Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008396.1 Hibiscus syriacus cultivar Beakdansim tig00111164_pilon, 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: 416257
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
File 2 of 2
Found at i:251019 original size:21 final size:21
Alignment explanation
Indices: 250993--251034 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
250983 CCAGAATGGG
*
250993 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
251014 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
251035 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:252476 original size:19 final size:20
Alignment explanation
Indices: 252452--252499 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
252442 AACGATTTTC
252452 TTTTGAAAACAAAAAT-AAA
1 TTTTGAAAACAAAAATGAAA
* *
252471 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
252491 TTTTGAAAA
1 TTTTGAAAA
252500 AGGATTTAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.54, C:0.06, G:0.10, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:254899 original size:21 final size:21
Alignment explanation
Indices: 254874--254914 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
254864 CAGAATGGGA
*
254874 GGAATCGGTACCCCTTCATAG
1 GGAATCGATACCCCTTCATAG
254895 GGAATCGATACCCCTTCATA
1 GGAATCGATACCCCTTCATA
254915 ATATTCAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (21 bp):
GGAATCGATACCCCTTCATAG
Found at i:255051 original size:21 final size:21
Alignment explanation
Indices: 255027--255105 Score: 73
Period size: 21 Copynumber: 4.0 Consensus size: 21
255017 AACCCATGCA
*
255027 GGGGGAATCTGTACCCTCTGGG
1 GGGGGAATCTGTACCCCCT-GG
*
255049 GGGGGAATCTGT--TCCC---
1 GGGGGAATCTGTACCCCCTGG
255065 -GGGGAATC-GATACCCCCTGG
1 GGGGGAATCTG-TACCCCCTGG
255085 GGGGGAATCTGTACCCCCTGG
1 GGGGGAATCTGTACCCCCTGG
255106 ACAATCTGAT
Statistics
Matches: 46, Mismatches: 3, Indels: 17
0.70 0.05 0.26
Matches are distributed among these distances:
14 1 0.02
15 9 0.20
17 3 0.07
20 2 0.04
21 18 0.39
22 13 0.28
ACGTcount: A:0.15, C:0.27, G:0.38, T:0.20
Consensus pattern (21 bp):
GGGGGAATCTGTACCCCCTGG
Found at i:255413 original size:36 final size:36
Alignment explanation
Indices: 255373--255564 Score: 224
Period size: 36 Copynumber: 5.3 Consensus size: 36
255363 GTTTTCAACA
* * *
255373 AAGTTGAACGGAGGGAAGCATCAGCACTTCTGATTC
1 AAGTTGAACGGAAGGAAGCATCGGCACTTCCGATTC
255409 AAGTTGAAC-GAAGGGAAGCATCGGCACTTCCGATTC
1 AAGTTGAACGGAA-GGAAGCATCGGCACTTCCGATTC
*
255445 AAGTTGAACGGAAGGAAGCATCGGCACTTCCGGTTC
1 AAGTTGAACGGAAGGAAGCATCGGCACTTCCGATTC
* * *
255481 AAGTCGAACGGAATGAAACATCGGCACTTCCGATTC
1 AAGTTGAACGGAAGGAAGCATCGGCACTTCCGATTC
* * * * * * *
255517 AAATCGAATGGAATGATGCATCTGCACTTCTGATTC
1 AAGTTGAACGGAAGGAAGCATCGGCACTTCCGATTC
* *
255553 AACTAGAACGGA
1 AAGTTGAACGGA
255565 TGGTTTACTA
Statistics
Matches: 137, Mismatches: 17, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
35 2 0.01
36 132 0.96
37 3 0.02
ACGTcount: A:0.32, C:0.21, G:0.26, T:0.21
Consensus pattern (36 bp):
AAGTTGAACGGAAGGAAGCATCGGCACTTCCGATTC
Found at i:262037 original size:21 final size:21
Alignment explanation
Indices: 262013--262065 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
262003 GTTTGAACAG
262013 GTTGCGTTTCATTAGTGAAGC
1 GTTGCGTTTCATTAGTGAAGC
262034 GTTGCGTTTCATTAGTGAAGC
1 GTTGCGTTTCATTAGTGAAGC
262055 GTTGCGTTTCA
1 GTTGCGTTTCA
262066 AGTCCACGAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.17, C:0.15, G:0.28, T:0.40
Consensus pattern (21 bp):
GTTGCGTTTCATTAGTGAAGC
Found at i:266873 original size:33 final size:33
Alignment explanation
Indices: 266828--267013 Score: 239
Period size: 33 Copynumber: 5.6 Consensus size: 33
266818 TTTATAGTCT
* * *
266828 ATATCTAACAGGCTTGGAATTAGTTAAGAGCTG
1 ATATCTAGCAGGCTTAGAATTAGTTAAGAGCCG
*
266861 ATATCTAGCAGGCTTGGAATTAGTTAAGAGCCG
1 ATATCTAGCAGGCTTAGAATTAGTTAAGAGCCG
* * * *
266894 ATATCTAGCAGTCTTGGAATTAGCTAAGAGCCC
1 ATATCTAGCAGGCTTAGAATTAGTTAAGAGCCG
** * *
266927 ATATCTAGCCTGCTTAGAACTAGTTAAGAGCCA
1 ATATCTAGCAGGCTTAGAATTAGTTAAGAGCCG
266960 ATATCTAGCCA-GCTTAGAATTAGTTAAGAGCCG
1 ATATCTAG-CAGGCTTAGAATTAGTTAAGAGCCG
*
266993 ATATCTAGCAGGTTTAGAATT
1 ATATCTAGCAGGCTTAGAATT
267014 CCAGTTCTAC
Statistics
Matches: 135, Mismatches: 16, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
32 2 0.01
33 132 0.98
34 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (33 bp):
ATATCTAGCAGGCTTAGAATTAGTTAAGAGCCG
Found at i:275842 original size:18 final size:18
Alignment explanation
Indices: 275821--275855 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
275811 AAAAATTAGA
275821 AAAGATATAAAAAAAATT
1 AAAGATATAAAAAAAATT
*
275839 AAAGTTATAAAAAAAAT
1 AAAGATATAAAAAAAAT
275856 GATACAAGCC
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:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (18 bp):
AAAGATATAAAAAAAATT
Found at i:279291 original size:21 final size:21
