG
* * * * *
363729 AATTTTTAGAAGTTTAGGGGTC--AAATGG
1 AATTTTTGGAAGATTCGAGGTCAAAAAGGG
* * *
363757 AATTTTTGGAAGTTTGGAGGT-AAAAATGG
1 AATTTTTGGAAGATTCGAGGTCAAAAAGGG
* * * * * *
363786 AATTTTTGAAAGTTTTGGGGTTAAAAATGG
1 AATTTTTGGAAGATTCGAGGTCAAAAAGGG
* *
363816 AATTTTTGGAAG-TTCGGGGGT-AAAAATGG
1 AATTTTTGGAAGATTC-GAGGTCAAAAAGGG
* * * *
363845 AATTTTTGAAAGTTTCGGGGT-AAAAATGG
1 AATTTTTGGAAGATTCGAGGTCAAAAAGGG
*
363874 AATTTTTGGAAG-TTCGAGGGT-AAAAATGG
1 AATTTTTGGAAGATTCGA-GGTCAAAAAGGG
363903 AATTTT
1 AATTTT
363909 AGGACAAATT
Statistics
Matches: 235, Mismatches: 23, Indels: 21
0.84 0.08 0.08
Matches are distributed among these distances:
28 46 0.20
29 97 0.41
30 92 0.39
ACGTcount: A:0.34, C:0.04, G:0.29, T:0.34
Consensus pattern (30 bp):
AATTTTTGGAAGATTCGAGGTCAAAAAGGG
Found at i:363686 original size:58 final size:58
Alignment explanation
Indices: 363624--363908 Score: 337
Period size: 58 Copynumber: 4.9 Consensus size: 58
363614 TTTGGGAAAA
* * ** * *
363624 TTCGAGGTTAAAAAGGGAATTTTTAGACA-TTCAAGGGT-AAAAGGGAATTTTTGGAAGT
1 TTCG-GGTTAAAAATGGAATTTTTGGA-AGTTCGGGGGTAAAAATGGAATTTTTGAAAGT
*
363682 TTCGAGGTCAAAAATGGAATTTTTGGAAGTTTC-GGGGTCAAAAATGGAATTTTT-AGAAGT
1 TTCG-GGTTAAAAATGGAATTTTTGGAAG-TTCGGGGGT-AAAAATGGAATTTTTGA-AAGT
* * * * *
363742 TTAGGGGT-CAAATGGAATTTTTGGAAGTTTGGAGGTAAAAATGGAATTTTTGAAAGTT
1 TTCGGGTTAAAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGAAAG-T
*
363800 TTGGGGTTAAAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGAAAGT
1 TTCGGGTTAAAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGAAAGT
* *
363858 TTCGGGGTAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTT
1 TTCGGGTTAAAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTT
363909 AGGACAAATT
Statistics
Matches: 198, Mismatches: 20, Indels: 18
0.84 0.08 0.08
Matches are distributed among these distances:
57 21 0.11
58 107 0.54
59 50 0.25
60 20 0.10
ACGTcount: A:0.34, C:0.04, G:0.29, T:0.34
Consensus pattern (58 bp):
TTCGGGTTAAAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGAAAGT
Found at i:365872 original size:37 final size:36
Alignment explanation
Indices: 365823--365908 Score: 120
Period size: 37 Copynumber: 2.4 Consensus size: 36
365813 TTTTAAATTT
*
365823 ATAATAATTTTAAATTTGAAAAAAAATTTAAGCTTAA
1 ATAATAAATTTAAATTTGAAAAAAAATTTAAGCTT-A
* * *
365860 ATAATAAATTTAAATTTTAAAACAAATTTAATCTTA
1 ATAATAAATTTAAATTTGAAAAAAAATTTAAGCTTA
365896 A-AATAAATTTAAA
1 ATAATAAATTTAAA
365909 ATGAGTTTGG
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
35 12 0.27
36 2 0.04
37 31 0.69
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.38
Consensus pattern (36 bp):
ATAATAAATTTAAATTTGAAAAAAAATTTAAGCTTA
Found at i:365888 original size:18 final size:18
Alignment explanation
Indices: 365814--365908 Score: 86
Period size: 18 Copynumber: 5.3 Consensus size: 18
365804 CTTTATTTAT
* *
365814 TTTAAA-TTTATAATAAT
1 TTTAAATTTTAAAATAAA
* *
365831 TTTAAATTTGAAAAAAAA
1 TTTAAATTTTAAAATAAA
** *
365849 TTTAAGCTTAAATAATAAA
1 TTTAAATTTTAA-AATAAA
*
365868 TTTAAATTTTAAAACAAA
1 TTTAAATTTTAAAATAAA
*
365886 TTT-AATCTTAAAATAAA
1 TTTAAATTTTAAAATAAA
365903 TTTAAA
1 TTTAAA
365909 ATGAGTTTGG
Statistics
Matches: 61, Mismatches: 14, Indels: 5
0.76 0.17 0.06
Matches are distributed among these distances:
17 21 0.34
18 26 0.43
19 14 0.23
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (18 bp):
TTTAAATTTTAAAATAAA
Found at i:365898 original size:17 final size:17
Alignment explanation
Indices: 365841--365907 Score: 71
Period size: 17 Copynumber: 3.8 Consensus size: 17
365831 TTTAAATTTG
* *
365841 AAAAAAAATTTAAGCTT
1 AAAATAAATTTAATCTT
*
365858 AAATAATAAATTTAAATTTT
1 -AA-AATAAATTT-AATCTT
*
365878 AAAACAAATTTAATCTT
1 AAAATAAATTTAATCTT
365895 AAAATAAATTTAA
1 AAAATAAATTTAA
365908 AATGAGTTTG
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
17 17 0.41
18 10 0.24
19 10 0.24
20 4 0.10
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.36
Consensus pattern (17 bp):
