Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007819.1 Hibiscus syriacus cultivar Beakdansim tig00110156_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: 3855360
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2745 characters in sequence are not A, C, G, or T
File 4 of 17
Found at i:629242 original size:16 final size:15
Alignment explanation
Indices: 629216--629249 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
629206 GCTACAATCT
629216 AACAAACTATTCTAG
1 AACAAACTATTCTAG
629231 AACAACACTATTCTAG
1 AACAA-ACTATTCTAG
629247 AAC
1 AAC
629250 TCACCACATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.47, C:0.24, G:0.06, T:0.24
Consensus pattern (15 bp):
AACAAACTATTCTAG
Found at i:631941 original size:30 final size:30
Alignment explanation
Indices: 631885--631975 Score: 103
Period size: 30 Copynumber: 3.0 Consensus size: 30
631875 TTTGATGAGT
* *
631885 CATGTGTTGATGGAG-AAGCACATGGTGGCA
1 CATGTGTTGATGGAGCAGGCAC-TGGTGGAA
* *
631915 GATGTGTTGATGGAGCAGGTACTGGTGGAA
1 CATGTGTTGATGGAGCAGGCACTGGTGGAA
***
631945 CACACGTTGATGGAGCAGGCACTGGTGGAA
1 CATGTGTTGATGGAGCAGGCACTGGTGGAA
631975 C
1 C
631976 GCACGTTGAT
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.25, C:0.14, G:0.38, T:0.22
Consensus pattern (30 bp):
CATGTGTTGATGGAGCAGGCACTGGTGGAA
Found at i:631981 original size:30 final size:30
Alignment explanation
Indices: 631920--631987 Score: 118
Period size: 30 Copynumber: 2.3 Consensus size: 30
631910 TGGCAGATGT
*
631920 GTTGATGGAGCAGGTACTGGTGGAACACAC
1 GTTGATGGAGCAGGCACTGGTGGAACACAC
*
631950 GTTGATGGAGCAGGCACTGGTGGAACGCAC
1 GTTGATGGAGCAGGCACTGGTGGAACACAC
631980 GTTGATGG
1 GTTGATGG
631988 GACTTGCAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.24, C:0.16, G:0.40, T:0.21
Consensus pattern (30 bp):
GTTGATGGAGCAGGCACTGGTGGAACACAC
Found at i:634919 original size:16 final size:15
Alignment explanation
Indices: 634893--634926 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
634883 GCTACAATCT
634893 AACAAACTATTCTAG
1 AACAAACTATTCTAG
634908 AACAACACTATTCTAG
1 AACAA-ACTATTCTAG
634924 AAC
1 AAC
634927 TCACAACATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.47, C:0.24, G:0.06, T:0.24
Consensus pattern (15 bp):
AACAAACTATTCTAG
Found at i:640528 original size:15 final size:16
Alignment explanation
Indices: 640505--640536 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
640495 CCCGACCACG
640505 GTGCTCCCGGAATCCT
1 GTGCTCCCGGAATCCT
640521 GTGC-CCCGGAATCCT
1 GTGCTCCCGGAATCCT
640536 G
1 G
640537 CGCGATTGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.12, C:0.38, G:0.28, T:0.22
Consensus pattern (16 bp):
GTGCTCCCGGAATCCT
Found at i:643484 original size:2 final size:2
Alignment explanation
Indices: 643477--643525 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
643467 TCAAAATGTG
643477 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
643519 TA TA TA T
1 TA TA TA T
643526 CAATTATAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:652334 original size:32 final size:33
Alignment explanation
Indices: 652261--652334 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 33
652251 AATTAAAACA
* *
652261 AAAAAATAAATTTGAAAGTTAAAGTGATTAAATT