Alignment explanation
Indices: 279262--279314 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
279252 ATTCTGACTA
279262 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
279283 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
279304 TCGCAATGCGA
1 TCGCATTGCGA
279315 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:279329 original size:20 final size:20
Alignment explanation
Indices: 279304--279376 Score: 119
Period size: 20 Copynumber: 3.6 Consensus size: 20
279294 TTTTCCTAAT
* *
279304 TCGCAATGCGAATACGTAAA
1 TCGCAACGCGATTACGTAAA
279324 TCGCAACGCGATTACGTAAA
1 TCGCAACGCGATTACGTAAA
279344 TCGCAACGCGATTACGTAAA
1 TCGCAACGCGATTACGTAAA
*
279364 TCGCAACGAGATT
1 TCGCAACGCGATT
279377 CTGACTATCG
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.21
Consensus pattern (20 bp):
TCGCAACGCGATTACGTAAA
Found at i:280253 original size:24 final size:24
Alignment explanation
Indices: 280226--280279 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
280216 GTATTCGAAA
280226 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
280250 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
280274 TTTGAT
1 TTTGAT
280280 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:282718 original size:20 final size:20
Alignment explanation
Indices: 282693--282741 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
282683 CAACGCAGAA
282693 ATCGCAACGC-GAATATGACT
1 ATCGCAACGCGGAA-ATGACT
*
282713 ATCGCAACGCGGAAATTACT
1 ATCGCAACGCGGAAATGACT
282733 ATCGCAACG
1 ATCGCAACG
282742 AGAGAATCGC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 24 0.89
21 3 0.11
ACGTcount: A:0.35, C:0.27, G:0.20, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:282770 original size:33 final size:34
Alignment explanation
Indices: 282733--282808 Score: 136
Period size: 33 Copynumber: 2.3 Consensus size: 34
282723 GGAAATTACT
282733 ATCGCAACGAGAGAATCGCAATGCG-AAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
*
282766 ATCGCAACGAGTGAATCGCAATGCGAAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
282800 ATCGCAACG
1 ATCGCAACG
282809 CGAAATTAGC
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
33 24 0.59
34 17 0.41
ACGTcount: A:0.43, C:0.20, G:0.24, T:0.13
Consensus pattern (34 bp):
ATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
Found at i:282804 original size:20 final size:19
Alignment explanation
Indices: 282746--282814 Score: 76
Period size: 19 Copynumber: 3.8 Consensus size: 19
282736 GCAACGAGAG
282746 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
282765 AATCGCAA--CG-AGTG--
1 AATCGCAATGCGAAATGAA
282779 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
282799 AATCGCAACGCGAAAT
1 AATCGCAATGCGAAAT
282815 TAGCGATTCT
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
14 8 0.20
16 5 0.12
17 2 0.05
18 3 0.07
19 12 0.29
20 11 0.27
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:282972 original size:14 final size:14
Alignment explanation
Indices: 282953--282989 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
282943 ACATCAATTA
282953 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
282967 ACAAATCATCTTTT
1 ACAAATCAACATTT
282981 ACAAATCAA
1 ACAAATCAA
282990 TTAACAATCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:284423 original size:42 final size:42
Alignment explanation
Indices: 284344--284436 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
284334 CCTCTTCAAC
* * *
284344 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
* * **
284386 GATGATAGGGGCCTCTTGAACGATAGGG-GAGGCCTCTTGAAC
1 GATGACAGGGGCCTCTTGAACGAT-GGGAGAGGACTCTTGAGG
284428 GATGACAGG
1 GATGACAGG
284437 TGAGTCGGGC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 39 0.93
43 3 0.07
ACGTcount: A:0.23, C:0.17, G:0.40, T:0.20
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
Found at i:285005 original size:20 final size:20
Alignment explanation
Indices: 284980--285048 Score: 111
Period size: 20 Copynumber: 3.5 Consensus size: 20
284970 CAACAACAAA
* **
284980 ATCGCAACGCGAAAATGACT
1 ATCGCAATGCGAATTTGACT
285000 ATCGCAATGCGAATTTGACT
1 ATCGCAATGCGAATTTGACT
285020 ATCGCAATGCGAATTTGACT
1 ATCGCAATGCGAATTTGACT
285040 ATCGCAATG
1 ATCGCAATG
285049 AGAGAATCGC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGAATTTGACT
Found at i:285118 original size:20 final size:20
Alignment explanation
Indices: 285093--285216 Score: 161
Period size: 20 Copynumber: 6.5 Consensus size: 20
285083 GATTCTTTCG
285093 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
285113 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
* * *
285133 TTGCGATAGTTATTTTTGCT
1 TTGCGATAGTCATTTTCGCA
285153 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
285173 TTGCGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
*
285187 TTGCGATAGTTATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
285207 TTGCGATAGT
1 TTGCGATAGT
285217 AAACTATTCT
Statistics
