Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008793.1 Hibiscus syriacus cultivar Beakdansim tig00111937_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: 720278
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:618965 original size:6 final size:6
Alignment explanation
Indices: 618948--618977 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
618938 AACTATTTAA
618948 TAATATT TAATAT TAATAT TAATAT TAATA
1 TAATA-T TAATAT TAATAT TAATAT TAATA
618978 ATCCTATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 18 0.78
7 5 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TAATAT
Found at i:620421 original size:12 final size:12
Alignment explanation
Indices: 620404--620493 Score: 71
Period size: 12 Copynumber: 7.4 Consensus size: 12
620394 ATATTTGCAA
620404 ATATAATAATAT
1 ATATAATAATAT
620416 ATATAATTAATAT
1 ATATAA-TAATAT
*
620429 ATTATATATAATAA
1 A-TATA-ATAATAT
* *
620443 ATAT-GTAAGAT
1 ATATAATAATAT
620454 A-ATAATAATACT
1 ATATAATAATA-T
*
620466 A-ATAATAACAT
1 ATATAATAATAT
620477 ATATAATTAATA-
1 ATATAA-TAATAT
620489 ATATA
1 ATATA
620494 TTATTATAAA
Statistics
Matches: 63, Mismatches: 8, Indels: 14
0.74 0.09 0.16
Matches are distributed among these distances:
10 2 0.03
11 11 0.17
12 25 0.40
13 14 0.22
14 10 0.16
15 1 0.02
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (12 bp):
ATATAATAATAT
Found at i:626711 original size:8 final size:8
Alignment explanation
Indices: 626698--626738 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
626688 CTCATTTTCA
626698 GAGAATTT
1 GAGAATTT
626706 GAGAATTT
1 GAGAATTT
*
626714 -AGAGTTT
1 GAGAATTT
*
626721 GGGAATTT
1 GAGAATTT
626729 GAGAATTT
1 GAGAATTT
626737 GA
1 GA
626739 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:627039 original size:128 final size:128
Alignment explanation
Indices: 626811--627558 Score: 1235
Period size: 128 Copynumber: 5.9 Consensus size: 128
626801 ATCGGAGTAT
**
626811 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCA
1 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATCA
*
626876 TTGCCTTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
66 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
*
626939 TATTCACATGAAGGCGTGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATCA
1 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATCA
627004 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
66 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
*
627067 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTAATCAGAGAATATGTTATCA
1 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATCA
*
627132 TTGCCCTATTATGCCACTCATGTCCCTCGGGGACACTAG--ATAT-A-T-CCTATTATTTCAC
66 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
627190 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATCA
1 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATCA
*
627255 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTC
66 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
*** *
627318 -AGGGGACATGAAGGCTCGTTCCC-GGGG-GCGCCTTCCATTATTTCATCAGAGAATATGTTATC
1 TA-TTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATC
* *
627380 ATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAATACCTATTATTTCTC
65 ATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
*** * ** *
627444 -AGGGGACATGAAGGCGCGTTCCCGGGGGTGCGCCTTCCATTATTTTGTCATAGAATATGTTATC
1 TA-TTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATC
627508 ATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
65 ATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
627559 AATCATGTAA
Statistics
Matches: 592, Mismatches: 20, Indels: 16
0.94 0.03 0.03
Matches are distributed among these distances:
123 115 0.19
124 1 0.00
125 5 0.01
126 125 0.21
127 10 0.02
128 336 0.57
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32
Consensus pattern (128 bp):
TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATCA
TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
Found at i:627507 original size:377 final size:379
Alignment explanation
Indices: 626811--627554 Score: 1273
Period size: 377 Copynumber: 2.0 Consensus size: 379
626801 ATCGGAGTAT
**
626811 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCA
1 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATCA
*
626876 TTGCCTTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACTA
66 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACTA
**
626941 TTCACATGAAGGCGTGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATCATT
131 GGCACATGAAGGCGTGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATCATT
* **
627006 GCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACTATT
196 GCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAATACCTATTATTTCACTAGG
627071 CACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTAATCAGAGAATATGTTATCATTGC
261 CACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTAATCAGAGAATATGTTATCATTGC
627136 CCTATTATGCCACTCATGTCCCTCGGGGACACTAGATATATCCTATTATTTCAC
326 CCTATTATGCCACTCATGTCCCTCGGGGACACTAGATATATCCTATTATTTCAC
627190 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATCA
1 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATCA
*
627255 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTC-A
66 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACTA
*
627319 GGGGACATGAAGGC-TCGTTCCC-GGGG-GCGCCTTCCATTATTTCATCAGAGAATATGTTATCA
131 -GGCACATGAAGGCGT-GTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATCA
*
627381 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAATACCTATTATTTCTC-A
194 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAATACCTATTATTTCACTA
* * ** *
627445 GGGGACATGAAGGCGCGTTCCCGGGGGTGCGCCTTCCATTATTTTGTCATAGAATATGTTATCAT
259 -GGCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTAATCAGAGAATATGTTATCAT
*
627510 TGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATC
