Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015273.1 Kokia drynarioides strain JFW-HI SEQ_130318, 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: 423685
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 472 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:293845 original size:19 final size:18
Alignment explanation
Indices: 293800--293846 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 18
293790 TGTTATTATT
293800 ATTATTATTATTATTAAA
1 ATTATTATTATTATTAAA
*
293818 AATAGTTATTATTATTAATA
1 ATTA-TTATTATTATTAA-A
293838 ATTATTATT
1 ATTATTATT
293847 GATATAACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 3 0.12
19 18 0.72
20 4 0.16
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (18 bp):
ATTATTATTATTATTAAA
Found at i:294594 original size:14 final size:15
Alignment explanation
Indices: 294571--294599 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
294561 AATTTGGACA
294571 TGTAATTTGGACTTT
1 TGTAATTTGGACTTT
294586 TGTAA-TTGGACTTT
1 TGTAATTTGGACTTT
294600 ATAATAATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.21, C:0.07, G:0.21, T:0.52
Consensus pattern (15 bp):
TGTAATTTGGACTTT
Found at i:294640 original size:12 final size:12
Alignment explanation
Indices: 294610--294702 Score: 50
Period size: 11 Copynumber: 8.0 Consensus size: 12
294600 ATAATAATCT
294610 TTTAAATTTTAAA
1 TTTAAA-TTTAAA
**
294623 AATAAATTTAAA
1 TTTAAATTTAAA
*
294635 TTTAAA-TTGAA
1 TTTAAATTTAAA
*
294646 TTTAAAATT-AA
1 TTTAAATTTAAA
* **
294657 TTTAAAATCGAA
1 TTTAAATTTAAA
*
294669 TTTAAA-ATAAA
1 TTTAAATTTAAA
* *
294680 TCTAAGTTTAAA
1 TTTAAATTTAAA
*
294692 -ATAAATTTAAA
1 TTTAAATTTAAA
294703 AGGGGCTCGG
Statistics
Matches: 63, Mismatches: 14, Indels: 8
0.74 0.16 0.09
Matches are distributed among these distances:
11 35 0.56
12 24 0.38
13 4 0.06
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.41
Consensus pattern (12 bp):
TTTAAATTTAAA
Found at i:294649 original size:11 final size:12
Alignment explanation
Indices: 294633--294676 Score: 65
Period size: 11 Copynumber: 3.8 Consensus size: 12
294623 AATAAATTTA
294633 AATTT-AAATTG
1 AATTTAAAATTG
294644 AATTTAAAATT-
1 AATTTAAAATTG
*
294655 AATTTAAAATCG
1 AATTTAAAATTG
294667 AATTTAAAAT
1 AATTTAAAAT
294677 AAATCTAAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 15 0.50
12 15 0.50
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.41
Consensus pattern (12 bp):
AATTTAAAATTG
Found at i:294656 original size:23 final size:24
Alignment explanation
Indices: 294625--294680 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 24
294615 ATTTTAAAAA
* *
294625 TAAATTTAAATTT-AAATTGAATT
1 TAAAATTAAATTTAAAATCGAATT
294648 TAAAATT-AATTTAAAATCGAATT
1 TAAAATTAAATTTAAAATCGAATT
294671 TAAAA-TAAAT
1 TAAAATTAAAT
294681 CTAAGTTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 6 0.21
23 23 0.79
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.41
Consensus pattern (24 bp):
TAAAATTAAATTTAAAATCGAATT
Found at i:294679 original size:28 final size:28
Alignment explanation
Indices: 294650--294703 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
294640 ATTGAATTTA
*
294650 AAAT-TAA-TTTAAAATCGAATTTAAAAT
1 AAATCTAAGTTTAAAAT-AAATTTAAAAT
294677 AAATCTAAGTTTAAAATAAATTTAAAA
1 AAATCTAAGTTTAAAATAAATTTAAAA
294704 GGGGCTCGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 4 0.17
28 12 0.50
29 8 0.33
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (28 bp):
AAATCTAAGTTTAAAATAAATTTAAAAT
Found at i:294680 original size:16 final size:17
Alignment explanation
Indices: 294661--294697 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
294651 AATTAATTTA
294661 AAATCGAA-TTTAAAAT
1 AAATCGAAGTTTAAAAT
*
294677 AAATCTAAGTTTAAAAT
1 AAATCGAAGTTTAAAAT
294694 AAAT
1 AAAT
294698 TTAAAAGGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.32
Consensus pattern (17 bp):
AAATCGAAGTTTAAAAT
Found at i:296190 original size:30 final size:29
Alignment explanation
Indices: 296146--296408 Score: 205
Period size: 29 Copynumber: 9.0 Consensus size: 29
296136 TTTTTGATGA
*
296146 TCGGGGG-TAAAATGGTGATTTTTGGAAGT
1 TCGGGGGCAAAAAT-GTGATTTTTGGAAGT
*
296175 TCGGGGGCAAAAATGGTGATTTTTGAAAGT
1 TCGGGGGCAAAAAT-GTGATTTTTGGAAGT
* *
296205 TCGGGGGTAAAAATGTAATTTTAT--AAGT
1 TCGGGGGCAAAAATGTGATTTT-TGGAAGT
* * *
296233 TC-AGGGCAAAAATGTAATTTTTAAGAAGT
1 TCGGGGGCAAAAATGTGATTTTT-GGAAGT
**
296262 TCGAGGGAAAAAAATGTGATTTTTGGAAGT
1 TCG-GGGGCAAAAATGTGATTTTTGGAAGT
* * * *
296292 ACAGGGGTAAAAATATGATTTTTGGAAGT
1 TCGGGGGCAAAAATGTGATTTTTGGAAGT
* * **
296321 ACGGGGGTAAAAATGTGATTTTTATAAGT
1 TCGGGGGCAAAAATGTGATTTTTGGAAGT
* * ** *
296350 T-TGGGGCAAAAATGTAATTTTCAAGAGGT
1 TCGGGGGCAAAAATGTGATTTT-TGGAAGT
* *
296379 TCGAGGGTC-AAAATGTAATTTTTGGAAGT
1 TCG-GGGGCAAAAATGTGATTTTTGGAAGT
296408 T
1 T
296409 TAAGAGTTAA
Statistics
Matches: 192, Mismatches: 32, Indels: 20
0.79 0.13 0.08
Matches are distributed among these distances:
26 1 0.01
27 17 0.09
28 23 0.12
29 78 0.41
30 53 0.28
31 20 0.10
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.33
Consensus pattern (29 bp):
TCGGGGGCAAAAATGTGATTTTTGGAAGT
Found at i:296284 original size:58 final size:57
Alignment explanation
Indices: 296146--296496 Score: 216
Period size: 58 Copynumber: 6.0 Consensus size: 57
296136 TTTTTGATGA
* * *
296146 TCGGGGGT-AAAATGGTGATTTT-TGGAAGTTCGGGGGCAAAAATGGTGATTTTTGA-AAGT
1 TCGGGGGTAAAAAT-GTGATTTTAT--AAGTTC-AGGGCAAAAAT-GTAATTTTTAAGAAGT
*
296205 TCGGGGGTAAAAATGTAATTTTATAAGTTCAGGGCAAAAATGTAATTTTTAAGAAGT
1 TCGGGGGTAAAAATGTGATTTTATAAGTTCAGGGCAAAAATGTAATTTTTAAGAAGT
** * * * * *
296262 TCGAGGGAAAAAAATGTGATTTT-TGGAAGTACAGGGGTAAAAATATGATTTTT-GGAAGT
1 TCG-GGGGTAAAAATGTGATTTTAT--AAGTTCA-GGGCAAAAATGTAATTTTTAAGAAGT
* ** * *
296321 ACGGGGGTAAAAATGTGATTTTTATAAGTTTGGGGCAAAAATGTAATTTTCAAGAGGT
1 TCGGGGGTAAAAATGTGA-TTTTATAAGTTCAGGGCAAAAATGTAATTTTTAAGAAGT
* * * * * ** *
296379 TCGAGGGTCAAAATGTAATTTT-TGGAAGTTTAAGAGTTAAAATGTAATTTTTGAGAAGT
1 TCGGGGGTAAAAATGTGATTTTAT--AAG-TTCAGGGCAAAAATGTAATTTTTAAGAAGT
* * * * * *
296438 TTGAGGGT-TAAATGTAATTTTTAGAAAGTTTAGGGTC-AAAATGTAATTTTTGAA-AAGT
1 TCGGGGGTAAAAATGTGA-TTTTA-TAAGTTCAGGG-CAAAAATGTAATTTTT-AAGAAGT
296496 T
1 T
296497 TAAGGTTTAA
Statistics
Matches: 231, Mismatches: 43, Indels: 37
0.74 0.14 0.12
Matches are distributed among these distances:
56 10 0.04
57 37 0.16
58 92 0.40
59 69 0.30
60 23 0.10
ACGTcount: A:0.35, C:0.04, G:0.27, T:0.34
Consensus pattern (57 bp):
TCGGGGGTAAAAATGTGATTTTATAAGTTCAGGGCAAAAATGTAATTTTTAAGAAGT
Found at i:296305 original size:117 final size:115
Alignment explanation
Indices: 296154--296555 Score: 382
Period size: 117 Copynumber: 3.4 Consensus size: 115
296144 GATCGGGGGT
* *
296154 AAAATGGTGATTTTTGGAAGTTCGGGGGCAAAAATGGTGATTTTTGAAAGTTCGGGGGTAAAAAT
1 AAAAT-GTGATTTTTGGAAGTTCAGGGGTAAAAAT-GTGATTTTTGAAAGTTCGGGGGTAAAAAT