Matches: 89, Mismatches: 9, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
14 7 0.08
16 5 0.06
18 6 0.07
20 71 0.80
ACGTcount: A:0.18, C:0.18, G:0.21, T:0.44
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:285138 original size:40 final size:39
Alignment explanation
Indices: 285055--285216 Score: 157
Period size: 40 Copynumber: 4.4 Consensus size: 39
285045 AATGAGAGAA
* **
285055 TCGCAATGCGATTTTCATTTCGCATTGCGAT--TC--TT
1 TCGCATTGCGATAGTCATTTCGCATTGCGATAGTCATTT
285090 TCG--TTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
1 TCGCATTGCGATAGTCA-TTTCGCATTGCGATAGTCATTT
* * *
285128 TCGCATTGCGATAGTTATTTTTGCTTTGCGATAGTCATTT
1 TCGCATTGCGATAGTCA-TTTCGCATTGCGATAGTCATTT
* *
285168 TCGCATTGCGAT--TC-TCTCG--TTGCGATAGTTATTT
1 TCGCATTGCGATAGTCATTTCGCATTGCGATAGTCATTT
285202 TCGCATTGCGATAGT
1 TCGCATTGCGATAGT
285217 AAACTATTCT
Statistics
Matches: 108, Mismatches: 10, Indels: 17
0.80 0.07 0.13
Matches are distributed among these distances:
33 9 0.08
34 40 0.37
35 3 0.03
36 6 0.06
38 6 0.06
40 44 0.41
ACGTcount: A:0.17, C:0.19, G:0.20, T:0.43
Consensus pattern (39 bp):
TCGCATTGCGATAGTCATTTCGCATTGCGATAGTCATTT
Found at i:287125 original size:20 final size:20
Alignment explanation
Indices: 287067--287136 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 20
287057 GAAACTTTAA
* **
287067 ATCGCAACACGAAAATGAAA
1 ATCGCAACGCGAAAATGACT
*
287087 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGACT
**
287107 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
287127 ATCGCAACGC
1 ATCGCAACGC
287137 AAGAATCGCA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.41, C:0.26, G:0.17, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:291668 original size:34 final size:33
Alignment explanation
Indices: 291615--291678 Score: 92
Period size: 34 Copynumber: 1.9 Consensus size: 33
291605 GTAAAATAAT
*
291615 AATTATTAATTAATAATTTATTGTTTATTAGAA
1 AATTATTAATTAATAATTTATTATTTATTAGAA
* *
291648 AATTATTGTATTAGTAATTTATTATTTATTA
1 AATTATT-AATTAATAATTTATTATTTATTA
291679 TTATCTATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
33 7 0.26
34 20 0.74
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (33 bp):
AATTATTAATTAATAATTTATTATTTATTAGAA
Found at i:293683 original size:13 final size:13
Alignment explanation
Indices: 293667--293691 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
293657 TCTATAAATA
293667 CCCTTTCCACTCC
1 CCCTTTCCACTCC
293680 CCCTTTCCACTC
1 CCCTTTCCACTC
293692 TCATCCAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.60, G:0.00, T:0.32
Consensus pattern (13 bp):
CCCTTTCCACTCC
Found at i:297355 original size:2 final size:2
Alignment explanation
Indices: 297348--297383 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
297338 CATCTGTTGT
297348 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
297384 ATTAATCCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:309561 original size:54 final size:53
Alignment explanation
Indices: 309493--309797 Score: 164
Period size: 54 Copynumber: 5.5 Consensus size: 53
309483 GGTGCTTGAT
*
309493 TTTAGATTGTAGCACAGAGGTGCTCAATCAT-TCCAATGCACAGAGGTGCCAG
1 TTTAGATTGAAGCACAGAGGTGCTCAATCATATCCAATGCACAGAGGTGCCAG
* **** *
309545 AATTTAGATTGAAGCACAGAGGTGCTCAGTCATAGTTGGTTGCACAGAGGTGTCAG
1 --TTTAGATTGAAGCACAGAGGTGCTCAATCATA-TCCAATGCACAGAGGTGCCAG
* * * * * * *
309601 TCATCGATTGAAGCACAGAGGTGCTCAATCATCT-TAGCTACACAGAGGTGTCAG
1 T-TTAGATTGAAGCACAGAGGTGCTCAATCATATCCA-ATGCACAGAGGTGCCAG
*** ** * * ** *
309655 CTCCCGGCTGAAGCACAGAGGTGCTCAGTCATTTTTTTTAACTGCACAGAGGTGTCAG
1 -TTTAGATTGAAGCACAGAGGTGCTCAATCA---TATCCAA-TGCACAGAGGTGCCAG
* * **** * *
309713 TTCTCGATTGAAGCACAGAGGTGCTCAATCACTTTTGGCTACACAGAGGTGTCAG
1 TT-TAGATTGAAGCACAGAGGTGCTCAATCA-TATCCAATGCACAGAGGTGCCAG
* * *
309768 CTCTCGATTGAAGCACAGAGGTACTCAATC
1 -TTTAGATTGAAGCACAGAGGTGCTCAATC
309798 GTTAATTCTA
Statistics
Matches: 204, Mismatches: 35, Indels: 23
0.78 0.13 0.09
Matches are distributed among these distances:
54 70 0.34
55 69 0.34
56 21 0.10
57 3 0.01
58 41 0.20
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (53 bp):
TTTAGATTGAAGCACAGAGGTGCTCAATCATATCCAATGCACAGAGGTGCCAG
Found at i:309589 original size:28 final size:28
Alignment explanation
Indices: 309495--309739 Score: 113
Period size: 27 Copynumber: 8.9 Consensus size: 28
309485 TGCTTGATTT
* *
309495 TAGATTGTAGCACAGAGGTGCTCAATCA
1 TAGATTGAAGCACAGAGGTGCTCAGTCA
** *
309523 T---TCCAATGCACAGAGGTGC-CAGAAT-T
1 TAGATTGAA-GCACAGAGGTGCTCAG--TCA
309549 TAGATTGAAGCACAGAGGTGCTCAGTCA
1 TAGATTGAAGCACAGAGGTGCTCAGTCA
**
309577 TAG-TTGGTTGCACAGAGGTG-TCAGTCA
1 TAGATT-GAAGCACAGAGGTGCTCAGTCA
* *
309604 TCGATTGAAGCACAGAGGTGCTCAATCA
1 TAGATTGAAGCACAGAGGTGCTCAGTCA
* *
309632 T--CTTAGCTA-CACAGAGGTG-TCAGCTC-
1 TAGATT-G-AAGCACAGAGGTGCTCAG-TCA
** **
309658 CCGGCTGAAGCACAGAGGTGCTCAGTCA
1 TAGATTGAAGCACAGAGGTGCTCAGTCA
*** *
309686 TTTTTTTTAACTGCACAGAGGTG-TCAGTTC-
1 -TAGATTGAA--GCACAGAGGTGCTCAG-TCA