1 AAAAAAT-AATCTGAAAGTTAAAGTAATTAAATT
**
652295 -AGGAATAATCTGAAAGTT-AAGTAATTAAATT
1 AAAAAATAATCTGAAAGTTAAAGTAATTAAATT
652326 AAAAAATAA
1 AAAAAATAA
652335 ACTTTAGTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
31 12 0.36
32 17 0.52
33 4 0.12
ACGTcount: A:0.57, C:0.01, G:0.12, T:0.30
Consensus pattern (33 bp):
AAAAAATAATCTGAAAGTTAAAGTAATTAAATT
Found at i:652527 original size:9 final size:9
Alignment explanation
Indices: 652515--652600 Score: 154
Period size: 9 Copynumber: 9.6 Consensus size: 9
652505 GAAACAAATC
*
652515 TGATAGTTT
1 TGATAATTT
*
652524 TGATAGTTT
1 TGATAATTT
652533 TGATAATTT
1 TGATAATTT
652542 TGATAATTT
1 TGATAATTT
652551 TGATAATTT
1 TGATAATTT
652560 TGATAATTT
1 TGATAATTT
652569 TGATAATTT
1 TGATAATTT
652578 TGATAATTT
1 TGATAATTT
652587 TGATAATTT
1 TGATAATTT
652596 TGATA
1 TGATA
652601 GTTTAGGTAT
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
9 76 1.00
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (9 bp):
TGATAATTT
Found at i:653251 original size:22 final size:22
Alignment explanation
Indices: 653200--653257 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
653190 TCACTCTCTA
*
653200 CGGTGACATCCGTCCCCATCTC
1 CGGTGAAATCCGTCCCCATCTC
* **
653222 TGACGAAATCCGTCCCCATCTC
1 CGGTGAAATCCGTCCCCATCTC
*
653244 CGGTGAAATTCGTC
1 CGGTGAAATCCGTC
653258 TATCTCCATC
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.19, C:0.38, G:0.19, T:0.24
Consensus pattern (22 bp):
CGGTGAAATCCGTCCCCATCTC
Found at i:655160 original size:19 final size:20
Alignment explanation
Indices: 655136--655205 Score: 67
Period size: 19 Copynumber: 3.6 Consensus size: 20
655126 CTAAAACCTA
655136 TTGCGAAATT-AAATTCATG
1 TTGCGAAATTGAAATTCATG
*
655155 TTGCG-AATTCGAAAATC-TAG
1 TTGCGAAATT-GAAATTCAT-G
*
655175 TTGCGAATTTGAAATTCA-G
1 TTGCGAAATTGAAATTCATG
*
655194 TTGCGAATTTGA
1 TTGCGAAATTGA
655206 CTTTTGTGTT
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
18 4 0.09
19 19 0.44
20 17 0.40
21 3 0.07
ACGTcount: A:0.33, C:0.11, G:0.20, T:0.36
Consensus pattern (20 bp):
TTGCGAAATTGAAATTCATG
Found at i:655179 original size:20 final size:19
Alignment explanation
Indices: 655154--655202 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 19
655144 TTAAATTCAT
655154 GTTGCGAATTCGAAAATCTA
1 GTTGCGAATTCGAAAATC-A
* *
655174 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTCGAAAATCA
655193 GTTGCGAATT
1 GTTGCGAATT
655203 TGACTTTTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 11 0.41
20 16 0.59
ACGTcount: A:0.31, C:0.12, G:0.22, T:0.35
Consensus pattern (19 bp):
GTTGCGAATTCGAAAATCA
Found at i:655197 original size:39 final size:38
Alignment explanation
Indices: 655128--655202 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 38
655118 TTGCGAAACT
655128 AAAACCTATTGCGAAATTAAATTCATGTTGCGAATTCG
1 AAAACCTATTGCGAAATTAAATTCATGTTGCGAATTCG
* *
655166 AAAATCTAGTTGCGAATTTGAAATTCA-GTTGCGAATT
1 AAAACCTA-TTGCGAAATT-AAATTCATGTTGCGAATT
655203 TGACTTTTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
38 7 0.21
39 19 0.58
40 7 0.21
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.33
Consensus pattern (38 bp):
AAAACCTATTGCGAAATTAAATTCATGTTGCGAATTCG
Found at i:655221 original size:20 final size:20
