Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003885.1 Hibiscus syriacus cultivar Beakdansim tig00008386_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: 757743
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 4 of 4
Found at i:602983 original size:20 final size:19
Alignment explanation
Indices: 602949--603003 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
602939 TTGTGATTTT
*
602949 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
602968 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
602988 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
603004 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:603501 original size:18 final size:18
Alignment explanation
Indices: 603475--603519 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
603465 GTCGATCAGA
*
603475 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
603493 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
603511 TGATGGCTC
1 TGATGGCTC
603520 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:604862 original size:20 final size:20
Alignment explanation
Indices: 604837--604874 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
604827 AATAGTTTCT
604837 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
604857 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
604875 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:605463 original size:20 final size:20
Alignment explanation
Indices: 605369--605463 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
605359 GATTATGTAT
*
605369 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
605389 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGATAGTCAG
* ** * *
605409 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-TAGTCAG
*
605430 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
605450 TATCGCATTGCGAT
1 TATCGCGTTGCGAT
605464 TTTCCCAATT
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 48 0.79
21 13 0.21
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:605482 original size:41 final size:41
Alignment explanation
Indices: 605391--605525 Score: 130
Period size: 41 Copynumber: 3.3 Consensus size: 41
605381 AAAGTCAGTA
* * * ** *
605391 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
605431 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* ** *
605473 TCGCGTTGCGAT-TTACTTATTCGCATTGCGAATTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
605514 TCGCGTTGCGAT
1 TCGCGTTGCGAT
605526 TTACTTATTC
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
40 3 0.04
41 73 0.94
42 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:605496 original size:20 final size:20
Alignment explanation
Indices: 605452--605544 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
605442 ATAGTCAGTA
* **
605452 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
605473 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
605493 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTTAT
*
605514 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
605534 TCGCATTGCGA
1 TCGCATTGCGA
605545 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:605526 original size:41 final size:41
Alignment explanation
Indices: 605452--605547 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
605442 ATAGTCAGTA
*
605452 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
605493 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
605534 TCGCATTGCGAATT
1 TCGCATTGCGAATT
605548 GGGAAAATCG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:614328 original size:2 final size:2
Alignment explanation
Indices: 614316--614362 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
614306 GTCAATGTAT
614316 TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
614356 TA TA TA T
1 TA TA TA T
614363 TTAGTTTAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 41 0.95
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:614447 original size:3 final size:3
Alignment explanation
Indices: 614439--614468 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
614429 TGTTTGCCCT
614439 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
614469 AGGATTAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:614980 original size:3 final size:3
Alignment explanation
Indices: 614972--615007 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
614962 AAAAATTCAG
614972 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
615008 ATTAATAGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:621784 original size:4 final size:4
Alignment explanation
Indices: 621768--621813 Score: 83
Period size: 4 Copynumber: 11.5 Consensus size: 4
621758 TTCGTTAATG
*
621768 TGTA TGCA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TG
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TG
621814 GTCATTGCTC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 40 1.00
ACGTcount: A:0.24, C:0.02, G:0.26, T:0.48
Consensus pattern (4 bp):
TGTA
Found at i:624343 original size:13 final size:13
Alignment explanation
Indices: 624325--624358 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
624315 CCAAAAAGAA
624325 ACTTTCCTGTTTT
1 ACTTTCCTGTTTT
*
624338 ACTTTCTTGTTTT
1 ACTTTCCTGTTTT
*
624351 TCTTTCCT
1 ACTTTCCT
624359 AATTCCCATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.06, C:0.24, G:0.06, T:0.65
Consensus pattern (13 bp):
ACTTTCCTGTTTT
Found at i:625532 original size:37 final size:35
Alignment explanation
Indices: 625450--625520 Score: 108
Period size: 37 Copynumber: 2.0 Consensus size: 35
625440 GCAACGAGAT
625450 AAAATATTTCAAATAAATTAAAAAAAAACCCTTAAAC
1 AAAATATTTCAAATAAATT--AAAAAAACCCTTAAAC
*
625487 AAAATATTTTAAATAAATT-AAAAAACCCTTAAAC
1 AAAATATTTCAAATAAATTAAAAAAACCCTTAAAC
625521 GCAGACATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
34 15 0.45
37 18 0.55
ACGTcount: A:0.61, C:0.13, G:0.00, T:0.27
Consensus pattern (35 bp):
AAAATATTTCAAATAAATTAAAAAAACCCTTAAAC
Found at i:629999 original size:60 final size:60
Alignment explanation
Indices: 629863--629977 Score: 160
Period size: 60 Copynumber: 1.9 Consensus size: 60
629853 ATAGTCGGAT
* * *
629863 GACCATTTTGTAACTTTTAATAATCGATGGACTCAACAAAGCAATATCCTATAGTAAAGG
1 GACCATTTTGTAACTTTTAATAATAGATGGACTCAACAAAACAATATCATATAGTAAAGG
* * *
629923 GACCATTTTGTAACTTTTAATACTTAGA-GGACTCAACAAAACAATTTTATATAGT
1 GACCATTTTGTAACTTTTAATA-ATAGATGGACTCAACAAAACAATATCATATAGT
629978 TGGGAGACCA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
60 45 0.94
61 3 0.06
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (60 bp):
GACCATTTTGTAACTTTTAATAATAGATGGACTCAACAAAACAATATCATATAGTAAAGG
Found at i:631100 original size:20 final size:20
Alignment explanation
Indices: 631042--631100 Score: 82
Period size: 20 Copynumber: 3.0 Consensus size: 20
631032 ATCCTATTCC
*
631042 CTGGTAATCTTACATTCCCA
1 CTGGTAATCTTACATTCCTA
*
631062 CTGATAATCTTACATTCCTA
1 CTGGTAATCTTACATTCCTA
* *
631082 TTGGTAATTTTACATTCCT
1 CTGGTAATCTTACATTCCT
631101 TGAACCAAAC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.25, C:0.24, G:0.08, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCTA
Found at i:632360 original size:2 final size:2
Alignment explanation
Indices: 632353--632381 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
632343 TAGATAAGTT
632353 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
632382 GTTTAAAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:642069 original size:44 final size:42
Alignment explanation
Indices: 641935--642075 Score: 69
Period size: 44 Copynumber: 3.3 Consensus size: 42
641925 AAAAATTAGA
* * *
641935 GGCCTTAATTATAAAGGTAGAAATTGAGATTGAAAAAA-AT-AG
1 GGCCTCAATTATAAAGGTA-AAAATGAGATT-AAAAAACTTAAG
* * * * **
641977 ATGCCTCAATTAT--A-CTATAATTGAGATTGAAAATTCTT-AG
1 -GGCCTCAATTATAAAGGTAAAAATGAGATT-AAAAAACTTAAG
* *
642017 GAGCCTCAATTAGAAAGTTAGAAAATGAGATTAAAAAAACTTAAG
1 G-GCCTCAATTATAAAGGTA-AAAATGAGATT-AAAAAACTTAAG
*
642062 GGACTCAATTATAA
1 GGCCTCAATTATAA
642076 GTGAGACTAA
Statistics
Matches: 74, Mismatches: 17, Indels: 13
0.71 0.16 0.12
Matches are distributed among these distances:
39 15 0.20
40 15 0.20
41 1 0.01
42 1 0.01
43 12 0.16
44 27 0.36
45 3 0.04
ACGTcount: A:0.45, C:0.09, G:0.17, T:0.28
Consensus pattern (42 bp):