*
309716 TCGATTGAAGCACAGAGGTGCTCA
1 TAGATTGAAGCACAGAGGTGCTCA
309740 ATCACTTTTG
Statistics
Matches: 162, Mismatches: 31, Indels: 48
0.67 0.13 0.20
Matches are distributed among these distances:
25 4 0.02
26 19 0.12
27 62 0.38
28 46 0.28
29 14 0.09
30 4 0.02
31 13 0.08
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (28 bp):
TAGATTGAAGCACAGAGGTGCTCAGTCA
Found at i:309616 original size:27 final size:28
Alignment explanation
Indices: 309551--309794 Score: 145
Period size: 27 Copynumber: 8.8 Consensus size: 28
309541 CCAGAATTTA
*
309551 GATTGAAGCACAGAGGTGCTCAGTCATA
1 GATTGAAGCACAGAGGTGCTCAGTCATC
**
309579 G-TTGGTTGCACAGAGGTG-TCAGTCATC
1 GATT-GAAGCACAGAGGTGCTCAGTCATC
*
309606 GATTGAAGCACAGAGGTGCTCAATCATC
1 GATTGAAGCACAGAGGTGCTCAGTCATC
* *
309634 --TTAGCTA-CACAGAGGTG-TCAGCTC-CC
1 GATT-G-AAGCACAGAGGTGCTCAG-TCATC
** *
309660 GGCTGAAGCACAGAGGTGCTCAGTCATTT
1 GATTGAAGCACAGAGGTGCTCAGTCA-TC
** *
309689 TTTTTAACTGCACAGAGGTG-TCAGTTC-TC
1 GATTGAA--GCACAGAGGTGCTCAG-TCATC
*
309718 GATTGAAGCACAGAGGTGCTCAATCA-C
1 GATTGAAGCACAGAGGTGCTCAGTCATC
** *
309745 TTTTGGCTA-CACAGAGGTG-TCAGCTC-TC
1 GATT-G-AAGCACAGAGGTGCTCAG-TCATC
*
309773 GATTGAAGCACAGAGGTACTCA
1 GATTGAAGCACAGAGGTGCTCA
309795 ATCGTTAATT
Statistics
Matches: 163, Mismatches: 30, Indels: 46
0.68 0.13 0.19
Matches are distributed among these distances:
26 8 0.05
27 78 0.48
28 51 0.31
29 9 0.06
30 4 0.02
31 13 0.08
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (28 bp):
GATTGAAGCACAGAGGTGCTCAGTCATC
Found at i:309621 original size:55 final size:54
Alignment explanation
Indices: 309497--309797 Score: 291
Period size: 55 Copynumber: 5.5 Consensus size: 54
309487 CTTGATTTTA
* **** * * * * *
309497 GATTGTAGCACAGAGGTGCTCAATCA-TTCCAATGCACAGAGGTGCCAGAATTTA
1 GATTGAAGCACAGAGGTGCTCAATCATTTTGGCTACACAGAGGTGTCAG-CTCTC
* * * *
309551 GATTGAAGCACAGAGGTGCTCAGTCATAGTTGGTTGCACAGAGGTGTCAG-TCATC
1 GATTGAAGCACAGAGGTGCTCAATCAT-TTTGGCTACACAGAGGTGTCAGCTC-TC
* * *
309606 GATTGAAGCACAGAGGTGCTCAATCATCTTAGCTACACAGAGGTGTCAGCTCCC
1 GATTGAAGCACAGAGGTGCTCAATCATTTTGGCTACACAGAGGTGTCAGCTCTC
** * ** * *
309660 GGCTGAAGCACAGAGGTGCTCAGTCATTTTTTTTAACTGCACAGAGGTGTCAGTTCTC
1 GATTGAAGCACAGAGGTGCTCAATCA----TTTTGGCTACACAGAGGTGTCAGCTCTC
309718 GATTGAAGCACAGAGGTGCTCAATCACTTTTGGCTACACAGAGGTGTCAGCTCTC
1 GATTGAAGCACAGAGGTGCTCAATCA-TTTTGGCTACACAGAGGTGTCAGCTCTC
*
309773 GATTGAAGCACAGAGGTACTCAATC
1 GATTGAAGCACAGAGGTGCTCAATC
309798 GTTAATTCTA
Statistics
Matches: 206, Mismatches: 33, Indels: 15
0.81 0.13 0.06
Matches are distributed among these distances:
54 67 0.33
55 77 0.37
56 16 0.08
58 46 0.22
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.25
Consensus pattern (54 bp):
GATTGAAGCACAGAGGTGCTCAATCATTTTGGCTACACAGAGGTGTCAGCTCTC
Found at i:310048 original size:81 final size:81
Alignment explanation
Indices: 309913--310070 Score: 253
Period size: 81 Copynumber: 2.0 Consensus size: 81
309903 GCGAGTTACA
* *
309913 AAGAATGGTTCACACACGAAATGGCGGAGCAACAAGCTCTCACAGAGGTGTAGAGTAGGAAGTTA
1 AAGAATGGTTCACACACGAAATGGCGGAGCAACAAGCTCTCACAGAGGTGTAGAGCAGGAAGCTA
* *
309978 CTGAGCCGGTTGCACC
66 CCGAGCCAGTTGCACC
* * *
309994 AAGAATGGTTCGCACACGAAATGGCGGATCGACAAGCTCTCACAGAGGTGTAGAGCAGGAAGCTA
1 AAGAATGGTTCACACACGAAATGGCGGAGCAACAAGCTCTCACAGAGGTGTAGAGCAGGAAGCTA
310059 CCGAGCCAGTTG
66 CCGAGCCAGTTG
310071 TGCAAGAGAC
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
81 70 1.00
ACGTcount: A:0.32, C:0.22, G:0.30, T:0.16
Consensus pattern (81 bp):
AAGAATGGTTCACACACGAAATGGCGGAGCAACAAGCTCTCACAGAGGTGTAGAGCAGGAAGCTA
CCGAGCCAGTTGCACC
Found at i:314595 original size:27 final size:29
Alignment explanation
Indices: 314564--314636 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 29
314554 TTATTATTAT
*
314564 TTAATTTTA-ATTTTATTAAGAA-TATAA
1 TTAATTTTATATTTTATTAAAAATTATAA
*
314591 TTAATTTATATTTTTTTATTAAAAATTATAA
1 TTAATTT-TA-TATTTTATTAAAAATTATAA
314622 TT-ATTTTATGATTTT
1 TTAATTTTAT-ATTTT
314637 TATTTGTTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
27 7 0.18
28 3 0.08
29 6 0.16
30 15 0.39
31 7 0.18
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (29 bp):
TTAATTTTATATTTTATTAAAAATTATAA
Found at i:314610 original size:30 final size:32
Alignment explanation
Indices: 314574--314637 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 32
314564 TTAATTTTAA
*
314574 TTTTATTAAGAA-TATAATTAATTTAT-ATTT
1 TTTTATTAAAAATTATAATTAATTTATGATTT
*
314604 TTTTATTAAAAATTATAATTATTTTATGATTT
1 TTTTATTAAAAATTATAATTAATTTATGATTT
314636 TT
1 TT
314638 ATTTGTTTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 11 0.37
31 13 0.43
32 6 0.20
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (32 bp):
TTTTATTAAAAATTATAATTAATTTATGATTT
Found at i:314638 original size:30 final size:30
Alignment explanation
Indices: 314574--314640 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 30
314564 TTAATTTTAA
* *
314574 TTTTATTAAGAATATAATTAATTTATATTT