323 TGCCCTATTATGCCACTCATGTCCCTCGGGGACACTAGATATATC
627555 AGTAAATCAT
Statistics
Matches: 345, Mismatches: 17, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
376 1 0.00
377 198 0.57
378 6 0.02
379 140 0.41
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32
Consensus pattern (379 bp):
TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATCA
TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCACTA
GGCACATGAAGGCGTGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATCATT
GCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAATACCTATTATTTCACTAGG
CACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTAATCAGAGAATATGTTATCATTGC
CCTATTATGCCACTCATGTCCCTCGGGGACACTAGATATATCCTATTATTTCAC
Found at i:628016 original size:33 final size:34
Alignment explanation
Indices: 627955--628054 Score: 139
Period size: 33 Copynumber: 3.0 Consensus size: 34
627945 AAATTTAATG
*
627955 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* * * *
627989 TTAAATTT-GAATAATATTATTTTTATTTTTATT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
*
628022 TTAAATTTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
628055 AACATTTATC
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 28 0.50
34 28 0.50
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAAT
Found at i:628604 original size:21 final size:21
Alignment explanation
Indices: 628574--628667 Score: 136
Period size: 21 Copynumber: 4.5 Consensus size: 21
628564 TATGGTATAA
*
628574 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
*
628595 AA-CCTGGCGGACTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
628616 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
*
628637 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
628658 AACCCTGCGG
1 AACCCTGCGG
628668 AGATGGCATA
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
20 3 0.04
21 61 0.91
22 3 0.04
ACGTcount: A:0.21, C:0.28, G:0.33, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:628697 original size:21 final size:21
Alignment explanation
Indices: 628671--628718 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
628661 CCTGCGGAGA
*
628671 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
628692 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
628713 GGGCAT
1 TGGCAT
628719 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:630486 original size:23 final size:22
Alignment explanation
Indices: 630417--630486 Score: 54
Period size: 22 Copynumber: 3.0 Consensus size: 22
630407 ATTAGCAAAA
630417 AAAAAT-TAATAATTCTAAATAAAT
1 AAAAATATAAT-ATT-T-AATAAAT
* * *
630441 AATATATATAATA-TTATTTAAT
1 AA-AAATATAATATTTAATAAAT
630463 AAAAATATAATATTTACATAAAT
1 AAAAATATAATATTTA-ATAAAT
630486 A
1 A
630487 TATTAATATA
Statistics
Matches: 36, Mismatches: 6, Indels: 9
0.71 0.12 0.18
Matches are distributed among these distances:
21 9 0.25
22 10 0.28
23 6 0.17
24 3 0.08
25 4 0.11
26 4 0.11
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.39
Consensus pattern (22 bp):
AAAAATATAATATTTAATAAAT
Found at i:630489 original size:19 final size:19
Alignment explanation
Indices: 630455--630522 Score: 58
Period size: 17 Copynumber: 3.8 Consensus size: 19
630445 TATATAATAT
630455 TATTTAATAAAAATA-TAA
1 TATTTAATAAAAATATTAA
*
630473 TATTTACATAAATATATTAA
1 TATTTA-ATAAAAATATTAA
630493 TA--TAA-AAATAATA--AA
1 TATTTAATAAA-AATATTAA
*
630508 TATTTAAAAAAAATA
1 TATTTAATAAAAATA
630523 CTAACATAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 13
0.74 0.04 0.23
Matches are distributed among these distances:
15 4 0.10
16 3 0.07
17 11 0.26
18 11 0.26
19 8 0.19
20 5 0.12
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (19 bp):
TATTTAATAAAAATATTAA
Found at i:630506 original size:23 final size:20
Alignment explanation
Indices: 630480--630522 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 20
630470 TAATATTTAC
630480 ATAAATATATTAATATAAAAATA
1 ATAAATAT-TTAA-A-AAAAATA
630503 ATAAATATTTAAAAAAAATA
1 ATAAATATTTAAAAAAAATA
630523 CTAACATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 7 0.35
21 1 0.05
22 4 0.20
23 8 0.40
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAAATATTTAAAAAAAATA
Found at i:630517 original size:17 final size:18
Alignment explanation
Indices: 630455--630514 Score: 56
Period size: 18 Copynumber: 3.4 Consensus size: 18
630445 TATATAATAT
630455 TATTTAATAAA-AATATAA
1 TATTTAATAAATAATA-AA
*
630473 TATTTACATAAATATATTAA
1 TATTTA-ATAAATA-ATAAA
630493 TA--TAA-AAATAATAAA
1 TATTTAATAAATAATAAA
630508 TATTTAA
1 TATTTAA
630515 AAAAAATACT
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
15 6 0.17
16 5 0.14
17 4 0.11
18 8 0.23
19 5 0.14
20 5 0.14
21 2 0.06
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (18 bp):
TATTTAATAAATAATAAA
Found at i:630535 original size:34 final size:34
Alignment explanation
Indices: 630461--630537 Score: 95
Period size: 34 Copynumber: 2.3 Consensus size: 34
630451 ATATTATTTA
* * * *
630461 ATAAAAAT-ATAATATTTACATAAATATATTAAT
1 ATAAAAATAATAATATTTACAAAAAAATACTAAC
630494 ATAAAAATAATAAATATTTA-AAAAAAATACTAAC
1 ATAAAAATAAT-AATATTTACAAAAAAATACTAAC
630528 ATAAAAATAA
1 ATAAAAATAA
630538 ATTCTTACCA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
33 8 0.21
34 22 0.58
35 8 0.21
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (34 bp):
ATAAAAATAATAATATTTACAAAAAAATACTAAC
Found at i:635872 original size:21 final size:20
Alignment explanation
Indices: 635846--635889 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
635836 GATTTCTGGG
* *
635846 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCC-TT
635867 CAAGGGGAACCGATACCCTT
1 CAAGGGGAACCGATACCCTT
635887 CAA
1 CAA
635890 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.32, C:0.27, G:0.25, T:0.16
Consensus pattern (20 bp):
CAAGGGGAACCGATACCCTT
Found at i:636490 original size:18 final size:18
Alignment explanation
Indices: 636467--636501 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