GGCCTCAATTATAAAGGTAAAAATGAGATTAAAAAACTTAAG
Found at i:642253 original size:32 final size:32
Alignment explanation
Indices: 642229--642293 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
642219 TTAGGGGCCT
642229 CAATTATAAAGGTAAAAAGGAATTAAAAAAAA
1 CAATTATAAAGGTAAAAAGGAATTAAAAAAAA
642261 CAATTATAAAGGTAAAAAGGAATTAAAAAAAA
1 CAATTATAAAGGTAAAAAGGAATTAAAAAAAA
642293 C
1 C
642294 TAAAGATTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.65, C:0.05, G:0.12, T:0.18
Consensus pattern (32 bp):
CAATTATAAAGGTAAAAAGGAATTAAAAAAAA
Found at i:642284 original size:19 final size:19
Alignment explanation
Indices: 642230--642285 Score: 61
Period size: 19 Copynumber: 3.3 Consensus size: 19
642220 TAGGGGCCTC
642230 AATTATAAAGGTAAAAAGG
1 AATTATAAAGGTAAAAAGG
*
642249 AA-T-TAAA---AAAAA-C
1 AATTATAAAGGTAAAAAGG
642262 AATTATAAAGGTAAAAAGG
1 AATTATAAAGGTAAAAAGG
642281 AATTA
1 AATTA
642286 AAAAAAACTA
Statistics
Matches: 29, Mismatches: 2, Indels: 12
0.67 0.05 0.28
Matches are distributed among these distances:
13 2 0.07
14 6 0.21
15 4 0.14
17 4 0.14
18 6 0.21
19 7 0.24
ACGTcount: A:0.62, C:0.02, G:0.14, T:0.21
Consensus pattern (19 bp):
AATTATAAAGGTAAAAAGG
Found at i:642404 original size:42 final size:44
Alignment explanation
Indices: 642302--642406 Score: 119
Period size: 43 Copynumber: 2.5 Consensus size: 44
642292 ACTAAAGATT
* * *
642302 TCAATTATAAAGAT-AAAAAGTTAGATTGAATAATATTAGGACC
1 TCAATTATAAAGATGAAAAAGTAAGATTGAATAAAATTAAGACC
* * *
642345 TCGATTATAAAGGTGAAAAA-TAAGATTTAA-AAAATTAAAGACC
1 TCAATTATAAAGATGAAAAAGTAAGATTGAATAAAATT-AAGACC
642388 T-AATTATAAAGATGAAAAA
1 TCAATTATAAAGATGAAAAA
642407 AATGAGGGCC
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
42 21 0.40
43 26 0.50
44 5 0.10
ACGTcount: A:0.53, C:0.06, G:0.13, T:0.28
Consensus pattern (44 bp):
TCAATTATAAAGATGAAAAAGTAAGATTGAATAAAATTAAGACC
Found at i:642435 original size:29 final size:30
Alignment explanation
Indices: 642389--642446 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
642379 TTAAAGACCT
*
642389 AATTATAAAGATGAAAAAAATGAGGGCCCC
1 AATTACAAAGATGAAAAAAATGAGGGCCCC
* *
642419 AATTACAAGGATG-AAAAAATGGGGGCCC
1 AATTACAAAGATGAAAAAAATGAGGGCCC
642447 TGAGCACTCG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.47, C:0.14, G:0.24, T:0.16
Consensus pattern (30 bp):
AATTACAAAGATGAAAAAAATGAGGGCCCC
Found at i:645476 original size:14 final size:13
Alignment explanation
Indices: 645457--645502 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 13
645447 GTAATTGGAT
645457 TTATGGAAATTGAA
1 TTATGGAAATT-AA
645471 TTATGGAAAATTAA
1 TTATGG-AAATTAA
645485 TTACTGGAAATTCAA
1 TTA-TGGAAATT-AA
645500 TTA
1 TTA
645503 CATTTCTGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
14 16 0.55
15 13 0.45
ACGTcount: A:0.43, C:0.04, G:0.15, T:0.37
Consensus pattern (13 bp):
TTATGGAAATTAA
Found at i:645501 original size:15 final size:14
Alignment explanation
Indices: 645460--645503 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 14
645450 ATTGGATTTA
645460 TGGAAATTGAATTA-
1 TGGAAATT-AATTAC
645474 TGGAAAATTAATTAC
1 TGG-AAATTAATTAC
645489 TGGAAATTCAATTAC
1 TGGAAATT-AATTAC
645504 ATTTCTGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 13 0.48
15 14 0.52
ACGTcount: A:0.43, C:0.07, G:0.16, T:0.34
Consensus pattern (14 bp):
TGGAAATTAATTAC
Found at i:646046 original size:17 final size:17
Alignment explanation
Indices: 646024--646067 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
646014 TTAAAATAAA
*
646024 ATATAATATCTTATATT
1 ATATAATATATTATATT
*
646041 ATATAATATATTATTTT
1 ATATAATATATTATATT
646058 ATTATAATAT
1 A-TATAATAT
646068 TAAAAATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 16 0.67
18 8 0.33
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (17 bp):
ATATAATATATTATATT
Found at i:646084 original size:30 final size:30
Alignment explanation
Indices: 646048--646112 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
646038 ATTATATAAT
* *
646048 ATATTATTTTATTA-TAATATTAAAAATATA
1 ATATTATATTATTAGAAATATTAAAAAT-TA
*
646078 ATATTATATTATTAGAAATATTAATAATTA
1 ATATTATATTATTAGAAATATTAAAAATTA
646108 ATATT
1 ATATT
646113 TTGATTAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 20 0.65
31 11 0.35
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (30 bp):
ATATTATATTATTAGAAATATTAAAAATTA
Found at i:646085 original size:22 final size:23
Alignment explanation
Indices: 646057--646112 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
646047 TATATTATTT
646057 TATTATAATATTAAAAATA-TAA
1 TATTATAATATTAAAAATATTAA
* *
646079 TATTATATTATTAGAAATATTAA
1 TATTATAATATTAAAAATATTAA
*
646102 TAAT-TAATATT
1 TATTATAATATT
646113 TTGATTAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 23 0.79
23 6 0.21
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (23 bp):
TATTATAATATTAAAAATATTAA
Found at i:646373 original size:42 final size:42
Alignment explanation
Indices: 646312--646402 Score: 146
Period size: 42 Copynumber: 2.2 Consensus size: 42
646302 TTCCTCCAAC
*
646312 CAAACACTGGAAAACATTTTCCGGAAAACAAATTACGTGAAA
1 CAAACACAGGAAAACATTTTCCGGAAAACAAATTACGTGAAA
* * *
646354 CAAACACAGGAAAATATTTTCCGGAAAATAAATTACTTGAAA
1 CAAACACAGGAAAACATTTTCCGGAAAACAAATTACGTGAAA
646396 CAAACAC
1 CAAACAC
646403 GAGATTTCGA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.49, C:0.19, G:0.12, T:0.20
Consensus pattern (42 bp):
CAAACACAGGAAAACATTTTCCGGAAAACAAATTACGTGAAA
Found at i:652365 original size:31 final size:31
Alignment explanation
Indices: 652342--652418 Score: 127
Period size: 31 Copynumber: 2.5 Consensus size: 31
652332 CATAGATTCT
* *
652342 GAAGAACCTAGGTAATCAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
*
652373 GAAGAACATAGGTAAACAATCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
652404 GAAGAACATAGGTAA
1 GAAGAACATAGGTAA
652419 CCCTCGACTC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.19
Consensus pattern (31 bp):
GAAGAACATAGGTAAACAGTCCATATGTCCC
Found at i:655103 original size:16 final size:16
Alignment explanation
Indices: 655082--655114 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
655072 CTAATTATAT
655082 AATTGATTCATTTCCA
1 AATTGATTCATTTCCA
655098 AATTGATTCATTTCCA
1 AATTGATTCATTTCCA
655114 A
1 A
655115 CCTTACTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.33, C:0.18, G:0.06, T:0.42
Consensus pattern (16 bp):
AATTGATTCATTTCCA
Found at i:659598 original size:13 final size:13
Alignment explanation
Indices: 659580--659604 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
659570 AGTTTAGTCT
659580 TTCTTCTTTTTTC
1 TTCTTCTTTTTTC
659593 TTCTTCTTTTTT
1 TTCTTCTTTTTT
659605 TTTATATGGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (13 bp):
TTCTTCTTTTTTC
Found at i:659650 original size:19 final size:20
Alignment explanation
Indices: 659611--659649 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
659601 TTTTTTTATA
*
659611 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
659631 TGGGGGTATCGATTCCCCC
1 TGGGGGAATCGATTCCCCC
659650 TCTAGCATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.10, C:0.33, G:0.33, T:0.23
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:659700 original size:21 final size:21
Alignment explanation
Indices: 659676--659718 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
659666 TTCATATTCG
*
659676 TTGAGGGGGTATCA-ATTCCCC
1 TTGAAGGGGTA-CAGATTCCCC
*
659697 TTGAATGGGTACAGATTCCCC
1 TTGAAGGGGTACAGATTCCCC
659718 T
1 T
659719 AGCCCAGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.21, C:0.23, G:0.26, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACAGATTCCCC
Found at i:666422 original size:13 final size:13
Alignment explanation
Indices: 666404--666428 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
666394 AGTTTAGTCT
666404 TTCTTCTTTTTTC
1 TTCTTCTTTTTTC
666417 TTCTTCTTTTTT
1 TTCTTCTTTTTT
666429 TTTATATGGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (13 bp):
TTCTTCTTTTTTC
Found at i:666523 original size:21 final size:21
Alignment explanation
Indices: 666499--666541 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
666489 TTCATATTCG
* *
666499 TTGAGGGGGTATCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
* *
666520 TTGAATGGTTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