*
296219 GTAATTTTATAAGTTCAGGGCAAAAATGTAATTTTTAAGAAGTTCGAGGGAAA
64 GTAATTTTATAAGTTTAGGGCAAAAATGTAATTTTTAAGAAGTTCGAGGG-AA
* * * *
296272 AAAATGTGATTTTTGGAAGTACAGGGGTAAAAATATGATTTTTGGAAGTACGGGGGTAAAAATGT
1 AAAATGTGATTTTTGGAAGTTCAGGGGTAAAAATGTGATTTTTGAAAGTTCGGGGGTAAAAATGT
* * * * **
296337 GATTTTTATAAGTTTGGGGCAAAAATGTAATTTTCAAGAGGTTCGAGGGTC
66 -AATTTTATAAGTTTAGGGCAAAAATGTAATTTTTAAGAAGTTCGAGGGAA
* * * * * * * * *
296388 AAAATGTAATTTTTGGAAGTTTAAGAGTTAAAATGTAATTTTTGAGAAGTTTGAGGGT-TAAATG
1 AAAATGTGATTTTTGGAAGTTCAGGGGTAAAAATGTGATTTTTGA-AAGTTCGGGGGTAAAAATG
* ** ***
296452 TAATTTTTAGAAAGTTTAGGGTC-AAAATGTAATTTTTGAA-AAGTTTAAGGTTT
65 TAA-TTTTA-TAAGTTTAGGG-CAAAAATGTAATTTTT-AAGAAGTTCGAGGGAA
* * * *
296505 AAAATGTAATTTTT-GAGGTT-AGGGGGTCAAAATGTAATTTTTGGAAAGTTC
1 AAAATGTGATTTTTGGAAGTTCA-GGGGTAAAAATGTGATTTTT-GAAAGTTC
296556 AGGTTTCAAA
Statistics
Matches: 236, Mismatches: 40, Indels: 18
0.80 0.14 0.06
Matches are distributed among these distances:
115 2 0.01
116 102 0.43
117 124 0.53
118 8 0.03
ACGTcount: A:0.35, C:0.04, G:0.26, T:0.35
Consensus pattern (115 bp):
AAAATGTGATTTTTGGAAGTTCAGGGGTAAAAATGTGATTTTTGAAAGTTCGGGGGTAAAAATGT
AATTTTATAAGTTTAGGGCAAAAATGTAATTTTTAAGAAGTTCGAGGGAA
Found at i:296439 original size:30 final size:30
Alignment explanation
Indices: 296358--296547 Score: 196
Period size: 29 Copynumber: 6.5 Consensus size: 30
296348 GTTTGGGGCA
** * ** *
296358 AAAATGTAATTTTCAAGAGGTTCGAGGGTC
1 AAAATGTAATTTTTGAGAAGTTTAAGGGTT
*
296388 AAAATGTAATTTTTG-GAAGTTTAAGAGTT
1 AAAATGTAATTTTTGAGAAGTTTAAGGGTT
*
296417 AAAATGTAATTTTTGAGAAGTTTGAGGGTT
1 AAAATGTAATTTTTGAGAAGTTTAAGGGTT
*
296447 -AAATGTAATTTTT-AGAAAGTTT-AGGGTC
1 AAAATGTAATTTTTGAG-AAGTTTAAGGGTT
* *
296475 AAAATGTAATTTTTGAAAAGTTTAAGGTTT
1 AAAATGTAATTTTTGAGAAGTTTAAGGGTT
* *
296505 AAAATGTAATTTTTGAG--G-TTAGGGGGTC
1 AAAATGTAATTTTTGAGAAGTTTA-AGGGTT
296533 AAAATGTAATTTTTG
1 AAAATGTAATTTTTG
296548 GAAAGTTCAG
Statistics
Matches: 137, Mismatches: 17, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
27 3 0.02
28 26 0.19
29 62 0.45
30 46 0.34
ACGTcount: A:0.35, C:0.03, G:0.23, T:0.39
Consensus pattern (30 bp):
AAAATGTAATTTTTGAGAAGTTTAAGGGTT
Found at i:296497 original size:58 final size:56
Alignment explanation
Indices: 296331--296554 Score: 202
Period size: 58 Copynumber: 3.9 Consensus size: 56
296321 ACGGGGGTAA
* * * * * * *
296331 AAATGTGATTTTTATAAGTTT-GGGGCAAAAATGTAA-TTTTCAAGAGGTTCGAGGGTCA
1 AAATGTAATTTTT-GAAGTTTAGGGTC-AAAATGTAATTTTTGAA-AAGTTTGAGGGT-T
* * *
296389 AAATGTAATTTTTGGAAGTTTAAGAGTTAAAATGTAATTTTTGAGAAGTTTGAGGGTT
1 AAATGTAATTTTT-GAAGTTT-AGGGTCAAAATGTAATTTTTGAAAAGTTTGAGGGTT
* *
296447 AAATGTAATTTTTAGAAAGTTTAGGGTCAAAATGTAATTTTTGAAAAGTTTAAGGTTT
1 AAATGTAATTTTT-G-AAGTTTAGGGTCAAAATGTAATTTTTGAAAAGTTTGAGGGTT
* *
296505 AAAATGTAATTTTTG-AGGTTAGGGGGTCAAAATGTAATTTTTGGAAAGTT
1 -AAATGTAATTTTTGAAGTTTA--GGGTCAAAATGTAATTTTTGAAAAGTT
296555 CAGGTTTCAA
Statistics
Matches: 140, Mismatches: 19, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
56 5 0.04
58 90 0.64
59 38 0.27
60 7 0.05
ACGTcount: A:0.35, C:0.03, G:0.24, T:0.39
Consensus pattern (56 bp):
AAATGTAATTTTTGAAGTTTAGGGTCAAAATGTAATTTTTGAAAAGTTTGAGGGTT
Found at i:296544 original size:87 final size:86
Alignment explanation
Indices: 296382--296554 Score: 251
Period size: 87 Copynumber: 2.0 Consensus size: 86
296372 AAGAGGTTCG
* * *
296382 AGGGTCAAAATGTAATTTTTGGAAGTTTAAGAGTTAAAATGTAATTTTTGAGAAGTTTGAGGGTT
1 AGGGTCAAAATGTAATTTTTGAAAGTTTAAGAGTTAAAATGTAATTTTTGAG-AGTTAGAGGGTA
296447 AAATGTAATTTTTAGAAAGTTT
65 AAATGTAATTTTTAGAAAGTTT
*
296469 AGGGTCAAAATGTAATTTTTGAAAAGTTTAAG-GTTTAAAATGTAATTTTTGAG-GTTAGGGGGT
1 AGGGTCAAAATGTAATTTTTG-AAAGTTTAAGAG-TTAAAATGTAATTTTTGAGAGTTAGAGGGT
*
296532 CAAAATGTAATTTTTGGAAAGTT
64 -AAAATGTAATTTTTAGAAAGTT
296555 CAGGTTTCAA
Statistics
Matches: 78, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
86 8 0.10
87 42 0.54
88 28 0.36
ACGTcount: A:0.35, C:0.02, G:0.24, T:0.39
Consensus pattern (86 bp):
AGGGTCAAAATGTAATTTTTGAAAGTTTAAGAGTTAAAATGTAATTTTTGAGAGTTAGAGGGTAA
AATGTAATTTTTAGAAAGTTT
Found at i:298394 original size:17 final size:17
Alignment explanation
Indices: 298369--298445 Score: 68
Period size: 17 Copynumber: 4.6 Consensus size: 17
298359 AATTTTTAAT
*
298369 TAAATTTAAATTTAAAA
1 TAAACTTAAATTTAAAA
* *
298386 TGAACTTAAATTCAAAA
1 TAAACTTAAATTTAAAA
* * *
298403 TAAATTTAAATTTATAC
1 TAAACTTAAATTTAAAA
*
298420 TAAA-TTCAAACTTAAAA
1 TAAACTT-AAATTTAAAA
298437 TAAA-TTAAA
1 TAAACTTAAA
298446 AACGGGTTCA
Statistics
Matches: 48, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
16 5 0.10
17 43 0.90
ACGTcount: A:0.56, C:0.06, G:0.01, T:0.36
Consensus pattern (17 bp):
TAAACTTAAATTTAAAA
Found at i:298406 original size:28 final size:28
Alignment explanation
Indices: 298375--298429 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
298365 TAATTAAATT
298375 TAAATTTAAAATGA-ACTTAAATTCAAAA
1 TAAATTTAAAATGATAC-TAAATTCAAAA
* *
298403 TAAATTTAAATTTATACTAAATTCAAA
1 TAAATTTAAAATGATACTAAATTCAAA
298430 CTTAAAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 22 0.92
29 2 0.08
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.36
Consensus pattern (28 bp):
TAAATTTAAAATGATACTAAATTCAAAA
Found at i:298437 original size:34 final size:34
Alignment explanation
Indices: 298369--298442 Score: 89
Period size: 34 Copynumber: 2.2 Consensus size: 34
298359 AATTTTTAAT
*
298369 TAAATTTAAATTTAAAATGAACTTAAATTCAAAA
1 TAAATTTAAATTTAAAATGAAATTAAATTCAAAA
* *
298403 TAAATTTAAATTTATACT-AAATTCAAACTT-AAAA
1 TAAATTTAAATTTAAAATGAAATT-AAA-TTCAAAA
298437 TAAATT
1 TAAATT
298443 AAAAACGGGT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
33 4 0.11
34 29 0.83
35 2 0.06
ACGTcount: A:0.54, C:0.07, G:0.01, T:0.38
Consensus pattern (34 bp):
TAAATTTAAATTTAAAATGAAATTAAATTCAAAA
Found at i:298956 original size:78 final size:77
Alignment explanation
Indices: 298822--299357 Score: 474
Period size: 78 Copynumber: 6.9 Consensus size: 77
298812 GAGAGGGTTA
* * ** *
298822 CAATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGGTGATGATCTGCCTTAGGCTCGGGGTAAGA
1 CAATCTTCCCTAAGCTCGGGGTAAGAGATT-GCTGGTGATGATCTGCCCCAAGCTCGGGGTAAGA
298887 GATCGAACGGCTG
65 GATCGAACGGCTG
* * * *
298900 CAATCTTCCCTAAACTCAGGGTAAGAGACTGACTGGTGATGATCTGCCCCAAGCTCGGGGTTAGA
1 CAATCTTCCCTAAGCTCGGGGTAAGAGATTG-CTGGTGATGATCTGCCCCAAGCTCGGGGTAAGA
*
298965 GATTGAACGGCTG
65 GATCGAACGGCTG
* * * * * * *
298978 CAATCTACCCTAGGCTCGGAGTAAGAGATCGAAC-GGCTGCA--ATCTTCCCTAAGTTCGGGGTA
1 CAATCTTCCCTAAGCTCGGGGTAAGAGATTG--CTGG-TG-ATGATCTGCCCCAAGCTCGGGGTA
**
299040 AGAGATCGAATAGCTG
62 AGAGATCGAACGGCTG
* * * * * * *
299056 CAATCTACCCTAAGCTCGAGGTAAGAAATTTGCTGATAATGATCTGCCCTAAGCTCGGGGTAAGT
1 CAATCTTCCCTAAGCTCGGGGTAAGAGA-TTGCTGGTGATGATCTGCCCCAAGCTCGGGGTAAGA
*
299121 GATCGAATGGCTG
65 GATCGAACGGCTG