Alignment explanation
Indices: 655193--655359 Score: 176
Period size: 20 Copynumber: 8.3 Consensus size: 20
655183 TTGAAATTCA
655193 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTTTGT
* * * *
655213 GTTGTGAATTTGACTATCGC
1 GTTGCGAATTTGACTTTTGT
*
655233 GTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACTTTTGT
* * * *
655253 GTTACG-ATTT-ACAAATTCGC
1 GTTGCGAATTTGAC--TTTTGT
655273 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTTTGT
655293 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTTTGT
* * *
655313 GTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACTTTTGT
* *
655333 GTTGAGAATTTGAATTTTGT
1 GTTGCGAATTTGACTTTTGT
655353 GTTGCGA
1 GTTGCGA
655360 TTTACAGATT
Statistics
Matches: 116, Mismatches: 27, Indels: 8
0.77 0.18 0.05
Matches are distributed among these distances:
18 2 0.02
19 4 0.03
20 104 0.90
21 4 0.03
22 2 0.02
ACGTcount: A:0.19, C:0.13, G:0.25, T:0.44
Consensus pattern (20 bp):
GTTGCGAATTTGACTTTTGT
Found at i:655305 original size:100 final size:100
Alignment explanation
Indices: 655193--655385 Score: 314
Period size: 100 Copynumber: 1.9 Consensus size: 100
655183 TTGAAATTCA
* * *
655193 GTTGCGAATTTGACTTTTGTGTTGTGAATTTGACTATCGCGTTGCGAATTTGACTTCTGTGTTAC
1 GTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTATCGCGTTGAGAATTTGAATTCTGTGTTAC
**
655258 GATTTACAAATTCGCGTTGCGAATTTGACTTTTGT
66 GATTTACAAATTCGCGACGCGAATTTGACTTTTGT
* *
655293 GTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTATCGCGTTGAGAATTTGAATTTTGTGTTGC
1 GTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTATCGCGTTGAGAATTTGAATTCTGTGTTAC
*
655358 GATTTACAGATTCGCGACGCGAATTTGA
66 GATTTACAAATTCGCGACGCGAATTTGA
655386 AAAATCGCAA
Statistics
Matches: 85, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
100 85 1.00
ACGTcount: A:0.20, C:0.13, G:0.24, T:0.42
Consensus pattern (100 bp):
GTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTATCGCGTTGAGAATTTGAATTCTGTGTTAC
GATTTACAAATTCGCGACGCGAATTTGACTTTTGT
Found at i:655382 original size:40 final size:40
Alignment explanation
Indices: 655296--655386 Score: 105
Period size: 40 Copynumber: 2.3 Consensus size: 40
655286 CTTTTGTGTT
* * **
655296 GCGAATTTGACTTTTGTGTTGCGAATTTGACTATCGCGTT
1 GCGAATTTGAATTTTGTGTTGCGAATTTGACGATCGCGAC
*
655336 GAGAATTTGAATTTTGTGTTGCG-ATTT-ACAGATTCGCGAC
1 GCGAATTTGAATTTTGTGTTGCGAATTTGAC-GA-TCGCGAC
655376 GCGAATTTGAA
1 GCGAATTTGAA
655387 AAATCGCAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.05
39 5 0.12
40 36 0.84
ACGTcount: A:0.23, C:0.13, G:0.25, T:0.38
Consensus pattern (40 bp):
GCGAATTTGAATTTTGTGTTGCGAATTTGACGATCGCGAC
Found at i:655499 original size:20 final size:20
Alignment explanation
Indices: 655474--655512 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
655464 TGTTGGTCAT
655474 TTTGACAAATTCAAAAAAGG
1 TTTGACAAATTCAAAAAAGG
655494 TTTGACAAATTCAAAAAAG
1 TTTGACAAATTCAAAAAAG
655513 ATTAGTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.51, C:0.10, G:0.13, T:0.26
Consensus pattern (20 bp):
TTTGACAAATTCAAAAAAGG
Found at i:656127 original size:29 final size:29
Alignment explanation
Indices: 656095--656154 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
656085 AACATTCTCT