666541 T
1 T
666542 AACCCAGAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.16, C:0.26, G:0.26, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:670078 original size:63 final size:65
Alignment explanation
Indices: 669982--670140 Score: 175
Period size: 63 Copynumber: 2.4 Consensus size: 65
669972 GGATTTTCGG
* *
669982 GCTAG-GGGAATCGGTACCCATTCA-AGGGGAACCGATACCCCTCAAT-G-AAATG-AATTCCAG
1 GCTAGAGGGAATCGGTACCC--CCAGGGGGGAACCGATACCCCTC-ATCGTAAATGAAATTCCAG
670042 AAT
63 AAT
* *
670045 GCTAGAGGGAATCGGTACCCCCAGGGGGGAACCGATACCCCTCATCGTATATGAAATTCCAGATT
1 GCTAGAGGGAATCGGTACCCCCAGGGGGGAACCGATACCCCTCATCGTAAATGAAATTCCAGAAT
* * *
670110 GCTTGAGGGGAATCGATACCCCTAAGGGGGG
1 GCTAGA-GGGAATCGGTACCCC-CAGGGGGG
670141 GGGAACCGAT
Statistics
Matches: 82, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
62 4 0.05
63 24 0.29
64 18 0.22
65 15 0.18
66 14 0.17
67 7 0.09
ACGTcount: A:0.29, C:0.24, G:0.28, T:0.19
Consensus pattern (65 bp):
GCTAGAGGGAATCGGTACCCCCAGGGGGGAACCGATACCCCTCATCGTAAATGAAATTCCAGAAT
Found at i:670526 original size:28 final size:28
Alignment explanation
Indices: 670451--670530 Score: 106
Period size: 29 Copynumber: 2.8 Consensus size: 28
670441 ATTACATTCC
**
670451 ATATTATGATACATGACATGAATTTGTATT
1 ATATTAT--TACATGACATGAATTCATATT
*
670481 AAATGTATTACATGACATGAATTCATATT
1 ATAT-TATTACATGACATGAATTCATATT
670510 ATATTATTACATGACATGAAT
1 ATATTATTACATGACATGAAT
670531 ATGCAGAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
28 17 0.38
29 22 0.49
30 3 0.07
31 3 0.07
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (28 bp):
ATATTATTACATGACATGAATTCATATT
Found at i:670586 original size:30 final size:31
Alignment explanation
Indices: 670544--670603 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
670534 CAGAAAAGTT
*
670544 ATATGCACTATGTGATAAAGGTATGTAAATG
1 ATATGCACTATGTGATAAAGGTATGGAAATG
*
670575 ATATGC-CTATGTGTTAAAGGTATGGAAAT
1 ATATGCACTATGTGATAAAGGTATGGAAAT
670604 ACTATGTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.33
Consensus pattern (31 bp):
ATATGCACTATGTGATAAAGGTATGGAAATG
Found at i:670897 original size:22 final size:22
Alignment explanation
Indices: 670823--670889 Score: 125
Period size: 22 Copynumber: 3.0 Consensus size: 22
670813 TTATGGACAT
*
670823 AATTCTACGGTCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
670845 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
670867 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
670889 A
1 A
670890 TTTATACGAG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.19, C:0.27, G:0.25, T:0.28
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:676967 original size:21 final size:21
Alignment explanation
Indices: 676925--676967 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
676915 TTTTCGGGCT
* * *
676925 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
676946 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
676967 A
1 A
676968 TGAAATGAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:677033 original size:67 final size:69
Alignment explanation
Indices: 676947--677099 Score: 213
Period size: 68 Copynumber: 2.2 Consensus size: 69
676937 ACCCATTCAA
* *
676947 GGGGAACCGATACCCCCTCAAT-G-AAATGAATTTCCAGAATGCTAGAGGGGAATCGGTACCCC-
1 GGGGAACCGATACCCCCTC-ATCGTAAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCT
*
677009 CAGGG
65 AAGGG
* * *
677014 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGATTGCTTGAGGGGAATCGATACCCCTA
1 GGGGAACCGATACCCCCTCATCGTAAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCTA
677079 AGGG
66 AGGG
*
677083 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
677100 ATGAGAAAAA
Statistics
Matches: 76, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
66 2 0.03
67 20 0.26
68 34 0.45
69 20 0.26
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.18
Consensus pattern (69 bp):
GGGGAACCGATACCCCCTCATCGTAAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCTA
AGGG
Found at i:677436 original size:29 final size:29
Alignment explanation
Indices: 677402--677473 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
677392 CATATTATGA
**
677402 TACATGACATGAATTTGTATTAAATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
*
677431 TACATGACATGAATTCATATTATATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
677460 TACATGACATGAAT
1 TACATGACATGAAT
677474 ATGCAGAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAATGTAT
Found at i:677530 original size:30 final size:31
Alignment explanation
Indices: 677488--677547 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
677478 AGAAAAAGTT
*
677488 ATATGCACTATGTGATAAAGGTATGTAAATG
1 ATATGCACTATGTGATAAAGGTATGGAAATG
*
677519 ATATGC-CTATGTGTTAAAGGTATGGAAAT
1 ATATGCACTATGTGATAAAGGTATGGAAAT
677548 ACTATGTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.33
Consensus pattern (31 bp):
ATATGCACTATGTGATAAAGGTATGGAAATG
Found at i:677841 original size:22 final size:22
Alignment explanation
Indices: 677767--677833 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
677757 TTATGGACAT
677767 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
677789 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
677811 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
677833 A
1 A
677834 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:678899 original size:23 final size:24
Alignment explanation
Indices: 678868--678913 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
678858 AATGTCATTT
*
678868 TTTTCAAAAATTACGAAAATAGCC
1 TTTTCAAAAATTACAAAAATAGCC
678892 TTTT-AAAAATTACAAAAATAGC
1 TTTTCAAAAATTACAAAAATAGC
678914 ACTATTTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.50, C:0.13, G:0.07, T:0.30
Consensus pattern (24 bp):
TTTTCAAAAATTACAAAAATAGCC
Found at i:679008 original size:18 final size:18
Alignment explanation
Indices: 678985--679040 Score: 76
Period size: 18 Copynumber: 3.1 Consensus size: 18
678975 AGATCAACGA
*
678985 TCAACGGGTCGGGTCGGG
1 TCAACGGGACGGGTCGGG
** *
679003 TCAACGAAACTGGTCGGG
1 TCAACGGGACGGGTCGGG
679021 TCAACGGGACGGGTCGGG
1 TCAACGGGACGGGTCGGG
679039 TC
1 TC
679041 GGAACCGGTC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.18, C:0.23, G:0.43, T:0.16
Consensus pattern (18 bp):
TCAACGGGACGGGTCGGG
Found at i:691842 original size:25 final size:25
Alignment explanation
Indices: 691810--691869 Score: 120
Period size: 25 Copynumber: 2.4 Consensus size: 25
691800 CCTGGTTAAT
691810 TTCATAATTTTTTACAAAGAAAAAA
1 TTCATAATTTTTTACAAAGAAAAAA
691835 TTCATAATTTTTTACAAAGAAAAAA
1 TTCATAATTTTTTACAAAGAAAAAA
691860 TTCATAATTT
1 TTCATAATTT
691870 GAGGGGTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.48, C:0.08, G:0.03, T:0.40
Consensus pattern (25 bp):
TTCATAATTTTTTACAAAGAAAAAA
Found at i:692602 original size:22 final size:23
Alignment explanation
Indices: 692574--692626 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 23
692564 GAGTTTATTA
*
692574 AAAAAATTA-AATTTTTTAATGC
1 AAAAAATTATAATTTTTAAATGC
**
692596 AAAAAA-TATAATTTTTAAATTT
1 AAAAAATTATAATTTTTAAATGC
692618 AAAAAATTA
1 AAAAAATTA
692627 GAGGAGCTCG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 2 0.08
22 22 0.85
23 2 0.08
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (23 bp):
AAAAAATTATAATTTTTAAATGC
Found at i:693568 original size:24 final size:24
Alignment explanation
Indices: 693525--693570 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
693515 CAAGGTAATT
*
693525 TTTTTTAACTTCATTTATTTAACC
1 TTTTTTAACTTCATTAATTTAACC
* *
693549 TTTTTTAATTTGATTAATTTAA
1 TTTTTTAACTTCATTAATTTAA
693571 TTATTTTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.28, C:0.09, G:0.02, T:0.61
Consensus pattern (24 bp):
TTTTTTAACTTCATTAATTTAACC
Found at i:695100 original size:24 final size:22
Alignment explanation
Indices: 695061--695111 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 22
695051 AAACAGTTAG
695061 TTTTTTTAATTT-AAAATTATAT
1 TTTTTTTAATTTAAAAATTA-AT
*
695083 TTTTTTTGTATTTAAAAAATTAAT
1 TTTTTTT-AATTT-AAAAATTAAT
695107 TTTTT
1 TTTTT
695112 AATAAACTCG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 7 0.28
23 4 0.16
24 7 0.28
25 7 0.28
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (22 bp):
TTTTTTTAATTTAAAAATTAAT