636457 CTAGGAGATT
636467 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
636485 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
636502 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:637499 original size:149 final size:149
Alignment explanation
Indices: 637318--637610 Score: 532
Period size: 149 Copynumber: 2.0 Consensus size: 149
637308 GGTTACGCGG
637318 TTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTATAGAAAGACACATACTTGATCC
1 TTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTATAGAAAGACACATACTTGATCC
* *
637383 CTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTATATGGCACT
66 CTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTATATGGCACT
*
637448 ACGGTGCAATTCTATGCGA
131 ACGGGGCAATTCTATGCGA
* * *
637467 TTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACATACTTGATCC
1 TTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTATAGAAAGACACATACTTGATCC
637532 CTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTATATGGCACT
66 CTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTATATGGCACT
637597 ACGGGGCAATTCTA
131 ACGGGGCAATTCTA
637611 CGGGGCACTT
Statistics
Matches: 138, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
149 138 1.00
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.35
Consensus pattern (149 bp):
TTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTATAGAAAGACACATACTTGATCC
CTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTATATGGCACT
ACGGGGCAATTCTATGCGA
Found at i:637635 original size:23 final size:23
Alignment explanation
Indices: 637591--637635 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
637581 ATCATTATAT
*
637591 GGCACTACGGGGCAATTCTACGG
1 GGCACTACGGGGCAATTATACGG
* * *
637614 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGGGCAATTATACG
637636 AGCTGTGGTG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.20, C:0.24, G:0.31, T:0.24
Consensus pattern (23 bp):
GGCACTACGGGGCAATTATACGG
Found at i:640859 original size:21 final size:21
Alignment explanation
Indices: 640833--640877 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
640823 GATTTCTGGG
* *
640833 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
640854 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
640875 CAA
1 CAA
640878 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:642560 original size:149 final size:149
Alignment explanation
Indices: 642281--642584 Score: 554
Period size: 149 Copynumber: 2.0 Consensus size: 149
642271 GAGTCGAGGG
642281 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
1 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
* *
642346 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
642411 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
* * *
642430 TCTATGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
*
642495 ACTTGATCCCTAGCATATGTATATGATTCTTAAATAATTCTACGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
642560 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
642579 TCTACG
1 TCTACG
642585 GGGCACTTCG
Statistics
Matches: 148, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
149 148 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:642607 original size:23 final size:23
Alignment explanation
Indices: 642563--642607 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
642553 ATCATTATAT
*
642563 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
642586 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
642608 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:659042 original size:284 final size:286
Alignment explanation
Indices: 658516--659095 Score: 1096
Period size: 284 Copynumber: 2.0 Consensus size: 286
658506 TTTATCAAAC
*
658516 AATGTGATGTATTATTTTGATTTTAAATTATGTGTCACAGAGCTCTGATTTGTAAAATATATTAA
1 AATGAGATGTATTATTTTGATTTTAAATTATGTGTCACAGAGCTCTGATTTGTAAAATATATTAA
*
658581 TAACTTTTTTATATGTTATATGATACCATTGAGTATGTTTTAAAAGAGAATGAGTAGATTATTTT
66 TAACTATTTTATATGTTATATGATACCATTGAGTATGTTTTAAAAGAGAATGAGTAGATTATTTT
*
658646 TTAATATTAGGGGTTACCTCGATAACCTAATATGGCACTTTAGGCCCAATCGGGTCTAGGGTGTT
131 TTAATATTAGGGGTTACCTCGATAACCCAATATGGCACTTTAGGCCCAATCGGGTCTAGGGTGTT
658711 ACATTTAGTAGTATTAGAGCGTCAGGTTGAAGTCGGTCCTAGACCCTATGGTCAG-TTTAGTAAG
196 ACATTTAGTAGTATTAGAGCGTCAGGTTGAAGTCGGTCCTAGACCCTATGGTCAGTTTTAGTAAG
658775 GTGTTAGTGAATAAATGTCCCTAAGT
261 GTGTTAGTGAATAAATGTCCCTAAGT
658801 -ATGAGATGTATTATTTTGATTTTAAATTATGTGTCACAGAGCTCTGATTTGTAAAATATATTAA
1 AATGAGATGTATTATTTTGATTTTAAATTATGTGTCACAGAGCTCTGATTTGTAAAATATATTAA
658865 TAACTATTTTATATGTTATATGATACCATTGAGTATGTTTTAAAAGAGAATGAGTAGATTATTTT
66 TAACTATTTTATATGTTATATGATACCATTGAGTATGTTTTAAAAGAGAATGAGTAGATTATTTT
658930 TTAATATTAGGGGTTACCTCGATAACCCAATATGGCACTTTAGGCCCAATCGGGTCTAGGGTGTT
131 TTAATATTAGGGGTTACCTCGATAACCCAATATGGCACTTTAGGCCCAATCGGGTCTAGGGTGTT
658995 ACATTTAGTAGTATTAGAGCGTCAGGTTG-AGTCGGTCCTAGGACCCTATGGTCAGTTTTAGTAA
196 ACATTTAGTAGTATTAGAGCGTCAGGTTGAAGTCGGTCCTA-GACCCTATGGTCAGTTTTAGTAA
659059 GGTGTTAGTGAATAAATGTCCCTAAGT
260 GGTGTTAGTGAATAAATGTCCCTAAGT
659086 AATGA-ATGTA
1 AATGAGATGTA
659096 CTTGTATAAG
Statistics
Matches: 289, Mismatches: 3, Indels: 6
0.97 0.01 0.02
Matches are distributed among these distances:
283 11 0.04
284 234 0.81
285 40 0.14
286 4 0.01
ACGTcount: A:0.30, C:0.11, G:0.21, T:0.38
Consensus pattern (286 bp):
AATGAGATGTATTATTTTGATTTTAAATTATGTGTCACAGAGCTCTGATTTGTAAAATATATTAA
TAACTATTTTATATGTTATATGATACCATTGAGTATGTTTTAAAAGAGAATGAGTAGATTATTTT
TTAATATTAGGGGTTACCTCGATAACCCAATATGGCACTTTAGGCCCAATCGGGTCTAGGGTGTT
ACATTTAGTAGTATTAGAGCGTCAGGTTGAAGTCGGTCCTAGACCCTATGGTCAGTTTTAGTAAG
GTGTTAGTGAATAAATGTCCCTAAGT
Found at i:659802 original size:23 final size:24
Alignment explanation
Indices: 659757--659802 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
659747 TTATCATAAT
*
659757 TCATTAATGGTGAAATTATAATTTC
1 TCATTAAT-GTGAAATTAAAATTTC
*