** * * *
299134 CAATCTATGTC-AAGCTCGGGGTAAGAGATTGGCTGGTGTTGATCTGCCTCAGGCTCGGGGTAAG
1 CAATCT-TCCCTAAGCTCGGGGTAAGAGATT-GCTGGTGATGATCTGCCCCAAGCTCGGGGTAAG
* *
299198 AGATCGGATGGCTG
64 AGATCGAACGGCTG
* * * * * *
299212 TAAT-TTGCCCCATGATCGGGGTAAGAGATTTGCTGATGATGATCTGCCCCAAGGTCGGGGTAAG
1 CAATCTT-CCCTAAGCTCGGGGTAAGAGA-TTGCTGGTGATGATCTGCCCCAAGCTCGGGGTAAG
299276 AGATCGAACGGCTG
64 AGATCGAACGGCTG
* * * * * * * * *
299290 CAATCTACCCCATGATCGAGGTAAGA-ATTTGCTGATGGTGATCTG-CCCAGGCTCGGGGTAAAA
1 CAATCTTCCCTAAGCTCGGGGTAAGAGA-TTGCTGGTGATGATCTGCCCCAAGCTCGGGGTAAGA
299353 GATCG
65 GATCG
299358 GATCTTTGAT
Statistics
Matches: 377, Mismatches: 67, Indels: 30
0.80 0.14 0.06
Matches are distributed among these distances:
76 22 0.06
77 25 0.07
78 319 0.85
79 10 0.03
80 1 0.00
ACGTcount: A:0.25, C:0.21, G:0.30, T:0.24
Consensus pattern (77 bp):
CAATCTTCCCTAAGCTCGGGGTAAGAGATTGCTGGTGATGATCTGCCCCAAGCTCGGGGTAAGAG
ATCGAACGGCTG
Found at i:299221 original size:117 final size:117
Alignment explanation
Indices: 298824--299240 Score: 403
Period size: 117 Copynumber: 3.6 Consensus size: 117
298814 GAGGGTTACA
* * *
298824 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGG-TGATGATCTGCCTTAGGCTCGGGGTAAGAG
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGATGGCTGATAATCTGCCCTAGGCTCGGGGTAAGAG
* * *
298888 ATCGAACGGCTGCAATCTTCCCTAAACTCAGGGTAAGAGACTGACTGGTGATG
66 ATCGAACGGCTGCAATCTTCCCTAAGCTCGGGGTAAGAGATTGACTGGTG-TG
* * * * * *
298941 ATCTGCCCCAAGCTCGGGGTTAGAGATTGAACGGCTG-CAATCTACCCTAGGCTCGGAGTAAGAG
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGATGGCTGATAATCTGCCCTAGGCTCGGGGTAAGAG
* * * * **
299005 ATCGAACGGCTGCAATCTTCCCTAAGTTCGGGGTAAGAGATCGAATAGCTGCA
66 ATCGAACGGCTGCAATCTTCCCTAAGCTCGGGGTAAGAGATTGACT-GGTGTG
* * * * * * * * * * *
299058 ATCTACCCTAAGCTCGAGGTAAGAAATTTGCT-GATAATGATCTGCCCTAAGCTCGGGGTAAGTG
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGATGGCTGATAATCTGCCCTAGGCTCGGGGTAAGAG
* ** *
299122 ATCGAATGGCTGCAATCTATGTC-AAGCTCGGGGTAAGAGATTGGCTGGTGTTG
66 ATCGAACGGCTGCAATCT-TCCCTAAGCTCGGGGTAAGAGATTGACTGGTG-TG
* * * * * * *
299175 ATCTGCCTCAGGCTCGGGGTAAGAGATCGGATGGCTG-TAATTTGCCCCATGATCGGGGTAAGAG
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGATGGCTGATAATCTGCCCTAGGCTCGGGGTAAGAG
299239 AT
66 AT
299241 TTGCTGATGA
Statistics
Matches: 232, Mismatches: 62, Indels: 12
0.76 0.20 0.04
Matches are distributed among these distances:
116 5 0.02
117 218 0.94
118 9 0.04
ACGTcount: A:0.25, C:0.21, G:0.30, T:0.24
Consensus pattern (117 bp):
ATCTGCCCCAAGCTCGGGGTAAGAGATTGGATGGCTGATAATCTGCCCTAGGCTCGGGGTAAGAG
ATCGAACGGCTGCAATCTTCCCTAAGCTCGGGGTAAGAGATTGACTGGTGTG
Found at i:299301 original size:39 final size:39
Alignment explanation
Indices: 298822--299315 Score: 253
Period size: 39 Copynumber: 12.7 Consensus size: 39
298812 GAGAGGGTTA
* *
298822 CAATCTGCCCCAAGCTCGGGGTAAGAGATTG-GCTGG-TG
1 CAATCTGCCCCAAGCTCGGGGTAAGAGATCGAAC-GGCTG
** *
298860 -ATGATCTGCCTTAGGCTCGGGGTAAGAGATCGAACGGCTG
1 CA--ATCTGCCCCAAGCTCGGGGTAAGAGATCGAACGGCTG
* * * *
298900 CAATCTTCCCTAAACTCAGGGTAAGAGA-CTG-ACTGG-TG
1 CAATCTGCCCCAAGCTCGGGGTAAGAGATC-GAAC-GGCTG
* *
298938 -ATGATCTGCCCCAAGCTCGGGGTTAGAGATTGAACGGCTG
1 CA--ATCTGCCCCAAGCTCGGGGTAAGAGATCGAACGGCTG
* * * *
298978 CAATCTACCCTAGGCTCGGAGTAAGAGATCGAACGGCTG
1 CAATCTGCCCCAAGCTCGGGGTAAGAGATCGAACGGCTG
* * * **
299017 CAATCTTCCCTAAGTTCGGGGTAAGAGATCGAATAGCTG
1 CAATCTGCCCCAAGCTCGGGGTAAGAGATCGAACGGCTG
* * * * * * *
299056 CAATCTACCCTAAGCTCGAGGTAAGAAATTTG--CTGAT-
1 CAATCTGCCCCAAGCTCGGGGTAAGAGA-TCGAACGGCTG
* * * *
299093 AATGATCTGCCCTAAGCTCGGGGTAAGTGATCGAATGGCTG
1 CA--ATCTGCCCCAAGCTCGGGGTAAGAGATCGAACGGCTG
**** * *
299134 CAATCTATGTCAAGCTCGGGGTAAGAGATTG-GCTGG-TG
1 CAATCTGCCCCAAGCTCGGGGTAAGAGATCGAAC-GGCTG
** * * * *
299172 TTGATCTGCCTCAGGCTCGGGGTAAGAGATCGGATGGCTG
1 -CAATCTGCCCCAAGCTCGGGGTAAGAGATCGAACGGCTG
* * * * * * *
299212 TAATTTGCCCCATGATCGGGGTAAGAGATTTG--CTGATG
1 CAATCTGCCCCAAGCTCGGGGTAAGAGA-TCGAACGGCTG
*
299250 -ATGATCTGCCCCAAGGTCGGGGTAAGAGATCGAACGGCTG
1 CA--ATCTGCCCCAAGCTCGGGGTAAGAGATCGAACGGCTG
* * * *
299290 CAATCTACCCCATGATCGAGGTAAGA
1 CAATCTGCCCCAAGCTCGGGGTAAGA
299316 ATTTGCTGAT
Statistics
Matches: 344, Mismatches: 83, Indels: 57
0.71 0.17 0.12
Matches are distributed among these distances:
37 4 0.01
38 16 0.05
39 301 0.88
40 19 0.06
41 4 0.01
ACGTcount: A:0.25, C:0.21, G:0.30, T:0.23
Consensus pattern (39 bp):
CAATCTGCCCCAAGCTCGGGGTAAGAGATCGAACGGCTG
Found at i:299313 original size:156 final size:152
Alignment explanation
Indices: 298822--299357 Score: 547
Period size: 156 Copynumber: 3.4 Consensus size: 152
298812 GAGAGGGTTA
* *
298822 CAATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGGTGATGATCTGCCTTAGGCTCGGGGTAAGA
1 CAATCTACCCCAAGCTCGGGGTAAGAGATTGGCTGGTG-TGATCTGCC-CAGGCTCGGGGTAAGA
* * * * *
298887 GATCGAACGGCTGCAATCTTCCCTAAACTCAGGGTAAGAGA-CTGACTGGTGATGATCTGCCCCA
64 GATCGAATGGCTGCAAT-TTCCCTAGA-TCGGGGTAAGAGATTTG-CTGATGATGATCTGCCCCA
* *
298951 AGCTCGGGGTTAGAGATTGAACGGCTG
126 AGCTCGGGGTAAGAGATCGAACGGCTG
* * * * * ** * * *
298978 CAATCTACCCTAGGCTCGGAGTAAGAGATCGAAC-GGCTGCAATCTTCCCTAAGTTCGGGGTAAG
1 CAATCTACCCCAAGCTCGGGGTAAGAGATTG-GCTGG-TGTGATCTGCCC-AGGCTCGGGGTAAG
* * * * * * *
299042 AGATCGAATAGCTGCAATCTACCCTAAGCTCGAGGTAAGAAATTTGCTGATAATGATCTGCCCTA
63 AGATCGAATGGCTGCAAT-TTCCCT-AGATCGGGGTAAGAGATTTGCTGATGATGATCTGCCCCA
* *
299107 AGCTCGGGGTAAGTGATCGAATGGCTG
126 AGCTCGGGGTAAGAGATCGAACGGCTG
***
299134 CAATCTATGTCAAGCTCGGGGTAAGAGATTGGCTGGTGTTGATCTGCCTCAGGCTCGGGGTAAGA
1 CAATCTACCCCAAGCTCGGGGTAAGAGATTGGCTGGTG-TGATCTGCC-CAGGCTCGGGGTAAGA
* * *
299199 GATCGGATGGCTGTAATTTGCCCCATGATCGGGGTAAGAGATTTGCTGATGATGATCTGCCCCAA
64 GATCGAATGGCTGCAATTT-CCCTA-GATCGGGGTAAGAGATTTGCTGATGATGATCTGCCCCAA
*
299264 GGTCGGGGTAAGAGATCGAACGGCTG
127 GCTCGGGGTAAGAGATCGAACGGCTG
* * * * * *
299290 CAATCTACCCCATGATCGAGGTAAGA-ATTTGCTGATGGTGATCTGCCCAGGCTCGGGGTAAAAG
1 CAATCTACCCCAAGCTCGGGGTAAGAGATTGGCTGGT-GTGATCTGCCCAGGCTCGGGGTAAGAG
299354 ATCG
65 ATCG
299358 GATCTTTGAT
Statistics
Matches: 306, Mismatches: 63, Indels: 24
0.78 0.16 0.06
Matches are distributed among these distances:
154 20 0.07
155 22 0.07
156 257 0.84
157 7 0.02
ACGTcount: A:0.25, C:0.21, G:0.30, T:0.24
Consensus pattern (152 bp):
CAATCTACCCCAAGCTCGGGGTAAGAGATTGGCTGGTGTGATCTGCCCAGGCTCGGGGTAAGAGA
TCGAATGGCTGCAATTTCCCTAGATCGGGGTAAGAGATTTGCTGATGATGATCTGCCCCAAGCTC
GGGGTAAGAGATCGAACGGCTG
Found at i:311717 original size:29 final size:29
Alignment explanation
Indices: 311685--311805 Score: 93
Period size: 29 Copynumber: 4.2 Consensus size: 29
311675 GAAGTCGAAC
*
311685 TTTTGGAAAATTGAGGGTAAAATGGTAAT
1 TTTTGGAAAATCGAGGGTAAAATGGTAAT
*** *
311714 TTTTGGATGCTCGAGGGTAAAATGGTGAT
1 TTTTGGAAAATCGAGGGTAAAATGGTAAT
**
311743 TTTTGGAAGTTCG-GCGGTAACAAT-GTAAT
1 TTTTGGAAAATCGAG-GGTAA-AATGGTAAT
* ** * * *