Found at i:700958 original size:28 final size:29
Alignment explanation
Indices: 700888--701128 Score: 101
Period size: 28 Copynumber: 8.5 Consensus size: 29
700878 TGATGCATTT
* *
700888 CTGATTCTGCATGGGATTATATTCC-CGT-
1 CTGATTCTGCATGGGCTTATA-TCCATGTC
* *
700916 CTCGATTCTACATGGGCTTA-GT-CATCGTC
1 CT-GATTCTGCATGGGCTTATATCCAT-GTC
* *
700945 CTGATTCTGTATGGGATTATATCCATGTC
1 CTGATTCTGCATGGGCTTATATCCATGTC
* * * *
700974 CTGATTCTGCACGGGCTT-TGTCCCTCTC
1 CTGATTCTGCATGGGCTTATATCCATGTC
* * * * *
701002 TTGATTATGAATGAGATTATATCC-TCGTC
1 CTGATTCTGCATGGGCTTATATCCAT-GTC
* * * *
701031 CTGATTCTACATGGGCTCA-GTCC-TCATC
1 CTGATTCTGCATGGGCTTATATCCAT-GTC
* * *
701059 CTGGTTCTCCATGGG-TTATATCTC-CGTC
1 CTGATTCTGCATGGGCTTATATC-CATGTC
* * * *
701087 CTGATTCTACATGTG-AT-TATCCTTGTC
1 CTGATTCTGCATGGGCTTATATCCATGTC
*
701114 CTGATTTTGCATGGG
1 CTGATTCTGCATGGG
701129 ATCCTCTACG
Statistics
Matches: 157, Mismatches: 45, Indels: 23
0.70 0.20 0.10
Matches are distributed among these distances:
26 2 0.01
27 22 0.14
28 75 0.48
29 55 0.35
30 3 0.02
ACGTcount: A:0.17, C:0.24, G:0.20, T:0.39
Consensus pattern (29 bp):
CTGATTCTGCATGGGCTTATATCCATGTC
Found at i:700959 original size:57 final size:57
Alignment explanation
Indices: 700888--701130 Score: 237
Period size: 57 Copynumber: 4.3 Consensus size: 57
700878 TGATGCATTT
*
700888 CTGATTCTGCATGGGATTATATTCC-CGT-CTCGATTCTACATGGGCTTAGTCATCGTC
1 CTGATTCTGCATGGGATTATA-TCCACGTCCT-GATTCTACATGGGCTTAGTCCTCGTC
* * * * *
700945 CTGATTCTGTATGGGATTATATCCATGTCCTGATTCTGCACGGGCTTTGTCCCTC-TC
1 CTGATTCTGCATGGGATTATATCCACGTCCTGATTCTACATGGGCTTAGT-CCTCGTC
* * * * * * *
701002 TTGATTATGAATGAGATTATATCCTCGTCCTGATTCTACATGGGCTCAGTCCTCATC
1 CTGATTCTGCATGGGATTATATCCACGTCCTGATTCTACATGGGCTTAGTCCTCGTC
* * * * *
701059 CTGGTTCTCCATGGG-TTATATCTC-CGTCCTGATTCTACATGTGATTA-TCCTTGTC
1 CTGATTCTGCATGGGATTATATC-CACGTCCTGATTCTACATGGGCTTAGTCCTCGTC
*
701114 CTGATTTTGCATGGGAT
1 CTGATTCTGCATGGGAT
701131 CCTCTACGGA
Statistics
Matches: 150, Mismatches: 30, Indels: 13
0.78 0.16 0.07
Matches are distributed among these distances:
55 18 0.12
56 35 0.23
57 92 0.61
58 5 0.03
ACGTcount: A:0.17, C:0.24, G:0.20, T:0.39
Consensus pattern (57 bp):
CTGATTCTGCATGGGATTATATCCACGTCCTGATTCTACATGGGCTTAGTCCTCGTC
Found at i:702790 original size:23 final size:23
Alignment explanation
Indices: 702764--702811 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
702754 ATAAAGTACA
* *
702764 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAACGCTTAT
**
702787 ATAATGTAATAGGTAACGCTTAT
1 ATAACATAATAGGTAACGCTTAT
702810 AT
1 AT
702812 TTACCTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAACGCTTAT
Found at i:703355 original size:23 final size:23
Alignment explanation
Indices: 703283--703347 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 23
703273 ATACTTTATA
* *
703283 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCAATTACATT
* *
703306 ATATAAACGATA-CATATTACATT
1 ATATAAGCGCTACCA-ATTACATT
703329 ATATAAGCGCTACCAATTA
1 ATATAAGCGCTACCAATTA
703348 TATCATATTT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
22 1 0.03
23 31 0.91
24 2 0.06
ACGTcount: A:0.43, C:0.18, G:0.06, T:0.32
Consensus pattern (23 bp):
ATATAAGCGCTACCAATTACATT
Found at i:703845 original size:23 final size:23
Alignment explanation
Indices: 703773--703838 Score: 96
Period size: 23 Copynumber: 2.9 Consensus size: 23
703763 ATACTTTACA
* **
703773 ATATAAGCACTATTTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
703796 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
703819 ATATAAGCGCTACCTATTAC
1 ATATAAGCGCTACCTATTAC
703839 GTCATATTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.38, C:0.20, G:0.06, T:0.36
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:703902 original size:490 final size:485
Alignment explanation
Indices: 702885--704054 Score: 2115
Period size: 490 Copynumber: 2.4 Consensus size: 485
702875 TTATAATATG
*
702885 TTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
*
702950 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCATCTACAATATTAATTTAATAATTTCATTTGCA
66 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
703015 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
131 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
703080 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
196 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
703145 CGTAACGTAAAAAAAATCATTAGACGCCTTAATTACTAAATTAATATCTTAAAACTCACTCAAAA
261 CGTAACGTAAAAAAAATCATTAGACGCCTTAATTACTAAATTAATATCTTAAAACTCACTCAAAA
*
703210 GATAACCTTAAATTAATGTTTTCCATAGTGAAAAAAATATGGACACTTTTATAAAAAGGATAGAT
326 GATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAATATGGACACTTTTATAAAAAGGATAGAT
*
703275 ACTTTATAATATAAGCACTACCTATTACATTATATAAACGATACATATTACATTATATAAGCGCT
391 ACTTTACAATATAAGCACTACCTATTACATTATATAAACGATACATATTACATTATATAAGCGCT
*
703340 ACCAATTATATCATATTTTTACCTATTATA
456 ACCAATTACATCATATTTTTACCTATTATA
* *
703370 TTGAAAGTGTCCATACTTTTTATAAAAGGGATCGATACTTTTTTTAAAATTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
*
703435 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACA
66 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
703500 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
131 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
703565 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
196 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAAT-A-ATAT
703630 ATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
259 ATCGTAACGT-AAAAA-AAATCATTAGACGCCT-TAATTACTAAATTAATATCTTAAAACTCACT
* *
703695 CAAAAGATAACCTTAAATTAATGTTTTCTACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGA
321 CAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAATATGGACACTTTTATAAAAAGGA
** * *
703760 TAGATACTTTACAATATAAGCACTATTTATTACATTATATAAACGCTACCTATTACATTATATAA
386 TAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGATACATATTACATTATATAA
* *
703825 GCGCTACCTATTACGTCATATTTTTACCTATTATA
451 GCGCTACCAATTACATCATATTTTTACCTATTATA
703860 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
*
703925 TCAATTTTTTTTAATAGTGTTTCATGTTTTCTACCTACAATATTAATTTAATAATTTCATTTGCA
66 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
* *
703990 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTTTAATTTAATAATA
131 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAA-TTTAAATTTAACAATA
704055 ATATATATCG
Statistics
Matches: 657, Mismatches: 22, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
485 248 0.38
486 1 0.00
487 14 0.02
488 5 0.01
489 16 0.02
490 359 0.55
491 14 0.02
ACGTcount: A:0.39, C:0.10, G:0.08, T:0.42
Consensus pattern (485 bp):
TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
CGTAACGTAAAAAAAATCATTAGACGCCTTAATTACTAAATTAATATCTTAAAACTCACTCAAAA
GATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAATATGGACACTTTTATAAAAAGGATAGAT
ACTTTACAATATAAGCACTACCTATTACATTATATAAACGATACATATTACATTATATAAGCGCT
ACCAATTACATCATATTTTTACCTATTATA
Found at i:704229 original size:21 final size:22
Alignment explanation
Indices: 704204--704276 Score: 83
Period size: 23 Copynumber: 3.2 Consensus size: 22
704194 ATACTTTACA
*
704204 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
704227 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
* * *
704250 ATATAAGCGTTACCTATTACATC
1 ATATAAAC-ATACCTATTACATT
704273 ATAT
1 ATAT
704277 TTTTACCTAT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
23 44 0.98
24 1 0.02
ACGTcount: A:0.40, C:0.21, G:0.04, T:0.36
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:704240 original size:23 final size:23
Alignment explanation
Indices: 704214--704276 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
704204 ATATAACCAC
704214 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
704237 TACCTATTACATTATATAAGCGT
1 TACCTATTACATTATATAAACGA
*
704260 TACCTATTACATCATAT
1 TACCTATTACATTATAT
704277 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.38
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:704725 original size:22 final size:22
Alignment explanation
Indices: 704684--704754 Score: 99
Period size: 22 Copynumber: 3.2 Consensus size: 22
704674 ATACTTTACA
*
704684 ATATAAGCACTATCTATTACATT
1 ATATAAGCGCTA-CTATTACATT