AAAATAAATTTAATCTT
Found at i:367951 original size:14 final size:14
Alignment explanation
Indices: 367932--367967 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
367922 GAAAAATAAT
367932 TCATTTTCCAGAAA
1 TCATTTTCCAGAAA
*
367946 TCATTTTCCGGAAA
1 TCATTTTCCAGAAA
367960 TCATTTTC
1 TCATTTTC
367968 AGTCAAACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (14 bp):
TCATTTTCCAGAAA
Found at i:368180 original size:18 final size:16
Alignment explanation
Indices: 368148--368191 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 16
368138 ATGGAATAAG
368148 AATAAATTTTTAATTA
1 AATAAATTTTTAATTA
368164 AATAAA--TTTAATTA
1 AATAAATTTTTAATTA
*
368178 ATTAAAATTTTTAA
1 AAT-AAATTTTTAA
368192 ACTCTAAACC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.42
15 3 0.12
16 6 0.25
17 5 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AATAAATTTTTAATTA
Found at i:368628 original size:161 final size:161
Alignment explanation
Indices: 368340--368656 Score: 503
Period size: 161 Copynumber: 2.0 Consensus size: 161
368330 CAAAGATTCA
*
368340 AAGATTCAATATTTTCTTCCCGTTAAGTTTGTTTGGGTTAATGGGTTTCAAATATTCAAGTTTTG
1 AAGATTCAATATTTTCTTCCCGTTAAGTTTGTTTGAGTTAATGGGTTTCAAATATTCAAGTTTTG
*
368405 AGACAGATTTATAATTAAAGATGTTAGAATCAAAAGGGGACAAGATAAAGATGAAAAAGACAAGT
66 AGACAGATTTATAATTAAAGATGTTAGAATCAAAAGGGAACAAGATAAAGATGAAAAAGACAAGT
* *
368470 GTGTAGAAATAGGTTTAGGGTTTTTTCAGTT
131 GTGTAGAAATAGGTTTAAGATTTTTTCAGTT
* *
368501 AAGATTCAATATTTTCTTCCTGTTAAGTTTTTTTGAGTTAATGGGTTTCAAATATTCAAGTTTTG
1 AAGATTCAATATTTTCTTCCCGTTAAGTTTGTTTGAGTTAATGGGTTTCAAATATTCAAGTTTTG
* * * *
368566 AGACAGATTTGTAATTAAAGATGTTGGAATC-AAAGGAGAAGAAGATGAAGAT-AAAGAAGACAA
66 AGACAGATTTATAATTAAAGATGTTAGAATCAAAAGG-GAACAAGATAAAGATGAAA-AAGACAA
*
368629 GTGTGTAGAAATGGGTTTAAGATTTTTT
129 GTGTGTAGAAATAGGTTTAAGATTTTTT
368657 TTCAGCTAAG
Statistics
Matches: 143, Mismatches: 11, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
160 8 0.06
161 135 0.94
ACGTcount: A:0.36, C:0.07, G:0.22, T:0.36
Consensus pattern (161 bp):
AAGATTCAATATTTTCTTCCCGTTAAGTTTGTTTGAGTTAATGGGTTTCAAATATTCAAGTTTTG
AGACAGATTTATAATTAAAGATGTTAGAATCAAAAGGGAACAAGATAAAGATGAAAAAGACAAGT
GTGTAGAAATAGGTTTAAGATTTTTTCAGTT
Found at i:368718 original size:16 final size:17
Alignment explanation
Indices: 368683--368722 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
368673 ATTTAAAAAT
*
368683 TTTAATTAATTAAATTTA
1 TTTAATTAA-TAAATCTA
368701 TTTAATTAA-AAATCTA
1 TTTAATTAATAAATCTA
368717 TTTAAT
1 TTTAAT
368723 CTCATTTGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 12 0.57
18 9 0.43
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTAATTAATAAATCTA
Found at i:369144 original size:19 final size:20
Alignment explanation
Indices: 369101--369150 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
369091 AATTTTGACA
369101 TAATTT-AATATTTCATTAAT
1 TAATTTAAATATTTCATT-AT
*
369121 TAATTTAAATATTTTATT-T
1 TAATTTAAATATTTCATTAT
*
369140 TAATTAAAATA
1 TAATTTAAATA
369151 ACATCATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 11 0.41
20 6 0.22
21 10 0.37
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (20 bp):
TAATTTAAATATTTCATTAT
Found at i:369146 original size:23 final size:23
Alignment explanation
Indices: 369075--369146 Score: 62
Period size: 23 Copynumber: 3.2 Consensus size: 23
369065 AATTTAAGAT
*
369075 TTAATTTATATACTTTAATTTTGACA
1 TTAATTTAAATA-TTTAATTTT-A-A
*
369101 -TAATTT-AATATTTCA--TTAA
1 TTAATTTAAATATTTAATTTTAA
*
369120 TTAATTTAAATATTTTATTTTAA
1 TTAATTTAAATATTTAATTTTAA
369143 TTAA
1 TTAA
369147 AATAACATCA
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
19 1 0.03
20 7 0.18
21 10 0.26
23 12 0.31
24 3 0.08
25 6 0.15
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.56
Consensus pattern (23 bp):
TTAATTTAAATATTTAATTTTAA
Found at i:372699 original size:59 final size:58
Alignment explanation
Indices: 372590--373210 Score: 471
Period size: 59 Copynumber: 10.5 Consensus size: 58