1 TTTTATTAAAAATATAATTAATTTATATAT
314604 TTTTATTAAAAATTATAATT-ATTT-TATGAT
1 TTTTATTAAAAA-TATAATTAATTTATAT-AT
314634 TTTTATT
1 TTTTATT
314641 TGTTTAGGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 3 0.09
30 23 0.70
31 7 0.21
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (30 bp):
TTTTATTAAAAATATAATTAATTTATATAT
Found at i:319072 original size:20 final size:20
Alignment explanation
Indices: 319043--319081 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
319033 TTTCCACCTC
*
319043 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
319063 ATGCATCTATATGATCCTA
1 ATGCAACTATATGATCCTA
319082 TATGGGATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:336035 original size:95 final size:95
Alignment explanation
Indices: 335872--336057 Score: 291
Period size: 95 Copynumber: 2.0 Consensus size: 95
335862 TCCGGTATCG
* * * *
335872 CAAATCAGTTTTCAGATTCGCAACGCGAATTTTGACTATCGCATTACGATTTACATATTCGCATT
1 CAAATCAATTTCCAGATTCGCAACGCGAACTTCGACTATCGCATTACGATTTACATATTCGCATT
*
335937 GCGATAGTCTAAGTTCGAGTTGCGATTTTC
66 GCGATAGTCGAAGTTCGAGTTGCGATTTTC
* * *
335967 CAAATCAATTTCCAGATTCGTAACGCGAACTTCGACTATCGTATTGCGATTTACATATTCGCATT
1 CAAATCAATTTCCAGATTCGCAACGCGAACTTCGACTATCGCATTACGATTTACATATTCGCATT
*
336032 GCGATAGTCGAAGTTCGCGTTGCGAT
66 GCGATAGTCGAAGTTCGAGTTGCGAT
336058 AGTCAAAGTT
Statistics
Matches: 82, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
95 82 1.00
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (95 bp):
CAAATCAATTTCCAGATTCGCAACGCGAACTTCGACTATCGCATTACGATTTACATATTCGCATT
GCGATAGTCGAAGTTCGAGTTGCGATTTTC
Found at i:336054 original size:21 final size:21
Alignment explanation
Indices: 336024--336249 Score: 130
Period size: 21 Copynumber: 11.0 Consensus size: 21
336014 GATTTACATA
* *
336024 TTCGCATTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
*
336045 TTCGCGTTGCGATAGTCAAAG
1 TTCGCGTTGCGATAGTCCAAG
** *
336066 TTCGCGTTGCGATTTTCCAAA
1 TTCGCGTTGCGATAGTCCAAG
*
336087 TT--CGTTGTGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
* * *
336106 TTCGCGTTGCGATTTATTCTAAA
1 TTCGCGTTGCGA--TAGTCCAAG
*
336129 TT--TGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
* * *
336148 TTCGCGTTGCGATTTATTACAAA
1 TTCGCGTTGCGA--TAGTCCAAG
* *
336171 TT--CGTTGTGATAGTCCAAA
1 TTCGCGTTGCGATAGTCCAAG
* * *
336190 TT--TGTTGCTATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* * *
336209 TTCGCTTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
336232 TT--CGTTGCGATAGTCCAA
1 TTCGCGTTGCGATAGTCCAA
336250 AATCGCATCG
Statistics
Matches: 155, Mismatches: 38, Indels: 26
0.71 0.17 0.12
Matches are distributed among these distances:
19 53 0.34
21 78 0.50
23 24 0.15
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.37
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:336076 original size:42 final size:40
Alignment explanation
Indices: 336049--336188 Score: 181
Period size: 42 Copynumber: 3.4 Consensus size: 40
336039 TCGAAGTTCG
* *
336049 CGTTGCGATAGTCAAAGTTCGCGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATATTCCAAATT
* *
336089 CGTTGTGATAGTCCAAGTTCGCGTTGCGATTTATTCTAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGA--TATTCCAAATT
* *
336131 TGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTACAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGA--TATTCCAAATT
*
336173 CGTTGTGATAGTCCAA
1 CGTTGCGATAGTCCAA
336189 ATTTGTTGCT
Statistics
Matches: 88, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
40 27 0.31
42 61 0.69
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.37
Consensus pattern (40 bp):
CGTTGCGATAGTCCAAGTTCGCGTTGCGATATTCCAAATT
Found at i:336155 original size:103 final size:102
Alignment explanation
Indices: 336030--336249 Score: 284
Period size: 103 Copynumber: 2.1 Consensus size: 102
336020 CATATTCGCA
* **
336030 TTGCGATAGTCGAAGTTCGCGTTGCGA-TAGT-CAAAGTTCGCGTTGCGATTTTCCAAATTCGTT
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTAGTACAAA-TT--CGTTGCGATAGTCCAAATTCGTT
* *
336093 G-TGATAGTCCAAGTTCGCGTTGCGATTTATTCTAAATTTG
63 GCT-ATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
* * *
336133 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTACAAATTCGTTGTGATAGTCCAAATTTGTTGC
1 TTGCGATAGTCCAAGTTCGCGTTGCGA-TTAGTACAAATTCGTTGCGATAGTCCAAATTCGTTGC
* *
336198 TATAGTCGAAGTTCGCTTTGCGATTTATTCCAAATTCG
65 TATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
336236 TTGCGATAGTCCAA
1 TTGCGATAGTCCAA
336250 AATCGCATCG
Statistics
Matches: 103, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
103 93 0.90
104 1 0.01
105 5 0.05
106 4 0.04
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.37
Consensus pattern (102 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATTAGTACAAATTCGTTGCGATAGTCCAAATTCGTTGCT
ATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
Found at i:336191 original size:61 final size:61
Alignment explanation
Indices: 336126--336250 Score: 205