704707 ATATAA-CGCTACCTATTACATT
1 ATATAAGCGCTA-CTATTACATT
*
704729 ATATAAGCGCTACTATTACATC
1 ATATAAGCGCTACTATTACATT
704751 ATAT
1 ATAT
704755 TTTTACCTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
22 33 0.75
23 11 0.25
ACGTcount: A:0.38, C:0.20, G:0.06, T:0.37
Consensus pattern (22 bp):
ATATAAGCGCTACTATTACATT
Found at i:704947 original size:480 final size:481
Alignment explanation
Indices: 704037--705096 Score: 1907
Period size: 480 Copynumber: 2.2 Consensus size: 481
704027 AATATTTAGA
704037 ATTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTAC
1 ATTTTTAA-TTAATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTAC
*
704102 TAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCATAGTGAAAAAA
65 TAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAA
704167 ATATAGACACTTTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATA
130 ATATAGACACTTTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATA
*
704232 AACGATACCTATTACATTATATAAGCGTTACCTATTACATCATATTTTTACCTATTATATTGAAA
195 AACGATACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAA
704297 GTGTCCATACTTTTTATAAAAGGATCGATACTTTGTTTAAAGTTATGTAATTTATGTTTCAATTT
260 GTGTCCATACTTTTTATAAAAGGATCGATACTTTGTTTAAAGTTATGTAATTTATGTTTCAATTT
704362 TTTTTAATAGTGTTTCATGTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAATT
325 TTTTTAATAGTGTTTCATGTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAATT
704427 ATTTGATTGTTTTGATATTTATAAAATAATATTAGAATTTAAATTTAACAATATTAACCAAAGAT
390 ATTTGATTGTTTTGATATTTATAAAATAATATTAGAATTTAAATTTAACAATATTAACCAAAGAT
704492 AAT-AATATGTAATATATATGTTTATT
455 AATAAATATGTAATATATATGTTTATT
704518 ATTTTTAATTAATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACT
1 ATTTTTAATTAATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACT
* *
704583 AAATTAATATCTTAAAACTCCCTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAG
66 AAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAA
* * * *
704648 TATGGACACTTTTATAAAAATGATAGATACTTTACAATATAAGCACTATCTATTACATTATAT-A
131 TATAGACACTTTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAA
*
704712 ACGCTACCTATTACATTATATAAGCGCTA-CTATTACATCATATTTTTACCTATTATATTGAAAG
196 ACGATACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAG
*
704776 TGTCCATAC-TTTTATAAAATGATCGATACTTCT-TTTAAAGTTATGTAATTTATGTTTCAA-TT
261 TGTCCATACTTTTTATAAAAGGATCGATACTT-TGTTTAAAGTTATGTAATTTATGTTTCAATTT
704838 TTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAA
325 TTTTTAATAGTGTTTCATG-TTTCCACCTACAATATTAATTTAATAATTTCATTTACAC-AAAAA
704903 TTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATTAACCAA
388 TTATTTGATTGTTTTGATA-TTTATAAAATAATA-TTAGAATTTAAATTTAACAATATTAACCAA
704968 AGATAATAAAAATATGTAATATATATGTTTATT
451 AGATAAT--AAATATGTAATATATATGTTTATT
*
705001 GTTTTTAATTAATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACT
1 ATTTTTAATTAATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACT
705066 AAATTAATATCTTAAAACTCACTCAAAAGAT
66 AAATTAATATCTTAAAACTCACTCAAAAGAT
705097 GTATATACCT
Statistics
Matches: 559, Mismatches: 12, Indels: 14
0.96 0.02 0.02
Matches are distributed among these distances:
476 21 0.04
477 87 0.16
478 69 0.12
479 42 0.08
480 215 0.38
481 8 0.01
483 117 0.21
ACGTcount: A:0.41, C:0.12, G:0.07, T:0.40
Consensus pattern (481 bp):
ATTTTTAATTAATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACT
AAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAA
TATAGACACTTTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAA
ACGATACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAG
TGTCCATACTTTTTATAAAAGGATCGATACTTTGTTTAAAGTTATGTAATTTATGTTTCAATTTT
TTTTAATAGTGTTTCATGTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAATTA
TTTGATTGTTTTGATATTTATAAAATAATATTAGAATTTAAATTTAACAATATTAACCAAAGATA
ATAAATATGTAATATATATGTTTATT
Found at i:704976 original size:921 final size:917
Alignment explanation
Indices: 703131--704959 Score: 3319
Period size: 921 Copynumber: 2.0 Consensus size: 917
703121 GTTTTTAATT
703131 TAATAATAATATATCGTAACGTAAAAAAAATCATTAGACGCCTTAATTACTAAATTAATATCTTA
1 TAATAATAATATATCGTAACGTAAAAAAAATCATTAGACGCCTTAATTACTAAATTAATATCTTA
*
703196 AAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCATAGTGAAAAAAATATGGACACTTTTA
66 AAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCATAGTGAAAAAAATATAGACACTTTTA
* *
703261 TAAAAAGGATAGATACTTTATAATATAAGCACTACCTATTACATTATATAAACGATACATATTAC
131 TAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACATATTAC
*
703326 ATTATATAAGCGCTACCAATTATATCATATTTTTACCTATTATATTGAAAGTGTCCATACTTTTT
196 ATTATATAAGCGCTACCAATTACATCATATTTTTACCTATTATATTGAAAGTGTCCATACTTTTT
*
703391 ATAAAAGGGATCGATACTTTTTTTAAAATTATGTAATTTATGTTTCAATTTTTTTTAATAGTGTT
261 ATAAAAGGGATCGATACTTTGTTTAAAATTATGTAATTTATGTTTCAATTTTTTTTAATAGTGTT
703456 TCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTT
326 TCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTT
703521 TGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAAT
391 TGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATTAACCAAAG--AATAATAAAT
*
703586 ATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAAT
454 ATGTAATATATATGTTTATTATTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAAT
703651 CATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAA
519 CATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAA
*
703716 TGTTTTCTACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGATACTTTACAATATAAGC
584 TGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGATACTTTACAATATAAGC
* *
703781 ACTATTTATTACATTATATAAACGCTACCTATTACATTATATAAGCGCTACCTATTACGTCATAT
649 ACTATCTATTACATTATATAAACGCTACCTATTACATTATATAAGCGCTACCTATTACATCATAT
*
703846 TTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTT
714 TTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTT
*
703911 ATGTAATTTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCTACCTACAATATTAATTTAA
779 ATGTAATTTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAA
*
703976 TAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTT
844 TAATTTCATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTT
704041 TTAATTTAA
909 TTAATTTAA
704050 TAATAAT-ATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATC
1 TAATAATAATATATCGTAACGT-AAAAA-AAATCATTAGACGCCT-TAATTACTAAATTAATATC
704114 TTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCATAGTGAAAAAAATATAGACACTT
63 TTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCATAGTGAAAAAAATATAGACACTT
*
704179 TTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTAT
128 TTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACATAT
* *
704244 TACATTATATAAGCGTTACCTATTACATCATATTTTTACCTATTATATTGAAAGTGTCCATACTT
193 TACATTATATAAGCGCTACCAATTACATCATATTTTTACCTATTATATTGAAAGTGTCCATACTT
*
704309 TTTATAAAA-GGATCGATACTTTGTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTTAATAGT
258 TTTATAAAAGGGATCGATACTTTGTTTAAAATTATGTAATTTATGTTTCAATTTTTTTTAATAGT
704373 GTTTCATG-TTTCCACCTACAATATTAATTTAATAATTTCATTTACAC-AAAAATTATTTGATTG
323 GTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTG
704436 TTTTGATA-TTTATAAAATAATA-TTAGAATTTAAATTTAACAATATTAACCAAAG-ATAAT-AA
388 TTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATTAACCAAAGAATAATAAA
704497 TATGTAATATATATGTTTATTATTTTTAA-TTAATAATAATATATATCGTAACGTAAAAAATAAA
453 TATGTAATATATATGTTTATTATTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAA
*
704561 TCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCCCTCAAAAGATAACCTTAAATTA
518 TCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTA
*
704626 ATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAATGATAGATACTTTACAATATAAG
583 ATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGATACTTTACAATATAAG
704691 CACTATCTATTACATTATAT-AACGCTACCTATTACATTATATAAGCGCTA-CTATTACATCATA
648 CACTATCTATTACATTATATAAACGCTACCTATTACATTATATAAGCGCTACCTATTACATCATA
*
704754 TTTTTACCTATTATATTGAAAGTGTCCATAC-TTTTAT-AAAATGATCGATACTTCTTTTAAAGT
713 TTTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGT
704817 TATGTAATTTATGTTTCAA-TTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTA
778 TATGTAATTTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTA
704881 ATAATTTCATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAA-T