*
656095 TGAAACGCACGTTTAAAAGATTTATTTCA
1 TGAAACGCACGTTTAAAAGATTCATTTCA
** *
656124 TGAAACGTTCGTTTAAAAGGTTCATTTCA
1 TGAAACGCACGTTTAAAAGATTCATTTCA
656153 TG
1 TG
656155 CGCGCTTTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (29 bp):
TGAAACGCACGTTTAAAAGATTCATTTCA
Found at i:661256 original size:14 final size:14
Alignment explanation
Indices: 661237--661263 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
661227 TTATATTACA
661237 TTTAAAAATTTATT
1 TTTAAAAATTTATT
661251 TTTAAAAATTTAT
1 TTTAAAAATTTAT
661264 AATTATCAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TTTAAAAATTTATT
Found at i:661321 original size:25 final size:25
Alignment explanation
Indices: 661271--661323 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
661261 TATAATTATC
* **
661271 AATAATGTATTTTTAATATATTTTA
1 AATAATGTATTTTTAATAAAACTTA
661296 AATAATGTAATTTTTAA-AAAACTTA
1 AATAATGT-ATTTTTAATAAAACTTA
661321 AAT
1 AAT
661324 TATAATATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 16 0.67
26 8 0.33
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (25 bp):
AATAATGTATTTTTAATAAAACTTA
Found at i:665715 original size:12 final size:12
Alignment explanation
Indices: 665698--665723 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
665688 AGTTTCAAGC
665698 TCTTGTTGAGGT
1 TCTTGTTGAGGT
665710 TCTTGTTGAGGT
1 TCTTGTTGAGGT
665722 TC
1 TC
665724 ACCTAGTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.12, G:0.31, T:0.50
Consensus pattern (12 bp):
TCTTGTTGAGGT
Found at i:669902 original size:18 final size:18
Alignment explanation
Indices: 669881--669920 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
669871 GGATAAGAGT
*
669881 AGAGCTCAGGAAAGAAGG
1 AGAGCTCAAGAAAGAAGG
669899 AGAGCTCAAGAAAGAAGG
1 AGAGCTCAAGAAAGAAGG
669917 AGAG
1 AGAG
669921 TCTAGGAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.47, C:0.10, G:0.38, T:0.05
Consensus pattern (18 bp):
AGAGCTCAAGAAAGAAGG
Found at i:670939 original size:28 final size:29
Alignment explanation
Indices: 670887--670945 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 29
670877 GGTAACCTAT
670887 TTTAGAAATAAGAATAAAAACACAT-TTA
1 TTTAGAAATAAGAATAAAAACACATCTTA
*
670915 TTTAGAAATTAAG-ATAATAGA-ACATCTTA
1 TTTAGAAA-TAAGAATAA-AAACACATCTTA
670944 TT
1 TT
670946 ATAGGAACAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
28 16 0.59
29 11 0.41
ACGTcount: A:0.51, C:0.07, G:0.08, T:0.34
Consensus pattern (29 bp):
TTTAGAAATAAGAATAAAAACACATCTTA
Found at i:673665 original size:50 final size:52
Alignment explanation
Indices: 673562--673669 Score: 118
Period size: 50 Copynumber: 2.1 Consensus size: 52
673552 ACATAAGAAC
*
673562 AAAATAAGATAAAAACAAAAGAAAAAAATAATAATAATTAAATAAATCAAAAGGG
1 AAAATAAGATAAAAAC-AAAGAAAAAAATAATAATAAGTAAATAAA-CAAAA-GG
*
673617 AAAATAAGAT-AAAAC-AA-AAAAAAAT-ATATTAAGTAAATCAAA-AGAAAGG
1 AAAATAAGATAAAAACAAAGAAAAAAATAATAATAAGTAAAT-AAACA-AAAGG
673666 AAAA
1 AAAA
673670 GAAAATGTAA
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
49 7 0.14
50 14 0.29
51 11 0.22
52 2 0.04
54 5 0.10
55 10 0.20
ACGTcount: A:0.71, C:0.04, G:0.09, T:0.16
Consensus pattern (52 bp):
AAAATAAGATAAAAACAAAGAAAAAAATAATAATAAGTAAATAAACAAAAGG