Period size: 61 Copynumber: 2.0 Consensus size: 61
336116 GATTTATTCT
*
336126 AAATTTGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTACAAATTCGTTGTGATAGTCC
1 AAATTTGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTACAAATTCGTTGCGATAGTCC
* * * *
336187 AAATTTGTTGCTATAGTCGAAGTTCGCTTTGCGATTTATTCCAAATTCGTTGCGATAGTCC
1 AAATTTGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTACAAATTCGTTGCGATAGTCC
336248 AAA
1 AAA
336251 ATCGCATCGA
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
61 59 1.00
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.38
Consensus pattern (61 bp):
AAATTTGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTACAAATTCGTTGCGATAGTCC
Found at i:346253 original size:20 final size:20
Alignment explanation
Indices: 346228--346265 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
346218 ATCCTATTAT
*
346228 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTATATTCCCA
346248 CTGGTAATCTTATATTCC
1 CTGGTAATCTTATATTCC
346266 GTGAATCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.24, G:0.11, T:0.45
Consensus pattern (20 bp):
CTGGTAATCTTATATTCCCA
Found at i:348045 original size:18 final size:17
Alignment explanation
Indices: 348004--348037 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
347994 TATTTTTAAA
* *
348004 CAATTAATTTTAAAACT
1 CAATAAATTTTAAAAAT
348021 CAATAAATTTTAAAAAT
1 CAATAAATTTTAAAAAT
348038 TATATAAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (17 bp):
CAATAAATTTTAAAAAT
Found at i:352790 original size:14 final size:15
Alignment explanation
Indices: 352752--352794 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 15
352742 TTGATTTTTC
352752 GGAAAATGAATTACT
1 GGAAAATGAATTACT
**
352767 GGAATTTGAATT-CT
1 GGAAAATGAATTACT
352781 GGAAAATGAATTAC
1 GGAAAATGAATTAC
352795 ATTTCTGGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.42, C:0.07, G:0.21, T:0.30
Consensus pattern (15 bp):
GGAAAATGAATTACT
Found at i:352800 original size:20 final size:20
Alignment explanation
Indices: 352777--352826 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
352767 GGAATTTGAA
352777 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
352797 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
*
352817 TTATGGAAAA
1 TTCTGGAAAA
352827 CGTTTTCCGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.42, C:0.08, G:0.16, T:0.34
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:353016 original size:22 final size:22
Alignment explanation
Indices: 352970--353010 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
352960 ATATAATAAA
352970 TAATATTATTTATTATAAAACT
1 TAATATTATTTATTATAAAACT
*
352992 TAATATTA-TTATTTTAAAA
1 TAATATTATTTATTATAAAA
353011 TTTTAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (22 bp):
TAATATTATTTATTATAAAACT
Found at i:353194 original size:23 final size:23
Alignment explanation
Indices: 353145--353207 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
353135 GTGTTATATT
* **
353145 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAATATATTAATTAAA
* *
353168 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAATATATTAATTAAA
353191 ATATTATTTAAATATAT
1 ATA-T-TTTAAATATAT
353208 AAATAATATT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
23 21 0.66
24 1 0.03
25 10 0.31
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAATATATTAATTAAA
Found at i:353217 original size:19 final size:19
Alignment explanation
Indices: 353183--353239 Score: 53
Period size: 19 Copynumber: 2.8 Consensus size: 19
353173 TTAAATATCT
*
353183 TTATTAAAATATTATTTAAA
1 TTATT-AAATAATATTTAAA
*
353203 -TATATAAATAATATTATTAA
1 TTAT-TAAATAATATT-TAAA
353223 TTATTAAATATATATTT
1 TTATTAAATA-ATATTT
353240 TTTTTTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
19 12 0.39
20 11 0.35
21 8 0.26
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TTATTAAATAATATTTAAA
Found at i:353218 original size:22 final size:20
Alignment explanation
Indices: 353190--353238 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 20
353180 TCTTTATTAA
353190 AATATTATTTAAATATATAAAT
1 AATATTA-TTAAATAT-TAAAT
*
353212 AATATTATTAATTATTAAAT
1 AATATTATTAAATATTAAAT
353232 ATATATT
1 A-ATATT
353239 TTTTTTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 6 0.24
21 12 0.48
22 7 0.28
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AATATTATTAAATATTAAAT
Found at i:353255 original size:60 final size:59
Alignment explanation
Indices: 353182--353342 Score: 150
Period size: 60 Copynumber: 2.7 Consensus size: 59
353172 TTTAAATATC
* * * **
353182 TTTATTAAAATATTATTTAAATATATAAATAATATTATTA-ATTATTA-AATATATATTTTTT
1 TTTATT-ATATATTATTAAAATAT--AAATTATATTATTATATTATTATAATATA-ATTGATT
*
353243 TTTATTATATATTATTAAAATA-AAATTATAATATCTTATATTATTATAATATAATTGATT
1 TTTATTATATATTATTAAAATATAAATTAT-AT-TATTATATTATTATAATATAATTGATT
* *
353303 ATT-TTATATAATATTAAAAATATAATATTATATTATTATA
1 TTTATTATATATTATT-AAAATATAA-ATTATATTATTATA