659782 TCATTAAT-TGAATTTAAAATT
1 TCATTAATGTGAAATTAAAATT
659803 CAATAAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.39, C:0.07, G:0.09, T:0.46
Consensus pattern (24 bp):
TCATTAATGTGAAATTAAAATTTC
Found at i:660165 original size:2 final size:2
Alignment explanation
Indices: 660158--660231 Score: 111
Period size: 2 Copynumber: 39.0 Consensus size: 2
660148 AATTGATTGG
660158 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
660198 CT AT AT AT AT AT AT AT AT -T AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
660232 TTGGCAAGTT
Statistics
Matches: 66, Mismatches: 2, Indels: 8
0.87 0.03 0.11
Matches are distributed among these distances:
1 4 0.06
2 62 0.94
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:661579 original size:2 final size:2
Alignment explanation
Indices: 661574--661610 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
661564 TTTATATAAC
661574 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
661611 TTCTGGAAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:662481 original size:44 final size:46
Alignment explanation
Indices: 662418--662505 Score: 162
Period size: 44 Copynumber: 2.0 Consensus size: 46
662408 ACCGTATCAG
662418 TAAGACATCTCAGGTTTTAA-TTAA-TTTTAGTGGCATGTATAAAT
1 TAAGACATCTCAGGTTTTAATTTAATTTTTAGTGGCATGTATAAAT
662462 TAAGACATCTCAGGTTTTAATTTAATTTTTAGTGGCATGTATAA
1 TAAGACATCTCAGGTTTTAATTTAATTTTTAGTGGCATGTATAA
662506 TTATCTAGTT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
44 20 0.48
45 4 0.10
46 18 0.43
ACGTcount: A:0.33, C:0.09, G:0.16, T:0.42
Consensus pattern (46 bp):
TAAGACATCTCAGGTTTTAATTTAATTTTTAGTGGCATGTATAAAT
Found at i:668360 original size:23 final size:23
Alignment explanation
Indices: 668334--668383 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
668324 ATCAAGCACA
*
668334 ATAACATATTAGGTA-TCGCTTAT
1 ATAACATAATAGGTAGT-GCTTAT
**
668357 ATAATGTAATAGGTAGTGCTTAT
1 ATAACATAATAGGTAGTGCTTAT
668380 ATAA
1 ATAA
668384 TAAAATTAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 22 0.96
24 1 0.04
ACGTcount: A:0.38, C:0.08, G:0.16, T:0.38
Consensus pattern (23 bp):
ATAACATAATAGGTAGTGCTTAT
Found at i:668380 original size:87 final size:86
Alignment explanation
Indices: 668234--668486 Score: 330
Period size: 87 Copynumber: 2.9 Consensus size: 86
668224 AACCGGAAAT
* * *
668234 ATTATCAATAC-CAATAACATATTAGGTACCGCTTATATAATGTAATACATAGCGTTTATAAAAT
1 ATTATCAA-ACACAATAACATATTAGGTACCGCTTATATAATGTAATAAATAGCGCTTATATAAT
668298 AAAATAGGTTAATTACT-AGAAAC
65 AAAATA-GTTAATTACTGA-AAAC
* * ** *
668321 ATTATCAAGCACAATAACATATTAGGTATCGCTTATATAATGTAATAGGTAGTGCTTATATAATA
1 ATTATCAAACACAATAACATATTAGGTACCGCTTATATAATGTAATAAATAGCGCTTATATAATA
668386 AAATTAGTTAATTACTGAAAAC
66 AAA-TAGTTAATTACTGAAAAC
* * * * *
668408 ATTATTAAACACAATAACATATTAGGTAGCGCTTATATAACGCAATAAATAGCACTTATATAATA
1 ATTATCAAACACAATAACATATTAGGTACCGCTTATATAATGTAATAAATAGCGCTTATATAATA
668473 AAATATGTTAATTA
66 AAATA-GTTAATTA
668487 TTAATTGTTA
Statistics
Matches: 146, Mismatches: 16, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
86 3 0.02
87 140 0.96
88 3 0.02
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.33
Consensus pattern (86 bp):
ATTATCAAACACAATAACATATTAGGTACCGCTTATATAATGTAATAAATAGCGCTTATATAATA
AAATAGTTAATTACTGAAAAC
Found at i:669161 original size:23 final size:23
Alignment explanation
Indices: 669127--669170 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
669117 TATTAAGTAC
* **
669127 CACTTATTTAATGTAATAGGTAG
1 CACTTATATAATAAAATAGGTAG
669150 CACTTATATAATAAAATAGGT
1 CACTTATATAATAAAATAGGT
669171 TAATTACTGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (23 bp):
CACTTATATAATAAAATAGGTAG
Found at i:669162 original size:87 final size:87
Alignment explanation
Indices: 669065--669263 Score: 308
Period size: 87 Copynumber: 2.3 Consensus size: 87
669055 ATTGGTAGTG
*
669065 CTTATATAATAAAATAGGTTAATTACTAGAAACATTATCAAGCACAATAACATATTAAGTACCAC
1 CTTATATAATAAAATAGGTTAATTACTAGAAACATTATCAAACACAATAACATATTAAGTACCAC
* * * *
669130 TTATTTAATGTAATAGGTAGCA
66 TTATATAACGCAATAGGTAACA
* * * *
669152 CTTATATAATAAAATAGGTTAATTACTGGAAACATTATCAAACACAATAACATATTAGGTAGCGC
1 CTTATATAATAAAATAGGTTAATTACTAGAAACATTATCAAACACAATAACATATTAAGTACCAC
669217 TTATATAACGCAATAGGTAACA
66 TTATATAACGCAATAGGTAACA
*
669239 CTTATATAATAAAATATGTTAATTA
1 CTTATATAATAAAATAGGTTAATTA
669264 TTTAATTTGT
Statistics
Matches: 102, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
87 102 1.00
ACGTcount: A:0.45, C:0.12, G:0.11, T:0.32
Consensus pattern (87 bp):
CTTATATAATAAAATAGGTTAATTACTAGAAACATTATCAAACACAATAACATATTAAGTACCAC
TTATATAACGCAATAGGTAACA
Found at i:670011 original size:23 final size:23
Alignment explanation
Indices: 669985--670034 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
669975 ATCAAACACA
* * *
669985 ATAACATATTAGGTAGCGCTTAT
1 ATAACACAATAGGTAGCACTTAT
*
670008 ATAACGCAATAGGTAGCACTTAT
1 ATAACACAATAGGTAGCACTTAT
670031 ATAA
1 ATAA
670035 TAAAATATGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (23 bp):
ATAACACAATAGGTAGCACTTAT
Found at i:670041 original size:23 final size:23
Alignment explanation
Indices: 669985--670041 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 23
669975 ATCAAACACA
* * *
669985 ATAACATATTAGGTAGCGCTTAT
1 ATAACAAAATAGGTAGCACTTAT
**
670008 ATAACGCAATAGGTAGCACTTAT
1 ATAACAAAATAGGTAGCACTTAT
*
670031 ATAATAAAATA
1 ATAACAAAATA
670042 TGTTAATTAT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.30
Consensus pattern (23 bp):
ATAACAAAATAGGTAGCACTTAT
Found at i:670797 original size:23 final size:23
Alignment explanation
Indices: 670771--670820 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
670761 ATCAAATACA
* * *
670771 ATAACATATTAGGTAGCGCTTAT
1 ATAACACAATAGGTAGCACTTAT
*
670794 ATAACGCAATAGGTAGCACTTAT
1 ATAACACAATAGGTAGCACTTAT
670817 ATAA
1 ATAA
670821 TAAAATATGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (23 bp):
ATAACACAATAGGTAGCACTTAT