843 ATAATTTCATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATT
*
704945 TTAAATTTAA
908 TTTAATTTAA
*
704955 CAATA
1 TAATA
704960 TTAACCAAAG
Statistics
Matches: 886, Mismatches: 21, Indels: 20
0.96 0.02 0.02
Matches are distributed among these distances:
905 14 0.02
906 106 0.12
907 43 0.05
908 6 0.01
909 43 0.05
910 30 0.03
911 181 0.20
912 30 0.03
913 5 0.01
916 32 0.04
917 14 0.02
918 38 0.04
919 51 0.06
920 77 0.09
921 216 0.24
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.41
Consensus pattern (917 bp):
TAATAATAATATATCGTAACGTAAAAAAAATCATTAGACGCCTTAATTACTAAATTAATATCTTA
AAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCATAGTGAAAAAAATATAGACACTTTTA
TAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACATATTAC
ATTATATAAGCGCTACCAATTACATCATATTTTTACCTATTATATTGAAAGTGTCCATACTTTTT
ATAAAAGGGATCGATACTTTGTTTAAAATTATGTAATTTATGTTTCAATTTTTTTTAATAGTGTT
TCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTT
TGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATTAACCAAAGAATAATAAATAT
GTAATATATATGTTTATTATTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAATCA
TTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATG
TTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGATACTTTACAATATAAGCAC
TATCTATTACATTATATAAACGCTACCTATTACATTATATAAGCGCTACCTATTACATCATATTT
TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTAT
GTAATTTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATA
ATTTCATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTTT
AATTTAA
Found at i:705124 original size:25 final size:25
Alignment explanation
Indices: 705096--705160 Score: 121
Period size: 25 Copynumber: 2.6 Consensus size: 25
705086 ACTCAAAAGA
*
705096 TGTATATACCTAAATATGTAGTTAT
1 TGTACATACCTAAATATGTAGTTAT
705121 TGTACATACCTAAATATGTAGTTAT
1 TGTACATACCTAAATATGTAGTTAT
705146 TGTACATACCTAAAT
1 TGTACATACCTAAAT
705161 TTAATGATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.40
Consensus pattern (25 bp):
TGTACATACCTAAATATGTAGTTAT
Found at i:707772 original size:21 final size:21
Alignment explanation
Indices: 707746--707802 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
707736 GATGTGTAAA
707746 TGTCGACACTTTTTTAAATGG
1 TGTCGACACTTTTTTAAATGG
707767 TGTCGACACTTTTTTAAATGG
1 TGTCGACACTTTTTTAAATGG
*
707788 TGTCGACACATTTTT
1 TGTCGACACTTTTTT
707803 CTTCCAATCT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.23, C:0.16, G:0.18, T:0.44
Consensus pattern (21 bp):
TGTCGACACTTTTTTAAATGG
Found at i:708079 original size:183 final size:183
Alignment explanation
Indices: 707767--708394 Score: 996
Period size: 183 Copynumber: 3.4 Consensus size: 183
707757 TTTTAAATGG
* *
707767 TGTCGACACTTTTTTAAATGGTGTCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACAC
1 TGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCAACAC
*
707832 AATATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCG
66 AATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCG
*
707897 GTTATATTACAAAATTATCTATTACATTATAAATCTGGTTTCCGATGTGTAAA
131 GTTATATTACAAAATTATCTATTACATTATAATTCTGGTTTCCGATGTGTAAA
* *
707950 TGTTGACACTTTTTTAAATGGTATCGATACATTTTTCTTCCAATCTGGACATAAAGTACCAACAC
1 TGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCAACAC
* *
708015 AATATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAATCGGTATATTTATACCG
66 AATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCG
*
708080 GTTATATTTCAAAATTATCTATTACATTATAATTCTGGGTTT-CGATGTGTAAA
131 GTTATATTACAAAATTATCTATTACATTATAATTCT-GGTTTCCGATGTGTAAA
* * *
708133 TGTCGACACTTTTTGACAAT-GTATCGACACATTTTTCTTCTAATCTGGACATAAAGTACCGACA
1 TGTCGACACTTTTTTA-AATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCAACA
* *
708197 CAATATTAAAAAGTGTCGATATTGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACT
65 CAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACC
* * *
708262 GGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTTTTTTCAA
130 GGTTATATTACAAAATTATCTATTACATTATAATTCTGGTTTCCGATG---TGTAAA
* *
708319 --TCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCATTCTGAACATAAAGTA-CAGACA
1 TGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCA-ACA
708381 CAATATTAAAAAGT
65 CAATATTAAAAAGT
708395 ATGAAAACTT
Statistics
Matches: 412, Mismatches: 25, Indels: 15
0.91 0.06 0.03
Matches are distributed among these distances:
182 4 0.01
183 331 0.80
184 73 0.18
186 4 0.01
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.37
Consensus pattern (183 bp):
TGTCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCAACAC
AATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCG
GTTATATTACAAAATTATCTATTACATTATAATTCTGGTTTCCGATGTGTAAA
Found at i:709607 original size:3 final size:3
Alignment explanation
Indices: 709599--709676 Score: 84
Period size: 3 Copynumber: 26.0 Consensus size: 3
709589 ACTTGTTTGG
* * * *
709599 ATC ATC ATC ATC ATC ATC ATC ATC ATC GTC ATC ATC TTC ATC GTC AGC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * * *
709647 TTC ATC GTC ATC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
709677 GTCAGCTTCA
Statistics
Matches: 59, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.24, C:0.33, G:0.06, T:0.36
Consensus pattern (3 bp):
ATC
Found at i:709652 original size:36 final size:36
Alignment explanation
Indices: 709612--709687 Score: 125
Period size: 36 Copynumber: 2.1 Consensus size: 36
709602 ATCATCATCA
*
709612 TCATCATCATCATCGTCATCATCTTCATCGTCAGCT
1 TCATCATCATCATCATCATCATCTTCATCGTCAGCT
* *
709648 TCATCGTCATCATCATCGTCATCTTCATCGTCAGCT
1 TCATCATCATCATCATCATCATCTTCATCGTCAGCT
709684 TCAT
1 TCAT
709688 ATTCATTGAC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.21, C:0.33, G:0.09, T:0.37
Consensus pattern (36 bp):
TCATCATCATCATCATCATCATCTTCATCGTCAGCT
Found at i:709677 original size:12 final size:12
Alignment explanation
Indices: 709600--709687 Score: 95
Period size: 12 Copynumber: 7.3 Consensus size: 12
709590 CTTGTTTGGA
* *
709600 TCATCATCATCA
1 TCATCGTCATCT
* *
709612 TCATCATCATCA
1 TCATCGTCATCT
* *
709624 TCGTCATCATCT
1 TCATCGTCATCT
*
709636 TCATCGTCAGCT
1 TCATCGTCATCT
*
709648 TCATCGTCATCA
1 TCATCGTCATCT
709660 TCATCGTCATCT
1 TCATCGTCATCT
*
709672 TCATCGTCAGCT
1 TCATCGTCATCT
709684 TCAT
1 TCAT
709688 ATTCATTGAC
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 67 1.00
ACGTcount: A:0.23, C:0.33, G:0.08, T:0.36
Consensus pattern (12 bp):
TCATCGTCATCT
Found at i:711501 original size:201 final size:200
Alignment explanation
Indices: 711157--711534 Score: 711
Period size: 201 Copynumber: 1.9 Consensus size: 200
711147 TTTAAATTAG
711157 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
711222 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
*
711287 TCAACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACC
131 TCAACACTTTTTATATATGGATCGACACTTTATGATTGCACCCTGTTTTCCATTCATTCTGGACC
711352 AAAAA
196 AAAAA
711357 TATCGACACAAACTAAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAT
1 TATCGACACAAACT-AAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAT
711422 ACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGG
65 ACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGG
* * *
711487 ATCGACACTTTTTATATATGGTTCGACACTTTATTATTGCACCCTGTT
130 ATCAACACTTTTTATATATGGATCGACACTTTATGATTGCACCCTGTT
711535 GGCCATATTG
Statistics
Matches: 173, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
200 14 0.08
201 159 0.92
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.37
Consensus pattern (200 bp):
TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
TCAACACTTTTTATATATGGATCGACACTTTATGATTGCACCCTGTTTTCCATTCATTCTGGACC
AAAAA
Found at i:713511 original size:33 final size:33
Alignment explanation
Indices: 713474--713539 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
713464 CATCTTAATA
*
713474 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
713507 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
713540 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:713598 original size:21 final size:21
Alignment explanation
Indices: 713573--713637 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
713563 CCCCTTATGC
* *
713573 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
713594 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