353343 AATATTAATA
Statistics
Matches: 84, Mismatches: 9, Indels: 15
0.78 0.08 0.14
Matches are distributed among these distances:
57 6 0.07
58 2 0.02
59 15 0.18
60 40 0.48
61 16 0.19
62 5 0.06
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.52
Consensus pattern (59 bp):
TTTATTATATATTATTAAAATATAAATTATATTATTATATTATTATAATATAATTGATT
Found at i:353334 original size:22 final size:23
Alignment explanation
Indices: 353309--353352 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
353299 GATTATTTTA
353309 TATAATATTAAAAATA-TAATAT
1 TATAATATTAAAAATATTAATAT
* *
353331 TATATTATTATAAATATTAATA
1 TATAATATTAAAAATATTAATA
353353 AATAAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TATAATATTAAAAATATTAATAT
Found at i:358805 original size:2 final size:2
Alignment explanation
Indices: 358798--358822 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
358788 AAATAAATAA
358798 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
358823 AGAATTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:360349 original size:5 final size:5
Alignment explanation
Indices: 360339--360388 Score: 50
Period size: 5 Copynumber: 9.8 Consensus size: 5
360329 ATACGTTTCA
*
360339 TATTT TATTT TA-TT T-TTT TATTT TATTCT TATTAT TCTTAT TATTT
1 TATTT TATTT TATTT TATTT TATTT TATT-T TATT-T TATT-T TATTT
360385 TATT
1 TATT
360389 ACTTTTACAA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
4 6 0.15
5 19 0.49
6 14 0.36
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (5 bp):
TATTT
Found at i:360394 original size:9 final size:8
Alignment explanation
Indices: 360343--360395 Score: 52
Period size: 9 Copynumber: 6.0 Consensus size: 8
360333 GTTTCATATT
360343 TTATTTTA
1 TTATTTTA
*
360351 TTTTTTTA
1 TTATTTTA
360359 TTTTATTCTTA
1 --TTATT-TTA
360370 TTATTCTTA
1 TTATT-TTA
360379 TTATTTTA
1 TTATTTTA
360387 TTACTTTTA
1 TTA-TTTTA
360396 CAATATTTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
8 13 0.33
9 19 0.49
10 4 0.10
11 3 0.08
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.74
Consensus pattern (8 bp):
TTATTTTA
Found at i:360540 original size:22 final size:22
Alignment explanation
Indices: 360515--360557 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
360505 TTATATTATA
360515 TTAC-TATTATTATTATTCTATT
1 TTACTTATTATTA-TATTCTATT
*
360537 TTACTTATTTTTATATTCTAT
1 TTACTTATTATTATATTCTAT
360558 CTATTTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.65
Consensus pattern (22 bp):
TTACTTATTATTATATTCTATT
Found at i:360553 original size:17 final size:17
Alignment explanation
Indices: 360533--360572 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
360523 ATTATTATTC
360533 TATTTTA-CTTATTTTTA
1 TATTTTATC-TATTTTTA
*
360550 TATTCTATCTATTTTTA
1 TATTTTATCTATTTTTA
360567 TATTTT
1 TATTTT
360573 CTTTTTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 19 0.95
18 1 0.05
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (17 bp):
TATTTTATCTATTTTTA
Found at i:360581 original size:19 final size:17
Alignment explanation
Indices: 360495--360584 Score: 54
Period size: 17 Copynumber: 4.8 Consensus size: 17
360485 TTTTTTTGTT
360495 TTCTATTTATTTATATTATA
1 TTCTATTTA-TT-T-TTATA
* *
360515 TTACTATTATTATTATTCTA
1 TT-CTA-T-TTATTTTTATA
* *
360535 TTTTACTTATTTTTATA
1 TTCTATTTATTTTTATA
*
360552 TTCTATCTATTTTTATA
1 TTCTATTTATTTTTATA
*
360569 TTTTCTTTTTATTTTT
1 --TTCTATTTATTTTT
360585 TAATCTTTTT
Statistics
Matches: 54, Mismatches: 11, Indels: 11
0.71 0.14 0.14
Matches are distributed among these distances:
17 23 0.43
19 14 0.26
20 8 0.15
21 3 0.06
22 3 0.06
23 3 0.06
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (17 bp):
TTCTATTTATTTTTATA
Found at i:360827 original size:17 final size:17
Alignment explanation
Indices: 360794--360839 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 17
360784 TTTTCATCTT
* *
360794 TTTTATTT-TTTTTTTG
1 TTTTATTTCATTTGTTG
360810 TTTTATTTCATTTGTTG
1 TTTTATTTCATTTGTTG
360827 TTTTATTTCATTT
1 TTTTATTTCATTT
360840 TATTTATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
16 8 0.30
17 19 0.70
ACGTcount: A:0.11, C:0.04, G:0.07, T:0.78
Consensus pattern (17 bp):
TTTTATTTCATTTGTTG
Found at i:367978 original size:24 final size:25
Alignment explanation
Indices: 367946--367996 Score: 77
Period size: 24 Copynumber: 2.0 Consensus size: 25
367936 CAAATCCAAT
367946 CCGATCCAAAAAA-ATAACCGAAAA
1 CCGATCCAAAAAACATAACCGAAAA
367970 CCGATCCAAAAAACCGATAACCGAAAA
1 CCGATCCAAAAAA-C-ATAACCGAAAA
367997 AAATCGAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 13 0.54
27 11 0.46
ACGTcount: A:0.55, C:0.27, G:0.10, T:0.08
Consensus pattern (25 bp):
CCGATCCAAAAAACATAACCGAAAA
Found at i:372458 original size:45 final size:44
Alignment explanation
Indices: 372390--372495 Score: 176
Period size: 45 Copynumber: 2.4 Consensus size: 44
372380 TCTGGAATGC
372390 TTTAAATTTGAACAATTGCACAACTTTTAGTAGTGTATTTAGGG