372580 AAAAAAAAAA
* * * * *
372590 TTTGGTGTTGGCCATTGCATGGTCGACACCCCCTTTTTATCTGATAAAAAAATCAAATT
1 TTTGGTGTTGGCCA-TGCATGGCCGACACCCCTTTTTTGTCAGATAAAAAATTCAAATT
* * *
372649 TTTGGATGTTGGCCATGCAATGGTCGACACCCCTTTTTTGTCAGATAAAAAATTTAATTT
1 TTTGG-TGTTGGCCATGC-ATGGCCGACACCCCTTTTTTGTCAGATAAAAAATTCAAATT
* * * * *
372709 TTTGGTGTTGGCCATGCCATGACCGACACTCC-TATTTGTCTGATAAAAAAAATCAAAATT
1 TTTGGTGTTGGCCATG-CATGGCCGACACCCCTTTTTTGTCAGAT-AAAAAATTC-AAATT
* *
372769 TTTGGTGTTAG-C---CAT-G-C-AC-CTCC-TTTTT-TCAGATAAAAAATTTTCAAATTTT
1 TTTGGTGTTGGCCATGCATGGCCGACACCCCTTTTTTGTCAGATAAAAAA--TTCAAA--TT
* * * * * *
372821 TTTGGTGTTAGCCATTGCATGGCCGACGCCCC-TTTTTATCTGCATAATAAA-TCAATTT
1 TTTGGTGTTGGCCA-TGCATGGCCGACACCCCTTTTTTGTCAG-ATAAAAAATTCAAATT
* *
372879 TTTGGGTGTTGGCCATGCCATGGTCGACACCCCTTTTTTGTCAGATAAAAAATTCGAATTTTT
1 TTT-GGTGTTGGCCATG-CATGGCCGACACCCCTTTTTTGTCAGATAAAAAATTC-AA--ATT
* * * ** * * * **
372942 TTTTGTGCTGGACATGCTATGATCGACACCTCCTTTTTTATCTGGTAAAAAA-TCATTTTTT
1 TTTGGTGTTGGCCATGC-ATGGCCGACACC-CCTTTTTTGTCAGATAAAAAATTCA--AATT
* * *
373003 TTTTGTGTTGGCCATGCAATGGCCGACACCCCCTTTTTGTCAGATAAAAAATTCGAATT
1 TTTGGTGTTGGCCATGC-ATGGCCGACACCCCTTTTTTGTCAGATAAAAAATTCAAATT
* * *
373062 TTTGGTGTAGGCCATTGCATGACCGACACCCCCTTTTTGTCAGATAAAAAATTCAAATT
1 TTTGGTGTTGGCCA-TGCATGGCCGACACCCCTTTTTTGTCAGATAAAAAATTCAAATT
* * * * * * *
373121 TTTGGTGTAGGCCATTGCATGACCGACACCCCCTTTTTTATCTGGTAAAATA-TCAATTTT
1 TTTGGTGTTGGCCA-TGCATGGCCGACA-CCCCTTTTTTGTCAGATAAAAAATTCAA-ATT
*
373181 TTTTGTGTTGGCCATGCAATGGCCGACACC
1 TTTGGTGTTGGCCATGC-ATGGCCGACACC
373211 AACTTTCCCT
Statistics
Matches: 464, Mismatches: 62, Indels: 72
0.78 0.10 0.12
Matches are distributed among these distances:
49 6 0.01
50 8 0.02
51 10 0.02
52 15 0.03
53 2 0.00
55 3 0.01
57 3 0.01
58 18 0.04
59 159 0.34
60 141 0.30
61 42 0.09
62 26 0.06
63 31 0.07
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.37
Consensus pattern (58 bp):
TTTGGTGTTGGCCATGCATGGCCGACACCCCTTTTTTGTCAGATAAAAAATTCAAATT
Found at i:372758 original size:119 final size:119
Alignment explanation
Indices: 372590--373210 Score: 550
Period size: 119 Copynumber: 5.3 Consensus size: 119
372580 AAAAAAAAAA
**
372590 TTTGGTGTTGGCCATTGCATGGTCGACACCCCCTTTTTATCTGATAAAAAAATCAAATTTTTGGA
1 TTTGGTGTTGGCCATTGCATGACCGACACCCCCTTTTTATCTGATAAAAAAATCAAATTTTTGG-
* *
372655 TGTTGGCCATGCAATGGTCGACACCCCTTTTTTGTCAGATAAAAAATTTAA-TTT
65 TGTTGGCCATGCAATGGCCGACACCCCTTTTTTGTCAGATAAAAAATTGAATTTT
* * *
372709 TTTGGTGTTGGCCA-TGCCATGACCGACA-CTCCTATTTGTCTGATAAAAAAAATCAAAATTTTT
1 TTTGGTGTTGGCCATTG-CATGACCGACACCCCCTTTTTATCTGAT-AAAAAAATC-AAATTTTT
* * *
372772 GGTGTT----A-GCCAT-G-C-AC-CTCC-TTTTT-TCAGATAAAAAATTTTCAAATTTT
63 GGTGTTGGCCATGCAATGGCCGACACCCCTTTTTTGTCAGATAAAAAA--TT-GAATTTT
* * * * *
372821 TTTGGTGTTAGCCATTGCATGGCCGAC-GCCCCTTTTTATCTGCAT-AATAAATCAATTTTTTGG
1 TTTGGTGTTGGCCATTGCATGACCGACACCCCCTTTTTATCTG-ATAAAAAAATCAAATTTTT-G
* *
372884 GTGTTGGCCATGCCATGGTCGACACCCCTTTTTTGTCAGATAAAAAATTCGAATTTTT
64 GTGTTGGCCATGCAATGGCCGACACCCCTTTTTTGTCAGATAAAAAATT-GAA-TTTT
* * * * * * **
372942 TTTTGTGCTGGACA-TGCTATGATCGACACCTCCTTTTTTATCTGGT-AAAAAATCATTTTTTTT
1 TTTGGTGTTGGCCATTGC-ATGACCGACACC-CCCTTTTTATCTGATAAAAAAATCA--AATTTT
* *
373005 TTGTGTTGGCCATGCAATGGCCGACACCCCCTTTTTGTCAGATAAAAAATTCGAA--TT
62 TGGTGTTGGCCATGCAATGGCCGACACCCCTTTTTTGTCAGATAAAAAATT-GAATTTT
* * * *
373062 TTTGGTGTAGGCCATTGCATGACCGACACCCCCTTTTTGTCAGATAAAAAATTCAAATTTTTGGT
1 TTTGGTGTTGGCCATTGCATGACCGACACCCCCTTTTTATCTGATAAAAAAATCAAATTTTTGGT
* * * * * * *
373127 GTAGGCCATTGC-ATGACCGACACCCCCTTTTTTATCTGGTAAAATA-TCAATTTT
66 GTTGGCCA-TGCAATGGCCGACA-CCCCTTTTTTGTCAGATAAAAAATTGAATTTT
* *
373181 TTTTGTGTTGGCCA-TGCAATGGCCGACACC
1 TTTGGTGTTGGCCATTGC-ATGACCGACACC
373211 AACTTTCCCT
Statistics
Matches: 411, Mismatches: 56, Indels: 70
0.77 0.10 0.13
Matches are distributed among these distances:
108 12 0.03
109 5 0.01
110 12 0.03
111 17 0.04
112 37 0.09
113 5 0.01
114 4 0.01
115 2 0.00
116 5 0.01
117 3 0.01