311772 TTTTAGAAGCTCGGGGGCAAAATTGTAAT
1 TTTTGGAAAATCGAGGGTAAAATGGTAAT
311801 TTTTG
1 TTTTG
311806 AGAAGTTTGA
Statistics
Matches: 76, Mismatches: 12, Indels: 8
0.79 0.12 0.08
Matches are distributed among these distances:
28 4 0.05
29 68 0.89
30 4 0.05
ACGTcount: A:0.29, C:0.07, G:0.29, T:0.36
Consensus pattern (29 bp):
TTTTGGAAAATCGAGGGTAAAATGGTAAT
Found at i:311747 original size:58 final size:57
Alignment explanation
Indices: 311685--311982 Score: 146
Period size: 60 Copynumber: 5.1 Consensus size: 57
311675 GAAGTCGAAC
* * * *
311685 TTTTGGAAAATTGAGGGTAAAATGGTAATTTTTGGATGCTCGAGGGTAAAATGGTGAT
1 TTTTGGAAAATTGAGGGTAAAAT-GTAATTTTTAGAAGCTCGAGGGCAAAATGGTAAT
* * *
311743 TTTTGG-AAGTTCG-GCGGTAACAATGTAATTTTTAGAAGCTCGGGGGCAAAATTGTAAT
1 TTTTGGAAAATT-GAG-GGTAA-AATGTAATTTTTAGAAGCTCGAGGGCAAAATGGTAAT
** * * * * * *
311801 TTTTGAGAAGTTTGAGGGGTAAAAATGTGATTTTTAAAAG-T-AAGGGGTAAAAAT-ATGAT
1 TTTTG-GAAAATTGA-GGGT-AAAATGTAATTTTTAGAAGCTCGA-GGG-CAAAATGGTAAT
* * * * **
311860 TTTT--AAAAGTACGGGGGTAAGAATGTAATTTTTGGAAGTTCGAGGAAAAAAAAT-GTAAT
1 TTTTGGAAAA-T-TGAGGGTAA-AATGTAATTTTTAGAAGCTCGAGG--GCAAAATGGTAAT
** * *
311919 TTTTGAGAAGTTTGAAGGCTAAAATGTAATTTTTAGAAAGTTCGAGGGTCAAAAT-GTAAT
1 TTTTG-GAAAATTG-AGGGTAAAATGTAATTTTTAG-AAGCTCGAGGG-CAAAATGGTAAT
311979 TTTT
1 TTTT
311983 AAGAAGTTTA
Statistics
Matches: 182, Mismatches: 35, Indels: 44
0.70 0.13 0.17
Matches are distributed among these distances:
56 4 0.02
57 24 0.13
58 49 0.27
59 30 0.16
60 54 0.30
61 19 0.10
62 2 0.01
ACGTcount: A:0.35, C:0.04, G:0.27, T:0.34
Consensus pattern (57 bp):
TTTTGGAAAATTGAGGGTAAAATGTAATTTTTAGAAGCTCGAGGGCAAAATGGTAAT
Found at i:311848 original size:28 final size:29
Alignment explanation
Indices: 311815--311892 Score: 113
Period size: 28 Copynumber: 2.7 Consensus size: 29
311805 GAGAAGTTTG
311815 AGGGGTAAAAATGTGATTTTTAAAAGTA-
1 AGGGGTAAAAATGTGATTTTTAAAAGTAC
*
311843 AGGGGTAAAAATATGATTTTTAAAAGTAC
1 AGGGGTAAAAATGTGATTTTTAAAAGTAC
* * *
311872 GGGGGTAAGAATGTAATTTTT
1 AGGGGTAAAAATGTGATTTTT
311893 GGAAGTTCGA
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
28 27 0.61
29 17 0.39
ACGTcount: A:0.40, C:0.01, G:0.26, T:0.33
Consensus pattern (29 bp):
AGGGGTAAAAATGTGATTTTTAAAAGTAC
Found at i:311849 original size:117 final size:118
Alignment explanation
Indices: 311739--311959 Score: 293
Period size: 117 Copynumber: 1.9 Consensus size: 118
311729 GGTAAAATGG
** * *** *
311739 TGATTTTTGGAAGTTCGGCGGTAACAATGTAATTTTTAGAAGCTCG-GGGGCAAAATTGTAATTT
1 TGATTTTTAAAAGTACGGCGGTAACAATGTAATTTTTAGAAGCTCGAGGAAAAAAAATGTAATTT
* * *
311803 TTGAGAAGTTTGAGGGGTAAAAATGTGATTTTTA-AAAGTAAGGGGTAAAAATA
66 TTGAGAAGTTTGAAGGCT-AAAATGTAATTTTTAGAAAGTAAGGGGTAAAAATA
* * * *
311856 TGATTTTTAAAAGTACGGGGGTAAGAATGTAATTTTTGGAAGTTCGAGGAAAAAAAATGTAATTT
1 TGATTTTTAAAAGTACGGCGGTAACAATGTAATTTTTAGAAGCTCGAGGAAAAAAAATGTAATTT
311921 TTGAGAAGTTTGAAGGCTAAAATGTAATTTTTAGAAAGT
66 TTGAGAAGTTTGAAGGCTAAAATGTAATTTTTAGAAAGT
311960 TCGAGGGTCA
Statistics
Matches: 88, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
117 53 0.60
118 35 0.40
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.34
Consensus pattern (118 bp):
TGATTTTTAAAAGTACGGCGGTAACAATGTAATTTTTAGAAGCTCGAGGAAAAAAAATGTAATTT
TTGAGAAGTTTGAAGGCTAAAATGTAATTTTTAGAAAGTAAGGGGTAAAAATA
Found at i:311890 original size:29 final size:28
Alignment explanation
Indices: 311699--312040 Score: 164
Period size: 29 Copynumber: 11.6 Consensus size: 28
311689 GGAAAATTGA
** * * *
311699 GGGTAAAATGGTAATTTTTGGATGCTCGA
1 GGGTAAAAT-GTAATTTTTAAAAGTTCGG
* **
311728 GGGTAAAATGGTGATTTTTGGAAGTTCGG
1 GGGTAAAAT-GTAATTTTTAAAAGTTCGG
* * *
311757 CGGTAACAATGTAATTTTTAGAAGCTCGG
1 GGGTAA-AATGTAATTTTTAAAAGTTCGG
* * *
311786 GGGCAAAATTGTAATTTTTGAGAAGTTTGAG
1 GGGTAAAA-TGTAATTTTT-AAAAGTTCG-G
* **
311817 GGGTAAAAATGTGATTTTTAAAAG-TAAG
1 GGGT-AAAATGTAATTTTTAAAAGTTCGG
* * *
311845 GGGTAAAAATATGATTTTTAAAAGTACGG
1 GGGT-AAAATGTAATTTTTAAAAGTTCGG
**
311874 GGGTAAGAATGTAATTTTTGGAAGTTCGAG
1 GGGTAA-AATGTAATTTTTAAAAGTTCG-G
*** * * *
311904 GAAAAAAAATGTAATTTTTGAGAAGTTTGAA
1 G-GGTAAAATGTAATTTTT-AAAAGTTCG-G
* *
311935 GGCTAAAATGTAATTTTTAGAAAGTTCGA
1 GGGTAAAATGTAATTTTTA-AAAGTTCGG
**
311964 GGGTCAAAATGTAATTTTTAAGAAGTTTAAG
1 GGGT-AAAATGTAATTTTTAA-AAG-TTCGG
** * **
311995 GATTAAAATGTAATTTTTGGAAAGTTTAG
1 GGGTAAAATGTAATTTTT-AAAAGTTCGG
*
312024 GGGTCAAAACGTAATTT
1 GGGT-AAAATGTAATTT
312041 CTAGACAATT
Statistics
Matches: 249, Mismatches: 48, Indels: 31
0.76 0.15 0.09
Matches are distributed among these distances:
28 28 0.11
29 94 0.38
30 94 0.38
31 29 0.12
32 4 0.02
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.34
Consensus pattern (28 bp):
GGGTAAAATGTAATTTTTAAAAGTTCGG
Found at i:312002 original size:60 final size:61
Alignment explanation
Indices: 311764--312040 Score: 225
Period size: 60 Copynumber: 4.7 Consensus size: 61
311754 CGGCGGTAAC
* * * * *
311764 AATGTAATTTTTAG-AAGCTCG-GGGGCAAAATTGTAATTTTTGAGAAGTTTGAGGGGTAAA
1 AATGTAATTTTTAGAAAGTTCGAGGGTCAAAA-TGTAATTTTTAAGAAGTTTGAAGGGTTAA
* ** * * * ** *
311824 AATGTGATTTTTA-AAAGTAAG-GGGTAAAAATATGATTTTTAA-AAGTACG--GGGGTAA
1 AATGTAATTTTTAGAAAGTTCGAGGGTCAAAATGTAATTTTTAAGAAGTTTGAAGGGTTAA
* *** * *
311880 GAATGTAATTTTT-GGAAGTTCGAGGAAAAAAAATGTAATTTTTGAGAAGTTTGAA-GGCTAA
1 -AATGTAATTTTTAGAAAGTTCGAGG-GTCAAAATGTAATTTTTAAGAAGTTTGAAGGGTTAA
*
311941 AATGTAATTTTTAGAAAGTTCGAGGGTCAAAATGTAATTTTTAAGAAGTTT-AAGGATTAA
1 AATGTAATTTTTAGAAAGTTCGAGGGTCAAAATGTAATTTTTAAGAAGTTTGAAGGGTTAA
* * *
312001 AATGTAATTTTTGGAAAGTT-TAGGGGTCAAAACGTAATTT
1 AATGTAATTTTTAGAAAGTTCGA-GGGTCAAAATGTAATTT
312041 CTAGACAATT
Statistics
Matches: 171, Mismatches: 35, Indels: 22
0.75 0.15 0.10
Matches are distributed among these distances:
56 5 0.03
57 16 0.09
58 7 0.04
59 26 0.15
60 101 0.59
61 16 0.09
ACGTcount: A:0.38, C:0.04, G:0.24, T:0.34
Consensus pattern (61 bp):
AATGTAATTTTTAGAAAGTTCGAGGGTCAAAATGTAATTTTTAAGAAGTTTGAAGGGTTAA
Found at i:312020 original size:30 final size:29
Alignment explanation
Indices: 311881--312040 Score: 133
Period size: 30 Copynumber: 5.3 Consensus size: 29
311871 CGGGGGTAAG
* ** **
311881 AATGTAATTTTTGGAAGTTCGAGGAAAAAA
1 AATGTAATTTTTGAAAGTTTAAGG-ATCAA
*
311911 AATGTAATTTTTGAGAAGTTTGAAGGCT-AA
1 AATGTAATTTTTGA-AAGTTT-AAGGATCAA
** *
311941 AATGTAATTTTTAGAAAGTTCGAGGGTCAA
1 AATGTAATTTTT-GAAAGTTTAAGGATCAA
* *
311971 AATGTAATTTTTAAGAAGTTTAAGGATTAA
1 AATGTAATTTTTGA-AAGTTTAAGGATCAA
* *
312001 AATGTAATTTTTGGAAAGTTTAGGGGTCAA
1 AATGTAATTTTT-GAAAGTTTAAGGATCAA
*
312031 AACGTAATTT
1 AATGTAATTT
312041 CTAGACAATT
Statistics
Matches: 106, Mismatches: 18, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
29 5 0.05
30 90 0.85
31 8 0.08
32 3 0.03
ACGTcount: A:0.39, C:0.04, G:0.22, T:0.36
Consensus pattern (29 bp):
AATGTAATTTTTGAAAGTTTAAGGATCAA
Found at i:312038 original size:90 final size:86
Alignment explanation