Found at i:670827 original size:23 final size:23
Alignment explanation
Indices: 670771--670827 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 23
670761 ATCAAATACA
* * *
670771 ATAACATATTAGGTAGCGCTTAT
1 ATAACAAAATAGGTAGCACTTAT
**
670794 ATAACGCAATAGGTAGCACTTAT
1 ATAACAAAATAGGTAGCACTTAT
*
670817 ATAATAAAATA
1 ATAACAAAATA
670828 TGTTAATTAT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.30
Consensus pattern (23 bp):
ATAACAAAATAGGTAGCACTTAT
Found at i:670917 original size:786 final size:789
Alignment explanation
Indices: 669152--672025 Score: 4469
Period size: 787 Copynumber: 3.6 Consensus size: 789
669142 ATAGGTAGCA
669152 CTTATATAATAAAATAGGTTAATTACTGGAAACATTATCAAACACAATAACATATTAGGTAGCGC
1 CTTATATAATAAAATAGGTTAATTACTGGAAACATTATCAAACACAATAACATATTAGGTAGCGC
*
669217 TTATATAACGCAATAGGTAACACTTATATAATAAAATATGTTAATTATTTAATTTGTTATTACAA
66 TTATATAACGCAATAGGTAGCACTTATATAATAAAATATGTTAATTATTTAATTTGTTATTACAA
669282 TATATTAGGTAAACGCCTAAAATATTACCAATGATAACATAACCGGTTATTTACTGGAAACATTA
131 TATATTAGGTAAACGCCTAAAATATTACCAATGATAACATAACCGGTTATTTACTGGAAACATTA
** *
669347 TCAAGTATAATAATGTAAACGGTAAAAAAAATAGGTTCTACCTATTACTTTAAACTACCTACCGG
196 TCAAGTATAATAATGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATTAAAC-A-CTACCGG
669412 ATATGTTGAAAGTATCGATTCCATTTAAATAAGTATCGACACTTTTGGAATTTAAAAGAAAAGCA
259 ATATGTTGAAAGTATCGATTCCATTTAAATAAGTATCGACACTTTTGGAATTTAAAAGAAAAGCA
*
669477 GTAATAGCGT-CTATAAAGTATCGATACTTTACAATATAACATGTAAAAATATGACAAAACCAGT
324 GTAATAGC-TCCTATAAAGTATCGATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGT
669541 TTCATTATGACAAAACCGGTAAAATTTAACTGATATGTTGAAAGTATAGATACTTTTTATAAAAA
388 TTCATTATGACAAAACCGGTAAAATTTAACTGATATGTTGAAAGTATAGATACTTTTTATAAAAA
669606 TGTATCGATACTTTGTTGAAAGTTATGTAATTTATGTTTC-AAAAA---AATAGTGCTTCATGTT
453 TGTATCGATACTTTGTTGAAAGTTATGTAATTTATGTTTCAAAAAATTTAATAGTGCTTCATGTT
669667 TTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAATATTATTTGATTGTTTTGATATT
518 TTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAATATTATTTGATTGTTTTGATATT
669732 TTATAAAATATTATTTAGAATTTAAATTTAACAATTTTAACCAAAGATAATAATAAATATGTAAT
583 TTATAAAATATTATTTAGAATTTAAATTTAACAATTTTAACCAAAGATAATAATAAATATGTAAT
*** *
669797 ATCTATGTTTATTATTTTTAAAAAAATAATAATATATATCGTAACATAAAATTAAAACATTAGAC
648 ATCTATGTTTATTATTTTTAATTTAATAATAATATATATCGTAACATAAAAATAAAACATTAGAC
669862 GCGTATAATTACTAAATTAATATCTTAAAACTCATTCAAAAGATAACCTTAAATTAATGTTTTTC
713 GCGTATAATTACTAAATTAATATCTTAAAACTCATTCAAAAGATAACCTTAAATTAATGTTTTTC
669927 ACAGAGGTAGTG
778 ACAGAGGTAGTG
669939 CTTATATAATAAAATAGGTTAATTACTGGAAACATTATCAAACACAATAACATATTAGGTAGCGC
1 CTTATATAATAAAATAGGTTAATTACTGGAAACATTATCAAACACAATAACATATTAGGTAGCGC
670004 TTATATAACGCAATAGGTAGCACTTATATAATAAAATATGTTAATTATTTAATTTGTTATTACAA
66 TTATATAACGCAATAGGTAGCACTTATATAATAAAATATGTTAATTATTTAATTTGTTATTACAA
*
670069 TATATTAGGTAAACGCCTAAAATATTACCAATGATAACATAACCGGTTATTTACTAGAAACATTA
131 TATATTAGGTAAACGCCTAAAATATTACCAATGATAACATAACCGGTTATTTACTGGAAACATTA
670134 TCAAGTATAATAATGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATT-AA-ACTACCGGAT
196 TCAAGTATAATAATGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATTAAACACTACCGGAT
670197 ATGTTGAAAGTATCGATTCCATTTAAATAAGTATCGACACTTTTGGAATTTAAAAGAAAAGCAGT
261 ATGTTGAAAGTATCGATTCCATTTAAATAAGTATCGACACTTTTGGAATTTAAAAGAAAAGCAGT
* * *
670262 AATAACTCCTATAAAGTATCGATACTTTACAATATAATAGGTAAAAATATGACAAAAACAGTTTC
326 AATAGCTCCTATAAAGTATCGATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTC
* *
670327 ATTATGACAAAATCGGTAAAATTTAACTGATATGTTGAAAGTATAGACACTTTTTATAAAAATGT
391 ATTATGACAAAACCGGTAAAATTTAACTGATATGTTGAAAGTATAGATACTTTTTATAAAAATGT
670392 ATCGATACTTTGTTGAAAGTTATGTAATTTATGTTTCAAAAAATTTAATAGTGCTTCATGTTTTC
456 ATCGATACTTTGTTGAAAGTTATGTAATTTATGTTTCAAAAAATTTAATAGTGCTTCATGTTTTC
670457 CACCTACAATATTAATTTAATAATTTCATTTACACAAAATATTATTTGATTGTTTTGATATTTTA
521 CACCTACAATATTAATTTAATAATTTCATTTACACAAAATATTATTTGATTGTTTTGATATTTTA
670522 TAAAATATTATTTAGAATTTAAATTTAACAATTTTAACCAAAGATAATAATAAATATGTAATATC
586 TAAAATATTATTTAGAATTTAAATTTAACAATTTTAACCAAAGATAATAATAAATATGTAATATC
*
670587 TATGTTTATTATTTTTAATTTAAT-A-AATAATATATCGTAACATAAAAATAAAATATTAGACGC
651 TATGTTTATTATTTTTAATTTAATAATAAT-ATATATCGTAACATAAAAATAAAACATTAGACGC
670650 GTATAATTACTAAATTAATATCTTAAAACTCATTCAAAAGATAACCTTAAATTAATGTTTTTCAC
715 GTATAATTACTAAATTAATATCTTAAAACTCATTCAAAAGATAACCTTAAATTAATGTTTTTCAC
670715 AGAGGTAGTG
780 AGAGGTAGTG
*
670725 CTTATATAATAAAATAGGTTAATTACTGGAAACATTATCAAATACAATAACATATTAGGTAGCGC
1 CTTATATAATAAAATAGGTTAATTACTGGAAACATTATCAAACACAATAACATATTAGGTAGCGC
670790 TTATATAACGCAATAGGTAGCACTTATATAATAAAATATGTTAATTATTTAATTTGTTATTACAA
66 TTATATAACGCAATAGGTAGCACTTATATAATAAAATATGTTAATTATTTAATTTGTTATTACAA
670855 TATATTAGGTAAACGCCTAAAATATTACCAATGATAACATAACCGGTTATTTACTGGAAACATTA
131 TATATTAGGTAAACGCCTAAAATATTACCAATGATAACATAACCGGTTATTTACTGGAAACATTA
670920 TCAAGTATAATAATGTAAACGGTAAAAAAAAAATAGGCGCTACCTATTACATTAAACTACATACC
196 TCAAGTATAATAATGTAAACGGT--AAAAAAAATAGGCGCTACCTATTACATTAAAC-AC-TACC
*
670985 GGATATGTTGAAAGTATCGATTCCATTTAAATAAGTATCGACACTTTTGGAATTTAAAAGAAAAT
257 GGATATGTTGAAAGTATCGATTCCATTTAAATAAGTATCGACACTTTTGGAATTTAAAAGAAAAG
* *
671050 CAGTAATAGCGCCTATAAAGTATCGATACTTTACAATATAACAGATAAAAATATGACAAAACCAG
322 CAGTAATAGCTCCTATAAAGTATCGATACTTTACAATATAACAGGTAAAAATATGACAAAACCAG
* * *
671115 TTTCATTATGATAAAACCGGTAAAATTTACCTGATATGTTGGAAGTATAGATACTTTTTATAAAA
387 TTTCATTATGACAAAACCGGTAAAATTTAACTGATATGTTGAAAGTATAGATACTTTTTATAAAA
*
671180 ATGTATCGATACTTTGTTGAAAGTTATGTAATTTATGTTTCAAAAAATTTTAACAGTGCTTCATG
452 ATGTATCGATACTTTGTTGAAAGTTATGTAATTTATGTTTCAAAAAA-TTTAATAGTGCTTCATG
*
671245 TTTTCCACCTACAATTTTAATTTAATAATTTCATTTACACAAAATATTATTTGATTGTTTTGATA
516 TTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAATATTATTTGATTGTTTTGATA
*
671310 TTTTATAAAATATAATTTAGAATTTAAATTTAACAATTTTAACCAAAGATAATAATAAATATGTA
581 TTTTATAAAATATTATTTAGAATTTAAATTTAACAATTTTAACCAAAGATAATAATAAATATGTA