118 43 0.10
119 95 0.23
120 52 0.13
121 29 0.07
122 22 0.05
123 62 0.15
124 6 0.01
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.37
Consensus pattern (119 bp):
TTTGGTGTTGGCCATTGCATGACCGACACCCCCTTTTTATCTGATAAAAAAATCAAATTTTTGGT
GTTGGCCATGCAATGGCCGACACCCCTTTTTTGTCAGATAAAAAATTGAATTTT
Found at i:373115 original size:182 final size:179
Alignment explanation
Indices: 372590--373210 Score: 556
Period size: 182 Copynumber: 3.5 Consensus size: 179
372580 AAAAAAAAAA
* * ** * * *
372590 TTTGGTGTTGGCCATTGCATGGTCGACACCCCC-TTTTTATCTGATAAAAAAATCAA-ATTTTTG
1 TTTGGTGTAGGACATTGCATGACCGACACCCCCTTTTTTATCTGGT-AAAAAATCAATTTTTTTT
* * * *
372653 GATGTTGGCCATGCAATGGTCGACACCCCTTTTTTGTCAG-ATAAAAAATTTAATTTTTT-GGTG
65 G-TGTTGGCCATGCAATGGCCGACACCCCCTTTTTATCAGCATAAAAAA-TCAATTTTTTGGGTG
* * * * *
372716 TTGGCCATGCCATGACCGACA-CTCCTATTTGTCTGATAAAAAAAATCAAAATT
128 TAGGCCATGCCATGACCGACACCCCCTTTTTGTCAGAT-AAAAAATTC-AAATT
* * *
372769 TTTGGTGTTA-G-C----CAT----G-CACCTCC-TTTTT-TCAGATAAAAAATTTTCAAATTTT
1 TTTGGTG-TAGGACATTGCATGACCGACACCCCCTTTTTTATCTGGTAAAAAA---TC-AATTTT
* * * * *
372821 TTTGGTGTTAGCCATTGC-ATGGCCGAC-GCCCCTTTTTATCTGCATAATAAATCAATTTTTTGG
61 TTTTGTGTTGGCCA-TGCAATGGCCGACACCCCCTTTTTATCAGCATAAAAAATCAATTTTTTGG
* ** * *
372884 GTGTTGGCCATGCCATGGTCGACACCCCTTTTTTGTCAGATAAAAAATTCGAATTTTT
125 GTGTAGGCCATGCCATGACCGACACCCCCTTTTTGTCAGATAAAAAATTC-AA--ATT
* * * *
372942 TTTTGTGCT-GGACA-TGCTATGATCGACACCTCCTTTTTTATCTGGTAAAAAATCATTTTTTTT
1 TTTGGTG-TAGGACATTGC-ATGACCGACACCCCCTTTTTTATCTGGTAAAAAATCA-ATTTTTT
*
373005 TTGTGTTGGCCATGCAATGGCCGACACCCCCTTTTTGTCAG-ATAAAAAATTCGAA-TTTTT-GG
63 TTGTGTTGGCCATGCAATGGCCGACACCCCCTTTTTATCAGCATAAAAAA-TC-AATTTTTTGGG
373067 TGTAGGCCATTG-CATGACCGACACCCCCTTTTTGTCAGATAAAAAATTCAAATT
126 TGTAGGCCA-TGCCATGACCGACACCCCCTTTTTGTCAGATAAAAAATTCAAATT
* *
373121 TTTGGTGTAGGCCATTGCATGACCGACACCCCCTTTTTTATCTGGTAAAATATCAATTTTTTTTG
1 TTTGGTGTAGGACATTGCATGACCGACACCCCCTTTTTTATCTGGTAAAAAATCAATTTTTTTTG
373186 TGTTGGCCATGCAATGGCCGACACC
66 TGTTGGCCATGCAATGGCCGACACC
373211 AACTTTCCCT
Statistics
Matches: 366, Mismatches: 43, Indels: 67
0.77 0.09 0.14
Matches are distributed among these distances:
167 6 0.02
168 5 0.01
169 11 0.03
170 23 0.06
171 58 0.16
172 22 0.06
173 10 0.03
174 4 0.01
177 1 0.00
178 38 0.10
179 54 0.15
180 4 0.01
181 6 0.02
182 79 0.22
183 28 0.08
184 7 0.02
185 10 0.03
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.37
Consensus pattern (179 bp):
TTTGGTGTAGGACATTGCATGACCGACACCCCCTTTTTTATCTGGTAAAAAATCAATTTTTTTTG
TGTTGGCCATGCAATGGCCGACACCCCCTTTTTATCAGCATAAAAAATCAATTTTTTGGGTGTAG
GCCATGCCATGACCGACACCCCCTTTTTGTCAGATAAAAAATTCAAATT
Found at i:376798 original size:12 final size:12
Alignment explanation
Indices: 376783--376830 Score: 51
Period size: 12 Copynumber: 3.7 Consensus size: 12
376773 TATTAGTGTA
376783 AAAATTAATTTG
1 AAAATTAATTTG
376795 AAAATTAATTTAAG
1 AAAATTAATTT--G
*
376809 TTGAAATTAATTTG
1 --AAAATTAATTTG
376823 AAAATTAA
1 AAAATTAA
376831 GGTACATGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
12 18 0.60
14 2 0.07
16 10 0.33
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (12 bp):
AAAATTAATTTG
Found at i:377273 original size:84 final size:86
Alignment explanation
Indices: 376944--377332 Score: 579
Period size: 84 Copynumber: 4.5 Consensus size: 86
376934 AATTTAACAT
* * * *
376944 TATTTAAATAAAAAAGATTATTATTATATTTCAATTTATATCAAATAATGTGTTGTTTTAACAAT
1 TATTTAAATAAAAAATATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTAACAAT
*
377009 ACATTGTTTATCAAATTTTAA
66 ACATTATTTATCAAATTTTAA
*
377030 TATTTAAATAAAAAAGATTATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGAC
1 TATTTAAAT-AAAAA-A-TATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTAAC
377095 AATACATTATTTATCAAATTTTAA
63 AATACATTATTTATCAAATTTTAA
* * * *
377119 TATTTAAATAAAAAACATTATTATTATATTACAATTTTTATCAAATAATGAGTTAATTTGACAAT
1 TATTTAAATAAAAAATATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTAACAAT
*