Indices: 311732--312045 Score: 251
Period size: 90 Copynumber: 3.5 Consensus size: 86
311722 GCTCGAGGGT
* * * * *
311732 AAAATGGTGATTTTTGGAAG-TTCGGCGGTAACAATGTAATTTTTAG-AAGCTCGGGGGCAAAAT
1 AAAAT-GTAATTTTTGAAAGTTTAGG-GGTAA-AATGTAATTTTTAGAAAGTTCGGGGTCAAAA-
* *
311795 TGTAATTTTTGAGAAGTTTGAGGGGTA
62 TGTAATTTTT-AGAAGTTT-AAGGATA
* * * * * *
311822 AAAATGTGATTTTTAAAAG-TAAGGGGTAAAAATATGATTTTTA-AAAGTACGGGGGT-AAGAAT
1 AAAATGTAATTTTTGAAAGTTTAGGGGT-AAAATGTAATTTTTAGAAAGTTC-GGGGTCAA-AAT
* ** *
311884 GTAATTTTTGGAAGTTCGAGGAAAA
63 GTAATTTTTAGAAGTTTAAGG-ATA
* *
311909 AAAATGTAATTTTTGAGAAGTTTGAAGGCTAAAATGTAATTTTTAGAAAGTTCGAGGGTCAAAAT
1 AAAATGTAATTTTTGA-AAGTTT-AGGGGTAAAATGTAATTTTTAGAAAGTTCG-GGGTCAAAAT
*
311974 GTAATTTTTAAGAAGTTTAAGGATT
63 GTAATTTTT-AGAAGTTTAAGGATA
* *
311999 AAAATGTAATTTTTGGAAAGTTTAGGGGTCAAAACGTAATTTCTAGA
1 AAAATGTAATTTTT-GAAAGTTTAGGGGT-AAAATGTAATTTTTAGA
312046 CAATTCAAGG
Statistics
Matches: 178, Mismatches: 32, Indels: 28
0.75 0.13 0.12
Matches are distributed among these distances:
86 2 0.01
87 21 0.12
88 33 0.19
89 42 0.24
90 67 0.38
91 13 0.07
ACGTcount: A:0.37, C:0.04, G:0.25, T:0.34
Consensus pattern (86 bp):
AAAATGTAATTTTTGAAAGTTTAGGGGTAAAATGTAATTTTTAGAAAGTTCGGGGTCAAAATGTA
ATTTTTAGAAGTTTAAGGATA
Found at i:312056 original size:60 final size:60
Alignment explanation
Indices: 311938--312056 Score: 152
Period size: 60 Copynumber: 2.0 Consensus size: 60
311928 GTTTGAAGGC
* * * * *
311938 TAAAATGTAATTTTTAGAAAGTTCGAGGGTCAAAATGTAATTTTTAAGAAGTTTAAGGAT
1 TAAAATGTAATTTTTAGAAAGTTAGAGGGTCAAAACGTAATTTCTAAGAAATTCAAGGAT
*
311998 TAAAATGTAATTTTTGGAAAGTTTAG-GGGTCAAAACGTAATTTCT-AGACAATTCAAGGA
1 TAAAATGTAATTTTTAGAAAG-TTAGAGGGTCAAAACGTAATTTCTAAGA-AATTCAAGGA
312057 CCTTTTAGGC
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
59 3 0.06
60 45 0.88
61 3 0.06
ACGTcount: A:0.39, C:0.06, G:0.20, T:0.34
Consensus pattern (60 bp):
TAAAATGTAATTTTTAGAAAGTTAGAGGGTCAAAACGTAATTTCTAAGAAATTCAAGGAT
Found at i:313452 original size:24 final size:24
Alignment explanation
Indices: 313407--313452 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
313397 TATGGCTTCG
* *
313407 TGTATCTGTATGGATTTAAAAAAC
1 TGTATATGTATGGATCTAAAAAAC
* *
313431 TGTATATGTATTGATCTCAAAA
1 TGTATATGTATGGATCTAAAAA
313453 TGGTTTTCCA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.39
Consensus pattern (24 bp):
TGTATATGTATGGATCTAAAAAAC
Found at i:313889 original size:17 final size:17
Alignment explanation
Indices: 313869--313911 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
313859 TTAATTAAAT
313869 TTAAATTTAAAATGAA-C
1 TTAAATTTAAAAT-AATC
* *
313886 TTAAATTCAAAATAATT
1 TTAAATTTAAAATAATC
313903 TTAAATTTA
1 TTAAATTTA
313912 TACTAAATTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 2 0.09
17 20 0.91
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (17 bp):
TTAAATTTAAAATAATC
Found at i:314561 original size:24 final size:24
Alignment explanation
Indices: 314534--314598 Score: 85
Period size: 25 Copynumber: 2.7 Consensus size: 24
314524 AAAATATTAG
* * *
314534 ATATGACACGATTACACAACATAA
1 ATATAACACGAATACAAAACATAA
*
314558 ATATAACACGACATAAAAAACATAA
1 ATATAACACGA-ATACAAAACATAA
314583 ATATAACACGAATACA
1 ATATAACACGAATACA
314599 TTATTCATAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
24 14 0.40
25 21 0.60
ACGTcount: A:0.57, C:0.18, G:0.06, T:0.18
Consensus pattern (24 bp):
ATATAACACGAATACAAAACATAA
Found at i:314927 original size:15 final size:15
Alignment explanation
Indices: 314906--315032 Score: 105
Period size: 15 Copynumber: 8.5 Consensus size: 15
314896 TTATCTTCCA
314906 CATTTGGTACCACAG
1 CATTTGGTACCACAG
* * *
314921 TATTTGGTGCAACAG
1 CATTTGGTACCACAG
314936 CATTTGGTATCC-CAG
1 CATTTGGTA-CCACAG
* *
314951 CATTTGG-AACATTAG
1 CATTTGGTACCA-CAG
* *
314966 CATTTGGTACGACAA
1 CATTTGGTACCACAG
* *
314981 CATTTGGTACAACTG
1 CATTTGGTACCACAG
* *
314996 CATTTGGTACCGCAA
1 CATTTGGTACCACAG
* *
315011 CATTTGGTACCCCAA
1 CATTTGGTACCACAG
315026 CATTTGG
1 CATTTGG
315033 CATAGCAGCA
Statistics
Matches: 88, Mismatches: 20, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
13 1 0.01
14 1 0.01
15 83 0.94
16 3 0.03
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (15 bp):
CATTTGGTACCACAG
Found at i:314940 original size:30 final size:30
Alignment explanation
Indices: 314906--315020 Score: 124
Period size: 30 Copynumber: 3.8 Consensus size: 30
314896 TTATCTTCCA
* *
314906 CATTTGGTACCACAGTATTTGGTGCAACAG
1 CATTTGGTACCACAGCATTTGGTACAACAG
* **
314936 CATTTGGTATCC-CAGCATTTGGAACATTAG
1 CATTTGGTA-CCACAGCATTTGGTACAACAG
* * *
314966 CATTTGGTACGACAACATTTGGTACAACTG
1 CATTTGGTACCACAGCATTTGGTACAACAG
* *
314996 CATTTGGTACCGCAACATTTGGTAC
1 CATTTGGTACCACAGCATTTGGTAC
315021 CCCAACATTT
Statistics
Matches: 70, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
29 1 0.01
30 67 0.96
31 2 0.03
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (30 bp):
CATTTGGTACCACAGCATTTGGTACAACAG
Found at i:320973 original size:21 final size:21
Alignment explanation
Indices: 320927--320973 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
320917 CTTGTGCTAA
*
320927 ATCTACCGATACAAGTATGGT
1 ATCTACCGATACAAGTATGGC
* *
320948 TTCTACCGGTACAAGTCAT-GC
1 ATCTACCGATACAAGT-ATGGC
320969 ATCTA
1 ATCTA
320974 TCGAAACCAA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (21 bp):
ATCTACCGATACAAGTATGGC
Found at i:325996 original size:8 final size:8
Alignment explanation
Indices: 325979--326013 Score: 63
Period size: 8 Copynumber: 4.5 Consensus size: 8
325969 TTTTCATGCT
325979 AAAA-ATA
1 AAAATATA
325986 AAAATATA
1 AAAATATA
325994 AAAATATA
1 AAAATATA
326002 AAAATATA
1 AAAATATA
326010 AAAA
1 AAAA
326014 AATCCAAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 4 0.15
8 23 0.85
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (8 bp):
AAAATATA
Found at i:334404 original size:10 final size:10
Alignment explanation
Indices: 334389--334428 Score: 53
Period size: 10 Copynumber: 3.8 Consensus size: 10
334379 TTAGTACCCA
334389 ACTAAATCTC
1 ACTAAATCTC
*
334399 ACTAAATACCC
1 ACTAAAT-CTC
334410 AACTAAATCTC
1 -ACTAAATCTC
334421 ACTAAATC
1 ACTAAATC
334429 AAACATTATG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
10 15 0.58
11 4 0.15
12 7 0.27
ACGTcount: A:0.45, C:0.30, G:0.00, T:0.25
Consensus pattern (10 bp):
ACTAAATCTC
Found at i:334411 original size:22 final size:22
Alignment explanation
Indices: 334383--334427 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
334373 TTTATATTAG
334383 TACCCAACTAAATCTCACTAAA
1 TACCCAACTAAATCTCACTAAA
334405 TACCCAACTAAATCTCACTAAA
1 TACCCAACTAAATCTCACTAAA
334427 T
1 T
334428 CAAACATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.44, C:0.31, G:0.00, T:0.24
Consensus pattern (22 bp):
TACCCAACTAAATCTCACTAAA
Found at i:336814 original size:22 final size:21