Found at i:673780 original size:16 final size:16
Alignment explanation
Indices: 673759--673807 Score: 64
Period size: 16 Copynumber: 2.9 Consensus size: 16
673749 ACAAATGCAG
673759 AATAAATAAAAAGA-AA
1 AATAAATAAAAA-ATAA
673775 AATAAATAAAAAATAA
1 AATAAATAAAAAATAA
673791 AATAAAATAAATAAATA
1 AAT-AAATAAA-AAATA
673808 TATATATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
15 1 0.03
16 17 0.57
17 7 0.23
18 5 0.17
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (16 bp):
AATAAATAAAAAATAA
Found at i:673789 original size:27 final size:27
Alignment explanation
Indices: 673723--673797 Score: 69
Period size: 27 Copynumber: 2.7 Consensus size: 27
673713 AACAAAAAGG
* * *
673723 AAATGAAAAGATAAATCAAAAGGAAAAC
1 AAAT-AAAAAATAAATAAAAAGAAAAAC
** * *
673751 AAATGCAGAATAAATAAAAAGAAAAAT
1 AAATAAAAAATAAATAAAAAGAAAAAC
673778 AAATAAAAAATAAAATAAAA
1 AAATAAAAAAT-AAATAAAA
673798 TAAATAAATA
Statistics
Matches: 36, Mismatches: 10, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
27 24 0.67
28 12 0.33
ACGTcount: A:0.73, C:0.04, G:0.09, T:0.13
Consensus pattern (27 bp):
AAATAAAAAATAAATAAAAAGAAAAAC
Found at i:673812 original size:2 final size:2
Alignment explanation
Indices: 673805--673829 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
673795 AAATAAATAA
673805 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
673830 AATTAAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:675018 original size:3 final size:3
Alignment explanation
Indices: 675012--675087 Score: 62
Period size: 3 Copynumber: 22.7 Consensus size: 3
675002 AAATAAATGT
* *
675012 ATA ATAA ATA ATA ATAA ATG ATA ATA ATAA ATA ATA ATAA ATA ACA ATA
1 ATA AT-A ATA ATA AT-A ATA ATA ATA AT-A ATA ATA AT-A ATA ATA ATA
675061 ATAA ATAA ATAA ATA ATA ATAA ATA AT
1 AT-A AT-A AT-A ATA ATA AT-A ATA AT
675088 TAATTATATT
Statistics
Matches: 63, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
3 37 0.59
4 26 0.41
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:675027 original size:10 final size:10
Alignment explanation
Indices: 675012--675087 Score: 91
Period size: 10 Copynumber: 7.2 Consensus size: 10
675002 AAATAAATGT
675012 ATAATAAATA
1 ATAATAAATA
675022 ATAATAAATGATA
1 ATAAT-AA--ATA
675035 ATAATAAATA
1 ATAATAAATA
675045 ATAATAAATA
1 ATAATAAATA
*
675055 ACAAT-AATAA
1 ATAATAAAT-A
675065 ATAAATAAATA
1 AT-AATAAATA
675076 ATAATAAATA
1 ATAATAAATA
675086 AT
1 AT
675088 TAATTATATT
Statistics
Matches: 58, Mismatches: 2, Indels: 12
0.81 0.03 0.17
Matches are distributed among these distances:
9 3 0.05
10 34 0.59
11 8 0.14
12 5 0.09
13 8 0.14
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.29
Consensus pattern (10 bp):
ATAATAAATA
Found at i:675035 original size:13 final size:13
Alignment explanation
Indices: 675018--675087 Score: 88
Period size: 13 Copynumber: 5.2 Consensus size: 13
675008 ATGTATAATA
675018 AATAATAATAAAT
1 AATAATAATAAAT
*
675031 GATAATAATAAAT
1 AATAATAATAAAT
*
675044 AATAATAA-ATAAC
1 AATAATAATA-AAT
675057 AATAATAAATAAAT
1 AATAAT-AATAAAT
675071 AAATAATAATAAAT
1 -AATAATAATAAAT
675085 AAT
1 AAT
675088 TAATTATATT
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
12 1 0.02
13 30 0.61
14 11 0.22
15 7 0.14