377184 ACATTATTTATCAAATTTGAA
66 ACATTATTTATCAAATTTTAA
* *
377205 TATTTAAAT-TAAAA-ATTATTATTATATTATAATTTTTATCAAATAATGTGTTGATTTAACAAT
1 TATTTAAATAAAAAATATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTAACAAT
377268 ACATTATTTATCAAATTTTAA
66 ACATTATTTATCAAATTTTAA
* * *
377289 TATTTAAAT-TAAAA-ATTATTATTTTATTAAAATTTTTATCAAAT
1 TATTTAAATAAAAAATATTATTATTATATTACAATTTTTATCAAAT
377333 TTTAAATTTA
Statistics
Matches: 282, Mismatches: 18, Indels: 8
0.92 0.06 0.03
Matches are distributed among these distances:
84 107 0.38
85 4 0.01
86 85 0.30
87 6 0.02
88 6 0.02
89 74 0.26
ACGTcount: A:0.43, C:0.05, G:0.04, T:0.47
Consensus pattern (86 bp):
TATTTAAATAAAAAATATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTAACAAT
ACATTATTTATCAAATTTTAA
Found at i:378561 original size:19 final size:19
Alignment explanation
Indices: 378523--378566 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
378513 TTTATAATAT
*
378523 TTTTTTTCTATTTTCAAAA
1 TTTTTTTATATTTTCAAAA
378542 TGTTTTTTATATTTTC-AAA
1 T-TTTTTTATATTTTCAAAA
378561 TTTTTT
1 TTTTTT
378567 AAAAAATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 5 0.22
19 5 0.22
20 13 0.57
ACGTcount: A:0.23, C:0.07, G:0.02, T:0.68
Consensus pattern (19 bp):
TTTTTTTATATTTTCAAAA
Found at i:379829 original size:17 final size:16
Alignment explanation
Indices: 379777--379831 Score: 53
Period size: 17 Copynumber: 3.5 Consensus size: 16
379767 TAAATTTAAT
379777 TTCTAATTTCTTGTATA
1 TTCTAATTTC-TGTATA
* *
379794 TTTTAATTT-T-AAT-
1 TTCTAATTTCTGTATA
379807 TTCTAATTTCCTGTATA
1 TTCTAATTT-CTGTATA
379824 TTCTAATT
1 TTCTAATT
379832 ATTATTTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
13 8 0.27
14 2 0.07
15 2 0.07
16 2 0.07
17 16 0.53
ACGTcount: A:0.25, C:0.11, G:0.04, T:0.60
Consensus pattern (16 bp):
TTCTAATTTCTGTATA
Found at i:379831 original size:30 final size:30
Alignment explanation
Indices: 379734--379831 Score: 124
Period size: 30 Copynumber: 3.3 Consensus size: 30
379724 TCCGTTTACT
* * * * *
379734 TTTTAAATTTAATTTGTAATTTCGTTTTTA
1 TTTTAATTTTAATTTCTAATTTCCTGTATA
* *
379764 TTTTAAATTTAATTTCTAATTTCTTGTATA
1 TTTTAATTTTAATTTCTAATTTCCTGTATA
379794 TTTTAATTTTAATTTCTAATTTCCTGTATA
1 TTTTAATTTTAATTTCTAATTTCCTGTATA
*
379824 TTCTAATT
1 TTTTAATT
379832 ATTATTTTTT
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 61 1.00
ACGTcount: A:0.28, C:0.07, G:0.04, T:0.61
Consensus pattern (30 bp):
TTTTAATTTTAATTTCTAATTTCCTGTATA
Found at i:380709 original size:59 final size:56
Alignment explanation
Indices: 380640--380851 Score: 162
Period size: 59 Copynumber: 3.6 Consensus size: 56
380630 AAGTTATGGC
*
380640 CAACATAAAAAAATTTGATTTTTTTATCAGATAAATAAGGGTGTCGGTCATGGCATGA
1 CAACACAAAAAAATTTGATTTTTTTATCAGATAAA-AAGGGTGTCGG-CATGGCATGA
* * * * * *
380698 CGAACACAAAAAAAATTGATTTTTTT-TTACA-AAAAGGGAGTATCGGCAATGGCATGGT
1 C-AACACAAAAAAATTTGATTTTTTTATCAGATAAAAAGG-GTGTCGGC-ATGGCAT-GA
* ** * *
380756 TAACACTCAAAAATTTGA-TTTTTTATTCAGATAAAAAGGGGTGTTGGCCAT-GCAATGGT
1 CAACACAAAAAAATTTGATTTTTTTA-TCAGATAAAAA-GGGTGTCGG-CATGGC-AT-GA
380815 CAACACAAAAAACATTTGAAATTTTTTTATCAGATAA
1 CAACACAAAAAA-ATTTG--ATTTTTTTATCAGATAA
380852 TGGTCGACAC
Statistics
Matches: 121, Mismatches: 19, Indels: 24
0.74 0.12 0.15
Matches are distributed among these distances:
56 10 0.08
57 30 0.25
58 10 0.08
59 47 0.39
60 8 0.07
62 9 0.07
63 7 0.06
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (56 bp):
CAACACAAAAAAATTTGATTTTTTTATCAGATAAAAAGGGTGTCGGCATGGCATGA
Found at i:380977 original size:59 final size:58
Alignment explanation
Indices: 380907--381076 Score: 152
Period size: 62 Copynumber: 2.9 Consensus size: 58
380897 GTTGGGCATG
* *
380907 GCATGGGCAACATCCAAAAATTTGATTTTTTATTTAGATAAAAAGGGGTGTAGGCTA-T
1 GCATGGCCAACA-CCAAAAATTTGATTTTTTATTTAGATAAAAAGGGGTGTAGACTATT
* *
380965 GCAATGGCCAACACCAAAAAAATTTGAAATTTTTTTATCT-GA-AAAAAGGGGATGTCGACTATT
1 GC-ATGGCCAACACC--AAAAATTTG--A-TTTTTTATTTAGATAAAAAGGGG-TGTAGACTATT
* * * *