Alignment explanation
Indices: 336789--336832 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
336779 GTTTAGGAAT
336789 AATGCAGACTTTTACCGATACA
1 AATG-AGACTTTTACCGATACA
* *
336811 AATGATAGTTTTACCGATACA
1 AATGAGACTTTTACCGATACA
336832 A
1 A
336833 GTGACTCTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.30
Consensus pattern (21 bp):
AATGAGACTTTTACCGATACA
Found at i:343752 original size:18 final size:18
Alignment explanation
Indices: 343724--343780 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
343714 TCACACATCA
343724 AAAAATAATTCAAAATTAT
1 AAAAAT-ATTCAAAATTAT
*
343743 AAAAATATTCAAAA-AAT
1 AAAAATATTCAAAATTAT
*
343760 AAAAA-ATTTATAAATTAT
1 AAAAATATTCA-AAATTAT
343778 AAA
1 AAA
343781 TTATAAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
16 4 0.12
17 10 0.30
18 13 0.39
19 6 0.18
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.30
Consensus pattern (18 bp):
AAAAATATTCAAAATTAT
Found at i:349768 original size:18 final size:19
Alignment explanation
Indices: 349721--349771 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
349711 TCTCAACAAA
*
349721 TCAAAATAATTT-TTAAAAT
1 TCAAAAT-ATTTATAAAAAT
349740 TCAAAATATTTATAAAAAT
1 TCAAAATATTTATAAAAAT
*
349759 TCCAAA-ATTTATA
1 TCAAAATATTTATA
349772 TTTTTTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 11 0.38
19 18 0.62
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (19 bp):
TCAAAATATTTATAAAAAT
Found at i:354071 original size:24 final size:24
Alignment explanation
Indices: 354044--354091 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
354034 CCCTCTCAAA
354044 AACA-AATTAAGCAATTGAATCCTT
1 AACATAATT-AGCAATTGAATCCTT
* *
354068 AACATTATTAGCAATTTAATCCTT
1 AACATAATTAGCAATTGAATCCTT
354092 CTCAATTTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 18 0.86
25 3 0.14
ACGTcount: A:0.42, C:0.17, G:0.06, T:0.35
Consensus pattern (24 bp):
AACATAATTAGCAATTGAATCCTT
Found at i:359054 original size:53 final size:53
Alignment explanation
Indices: 358972--359198 Score: 292
Period size: 53 Copynumber: 4.3 Consensus size: 53
358962 GTAAATGCAA
* * * * *
358972 AAAGGTCTGATGATTCTTTGTCATTGTAAGTTATATGAATCTTATTACGGATT
1 AAAGGTCCGATGACTCTGTGTCATCGTAAGTTATATGAATCCTATTACGGATT
*
359025 AAAGGTCCGATGACTCTGTGTCATCGTAAGTTATATGAATCCTATTACAGATT
1 AAAGGTCCGATGACTCTGTGTCATCGTAAGTTATATGAATCCTATTACGGATT
* * * * *
359078 AAAGGTCCGATGACTTTATGTCATCGTGAGTTATATGAAATCTTATTACGTATT
1 AAAGGTCCGATGACTCTGTGTCATCGTAAGTTATATG-AATCCTATTACGGATT
* * * * * *
359132 AAAGATCCTATGACTTTGTTTCATCGTGAGTTATATGAATCCTATTATGGATT
1 AAAGGTCCGATGACTCTGTGTCATCGTAAGTTATATGAATCCTATTACGGATT
359185 AAAGGTCCGATGAC
1 AAAGGTCCGATGAC
359199 AGCTCCTGCA
Statistics
Matches: 152, Mismatches: 21, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
53 106 0.70
54 46 0.30
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.38
Consensus pattern (53 bp):
AAAGGTCCGATGACTCTGTGTCATCGTAAGTTATATGAATCCTATTACGGATT
Found at i:359157 original size:107 final size:107
Alignment explanation
Indices: 358972--359198 Score: 323
Period size: 107 Copynumber: 2.1 Consensus size: 107
358962 GTAAATGCAA
* * * *
358972 AAAGGTCTGATGA-TTCTTTGTCATTGTAAGTTATATGAATCTTATTACGGATTAAAGGTCCGAT
1 AAAGGTCCGATGACTTCTATGTCATCGTAAGTTATATGAATCTTATTACGGATTAAAGATCCGAT
359036 GACTCTGTGTCATCGTAAGTTATATGAATCCTATTACAGATT
66 GACTCTGTGTCATCGTAAGTTATATGAATCCTATTACAGATT
* * *
359078 AAAGGTCCGATGACTT-TATGTCATCGTGAGTTATATGAAATCTTATTACGTATTAAAGATCCTA
1 AAAGGTCCGATGACTTCTATGTCATCGTAAGTTATATG-AATCTTATTACGGATTAAAGATCCGA
* * * **
359142 TGACTTTGTTTCATCGTGAGTTATATGAATCCTATTATGGATT
65 TGACTCTGTGTCATCGTAAGTTATATGAATCCTATTACAGATT
359185 AAAGGTCCGATGAC
1 AAAGGTCCGATGAC
359199 AGCTCCTGCA
Statistics
Matches: 107, Mismatches: 12, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
106 30 0.28
107 77 0.72
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.38
Consensus pattern (107 bp):
AAAGGTCCGATGACTTCTATGTCATCGTAAGTTATATGAATCTTATTACGGATTAAAGATCCGAT
GACTCTGTGTCATCGTAAGTTATATGAATCCTATTACAGATT
Found at i:360760 original size:40 final size:38
Alignment explanation
Indices: 360703--360815 Score: 147
Period size: 38 Copynumber: 2.9 Consensus size: 38
360693 AAACATGTAC
* *
360703 AACATGTGCTCAGTTCATTATTACAATAGTAGACATGTTT
1 AACATGTACTCAATTCATTATT--AATAGTAGACATGTTT
*
360743 AACATGTACTCAATTCATCATTAATAGTA-AGCATGTTT
1 AACATGTACTCAATTCATTATTAATAGTAGA-CATGTTT
* *
360781 AACACGTACTCAATTCATTATTAACAGTAGACATG
1 AACATGTACTCAATTCATTATTAATAGTAGACATG
360816 GAAATCATGT
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
37 1 0.02
38 44 0.68
39 1 0.02
40 19 0.29
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (38 bp):
AACATGTACTCAATTCATTATTAATAGTAGACATGTTT
Found at i:360778 original size:38 final size:39
Alignment explanation
Indices: 360690--360815 Score: 143
Period size: 38 Copynumber: 3.3 Consensus size: 39
360680 CAAAACTAGC
** * *
360690 AGTAA-ACATGTACAACATGTGCTCAGTTCATTATTACAAT
1 AGTAAGACATGTTTAACATGTACTCAATTCATTATT--AAT
*
360730 AGT-AGACATGTTTAACATGTACTCAATTCATCATTAAT
1 AGTAAGACATGTTTAACATGTACTCAATTCATTATTAAT
* *
360768 AGTAAG-CATGTTTAACACGTACTCAATTCATTATTAAC
1 AGTAAGACATGTTTAACATGTACTCAATTCATTATTAAT
360806 AGT-AGACATG
1 AGTAAGACATG
360816 GAAATCATGT
Statistics
Matches: 75, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
37 2 0.03
38 42 0.56
39 3 0.04
40 28 0.37
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (39 bp):
AGTAAGACATGTTTAACATGTACTCAATTCATTATTAAT
Found at i:361082 original size:24 final size:24
Alignment explanation
Indices: 361054--361101 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
361044 TACTGGGTAA
361054 AACTATAAAATTTGCAAATCAGGG
1 AACTATAAAATTTGCAAATCAGGG
361078 AACTATAAAATTTGCAAATCAGGG
1 AACTATAAAATTTGCAAATCAGGG
361102 GTCACACGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.46, C:0.12, G:0.17, T:0.25
Consensus pattern (24 bp):
AACTATAAAATTTGCAAATCAGGG
Found at i:362263 original size:243 final size:244
Alignment explanation
Indices: 361816--362293 Score: 773
Period size: 243 Copynumber: 2.0 Consensus size: 244
361806 AAGAAGAGAA
* * *
361816 AAAGATGGTGGAATGTTAATTATGTTGGATTTTGAGAAGGGGCAAGTTATGAATTCTAATTAGGA
1 AAAGATGGTGGAATGCTAATTATGTTGGATTTTGAGAAGGGACAAATTATGAATTCTAATTAGGA
* *
361881 AGGAATTGGGTAAATTCCTAAGATTTGTAAACCCTAAGGGCTACACATGCAAATTTCCCAACTTA
66 AGGAATTGGGTAAATTCCTAAGATTTGCAAACCCTAAGGGCTACACATGCAAATTTCCCAAATTA
* *
361946 GGAGCAAGGGGCGGCAATTTGTAAATTCTCCTATTTTTGGTCAAATTTAAAAGGAAATGGAAGGG
131 GAAGCAAGGGGCGGCAATTTGCAAATTCTCCTATTTTTGGTCAAATTTAAAAGGAAATGGAAGGG
362011 AGATGCATGGCTCAAACTCGGGTCACTTGGGGGGCTCTAGCGTTTTCCC
196 AGATGCATGGCTCAAACTCGGGTCACTTGGGGGGCTCTAGCGTTTTCCC
* *
362060 AAAGA-GGTGGAATGCTAATTCTGTTGGAATTTTGAGTAGGGACAAATTATGAATTCTAATTAGG
1 AAAGATGGTGGAATGCTAATTATGTTGG-ATTTTGAGAAGGGACAAATTATGAATTCTAATTAGG