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.29
Consensus pattern (13 bp):
AATAATAATAAAT
Found at i:675205 original size:34 final size:33
Alignment explanation
Indices: 675154--675244 Score: 130
Period size: 33 Copynumber: 2.7 Consensus size: 33
675144 CTAAATATTA
675154 TATATAAATTTTC-AAAAATGTTTTTTTAAAAAAC
1 TATAT-AATTTTCAAAAAATGTTTTTTT-AAAAAC
**
675188 TATATAATTTTCAAAAAATACTTTTTTAAAAAC
1 TATATAATTTTCAAAAAATGTTTTTTTAAAAAC
*
675221 TATATGATTTTCAAAAAATGTTTT
1 TATATAATTTTCAAAAAATGTTTT
675245 CAAAAATTAT
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
33 34 0.67
34 17 0.33
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (33 bp):
TATATAATTTTCAAAAAATGTTTTTTTAAAAAC
Found at i:675263 original size:38 final size:37
Alignment explanation
Indices: 675221--675486 Score: 276
Period size: 38 Copynumber: 7.2 Consensus size: 37
675211 TTTTAAAAAC
* * *
675221 TATATGATTTTCAAAAAATGTTTTCAAAAATTATATTT
1 TATATAATTTTCAAAAAATGTTTT-AAAAACTATATAT
675259 TATATAAGTTTTC-AAAAATGTTTTTAAAAACTATATAT
1 TATATAA-TTTTCAAAAAATG-TTTTAAAAACTATATAT
*
675297 TATATAAATTTCAAAAAATGTTTTTAAAAACTATATAT
1 TATATAATTTTCAAAAAATG-TTTTAAAAACTATATAT
* *
675335 TATATAAGTTTTCCAAAAATGATTTTAAAGACTATATAT
1 TATATAA-TTTTCAAAAAATG-TTTTAAAAACTATATAT
** *
675374 TATAT-ATTTTCCTAAAATATTTTAAAAACTATATAT
1 TATATAATTTTCAAAAAATGTTTTAAAAACTATATAT
* * * *
675410 TATACAGTTTTC---AAGTGTTTTAAAAACCATATAT
1 TATATAATTTTCAAAAAATGTTTTAAAAACTATATAT
* *
675444 TATATACATTTT--TAAAATGTTTTTAGAAACTATATAT
1 TATATA-ATTTTCAAAAAATG-TTTTAAAAACTATATAT
675481 TATATA
1 TATATA
675487 TGTATTTTTA
Statistics
Matches: 198, Mismatches: 21, Indels: 19
0.83 0.09 0.08
Matches are distributed among these distances:
34 24 0.12
35 4 0.02
36 24 0.12
37 41 0.21
38 64 0.32
39 41 0.21
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.45
Consensus pattern (37 bp):
TATATAATTTTCAAAAAATGTTTTAAAAACTATATAT
Found at i:675505 original size:39 final size:37
Alignment explanation
Indices: 675273--675505 Score: 133
Period size: 39 Copynumber: 6.3 Consensus size: 37
675263 TAAGTTTTCA
* * * **
675273 AAAATGTTTTTAAAAACTATATATTATATAAATTTCAA
1 AAAACGTTTTTAAAAACCATATATTATATACATTT-TT
* * *
675311 AAAATGTTTTTAAAAACTATATATTATATA-AGTTTTCCA
1 AAAACGTTTTTAAAAACCATATATTATATACA-TTTT--T
* * * *
675350 AAAATGATTTTAAAGACTATATATTATAT--ATTTTCCT
1 AAAACGTTTTTAAAAACCATATATTATATACATTTT--T
* *
675387 AAAA--TATTTTAAAAACTATATA-T-TATACAGTTTT
1 AAAACGT-TTTTAAAAACCATATATTATATACATTTTT
*
675421 -CAA-GTGTTTTAAAAACCATATATTATATACATTTTT
1 AAAACGT-TTTTAAAAACCATATATTATATACATTTTT
* * * *
675457 AAAATGTTTTTAGAAACTATATATTATATATGTATTTTT
1 AAAACGTTTTTAAAAACCATATATTATATA--CATTTTT
*
675496 AAACCGTTTT
1 AAAACGTTTT
675506 CAAACTATAA
Statistics
Matches: 165, Mismatches: 17, Indels: 25
0.80 0.08 0.12
Matches are distributed among these distances:
33 2 0.01
34 20 0.12
35 2 0.01
36 29 0.18
37 34 0.21
38 36 0.22
39 42 0.25
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.45
Consensus pattern (37 bp):
AAAACGTTTTTAAAAACCATATATTATATACATTTTT
Found at i:676303 original size:84 final size:84
Alignment explanation
Indices: 676093--676939 Score: 822
Period size: 84 Copynumber: 10.2 Consensus size: 84
676083 TGCATTGAAC
* * * * *