*
713615 CTATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
713636 CT
1 CT
713638 TGATTGTCTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.17, C:0.31, G:0.11, T:0.42
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:715904 original size:20 final size:19
Alignment explanation
Indices: 715849--715895 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
715839 TCCGGTATCA
*
715849 TTTTACCGGTTTTATCATT
1 TTTTACCAGTTTTATCATT
*
715868 TTGATACCAGTTTTATCATAT
1 TT-TTACCAGTTTTATCAT-T
715889 TTTTACC
1 TTTTACC
715896 TGTTATATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.21, C:0.17, G:0.09, T:0.53
Consensus pattern (19 bp):
TTTTACCAGTTTTATCATT
Found at i:716075 original size:20 final size:19
Alignment explanation
Indices: 716030--716090 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 19
716020 TCCGGTAACG
716030 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
716049 TTGTTACTGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
* * *
716070 TTTTACCTGTTATATCGTT
1 TTTTACCGGTTTTATCATT
716089 TT
1 TT
716091 GGATCGATAC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 5 0.14
20 27 0.77
21 3 0.09
ACGTcount: A:0.16, C:0.13, G:0.11, T:0.59
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:716120 original size:181 final size:182
Alignment explanation
Indices: 715816--716288 Score: 707
Period size: 181 Copynumber: 2.6 Consensus size: 182
715806 CGTACTTACG
* * *
715816 AAAGTATCGACACTTTCAATATATCCGGTATCATTTTACCGGTTTTATCATTTTGATACCAGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* ** *
715881 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATATTTTTTTTTAAAGTATCGACACATTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
* *
715946 AGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
131 AGGAGCTAAAACTGCTTCTCTTTTAAAATCACAAAGTGTCGATCCTTATATT
* *
715997 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGTTACTGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
*
716062 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
** * *
716127 AGGATTTAAAACTGCTTCTCTTTTAAAATCACGAAGTGTCGATCTTTATATT
131 AGGAGCTAAAACTGCTTCTCTTTTAAAATCACAAAGTGTCGATCCTTATATT
* * * * *
716179 AAAGTACCGACACTTTAAATGTATCCGGTAGCGCTTTACCGGTTTTATCATTTCT-ATACCGGTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTT-TGATACCGGTT
* * *
716243 TTGTCATAGTTTTACCTGTTATATCGTTTTGGATCGACACATTTTT
65 TTATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
716289 AATTTGGATC
Statistics
Matches: 264, Mismatches: 26, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
181 164 0.62
182 99 0.38
183 1 0.00
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (182 bp):
AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
AGGAGCTAAAACTGCTTCTCTTTTAAAATCACAAAGTGTCGATCCTTATATT
Found at i:716296 original size:21 final size:21
Alignment explanation
Indices: 716270--716324 Score: 110
Period size: 21 Copynumber: 2.6 Consensus size: 21
716260 GTTATATCGT
716270 TTTGGATCGACACATTTTTAA
1 TTTGGATCGACACATTTTTAA
716291 TTTGGATCGACACATTTTTAA
1 TTTGGATCGACACATTTTTAA
716312 TTTGGATCGACAC
1 TTTGGATCGACAC
716325 GAACCGGTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.40
Consensus pattern (21 bp):
TTTGGATCGACACATTTTTAA
Found at i:716975 original size:32 final size:32
Alignment explanation
Indices: 716939--717014 Score: 84
Period size: 31 Copynumber: 2.4 Consensus size: 32
716929 GGGGCCGTGA
*
716939 GGCCTACCTAAGAACAT-ATCTTAGGGCCGCAG
1 GGCCTACCTAAGAA-ATGATCTCAGGGCCGCAG
** *
716971 GGCCTACCCGAG-AATGATCTCAGGGTCGCAG
1 GGCCTACCTAAGAAATGATCTCAGGGCCGCAG
*
717002 AGCCTACCTAAGA
1 GGCCTACCTAAGA
717015 GTCACATTAG
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
30 2 0.06
31 23 0.66
32 10 0.29
ACGTcount: A:0.28, C:0.29, G:0.26, T:0.17
Consensus pattern (32 bp):
GGCCTACCTAAGAAATGATCTCAGGGCCGCAG
Found at i:717906 original size:13 final size:13
Alignment explanation
Indices: 717888--717913 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
717878 AAGAAAGTCA
717888 ACGGTCAACGGTC
1 ACGGTCAACGGTC
717901 ACGGTCAACGGTC
1 ACGGTCAACGGTC
717914 GGGTCGGGTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.31, G:0.31, T:0.15
Consensus pattern (13 bp):
ACGGTCAACGGTC
Found at i:717924 original size:30 final size:32
Alignment explanation
Indices: 717890--717961 Score: 94
Period size: 35 Copynumber: 2.2 Consensus size: 32
717880 GAAAGTCAAC
*
717890 GGTCAACGGTCA-C-GGTCAACGGTCGGGTCG
1 GGTCAACGGTCAGCGGGTCAACAGTCGGGTCG
717920 GGTCAACGGTCAGGTCGGGGTCAACAGTCGGGTCG
1 GGTCAACGGTCA-G-C-GGGTCAACAGTCGGGTCG
717955 GGTCAAC
1 GGTCAAC
717962 CCGGTTCAGA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
30 12 0.33
33 1 0.03
35 23 0.64
ACGTcount: A:0.18, C:0.25, G:0.40, T:0.17
Consensus pattern (32 bp):
GGTCAACGGTCAGCGGGTCAACAGTCGGGTCG
Found at i:717925 original size:17 final size:17
Alignment explanation
Indices: 717903--717961 Score: 91
Period size: 17 Copynumber: 3.4 Consensus size: 17
717893 CAACGGTCAC
717903 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
*
717920 GGTCAACGGTCAGGTCGG
1 GGTCAACGGTCGGGTC-G
*
717938 GGTCAACAGTCGGGTCG
1 GGTCAACGGTCGGGTCG
717955 GGTCAAC
1 GGTCAAC
717962 CCGGTTCAGA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
17 23 0.61
18 15 0.39
ACGTcount: A:0.17, C:0.24, G:0.42, T:0.17
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:717931 original size:7 final size:7
Alignment explanation
Indices: 717884--717913 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
717874 GTCAAAGAAA
717884 GTCAACG
1 GTCAACG
717891 GTCAACG
1 GTCAACG
717898 GTC-ACG
1 GTCAACG
717904 GTCAACG
1 GTCAACG
717911 GTC
1 GTC
717914 GGGTCGGGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.23, C:0.30, G:0.30, T:0.17
Consensus pattern (7 bp):
GTCAACG
Found at i:717979 original size:19 final size:19
Alignment explanation
Indices: 717955--718019 Score: 96
Period size: 19 Copynumber: 3.4 Consensus size: 19
717945 AGTCGGGTCG
*
717955 GGTCAACCCGGTTC-AGACC
1 GGTCAAACCGGTTCGA-ACC
717974 GGTCAAACCGGTTCGAACC
1 GGTCAAACCGGTTCGAACC
717993 GGTCAAACCGGTTCGAACC
1 GGTCAAACCGGTTCGAACC
718012 GGTTCAAA
1 GG-TCAAA
718020 ACTGGTCAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
19 37 0.86
20 6 0.14
ACGTcount: A:0.26, C:0.31, G:0.26, T:0.17
Consensus pattern (19 bp):
GGTCAAACCGGTTCGAACC
Found at i:717992 original size:10 final size:10
Alignment explanation
Indices: 717957--718035 Score: 83
Period size: 10 Copynumber: 8.1 Consensus size: 10
717947 TCGGGTCGGG
*
717957 TCAACCCGGT
1 TCAAACCGGT
*
717967 TCAGACCGG-
1 TCAAACCGGT
717976 TCAAACCGGT
1 TCAAACCGGT
*
717986 TCGAACCGG-
1 TCAAACCGGT
717995 TCAAACCGGT
1 TCAAACCGGT
*
718005 TCGAACCGGT
1 TCAAACCGGT
*
718015 TCAAAACTGG-
1 TC-AAACCGGT
718025 TCAAACCGGT
1 TCAAACCGGT
718035 T
1 T
718036 TTCCAGCAGC
Statistics
Matches: 56, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
9 22 0.39
10 29 0.52
11 5 0.09
ACGTcount: A:0.27, C:0.30, G:0.24, T:0.19
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:724326 original size:32 final size:31
Alignment explanation
Indices: 724290--724365 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
724280 GGGGCCGTGA
*
724290 GGCCTACCTAAGAACACATCTTAGGGCCGCAG
1 GGCCTACCTAAGAA-ACATCTCAGGGCCGCAG
** **
724322 GGCCTACCCGAGAATGATCTCAGGGCCGCAG
1 GGCCTACCTAAGAAACATCTCAGGGCCGCAG
*
724353 AGCCTACCTAAGA
1 GGCCTACCTAAGA
724366 GTCACATTAG
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
31 24 0.67
32 12 0.33
ACGTcount: A:0.28, C:0.32, G:0.26, T:0.14
Consensus pattern (31 bp):
GGCCTACCTAAGAAACATCTCAGGGCCGCAG
Found at i:724348 original size:63 final size:63
Alignment explanation
Indices: 724242--724365 Score: 155
Period size: 63 Copynumber: 2.0 Consensus size: 63
724232 CCCTAAGGGA
* * *
724242 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCG-TGAGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGA-GCCTACCTAAGAAC
* *
724305 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
724366 GTCACATTAG
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
62 2 0.04
63 49 0.92
64 2 0.04
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:725257 original size:13 final size:13
Alignment explanation
Indices: 725239--725277 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