381028 GCATGACCAACACAATAAAATTTGA-TTTTTA-TCAGATAAATAGGGGTGT
1 GCATGGCCAACACCA-AAAATTTGATTTTTTATTTAGATAAAAAGGGGTGT
381077 CGGCCATGAA
Statistics
Matches: 92, Mismatches: 9, Indels: 23
0.74 0.07 0.19
Matches are distributed among these distances:
57 11 0.12
58 12 0.13
59 10 0.11
60 10 0.11
61 17 0.18
62 20 0.22
63 12 0.13
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (58 bp):
GCATGGCCAACACCAAAAATTTGATTTTTTATTTAGATAAAAAGGGGTGTAGACTATT
Found at i:381048 original size:61 final size:63
Alignment explanation
Indices: 380932--381076 Score: 155
Period size: 61 Copynumber: 2.4 Consensus size: 63
380922 AAAAATTTGA
* * *
380932 TTTTTTATTTAGATAAAAAGGGGTGTAGGCTATGCAATGGCCAACACCAAAAAAATTTGAAAT
1 TTTTTTATCTAGATAAAAAGGGGTGTAGACTATGCAATGACCAACACCAAAAAAATTTGAAAT
* *
380995 TTTTTTATCT-GA-AAAAAGGGGATGTCGACTATTGC-ATGACCAACA-CAATAAAATTTG--A-
1 TTTTTTATCTAGATAAAAAGGGG-TGTAGACTA-TGCAATGACCAACACCAAAAAAATTTGAAAT
*
381053 -TTTTTATC-AGATAAATAGGGGTGT
1 TTTTTTATCTAGATAAAAAGGGGTGT
381077 CGGCCATGAA
Statistics
Matches: 72, Mismatches: 6, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
57 13 0.18
58 8 0.11
59 1 0.01
61 20 0.28
62 18 0.25
63 12 0.17
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.32
Consensus pattern (63 bp):
TTTTTTATCTAGATAAAAAGGGGTGTAGACTATGCAATGACCAACACCAAAAAAATTTGAAAT
Found at i:390035 original size:14 final size:14
Alignment explanation
Indices: 390016--390042 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
390006 CCATATGCTT
390016 TTTTGCTTCGGCCC
1 TTTTGCTTCGGCCC
390030 TTTTGCTTCGGCC
1 TTTTGCTTCGGCC
390043 ATCTGGTCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.33, G:0.22, T:0.44
Consensus pattern (14 bp):
TTTTGCTTCGGCCC
Found at i:391020 original size:23 final size:24
Alignment explanation
Indices: 390975--391039 Score: 62
Period size: 24 Copynumber: 2.6 Consensus size: 24
390965 TTTTATATAA
*
390975 AACAAATTTGAAACATATAATA-TATT
1 AACAAAATT-AAA-ATA-AATATTATT
391001 AA-AAACATTAAAATAAATATTATT
1 AACAAA-ATTAAAATAAATATTATT
*
391025 AACAAATTTAAAATA
1 AACAAAATTAAAATA
391040 TATTAAAAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
23 4 0.12
24 17 0.50
25 9 0.26
26 4 0.12
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.32
Consensus pattern (24 bp):
AACAAAATTAAAATAAATATTATT
Found at i:391509 original size:2 final size:2
Alignment explanation
Indices: 391502--391541 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
391492 ATTTTATTAA
391502 AT AT AT 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 AT AT AT
391542 GTATTTAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:397487 original size:22 final size:22
Alignment explanation
Indices: 397430--397490 Score: 106
Period size: 22 Copynumber: 2.8 Consensus size: 22
397420 CGATCTGAGA
397430 AAAAATAAAAG-AAACAGAATT
1 AAAAATAAAAGAAAACAGAATT
397451 AAAAATAAAAGAAAACAGAATT
1 AAAAATAAAAGAAAACAGAATT
*
397473 AAAAGTAAAAGAAAACAG
1 AAAAATAAAAGAAAACAG
397491 GGAAGTCGAA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
21 11 0.29
22 27 0.71
ACGTcount: A:0.72, C:0.05, G:0.11, T:0.11
Consensus pattern (22 bp):
AAAAATAAAAGAAAACAGAATT
Found at i:398259 original size:14 final size:14
Alignment explanation
Indices: 398242--398282 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
398232 TTTAAACTTT
398242 AAAAGATAAATACA
1 AAAAGATAAATACA
398256 AAAAGATAAA-A-A
1 AAAAGATAAATACA
*
398268 TAAA-ATAAATACA
1 AAAAGATAAATACA
398281 AA
1 AA
398283 TTTAAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
11 5 0.22
12 5 0.22
13 3 0.13
14 10 0.43
ACGTcount: A:0.76, C:0.05, G:0.05, T:0.15
Consensus pattern (14 bp):
AAAAGATAAATACA
Found at i:398295 original size:19 final size:19
Alignment explanation
Indices: 398271--398315 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
398261 ATAAAAATAA
398271 AATAAATACAAAT-TTAAAT
1 AATAAATA-AAATCTTAAAT
*
398290 AATAAATAATATCTTAAAT
1 AATAAATAAAATCTTAAAT
*
398309 ATTAAAT
1 AATAAAT