* * * *
362124 AAGGAATTGGGTGAATTCCTAGGGTTTGCAAACCTTAAGGGCTACACATGCAAATTTCCCAAATT
65 AAGGAATTGGGTAAATTCCTAAGATTTGCAAACCCTAAGGGCTACACATGCAAATTTCCCAAATT
* *
362189 AGAAGTAA-GGGCGGCAATTTGCAAATTC-CTCTATTTTTGGTCGAATTTAAAAGGAAATGGAAG
130 AGAAGCAAGGGGCGGCAATTTGCAAATTCTC-CTATTTTTGGTCAAATTTAAAAGGAAATGGAAG
*
362252 GGAGATGCATGGCTTAAACTCGGGTCACTTGGGGGGCTCTAG
194 GGAGATGCATGGCTCAAACTCGGGTCACTTGGGGGGCTCTAG
362294 AATTTTAACC
Statistics
Matches: 216, Mismatches: 16, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
242 1 0.00
243 112 0.52
244 103 0.48
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.29
Consensus pattern (244 bp):
AAAGATGGTGGAATGCTAATTATGTTGGATTTTGAGAAGGGACAAATTATGAATTCTAATTAGGA
AGGAATTGGGTAAATTCCTAAGATTTGCAAACCCTAAGGGCTACACATGCAAATTTCCCAAATTA
GAAGCAAGGGGCGGCAATTTGCAAATTCTCCTATTTTTGGTCAAATTTAAAAGGAAATGGAAGGG
AGATGCATGGCTCAAACTCGGGTCACTTGGGGGGCTCTAGCGTTTTCCC
Found at i:363672 original size:19 final size:20
Alignment explanation
Indices: 363631--363678 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
363621 TAGTGAAATG
363631 ACAACAAAATAGTGAAAAAA
1 ACAACAAAATAGTGAAAAAA
* *
363651 ACAAGAAAATAGT-AACAAA
1 ACAACAAAATAGTGAAAAAA
*
363670 ACAATAAAA
1 ACAACAAAA
363679 AACAACAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 13 0.52
20 12 0.48
ACGTcount: A:0.71, C:0.10, G:0.08, T:0.10
Consensus pattern (20 bp):
ACAACAAAATAGTGAAAAAA
Found at i:363679 original size:20 final size:20
Alignment explanation
Indices: 363631--363679 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
363621 TAGTGAAATG
*
363631 ACAACAAAATAGTGAAAAAA
1 ACAAAAAAATAGTGAAAAAA
* *
363651 ACAAGAAAATAGT-AACAAA
1 ACAAAAAAATAGTGAAAAAA
363670 ACAATAAAAA
1 ACAA-AAAAA
363680 ACAACAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.71, C:0.10, G:0.08, T:0.10
Consensus pattern (20 bp):
ACAAAAAAATAGTGAAAAAA
Found at i:368697 original size:20 final size:21
Alignment explanation
Indices: 368663--368723 Score: 67
Period size: 19 Copynumber: 3.0 Consensus size: 21
368653 ATTTTTTAAG
368663 TAAAAATCATT-AAAATTATTT
1 TAAAAAT-ATTAAAAATTATTT
*
368684 TAAAAGTA-TAAAAATTA--T
1 TAAAAATATTAAAAATTATTT
*
368702 TAAAAATATTAAAAAATATTT
1 TAAAAATATTAAAAATTATTT
368723 T
1 T
368724 CTTTTAAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
18 8 0.24
19 9 0.27
20 8 0.24
21 8 0.24
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (21 bp):
TAAAAATATTAAAAATTATTT
Found at i:368707 original size:10 final size:10
Alignment explanation
Indices: 368663--368721 Score: 52
Period size: 9 Copynumber: 6.1 Consensus size: 10
368653 ATTTTTTAAG
*
368663 TAAAAATCAT
1 TAAAAATTAT
368673 T-AAAATTATT
1 TAAAAATTA-T
* *
368683 TTAAAAGTA-
1 TAAAAATTAT
368692 TAAAAATTAT
1 TAAAAATTAT
368702 TAAAAA-TAT
1 TAAAAATTAT
*
368711 TAAAAAATAT
1 TAAAAATTAT
368721 T
1 T
368722 TTCTTTTAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
9 22 0.54
10 13 0.32
11 6 0.15
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (10 bp):
TAAAAATTAT
Found at i:371739 original size:132 final size:130
Alignment explanation
Indices: 371461--371885 Score: 478
Period size: 132 Copynumber: 3.3 Consensus size: 130
371451 GAACACAAAT
** * * * * ** **
371461 CAAAGGTTAAATGGCTCGAAGATTCAATGTTTGCTCTTGCTAGTGATTGACCACCAATCAGCTGG
1 CAAAGGTTAAACAGCTCGAAGATTCAATCTTTACTCTTGCTGGTGATCGAATACCAATCAGCAAG
* * * * *
371526 AGC-ATTTC-TAGG-CAGGGACAACAAG-ATGACCTTTTTTTCTTTTCTTTTCCTGAGAATTC-A
66 AGCAATTTCTTAGGTAAGGG-CACCAAGCA-GGCCTTTTTTTC-TTTCTTTTTCTGAGAATACAA
371586 AAG
128 AAG
* * *
371589 CAAAGGTTAAACAACTCGATGATTCAATCTTTACTCTTGCTGGTGATCGAATATCAATCAGCAAG
1 CAAAGGTTAAACAGCTCGAAGATTCAATCTTTACTCTTGCTGGTGATCGAATACCAATCAGCAAG
*
371654 AGCAATTTCTTA-G-ACA-GGCACCAAGCAGGCCTTATTTTTTTTCTTTCTTTTTCTGATAATAC
66 AGCAATTTCTTAGGTA-AGGGCACCAAGCAGGCC----TTTTTTTCTTTCTTTTTCTGAGAATAC
371716 AAAAG
126 AAAAG
371721 CAAAGGTTAAACAGCTCGAAGATTCAATCTTTACTCTTGCTGGTGATCGAATACCAATCAGCAAG
1 CAAAGGTTAAACAGCTCGAAGATTCAATCTTTACTCTTGCTGGTGATCGAATACCAATCAGCAAG
* * * *
371786 AGCATTTTCTTAGGTAAGGGGACCAAGCAGGCC-TTTTCT-TTTC-TTTTCTGAGAATA-AAAAT
66 AGCAATTTCTTAGGTAAGGGCACCAAGCAGGCCTTTTTTTCTTTCTTTTTCTGAGAATACAAAAG
*
371847 CAAAGGTTAAACAGCTTGAAGATTCAATCTTTACTCTTG
1 CAAAGGTTAAACAGCTCGAAGATTCAATCTTTACTCTTG
371886 TTAGTGACAA
Statistics
Matches: 257, Mismatches: 28, Indels: 26
0.83 0.09 0.08
Matches are distributed among these distances:
126 42 0.16
127 12 0.05
128 68 0.26
129 14 0.05
130 3 0.01
131 16 0.06
132 85 0.33
133 2 0.01
134 15 0.06
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (130 bp):
CAAAGGTTAAACAGCTCGAAGATTCAATCTTTACTCTTGCTGGTGATCGAATACCAATCAGCAAG
AGCAATTTCTTAGGTAAGGGCACCAAGCAGGCCTTTTTTTCTTTCTTTTTCTGAGAATACAAAAG
Found at i:386571 original size:23 final size:24
Alignment explanation
Indices: 386531--386581 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
386521 ATAAAATCAT
*
386531 AAAATAATATTATAATAT-TTTTA
1 AAAAGAATATTATAATATATTTTA
386554 AAAAGAAT-TTATATATATATTTTA
1 AAAAGAATATTATA-ATATATTTTA
386578 AAAA
1 AAAA
386582 TATATGTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 5 0.20
23 11 0.44
24 9 0.36
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (24 bp):
AAAAGAATATTATAATATATTTTA
Found at i:391678 original size:4 final size:4
Alignment explanation
Indices: 391661--391726 Score: 55
Period size: 4 Copynumber: 16.5 Consensus size: 4
391651 ACGGTAGAAC
* * *
391661 AAAG AAAA AAAG AAAG AAAAG AGAG AAAAA AAAG AAAG AAAG AAAG -AAG
1 AAAG AAAG AAAG AAAG -AAAG AAAG -AAAG AAAG AAAG AAAG AAAG AAAG
* *
391710 GAAG -AAG GAAG AAAG AA
1 AAAG AAAG AAAG AAAG AA
391727 GAAGGAAGAA
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
3 6 0.12
4 39 0.76
5 6 0.12
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:391693 original size:13 final size:13
Alignment explanation
Indices: 391665--391715 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
391655 TAGAACAAAG
*
391665 AAAA-AAAGAAAG
1 AAAAGAAAGAAAA
*
391677 AAAAGAGAGAAAA
1 AAAAGAAAGAAAA
391690 AAAAGAAAGAAAGA
1 AAAAGAAAGAAA-A
*
391704 AAGAAGGAAGAA
1 AA-AAGAAAGAA
391716 GGAAGAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
12 4 0.12
13 17 0.53
14 3 0.09
15 8 0.25
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (13 bp):
AAAAGAAAGAAAA
Found at i:391716 original size:7 final size:7
Alignment explanation
Indices: 391704--391736 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
391694 GAAAGAAAGA
391704 AAGAAGG
1 AAGAAGG
391711 AAGAAGG
1 AAGAAGG
*
391718 AAGAAAG
1 AAGAAGG
391725 AAGAAGG
1 AAGAAGG
391732 AAGAA
1 AAGAA
391737 TGAGAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (7 bp):
AAGAAGG
Found at i:391727 original size:14 final size:14
Alignment explanation
Indices: 391692--391736 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
391682 AGAGAAAAAA
*
391692 AAGAAAG-A-AAGA