671375 ATATCTATGTTTATTATTTTTAATTTAATAATAATATATATCGTAACATAAAAATAAAACATTAG
646 ATATCTATGTTTATTATTTTTAATTTAATAATAATATATATCGTAACATAAAAATAAAACATTAG
*
671440 ACGCGTATAATTACTAAATTAATATATTAAAACTCATTCAAAAGATAACCTTAAATTAATGTTTT
711 ACGCGTATAATTACTAAATTAATATCTTAAAACTCATTCAAAAGATAACCTTAAATTAATGTTTT
*
671505 CCACAGAGGTAGTG
776 TCACAGAGGTAGTG
* * * * * * *
671519 CTTATATATTCAAATAGGTTAATTACTGGAAACATTATCAATCGCAATGACATATTAAGTA-CTA
1 CTTATATAATAAAATAGGTTAATTACTGGAAACATTATCAAACACAATAACATATTAGGTAGC-G
* * * * * ** * *
671583 CTTATATAATGTAATAGGTAGCGCTTGTATAATAAAATAGGTTAATTACTAGAAATATTATTAAA
65 CTTATATAACGCAATAGGTAGCACTTATATAATAAAATATGTTAATTA-T-TTAAT-TTGTT-AT
* * * * * *
671648 CACAATAACATATTAGGT-AGCGCTTATATAACGCAATAGATAGCACTTATATAATAAAATATGT
126 TACAAT---ATATTAGGTAAACGC----CTAA---AATA-TTA-C-C--A-ATGAT--AACA---
**** * ** * * *
671712 TAATTATTTAATTTATTATTACAATATATTAGGTAAACGCCTAAAATATTACCAATGATAACATA
170 TAACCGGTT-A--T-TTACTGGAA-ACATTA--TCAA-G--T---ATA--A-TAATG-T---A-A
* *
671777 ACGGT-AAAAAAATAGGCGCTACCTATTACATTAAACTACCTACCAGATATGTTGAAAGTATTGA
214 ACGGTAAAAAAAATAGGCGCTACCTATTACATTAAAC-A-CTACCGGATATGTTGAAAGTATCGA
** * ** *
671841 TTTTATTTAAATAAGTATCGACACTTTTGAAATTTAAAAGAAAAGTTGTAATAGCGCCTATAAAG
277 TTCCATTTAAATAAGTATCGACACTTTTGGAATTTAAAAGAAAAGCAGTAATAGCTCCTATAAAG
* *
671906 TATCGATACTTTACAATATAACAAGTAAAAATATGACAAAACCAATTTCATTATGACAAAACCGG
342 TATCGATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTATGACAAAACCGG
* * * *
671971 TAAAATTTACCTGATATGTTGAAAGTATCGATCCTTTTTATAAAAA-GGATCGATA
407 TAAAATTTAACTGATATGTTGAAAGTATAGATACTTTTTATAAAAATGTATCGATA
672026 TTTTACAATA
Statistics
Matches: 1940, Mismatches: 84, Indels: 78
0.92 0.04 0.04
Matches are distributed among these distances:
782 1 0.00
783 233 0.12
784 6 0.00
785 3 0.00
786 326 0.17
787 411 0.21
788 28 0.01
789 2 0.00
791 2 0.00
792 235 0.12
793 174 0.09
794 204 0.11
795 4 0.00
796 3 0.00
797 4 0.00
798 6 0.00
800 4 0.00
801 9 0.00
804 3 0.00
807 4 0.00
808 2 0.00
809 1 0.00
810 1 0.00
812 1 0.00
813 4 0.00
815 3 0.00
818 5 0.00
819 1 0.00
821 1 0.00
822 6 0.00
823 5 0.00
825 3 0.00
826 1 0.00
828 1 0.00
831 3 0.00
833 1 0.00
834 4 0.00
835 9 0.00
836 218 0.11
837 1 0.00
838 1 0.00
839 6 0.00
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.35
Consensus pattern (789 bp):
CTTATATAATAAAATAGGTTAATTACTGGAAACATTATCAAACACAATAACATATTAGGTAGCGC
TTATATAACGCAATAGGTAGCACTTATATAATAAAATATGTTAATTATTTAATTTGTTATTACAA
TATATTAGGTAAACGCCTAAAATATTACCAATGATAACATAACCGGTTATTTACTGGAAACATTA
TCAAGTATAATAATGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATTAAACACTACCGGAT
ATGTTGAAAGTATCGATTCCATTTAAATAAGTATCGACACTTTTGGAATTTAAAAGAAAAGCAGT
AATAGCTCCTATAAAGTATCGATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTC
ATTATGACAAAACCGGTAAAATTTAACTGATATGTTGAAAGTATAGATACTTTTTATAAAAATGT
ATCGATACTTTGTTGAAAGTTATGTAATTTATGTTTCAAAAAATTTAATAGTGCTTCATGTTTTC
CACCTACAATATTAATTTAATAATTTCATTTACACAAAATATTATTTGATTGTTTTGATATTTTA
TAAAATATTATTTAGAATTTAAATTTAACAATTTTAACCAAAGATAATAATAAATATGTAATATC
TATGTTTATTATTTTTAATTTAATAATAATATATATCGTAACATAAAAATAAAACATTAGACGCG
TATAATTACTAAATTAATATCTTAAAACTCATTCAAAAGATAACCTTAAATTAATGTTTTTCACA
GAGGTAGTG
Found at i:671628 original size:87 final size:87
Alignment explanation
Indices: 671511--671717 Score: 245
Period size: 87 Copynumber: 2.4 Consensus size: 87
671501 TTTTCCACAG
* * * * * * *
671511 AGGTAGTGCTTATATATTCAAATAGGTTAATTACTGGAAACATTATCAATCGCAATGACATATTA
1 AGGTAGCGCTTATATAATAAAATAGGTTAATTACTAGAAACATTATCAAACACAATAACATATTA
* *
671576 AGTA-CTACTTATATAATGTAAT
66 AGTAGC-ACTTATATAACGCAAT
* * *
671598 AGGTAGCGCTTGTATAATAAAATAGGTTAATTACTAGAAATATTATTAAACACAATAACATATTA
1 AGGTAGCGCTTATATAATAAAATAGGTTAATTACTAGAAACATTATCAAACACAATAACATATTA
* *
671663 GGTAGCGCTTATATAACGCAAT
66 AGTAGCACTTATATAACGCAAT
* * *
671685 AGATAGCACTTATATAATAAAATATGTTAATTA
1 AGGTAGCGCTTATATAATAAAATAGGTTAATTA
671718 TTTAATTTAT
Statistics
Matches: 101, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
87 100 0.99
88 1 0.01
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.34
Consensus pattern (87 bp):
AGGTAGCGCTTATATAATAAAATAGGTTAATTACTAGAAACATTATCAAACACAATAACATATTA
AGTAGCACTTATATAACGCAAT
Found at i:672104 original size:112 final size:112
Alignment explanation
Indices: 671902--672255 Score: 600
Period size: 112 Copynumber: 3.2 Consensus size: 112
671892 TAGCGCCTAT
*
671902 AAAGTATCGATACTTTACAATATAACAAGTAAAAATATGACAAAACCAATTTCATTATGACAAAA
1 AAAGGATCGATACTTTACAATATAACAAGTAAAAATATGACAAAACCAATTTCATTATGACAAAA
671967 CCGGTAAAATTTACCTGATATGTTGAAAGTATCGATCCTTTTTATAA
66 CCGGTAAAATTTACCTGATATGTTGAAAGTATCGATCCTTTTTATAA
* *
672014 AAAGGATCGATATTTTACAATATAACAAGTAAAAATATGACAAAACCAGTTTCATTATGACAAAA
1 AAAGGATCGATACTTTACAATATAACAAGTAAAAATATGACAAAACCAATTTCATTATGACAAAA
*
672079 CCGGTAAAATTTACCTGATATGTTGAAAGTATCGATCGTTTTTATAA
66 CCGGTAAAATTTACCTGATATGTTGAAAGTATCGATCCTTTTTATAA
* *
672126 AAAGGATCGATACTTTACAATATAACAGGTAAAAATATGATAAAACCAATTTCATTATGACAAAA
1 AAAGGATCGATACTTTACAATATAACAAGTAAAAATATGACAAAACCAATTTCATTATGACAAAA
* * *
672191 CCGGTAAAATTTACCTAATATGTTGAAAGTATAGATACTTTTTATAA
66 CCGGTAAAATTTACCTGATATGTTGAAAGTATCGATCCTTTTTATAA
* *
672238 AATTGTATCGATACTTTA
1 AA-AGGATCGATACTTTA
672256 TTGAAACTTA
Statistics
Matches: 227, Mismatches: 14, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
112 214 0.94
113 13 0.06
ACGTcount: A:0.44, C:0.13, G:0.12, T:0.32
Consensus pattern (112 bp):
AAAGGATCGATACTTTACAATATAACAAGTAAAAATATGACAAAACCAATTTCATTATGACAAAA
CCGGTAAAATTTACCTGATATGTTGAAAGTATCGATCCTTTTTATAA
Found at i:672687 original size:87 final size:87
Alignment explanation
Indices: 672571--672777 Score: 335
Period size: 87 Copynumber: 2.4 Consensus size: 87
672561 TTTTCCACAG
* *
672571 AGGTAGTGCTTATATAATAAAATATGTTAATTACTGGAAACATTATCAAACACAATAACATATTA
1 AGGTAGCGCTTATATAATAAAATAGGTTAATTACTGGAAACATTATCAAACACAATAACATATTA
*
672636 GGTA-CTGGTTATATAATGTAAT
66 GGTAGC-GGTTATATAACGTAAT