725229 AAGAAAGTCA
725239 ACGGTCAACGGTC
1 ACGGTCAACGGTC
725252 ACGGTCAACGGTC
1 ACGGTCAACGGTC
725265 ACGGTCAACGGTC
1 ACGGTCAACGGTC
725278 GGGTCGGGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.23, C:0.31, G:0.31, T:0.15
Consensus pattern (13 bp):
ACGGTCAACGGTC
Found at i:725260 original size:20 final size:20
Alignment explanation
Indices: 725235--725277 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 20
725225 GTCAAAGAAA
725235 GTCAACGGTCAACGGTCACG
1 GTCAACGGTCAACGGTCACG
725255 GTCAACGGTC-ACGGTCAACG
1 GTCAACGGTCAACGGTC-ACG
725275 GTC
1 GTC
725278 GGGTCGGGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.23, C:0.30, G:0.30, T:0.16
Consensus pattern (20 bp):
GTCAACGGTCAACGGTCACG
Found at i:725289 original size:17 final size:17
Alignment explanation
Indices: 725267--725324 Score: 98
Period size: 17 Copynumber: 3.4 Consensus size: 17
725257 CAACGGTCAC
725267 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
725284 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
* *
725301 GGTCAACAGTCAGGTCG
1 GGTCAACGGTCGGGTCG
725318 GGTCAAC
1 GGTCAAC
725325 CCGGTTCAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.17, C:0.24, G:0.41, T:0.17
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:725294 original size:7 final size:7
Alignment explanation
Indices: 725235--725277 Score: 72
Period size: 7 Copynumber: 6.4 Consensus size: 7
725225 GTCAAAGAAA
725235 GTCAACG
1 GTCAACG
725242 GTCAACG
1 GTCAACG
725249 GTC-ACG
1 GTCAACG
725255 GTCAACG
1 GTCAACG
725262 GTC-ACG
1 GTCAACG
725268 GTCAACG
1 GTCAACG
725275 GTC
1 GTC
725278 GGGTCGGGTC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 12 0.35
7 22 0.65
ACGTcount: A:0.23, C:0.30, G:0.30, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:725342 original size:19 final size:19
Alignment explanation
Indices: 725318--725407 Score: 119
Period size: 19 Copynumber: 4.7 Consensus size: 19
725308 AGTCAGGTCG
*
725318 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
725337 GGTCAAACCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
*
725356 GATCAAACCGGTTC-GAACC
1 GGTCAAACCGGTTCAG-ACC
* *
725375 GGTCAAACCGGTTCAAAACT
1 GGTCAAACCGGTTC-AGACC
725395 GGTCAAACCGGTT
1 GGTCAAACCGGTT
725408 TTCCAGCAGC
Statistics
Matches: 63, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
18 1 0.02
19 47 0.75
20 15 0.24
ACGTcount: A:0.28, C:0.30, G:0.24, T:0.18
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Found at i:725390 original size:10 final size:10
Alignment explanation
Indices: 725320--725407 Score: 85
Period size: 9 Copynumber: 9.1 Consensus size: 10
725310 TCAGGTCGGG
*
725320 TCAACCCGGT
1 TCAAACCGGT
*
725330 TCAGACCGG-
1 TCAAACCGGT
725339 TCAAACCGGT
1 TCAAACCGGT
* *
725349 TCAGACC-GA
1 TCAAACCGGT
725358 TCAAACCGGT
1 TCAAACCGGT
*
725368 TCGAACCGG-
1 TCAAACCGGT
725377 TCAAACCGGT
1 TCAAACCGGT
*
725387 TCAAAACTGG-
1 TC-AAACCGGT
725397 TCAAACCGGT
1 TCAAACCGGT
725407 T
1 T
725408 TTCCAGCAGC
Statistics
Matches: 62, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
9 29 0.47
10 27 0.44
11 6 0.10
ACGTcount: A:0.28, C:0.31, G:0.23, T:0.18
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:726591 original size:229 final size:229
Alignment explanation
Indices: 726189--726684 Score: 915
Period size: 229 Copynumber: 2.2 Consensus size: 229
726179 ACCTACTTTT
726189 ATAAGTATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCA
1 ATAAGTATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCA
726254 ATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAA
66 ATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAA
726319 AAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAA
131 AAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAA
* *
726384 CCAAATATAATAATAAATATGTTTTCCACAGTGAA
196 CCAAAGATAATAATAAATATATTTT-CACAGTGAA
* *
726419 ATAAGTATGTACACTTTTATAAAAATGATATATA-TATTTTTTAAAGTTATGTAATTTATGTTTT
1 ATAAGTATGGACACTTTTATAAAAATGATATATACT-TTTTTTAAAGTTATGTAATTTATGTTTC
726483 AATTTTTTTTAATAGTGTTTCATG-TTTCCACCTACAATATTAATTTAATAATTTCATTTACACA
65 AATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACA
726547 AAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTA
130 AAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTA
726612 ACCAAAGATAATAATAAATATATTTTCACAGTGAA
195 ACCAAAGATAATAATAAATATATTTTCACAGTGAA
*
726647 ATAAGTATGGACACTTTTATAAAAATGATAAATACTTT
1 ATAAGTATGGACACTTTTATAAAAATGATATATACTTT
726685 ACAATATAAC
Statistics
Matches: 258, Mismatches: 6, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
228 43 0.17
229 131 0.51
230 84 0.33
ACGTcount: A:0.40, C:0.08, G:0.07, T:0.45
Consensus pattern (229 bp):
ATAAGTATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCA
ATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAA
AAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAA
CCAAAGATAATAATAAATATATTTTCACAGTGAA
Found at i:729454 original size:34 final size:34
Alignment explanation
Indices: 729411--729483 Score: 146
Period size: 34 Copynumber: 2.1 Consensus size: 34
729401 AAATTGGAAT
729411 CAAATAATACCATAACATTATACTTATTTACAAC
1 CAAATAATACCATAACATTATACTTATTTACAAC
729445 CAAATAATACCATAACATTATACTTATTTACAAC
1 CAAATAATACCATAACATTATACTTATTTACAAC
729479 CAAAT
1 CAAAT
729484 TTAAACAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.48, C:0.21, G:0.00, T:0.32
Consensus pattern (34 bp):
CAAATAATACCATAACATTATACTTATTTACAAC
Found at i:737274 original size:50 final size:50
Alignment explanation
Indices: 737195--737294 Score: 164
Period size: 50 Copynumber: 2.0 Consensus size: 50
737185 GTTTATTATA
* * *
737195 AAGATAAAGTATTCAAATAGTAACTCAATCGTGTTTCATGATTGAGTATG
1 AAGATAAAGTATTCAAATAGCAACCCAATCGTGTTTCACGATTGAGTATG
*
737245 AAGATAAAGTATTCAAATTGCAACCCAATCGTGTTTCACGATTGAGTATG
1 AAGATAAAGTATTCAAATAGCAACCCAATCGTGTTTCACGATTGAGTATG
737295 GATCACATTC
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.32
Consensus pattern (50 bp):
AAGATAAAGTATTCAAATAGCAACCCAATCGTGTTTCACGATTGAGTATG
Found at i:739566 original size:15 final size:16
Alignment explanation
Indices: 739541--739583 Score: 63
Period size: 15 Copynumber: 2.8 Consensus size: 16
739531 TAGCTTTTTT
739541 TTTTGTCTTAAAATT-A
1 TTTT-TCTTAAAATTAA
739557 TTTTTCTTAAAATTAA
1 TTTTTCTTAAAATTAA
739573 TTTTT-TTAAAA
1 TTTTTCTTAAAA
739584 GACGTTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 16 0.62
16 10 0.38
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (16 bp):
TTTTTCTTAAAATTAA
Found at i:742290 original size:52 final size:52
Alignment explanation
Indices: 742225--742363 Score: 190
Period size: 52 Copynumber: 2.7 Consensus size: 52
742215 CGCATGATGA
* * *
742225 ATGCAAAGATGCCTTAATGCATCTGTTGCCTATGCTGAGGCATGTTGCATGC
1 ATGCAAAGATGCCTTAATGCATCTGTTGCCCATGCAGAGGCATGCTGCATGC
*
742277 ATGCAAAGCTGCCTTAATGCAGT-TGTTGCCCATGCAGAGGCATGCTGCATGC
1 ATGCAAAGATGCCTTAATGCA-TCTGTTGCCCATGCAGAGGCATGCTGCATGC
* * * *
742329 ATGAAAAGTTGCCTTAATGCAACTGCTGCCCATGC
1 ATGCAAAGATGCCTTAATGCATCTGTTGCCCATGC
742364 CTCGTTTAAT
Statistics
Matches: 77, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
52 76 0.99
53 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.27
Consensus pattern (52 bp):
ATGCAAAGATGCCTTAATGCATCTGTTGCCCATGCAGAGGCATGCTGCATGC
Found at i:743633 original size:19 final size:21
Alignment explanation
Indices: 743611--743649 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
743601 TTTTAAGTAT
743611 TTTAA-TTAGGATTT-TCTTC
1 TTTAATTTAGGATTTATCTTC
743630 TTTAATTTAGGATTTATCTT
1 TTTAATTTAGGATTTATCTT
743650 TATCTTGTTT
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:0.23, C:0.08, G:0.10, T:0.59
Consensus pattern (21 bp):
TTTAATTTAGGATTTATCTTC
Found at i:747841 original size:24 final size:23
Alignment explanation
Indices: 747807--747873 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 23
747797 GAGATATCAT
747807 AAATCAAAACAGAATTCAGAACA-
1 AAATC-AAACAGAATTCAGAACAG
* * *
747830 AATATCAGAACAAAATCCAGATCAG
1 AA-ATCA-AACAGAATTCAGAACAG
747855 AAATCAATACAGAATTCAG
1 AAATCAA-ACAGAATTCAG
747874 GTTATGTATC
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
23 4 0.11
24 29 0.83
25 2 0.06
ACGTcount: A:0.55, C:0.18, G:0.10, T:0.16
Consensus pattern (23 bp):
AAATCAAACAGAATTCAGAACAG
Done.