1 TTTAAATTTGAACAATTGCACAACTTTTAGTAGTGTATTTAGGG
* *
372434 TTTAGAATTTAAACAATTGCACAACTTTTAGTAGTGTATTTGGGG
1 TTTA-AATTTGAACAATTGCACAACTTTTAGTAGTGTATTTAGGG
372479 TTTAAAATTTGAACAAT
1 TTT-AAATTTGAACAAT
372496 GTGCTATTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
44 4 0.07
45 52 0.91
46 1 0.02
ACGTcount: A:0.34, C:0.08, G:0.17, T:0.41
Consensus pattern (44 bp):
TTTAAATTTGAACAATTGCACAACTTTTAGTAGTGTATTTAGGG
Found at i:373656 original size:45 final size:44
Alignment explanation
Indices: 373592--373697 Score: 176
Period size: 45 Copynumber: 2.4 Consensus size: 44
373582 CAAATAGCAC
373592 ATTGTTCAAATTTTAAACCCCAAATACACTACTAAAAGTTGTGCA
1 ATTGTTCAAA-TTTAAACCCCAAATACACTACTAAAAGTTGTGCA
* *
373637 ATTGTTTAAATTCTAAACCCTAAATACACTACTAAAAGTTGTGCA
1 ATTGTTCAAATT-TAAACCCCAAATACACTACTAAAAGTTGTGCA
373682 ATTGTTCAAATTTAAA
1 ATTGTTCAAATTTAAA
373698 GCATTCTAGA
Statistics
Matches: 57, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
44 6 0.11
45 51 0.89
ACGTcount: A:0.41, C:0.17, G:0.08, T:0.34
Consensus pattern (44 bp):
ATTGTTCAAATTTAAACCCCAAATACACTACTAAAAGTTGTGCA
Found at i:382514 original size:59 final size:56
Alignment explanation
Indices: 382380--382550 Score: 180
Period size: 59 Copynumber: 2.9 Consensus size: 56
382370 GTATATACAT
* * * ** *
382380 ATAGTTTAGGATGAAATTGGAATGTCCAAAAAGTTTGGGGACCAATTTAGAATGGTC
1 ATAGTTTAGGATGAAATTGAAATATTC-AAAAGTTTGAAGAACAATTTAGAATGGTC
* * *
382437 ATAGTTCGAGGATGAAATTGAAATATTCAAAAGTTTGAAGAATAATTTAGAATTATGTC
1 ATAGTT-TAGGATGAAATTGAAATATTCAAAAGTTTGAAGAACAATTTAGAA-T-GGTC
* * *
382496 ATAGTTTATGGATGAAATTGAAATATTCAAAGGTTTTAAGAACCAATTTAAAATG
1 ATAGTTTA-GGATGAAATTGAAATATTCAAAAGTTTGAAGAA-CAATTTAGAATG
382551 AGGATCATAC
Statistics
Matches: 94, Mismatches: 15, Indels: 9
0.80 0.13 0.08
Matches are distributed among these distances:
57 26 0.28
58 19 0.20
59 41 0.44
60 8 0.09
ACGTcount: A:0.40, C:0.06, G:0.20, T:0.33
Consensus pattern (56 bp):
ATAGTTTAGGATGAAATTGAAATATTCAAAAGTTTGAAGAACAATTTAGAATGGTC
Found at i:389784 original size:11 final size:11
Alignment explanation
Indices: 389768--389805 Score: 58
Period size: 11 Copynumber: 3.3 Consensus size: 11
389758 ACAGCAGCCC
389768 CCCCTTAGCAG
1 CCCCTTAGCAG
389779 CCCCTTAGCAG
1 CCCCTTAGCAG
389790 CCCCCCTTAGCAG
1 --CCCCTTAGCAG
389803 CCC
1 CCC
389806 ATGTGTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 14 0.56
13 11 0.44
ACGTcount: A:0.16, C:0.53, G:0.16, T:0.16
Consensus pattern (11 bp):
CCCCTTAGCAG
Found at i:389795 original size:13 final size:13
Alignment explanation
Indices: 389760--389805 Score: 69
Period size: 13 Copynumber: 3.6 Consensus size: 13
389750 AAAAAATTAC
389760 AGCAGCCCCCCCTT
1 AGCAG-CCCCCCTT
389774 AGCAG--CCCCTT
1 AGCAGCCCCCCTT
389785 AGCAGCCCCCCTT
1 AGCAGCCCCCCTT
389798 AGCAGCCC
1 AGCAGCCC
389806 ATGTGTTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
11 11 0.37
13 14 0.47
14 5 0.17
ACGTcount: A:0.17, C:0.52, G:0.17, T:0.13
Consensus pattern (13 bp):
AGCAGCCCCCCTT
Found at i:393093 original size:15 final size:16
Alignment explanation
Indices: 393065--393096 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
393055 AAAATCTTTC
393065 TTTCCCGTTCTGGATT
1 TTTCCCGTTCTGGATT
393081 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTGGATT
393096 T
1 T
393097 GGATCTGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.06, C:0.25, G:0.19, T:0.50
Consensus pattern (16 bp):
TTTCCCGTTCTGGATT
Found at i:394013 original size:12 final size:13
Alignment explanation
Indices: 393990--394034 Score: 83
Period size: 13 Copynumber: 3.5 Consensus size: 13
393980 AAAAAATTAC
393990 AGCAGCCCCCCTT
1 AGCAGCCCCCCTT
394003 AGCAG-CCCCCTT
1 AGCAGCCCCCCTT
394015 AGCAGCCCCCCTT
1 AGCAGCCCCCCTT
394028 AGCAGCC
1 AGCAGCC
394035 ATGTGTTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.39
13 19 0.61
ACGTcount: A:0.18, C:0.51, G:0.18, T:0.13
Consensus pattern (13 bp):
AGCAGCCCCCCTT
Found at i:395779 original size:8 final size:10
Alignment explanation
Indices: 395757--395781 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
395747 AACCTATGCT
395757 TATATTAAAA
1 TATATTAAAA
395767 TATATTAAAA
1 TATATTAAAA
395777 TATAT
1 TATAT
395782 AATTTTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
TATATTAAAA
Found at i:407950 original size:12 final size:12
Alignment explanation
Indices: 407933--407957 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
407923 TAAAATTTGA
407933 ACTTCCAATCTT
1 ACTTCCAATCTT
407945 ACTTCCAATCTT
1 ACTTCCAATCTT
407957 A
1 A
407958 TTTAAAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.32, G:0.00, T:0.40
Consensus pattern (12 bp):
ACTTCCAATCTT
Found at i:408380 original size:2 final size:2
Alignment explanation
Indices: 408373--408404 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
408363 ATTCTAATCT
408373 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
408405 ATTTTTCAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.