* *
672658 ATGTAGCGCTTATATAATAAAATAGGTTAATTACTGGAAACATTATCAAGCACAATAACATATTA
1 AGGTAGCGCTTATATAATAAAATAGGTTAATTACTGGAAACATTATCAAACACAATAACATATTA
*
672723 GGTAGCGTTTATATAACGTAAT
66 GGTAGCGGTTATATAACGTAAT
*
672745 AGGTAGCGCTTATATAATAAAAGAGGTTAATTA
1 AGGTAGCGCTTATATAATAAAATAGGTTAATTA
672778 TTTAATTTGT
Statistics
Matches: 111, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
87 110 0.99
88 1 0.01
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (87 bp):
AGGTAGCGCTTATATAATAAAATAGGTTAATTACTGGAAACATTATCAAACACAATAACATATTA
GGTAGCGGTTATATAACGTAAT
Found at i:672738 original size:23 final size:23
Alignment explanation
Indices: 672712--672761 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
672702 ATCAAGCACA
* *
672712 ATAACATATTAGGTAGCGTTTAT
1 ATAACATAATAGGTAGCGCTTAT
*
672735 ATAACGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
672758 ATAA
1 ATAA
672762 TAAAAGAGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:672771 original size:23 final size:23
Alignment explanation
Indices: 672722--672771 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
672712 ATAACATATT
* ** *
672722 AGGTAGCGTTTATATAACGTAAT
1 AGGTAGCGCTTATATAACAAAAG
*
672745 AGGTAGCGCTTATATAATAAAAG
1 AGGTAGCGCTTATATAACAAAAG
672768 AGGT
1 AGGT
672772 TAATTATTTA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.38, C:0.08, G:0.24, T:0.30
Consensus pattern (23 bp):
AGGTAGCGCTTATATAACAAAAG
Found at i:673159 original size:113 final size:112
Alignment explanation
Indices: 673018--673501 Score: 511
Period size: 113 Copynumber: 4.2 Consensus size: 112
673008 GTATCGATAC
* *
673018 TTTATAAAAATGTATCGATACTTTACAATATAACAAGTAAAAATATGACAAAATCAGTTTCATTA
1 TTTATAAAAATGTATCGATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTA
*
673083 TGACAAAACCGGTAAAATTTACCGGATATATTGAAAGTATCGATCCTT
66 TGACAAAACCGGTAAAATTTACC-AATATATTGAAAGTATCGATCCTT
*
673131 TTTATAAAAATGTATC-ATTACTTTACAATATAACAGGTAAAAGTATGACAAAACCAGTTTCATT
1 TTTATAAAAATGTATCGA-TACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATT
*
673195 ATGACAAAACCGGTAAAATTTACCTAATATATTGAAAGTATCGATCATTTTT
65 ATGACAAAACCGGTAAAATTTACC-AATATATTGAAAGTATCGATC---CTT
* *
673247 ATGTTGAAAAAGAATAAAAATGTATC-ATCACTTTATAATATAACAGGTAAAAGTATGACAAAAC
1 -T-TT--------ATAAAAATGTATCGAT-ACTTTACAATATAACAGGTAAAAATATGACAAAAC
* * *
673311 CAATTTCATTATGACAAAACCGATAAAATTTACCTAATATA---AAAG----GATCCTAA
55 CAGTTTCATTATGACAAAACCGGTAAAATTTACC-AATATATTGAAAGTATCGATCCT-T
* * * ** * *
673364 TATATTAAAAA-GGATCGATATTTTACAATATAATTGGTAAAAATATGACAAAATCAGTTTCATG
1 TTTA-TAAAAATGTATCGATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATT
* * **
673428 ATGACAAAACCGGTAAAATTTACCAAATATGTTGAAAGTATAGATATTTT
65 ATGACAAAACCGGTAAAATTTACC-AATATATTGAAAGTATCGAT-CCTT
673478 TTTATAAAAATGTATCGATACTTT
1 TTTATAAAAATGTATCGATACTTT
673502 GTTGAAAGTT
Statistics
Matches: 314, Mismatches: 30, Indels: 53
0.79 0.08 0.13
Matches are distributed among these distances:
107 70 0.22
108 8 0.03
110 4 0.01
112 1 0.00
113 109 0.35
114 17 0.05
115 2 0.01
116 4 0.01
117 1 0.00
118 2 0.01
119 4 0.01
123 4 0.01
125 1 0.00
126 87 0.28
ACGTcount: A:0.45, C:0.12, G:0.11, T:0.32
Consensus pattern (112 bp):
TTTATAAAAATGTATCGATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTA
TGACAAAACCGGTAAAATTTACCAATATATTGAAAGTATCGATCCTT
Found at i:677693 original size:2 final size:2
Alignment explanation
Indices: 677686--677719 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
677676 AAATAATTTA
677686 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
677720 CATTTTTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:687157 original size:20 final size:20
Alignment explanation
Indices: 687127--687165 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
687117 GCATAAGTCG
687127 GTTTAGAATTTTAACATTTTC
1 GTTTAGAATTTTAA-ATTTTC
687148 GTTT-GAATTTTAAATTTT
1 GTTTAGAATTTTAAATTTT
687166 AATGTTTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 9 0.50
21 4 0.22
ACGTcount: A:0.28, C:0.05, G:0.10, T:0.56
Consensus pattern (20 bp):
GTTTAGAATTTTAAATTTTC
Found at i:693041 original size:343 final size:347
Alignment explanation
Indices: 692304--693046 Score: 1022
Period size: 343 Copynumber: 2.2 Consensus size: 347
692294 GGGTATTACA
* * * *
692304 CGACTC-TACTCGAAAATATGCATCCTCTAA-CAAAACTGACCTGATTC-AAAATTATATATCCT
1 CGACTCAT-CTCGAAAATATGTATCCTCTAACCAAAACCGACCCGATTCGAAAGTTATATATCCT
* *
692366 CCTTCTAACCCGACCCGAAATTATAAAGAAAAACTAATAATACTTTTAGGTTGGTAACTAATATT
65 CCATCTAACCCGACCCAAAATTATAAAGAAAAAC-AATAATACTTTTAGGTTGGTAACTAATATT
* * *
692431 TACTAATAGGGTTCCCAATATTGAAGGAAGTAGGGATTTTTTTTTTAAATAGTATCGAGTGATTA
129 TACTAATAGAGTTCCCAATATCGAAGGAAGTA-GGATTTTTTTTTGAAATAGTATCGAGTGATTA
* * *
692496 TAAAATAGTTTATGTTCATAATCTTTCTTAGCCATTGATAGCACACACATAACATGTAGATGAAA
193 TAAAATAATTTATGTTCATAATCTTTCGTAGCCATTGATAACACACACATAACATGTAGATGAAA
* * *
692561 CTGTTCAAACTCATGAACTCTATGGATAATAATACTCCCCTTAATTAGGTATAGCAACAAGTTGA
258 CTGTTCAAACTCATGAACTATATGGATAATAATACTCCCCTTAATTAGGGATAGCAACAAGTTCA
692626 GTTAGGGTCGAGTTTTTGGTTAACC
323 GTTAGGGTCGAGTTTTTGGTTAACC
* * * * *
692651 CAACTCGA-CTCGAAAATATGTATCATCCAACCAAAATCGATCCGATTCGAAAGTTATATATCCT
1 CGACTC-ATCTCGAAAATATGTATCCTCTAACCAAAACCGACCCGATTCGAAAGTTATATATCCT
* * * *
692715 CCATCTGACCCGACCCAAAATTCTAAAG-AAAA-AATATTACTTTTAGGTTGGTAATTAATATTT
65 CCATCTAACCCGACCCAAAATTATAAAGAAAAACAATAATACTTTTAGGTTGGTAACTAATATTT
* * *
692778 ACTATTAGAGTTCCTAATATCGAAGGAAGTA-GA-TTTTTTTTGAAATAGTCTCGAGTGATTATA
130 ACTAATAGAGTTCCCAATATCGAAGGAAGTAGGATTTTTTTTTGAAATAGTATCGAGTGATTATA
* * ** * *
692841 ATATAATTTATGTTCATAATCTTTCGTAGTCATTGATAACACACGTATAACCTGTAGAT-ACAAT
195 AAATAATTTATGTTCATAATCTTTCGTAGCCATTGATAACACACACATAACATGTAGATGA-AAC
*
692905 TGTTCAAACTCATGAACTATATGGATAATAATACTCCCCTTAATTAGGGAT-GTTAACAAG-TCA
259 TGTTCAAACTCATGAACTATATGGATAATAATACTCCCCTTAATTAGGGATAG-CAACAAGTTCA
*
692968 TGTTAGGGTCGTGTTTTTGGTTAACC
323 -GTTAGGGTCGAGTTTTTGGTTAACC