1 AAGAAAGAAGAAGG
*
391704 AAGAAGGAAGAAGG
1 AAGAAAGAAGAAGG
391718 AAGAAAGAAGAAGG
1 AAGAAAGAAGAAGG
391732 AAGAA
1 AAGAA
391737 TGAGAAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
12 6 0.21
13 1 0.04
14 21 0.75
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (14 bp):
AAGAAAGAAGAAGG
Found at i:392104 original size:21 final size:21
Alignment explanation
Indices: 392078--392117 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
392068 TAATTTACTT
392078 TAATTTAATTTTGTTAGTAAG
1 TAATTTAATTTTGTTAGTAAG
*
392099 TAATTTTATTTTGTTAGTA
1 TAATTTAATTTTGTTAGTA
392118 GTAGTAAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.57
Consensus pattern (21 bp):
TAATTTAATTTTGTTAGTAAG
Found at i:392488 original size:16 final size:16
Alignment explanation
Indices: 392444--392492 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
392434 AAATACTTTA
392444 AATTAATTACCAAAAT
1 AATTAATTACCAAAAT
*
392460 -A-TAATATA-AAAAAT
1 AATTAAT-TACCAAAAT
392474 AATTAATTACCAAAAT
1 AATTAATTACCAAAAT
392490 AAT
1 AAT
392493 ACCTCATCCC
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
14 9 0.33
15 6 0.22
16 12 0.44
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.31
Consensus pattern (16 bp):
AATTAATTACCAAAAT
Found at i:393853 original size:43 final size:43
Alignment explanation
Indices: 393771--393855 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 43
393761 ATTAACATGT
* *
393771 TAAATTATATTACTTGACTCGTGTTAATATGGTTGCATGTTAC
1 TAAATTATATTACTTGACTCGTATTAATATGCTTGCATGTTAC
* *
393814 TAAATTATATTACTTTACTCTTATTAATAT-CTTGACATGTTA
1 TAAATTATATTACTTGACTCGTATTAATATGCTTG-CATGTTA
393856 TTAATTGTGC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
42 3 0.08
43 34 0.92
ACGTcount: A:0.31, C:0.12, G:0.11, T:0.47
Consensus pattern (43 bp):
TAAATTATATTACTTGACTCGTATTAATATGCTTGCATGTTAC
Found at i:394545 original size:21 final size:21
Alignment explanation
Indices: 394501--394541 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
394491 CAAGCTACCA
394501 CAATACTCTACTCCTCTCGGG
1 CAATACTCTACTCCTCTCGGG
394522 CAATACTCTACTCCTC-CGGG
1 CAATACTCTACTCCTCTCGGG
394542 GCAAATAGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.20, C:0.39, G:0.15, T:0.27
Consensus pattern (21 bp):
CAATACTCTACTCCTCTCGGG
Found at i:394797 original size:21 final size:21
Alignment explanation
Indices: 394772--394818 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
394762 TTTCATACCT
394772 ATAAACCCTAAATCCTAAACC
1 ATAAACCCTAAATCCTAAACC
*
394793 ATAAACTCTAAATCCTAAACC
1 ATAAACCCTAAATCCTAAACC
*
394814 TTAAA
1 ATAAA
394819 TTAAAAACCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.49, C:0.28, G:0.00, T:0.23
Consensus pattern (21 bp):
ATAAACCCTAAATCCTAAACC
Found at i:397313 original size:24 final size:24
Alignment explanation
Indices: 397286--397331 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
397276 ACCAGACACG
*
397286 AAGTTGGATCTTCATTTTCTACTA
1 AAGTAGGATCTTCATTTTCTACTA
*
397310 AAGTAGGATCTTTATTTTCTAC
1 AAGTAGGATCTTCATTTTCTAC
397332 AAGTTCAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.26, C:0.15, G:0.13, T:0.46
Consensus pattern (24 bp):
AAGTAGGATCTTCATTTTCTACTA
Found at i:398186 original size:30 final size:30
Alignment explanation
Indices: 398152--398214 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
398142 TAGTCAAATA
*
398152 AAATAAATAATTTTTGTATATTATTTTAGT
1 AAATAAATAATTTTTATATATTATTTTAGT
* * *
398182 AAATAAATATTTTTTATATTTTATTTTGGT
1 AAATAAATAATTTTTATATATTATTTTAGT
398212 AAA
1 AAA
398215 AAACCAAAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (30 bp):
AAATAAATAATTTTTATATATTATTTTAGT
Found at i:398186 original size:35 final size:36
Alignment explanation
Indices: 398121--398188 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
398111 TTATTAAACT
398121 AATAATTTTTTAATATTACTTTAGTCAAATAAAATA
1 AATAATTTTTTAATATTACTTTAGTCAAATAAAATA
*
398157 AATAATTTTTGT-ATATTATTTTAGT-AAATAAA
1 AATAATTTTT-TAATATTACTTTAGTCAAATAAA
398189 TATTTTTTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
35 7 0.23
36 22 0.73
37 1 0.03
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (36 bp):
AATAATTTTTTAATATTACTTTAGTCAAATAAAATA
Found at i:407178 original size:61 final size:61
Alignment explanation
Indices: 407103--407227 Score: 241
Period size: 61 Copynumber: 2.0 Consensus size: 61
407093 TCCAGTAAGT
407103 TAGGACATAACAATTCGAATTTTTAAAAATAACAAGCATTCTTAATTATTATCCCAAAATC
1 TAGGACATAACAATTCGAATTTTTAAAAATAACAAGCATTCTTAATTATTATCCCAAAATC
*
407164 TAGGACATAACAATTCGAATTTTTAAAAATATCAAGCATTCTTAATTATTATCCCAAAATC
1 TAGGACATAACAATTCGAATTTTTAAAAATAACAAGCATTCTTAATTATTATCCCAAAATC
407225 TAG
1 TAG
407228 TATTTTTAAT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 63 1.00
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.34
Consensus pattern (61 bp):
TAGGACATAACAATTCGAATTTTTAAAAATAACAAGCATTCTTAATTATTATCCCAAAATC
Found at i:407495 original size:22 final size:24
Alignment explanation
Indices: 407456--407507 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
407446 ATGAATGTAA
* *
407456 ATAATTAAATGAAGACAATCAA-AT
1 ATAA-TAAATGAACACAATAAAGAT
407480 ATAATAAAT-AACACAATAAAGAT
1 ATAATAAATGAACACAATAAAGAT
407503 ATAAT
1 ATAAT
407508 TATAGTATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 9 0.36
23 12 0.48
24 4 0.16
ACGTcount: A:0.62, C:0.08, G:0.06, T:0.25
Consensus pattern (24 bp):
ATAATAAATGAACACAATAAAGAT
Found at i:408575 original size:24 final size:24
Alignment explanation
Indices: 408548--408594 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
408538 AAACTCGTTC
* *
408548 ATTAGTAAATAATAATTTGAATTA
1 ATTAGAAAATAATAATTTAAATTA
408572 ATTAGAAAATAATAATTTAAATT
1 ATTAGAAAATAATAATTTAAATT
408595 GGACCAAAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.40
Consensus pattern (24 bp):
ATTAGAAAATAATAATTTAAATTA
Found at i:408836 original size:8 final size:8
Alignment explanation
Indices: 408823--408849 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
408813 GAATGAAATT
408823 AAAAAAGA
1 AAAAAAGA
408831 AAAAAAGA
1 AAAAAAGA
408839 AAAAAAGA
1 AAAAAAGA
408847 AAA
1 AAA
408850 CAAGTTTGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:415901 original size:2 final size:2
Alignment explanation
Indices: 415894--415925 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
415884 TGTAATCATA
*
415894 AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
415926 GAGTAAACAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:416092 original size:9 final size:10
Alignment explanation
Indices: 416076--416103 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
416066 ATAATCATAT
416076 TAAAAAAAAA
1 TAAAAAAAAA
416086 TAAAAAAAAA
1 TAAAAAAAAA
416096 TAAAAAAA
1 TAAAAAAA
416104 TCAGTCAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (10 bp):
TAAAAAAAAA
Done.