398316 CCTAATATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 3 0.13
19 20 0.87
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (19 bp):
AATAAATAAAATCTTAAAT
Found at i:399092 original size:106 final size:108
Alignment explanation
Indices: 398918--399114 Score: 247
Period size: 106 Copynumber: 1.8 Consensus size: 108
398908 AAATTGGACT
* * * * * **
398918 TTTTGACGCAAAATGAAATGACACCCAAGCACTTCATCCCGGTTACTCAGCCCAACATGCTCTCA
1 TTTTGACGCAAAATGAAATGACAACCAAGCACTCCACCCCGATTACTCAACCCAACACACTCTCA
*
398983 ATTT-TTTTTCTTCT-TTTT-TTTTTTGTAGAATGTGTTAGCCC
66 ATTTATTTAT-TTCTATTTTATTTTTTGTAGAATGTGTTAGCCC
* * * * *
399024 TTTTGACGCGAAGTGAAATGACAACCAAGCACTCCACCCCGATTACTCAATCTAACACACTCTGA
1 TTTTGACGCAAAATGAAATGACAACCAAGCACTCCACCCCGATTACTCAACCCAACACACTCTCA
399089 ATTTATTTATTTCTATTTTATTTTTT
66 ATTTATTTATTTCTATTTTATTTTTT
399115 TCGGGTTAGC
Statistics
Matches: 75, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
106 61 0.81
107 8 0.11
108 6 0.08
ACGTcount: A:0.26, C:0.24, G:0.12, T:0.38
Consensus pattern (108 bp):
TTTTGACGCAAAATGAAATGACAACCAAGCACTCCACCCCGATTACTCAACCCAACACACTCTCA
ATTTATTTATTTCTATTTTATTTTTTGTAGAATGTGTTAGCCC
Found at i:399373 original size:15 final size:16
Alignment explanation
Indices: 399345--399374 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
399335 TAATTAAAAA
399345 TAAAAGAGAATAGAAT
1 TAAAAGAGAATAGAAT
399361 TAAAAGA-AATAGAA
1 TAAAAGAGAATAGAA
399375 AATAGGGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.67, C:0.00, G:0.17, T:0.17
Consensus pattern (16 bp):
TAAAAGAGAATAGAAT
Found at i:399378 original size:22 final size:22
Alignment explanation
Indices: 399336--399379 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
399326 AAAAAAACAT
*
399336 AATTAAAAATAAAAGAGAATAG
1 AATTAAAAATAAAAGAAAATAG
*
399358 AATTAAAAGA-AATAGAAAATAG
1 AATTAAAA-ATAAAAGAAAATAG
399380 GGAAGTCGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.68, C:0.00, G:0.14, T:0.18
Consensus pattern (22 bp):
AATTAAAAATAAAAGAAAATAG
Found at i:400193 original size:19 final size:19
Alignment explanation
Indices: 400169--400211 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
400159 AAACATAAAT
400169 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
400188 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
400207 TAAAT
1 TAAAT
400212 CCTAATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:404366 original size:16 final size:16
Alignment explanation
Indices: 404345--404376 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
404335 CTCTTGCTCG
404345 TTGAGGAGTCATATTA
1 TTGAGGAGTCATATTA
404361 TTGAGGAGTCATATTA
1 TTGAGGAGTCATATTA
404377 ACTAATGCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.06, G:0.25, T:0.38
Consensus pattern (16 bp):
TTGAGGAGTCATATTA
Found at i:405488 original size:22 final size:22
Alignment explanation
Indices: 405431--405488 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
405421 CGATCTGAGG
*
405431 AAAAATAAAAG-AAACAGAATT
1 AAAAAGAAAAGAAAACAGAATT
*
405452 AAAAAGAAAATAAAACAGAATT
1 AAAAAGAAAAGAAAACAGAATT
*
405474 -GAAAGAAATAGAAAA
1 AAAAAGAAA-AGAAAA
405489 TAGGGAAGTC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 16 0.52
22 15 0.48
ACGTcount: A:0.72, C:0.03, G:0.12, T:0.12
Consensus pattern (22 bp):
AAAAAGAAAAGAAAACAGAATT
Found at i:406318 original size:19 final size:19
Alignment explanation
Indices: 406294--406336 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
406284 AAATATAAAT
406294 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
406313 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
406332 TAAAT
1 TAAAT
406337 CCTAATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:406644 original size:347 final size:347
Alignment explanation
Indices: 406009--406674 Score: 1210
Period size: 347 Copynumber: 1.9 Consensus size: 347
405999 ATTTGATAAC
*
406009 CTTTGGCTAGAATGGTTTTTTAGTTACTAATGATTTTTGGGGAAGAACACAAAATAAAAAGAATA