*
692994 CGACTCATCTCGAAAATATGTATCCTCTAACCGAAACCGACCCGATTCGAAAG
1 CGACTCATCTCGAAAATATGTATCCTCTAACCAAAACCGACCCGATTCGAAAG
693047 GATATTCGAC
Statistics
Matches: 347, Mismatches: 41, Indels: 20
0.85 0.10 0.05
Matches are distributed among these distances:
342 5 0.01
343 205 0.59
344 2 0.01
346 56 0.16
347 24 0.07
348 17 0.05
349 38 0.11
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.33
Consensus pattern (347 bp):
CGACTCATCTCGAAAATATGTATCCTCTAACCAAAACCGACCCGATTCGAAAGTTATATATCCTC
CATCTAACCCGACCCAAAATTATAAAGAAAAACAATAATACTTTTAGGTTGGTAACTAATATTTA
CTAATAGAGTTCCCAATATCGAAGGAAGTAGGATTTTTTTTTGAAATAGTATCGAGTGATTATAA
AATAATTTATGTTCATAATCTTTCGTAGCCATTGATAACACACACATAACATGTAGATGAAACTG
TTCAAACTCATGAACTATATGGATAATAATACTCCCCTTAATTAGGGATAGCAACAAGTTCAGTT
AGGGTCGAGTTTTTGGTTAACC
Found at i:695165 original size:19 final size:19
Alignment explanation
Indices: 695141--695205 Score: 58
Period size: 19 Copynumber: 3.2 Consensus size: 19
695131 CCACAAATAC
695141 ACCAAACTAACATATTAAA
1 ACCAAACTAACATATTAAA
* **
695160 ACCAAAGTAACATTCCACAAATA
1 ACCAAACTAACA-T--ATTAA-A
695183 CACCAAACTAACATATTAAA
1 -ACCAAACTAACATATTAAA
695203 ACC
1 ACC
695206 TAAGTAACAA
Statistics
Matches: 35, Mismatches: 6, Indels: 10
0.69 0.12 0.20
Matches are distributed among these distances:
19 14 0.40
20 2 0.06
21 3 0.09
22 3 0.09
23 2 0.06
24 11 0.31
ACGTcount: A:0.54, C:0.26, G:0.02, T:0.18
Consensus pattern (19 bp):
ACCAAACTAACATATTAAA
Found at i:695179 original size:43 final size:43
Alignment explanation
Indices: 695118--695227 Score: 193
Period size: 43 Copynumber: 2.6 Consensus size: 43
695108 AATCTAAACT
*
695118 CCAAATTAACAATCCACAAATACACCAAACTAACATATTAAAA
1 CCAAAGTAACAATCCACAAATACACCAAACTAACATATTAAAA
*
695161 CCAAAGTAACATTCCACAAATACACCAAACTAACATATTAAAA
1 CCAAAGTAACAATCCACAAATACACCAAACTAACATATTAAAA
*
695204 CCTAAGTAACAATCCACAAATACA
1 CCAAAGTAACAATCCACAAATACA
695228 TTAACTAATA
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 63 1.00
ACGTcount: A:0.54, C:0.26, G:0.02, T:0.18
Consensus pattern (43 bp):
CCAAAGTAACAATCCACAAATACACCAAACTAACATATTAAAA
Found at i:695196 original size:24 final size:24
Alignment explanation
Indices: 695118--695196 Score: 78
Period size: 24 Copynumber: 3.5 Consensus size: 24
695108 AATCTAAACT
* *
695118 CCAAATTAACAATCCACAAATACA
1 CCAAACTAACATTCCACAAATACA
**
695142 CCAAACTAACA-T--ATTAA-A-A
1 CCAAACTAACATTCCACAAATACA
*
695161 CCAAAGTAACATTCCACAAATACA
1 CCAAACTAACATTCCACAAATACA
695185 CCAAACTAACAT
1 CCAAACTAACAT
695197 ATTAAAACCT
Statistics
Matches: 43, Mismatches: 7, Indels: 10
0.72 0.12 0.17
Matches are distributed among these distances:
19 11 0.26
20 2 0.05
21 3 0.07
22 3 0.07
23 2 0.05
24 22 0.51
ACGTcount: A:0.53, C:0.28, G:0.01, T:0.18
Consensus pattern (24 bp):
CCAAACTAACATTCCACAAATACA
Found at i:695691 original size:13 final size:13
Alignment explanation
Indices: 695673--695701 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
695663 TAATTTCAAA
695673 AAAAGAAAAAAAT
1 AAAAGAAAAAAAT
695686 AAAAGAAAAAAAT
1 AAAAGAAAAAAAT
695699 AAA
1 AAA
695702 CGCTTGGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.86, C:0.00, G:0.07, T:0.07
Consensus pattern (13 bp):
AAAAGAAAAAAAT
Found at i:696565 original size:13 final size:13
Alignment explanation
Indices: 696531--696577 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
696521 TCTGCTTTTC
696531 TTTCTTCTCTATT-T
1 TTTCTT-TCT-TTAT
*
696545 TTTTTTTCTTTAT
1 TTTCTTTCTTTAT
*
696558 TTTCTTTCATTAT
1 TTTCTTTCTTTAT
696571 TTTCTTT
1 TTTCTTT
696578 TCACAATGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
12 2 0.07
13 22 0.76
14 5 0.17
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTCTTTCTTTAT
Found at i:698354 original size:23 final size:23
Alignment explanation
Indices: 698323--698367 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
698313 TAATTTTTAT
*
698323 ATTTATTAATATTTTATATTTTC
1 ATTTATTAATATTTTAGATTTTC
* *
698346 ATTTTTTAATGTTTTAGATTTT
1 ATTTATTAATATTTTAGATTTT
698368 TAAAGAATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (23 bp):
ATTTATTAATATTTTAGATTTTC
Found at i:709344 original size:18 final size:18
Alignment explanation
Indices: 709302--709347 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
709292 TAGTTTGATT
*
709302 AATGAAATAACATTATTC
1 AATGAACTAACATTATTC
*
709320 AATGAACTAACTTTATTC
1 AATGAACTAACATTATTC
709338 AATGAACTAA
1 AATGAACTAA
709348 ATGCATGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.48, C:0.13, G:0.07, T:0.33
Consensus pattern (18 bp):
AATGAACTAACATTATTC
Found at i:709436 original size:17 final size:17
Alignment explanation
Indices: 709381--709444 Score: 65
Period size: 17 Copynumber: 3.8 Consensus size: 17
709371 AAATAACTAG
* *
709381 ATGCATAAATGAACTAC
1 ATGCTTAAATGAAATAC
* *
709398 TTGCCTAAATGAAATAC
1 ATGCTTAAATGAAATAC
* *
709415 ATGCTTAAATGCAATGC
1 ATGCTTAAATGAAATAC
*
709432 ATGCTTTAATGAA
1 ATGCTTAAATGAA
709445 TAACATACTT
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 38 1.00
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.30
Consensus pattern (17 bp):
ATGCTTAAATGAAATAC
Found at i:710824 original size:24 final size:24
Alignment explanation
Indices: 710780--710826 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
710770 ATAAAGAACC
*
710780 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
710804 AAAATAAAGTTTAAACA-ACCATT
1 AAAATAAA-CTTAAACATACCATT
710827 CAACCAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:714129 original size:19 final size:20
Alignment explanation
Indices: 714107--714150 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
714097 GAGAAAAGGT
*
714107 AAAAGTTAA-AATGAAAGAG
1 AAAAGTTAATAATGAAAGAC
*
714126 AAAAATTAATAATGAAAGAC
1 AAAAGTTAATAATGAAAGAC
714146 AAAAG
1 AAAAG
714151 AAAAAGTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.66, C:0.02, G:0.16, T:0.16
Consensus pattern (20 bp):
AAAAGTTAATAATGAAAGAC
Done.