1 CTTTGGCTAGAAAGGTTTTTTAGTTACTAATGATTTTTGGGGAAGAACACAAAATAAAAAGAATA
406074 GAGCTTTTTATTGAACTAAGATTTTGGGAGATGAAGGATTTTCTCAATGAATGAGGCATGAATAA
66 GAGCTTTTTATTGAACTAAGATTTTGGGAGATGAAGGATTTTCTCAATGAATGAGGCATGAATAA
*
406139 TTCAATTACTCCACCCCCTGTTTATAGTACATAATATTCCTAGTTGAATCCAATCTAAATTCTAA
131 TTCAATTACTCCACCCCCTATTTATAGTACATAATATTCCTAGTTGAATCCAATCTAAATTCTAA
*
406204 AAGATAATTAGAATTTTATCTAACATTTAATTTCTCTAATTGGATTCAATTTAAACTTTAAAAGA
196 AAGATAATTAGAATTTTATCTAACATTTAATTTCTCTAATTGGATTCAATTTAAACTCTAAAAGA
406269 TAAATACAAAAGGATAAATATAAATTAAATACAAATTTAAATAATAAATAATATCTTAAATATTA
261 TAAATACAAAAGGATAAATATAAATTAAATACAAATTTAAATAATAAATAATATCTTAAATATTA
406334 AATCCTAATAAAAAGAATAGAG
326 AATCCTAATAAAAAGAATAGAG
**
406356 CTTTGGCTAGAAAGGTTTTTTAGTTACTCGTGATTTTTGGGGAAGAACACAAAATAAAAAGAATA
1 CTTTGGCTAGAAAGGTTTTTTAGTTACTAATGATTTTTGGGGAAGAACACAAAATAAAAAGAATA
* *
406421 GAGCTTTTTATTGAACTAGGATTTTGGGAGAT-AGAGGATTTTCTCAATGAATGGGGCATGAATA
66 GAGCTTTTTATTGAACTAAGATTTTGGGAGATGA-AGGATTTTCTCAATGAATGAGGCATGAATA
* * *
406485 ATTCAATTACTCCACCCCTTATTTATGGTACATAATATTCTTAGTTGAATCCAATCTAAACTT-T
130 ATTCAATTACTCCACCCCCTATTTATAGTACATAATATTCCTAGTTGAATCCAATCTAAA-TTCT
406549 AAAAGATAATTAGAATTTTATCTAACATTTAATTTCTCTAATTGGATTCAATTTAAACTCTAAAA
194 AAAAGATAATTAGAATTTTATCTAACATTTAATTTCTCTAATTGGATTCAATTTAAACTCTAAAA
406614 GATAAATACAAAAGGATAAATATAAATTAAATACAAATTTAAATAATAAATAATATCTTAA
259 GATAAATACAAAAGGATAAATATAAATTAAATACAAATTTAAATAATAAATAATATCTTAA
406675 TTATCTTAAA
Statistics
Matches: 307, Mismatches: 10, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
346 1 0.00
347 304 0.99
348 2 0.01
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Consensus pattern (347 bp):
CTTTGGCTAGAAAGGTTTTTTAGTTACTAATGATTTTTGGGGAAGAACACAAAATAAAAAGAATA
GAGCTTTTTATTGAACTAAGATTTTGGGAGATGAAGGATTTTCTCAATGAATGAGGCATGAATAA
TTCAATTACTCCACCCCCTATTTATAGTACATAATATTCCTAGTTGAATCCAATCTAAATTCTAA
AAGATAATTAGAATTTTATCTAACATTTAATTTCTCTAATTGGATTCAATTTAAACTCTAAAAGA
TAAATACAAAAGGATAAATATAAATTAAATACAAATTTAAATAATAAATAATATCTTAAATATTA
AATCCTAATAAAAAGAATAGAG
Found at i:413727 original size:16 final size:16
Alignment explanation
Indices: 413699--413731 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
413689 AAGTTAAAAC
413699 AATAATGTATTTTGAAA
1 AATAATGTATTTT-AAA
413716 AATAAT-TATTTTAAA
1 AATAATGTATTTTAAA
413731 A
1 A
413732 TTTAATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 6 0.38
17 6 0.38
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (16 bp):
AATAATGTATTTTAAA
Found at i:414312 original size:33 final size:33
Alignment explanation
Indices: 414248--414317 Score: 81
Period size: 33 Copynumber: 2.1 Consensus size: 33
414238 CAAAAAAATA
*
414248 ATATCTATTATTATAACTATATGTATCAATATC
1 ATATCTATTATTATAACTATATGAATCAATATC
* *
414281 TATATCTA-TATTCTATA-TATATGAATTAATATC
1 -ATATCTATTATTATA-ACTATATGAATCAATATC
414314 ATAT
1 ATAT
414318 TTGTTTTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
32 4 0.12
33 20 0.62
34 8 0.25
ACGTcount: A:0.40, C:0.10, G:0.03, T:0.47
Consensus pattern (33 bp):
ATATCTATTATTATAACTATATGAATCAATATC
Found at i:414918 original size:16 final size:18
Alignment explanation
Indices: 414890--414926 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
414880 ACGTTAAAAG
414890 AAACAAAGAAAGGA-GGA
1 AAACAAAGAAAGGATGGA
414907 AAACAAAG-AAGGATGGA
1 AAACAAAGAAAGGATGGA
414924 AAA
1 AAA
414927 TGAAGAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.65, C:0.05, G:0.27, T:0.03
Consensus pattern (18 bp):
AAACAAAGAAAGGATGGA
Found at i:416846 original size:23 final size:23
Alignment explanation
Indices: 416814--416876 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
416804 TATATGTTCA
* *
416814 TGAACGTGTTCGTTTAATATCCC
1 TGAACATGTTCGATTAATATCCC
* * *
416837 TGAACATGTTCGATTAATGTTCG
1 TGAACATGTTCGATTAATATCCC
416860 TGAACATGTTCGATTAA
1 TGAACATGTTCGATTAA
416877 ATTAAACGAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.38
Consensus pattern (23 bp):
TGAACATGTTCGATTAATATCCC
Done.