676093 TATGCTGCAAATGGTGTGTCTTGGAGCTAAGCGTAATAGAACTCAAAGGTCTTTGG-TGGCAGAT
1 TATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTTGGCAGAT
* *
676157 AACCCTTCTAGCCTTGAGT
66 AACCCTTCTAGACTTAAGT
* * *
676176 TATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGCAGA
1 TATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTTGGCAGA
* *
676241 TAACCCTTCTCGACTTAAGC
65 TAACCCTTCTAGACTTAAGT
* * *
676261 TATGCTGCAAATGATGTGCCTTGGAGCTGAACGTAGTCGAACTCGAAGGTCTTTTGG-TGACAGA
1 TATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTC-TTTGGTTGGCAGA
* *
676325 TAACCCTTCTAGCCTTGAGT
65 TAACCCTTCTAGACTTAAGT
* * * * * *
676345 TATGCTGTAAATGATGTACCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTC--T--TTGGCAGA
1 TATGCTGCAAATGATGT-GCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTTGGCAGA
** * *
676406 TAGTCCTTCTCGACTTAAGC
65 TAACCCTTCTAGACTTAAGT
* * * * * *
676426 TATGTTGCAAATGATGTTCCTTGGAGCTGAACGTAGTCAAACTCGAAGGTCTTTTGG-TGACAGA
1 TATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTC-TTTGGTTGGCAGA
* *
676490 TAACCCTTCTAGCCTTGAGT
65 TAACCCTTCTAGACTTAAGT
* * * * *
676510 TATGCTGTAAATGATATGCCTTGGAGCTTAGCGTAGTCAAACTCGAAGGTCTTTGGTTGGCAGAT
1 TATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTTGGCAGAT
* *
676575 AACCTTTCTCGACTTAAGT
66 AACCCTTCTAGACTTAAGT
* * * * * ** *
676594 TATGCTGCAAATGACGTACCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC--T--TTGGAAGA
1 TATGCTGCAAATGATGT-GCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTTGGCAGA
* * *
676655 TAGCCCTTCTCGACTTAAGC
65 TAACCCTTCTAGACTTAAGT
* * * *
676675 TATGCTGCAAATGATGTGTCATT-GAGCTGAGTGTAATCGAACTCAAAGGTC-ATGAGTTGGCAG
1 TATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTG-GTTGGCAG
* *
676738 ACAACCCTTATAGACTTAAGT
64 ATAACCCTTCTAGACTTAAGT
* * * * *
676759 TGTGCTGTAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-TGACAGAT
1 TATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTTGGCAGAT
* *
676823 AACCCTTCTAGCCTTGAGT
66 AACCCTTCTAGACTTAAGT
* * * * * * * * * *
676842 TATGTTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGAATGACTTTTGTTAGCAGA
1 TATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTTGGCAGA
*
676907 TAACCCTTCTCGACTTAAGT
65 TAACCCTTCTAGACTTAAGT
*
676927 TATACTGCAAATG
1 TATGCTGCAAATG
676940 TTGTATTAAA
Statistics
Matches: 618, Mismatches: 125, Indels: 40
0.79 0.16 0.05
Matches are distributed among these distances:
80 50 0.08
81 78 0.13
82 1 0.00
83 65 0.11
84 292 0.47
85 132 0.21
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.30
Consensus pattern (84 bp):
TATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTTGGCAGAT
AACCCTTCTAGACTTAAGT
Found at i:676487 original size:165 final size:166
Alignment explanation
Indices: 676092--676939 Score: 1010
Period size: 165 Copynumber: 5.1 Consensus size: 166
676082 ATGCATTGAA
* * * * * *
676092 CTATGCTGCAAATGGTGTGTCTTGGAGCT-AAGCGTAATAGAACTCAAAGGTCTTTGGTGGCAGA
1 CTATGCTGCAAATGATGTGCCTTGGAGCTGAA-CGTAGTCGAACTCGAAGGTCTTTGGTGACAGA
*
676156 TAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTC
65 TAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTC
676221 GAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAG
130 GAAGGTC-TT-GTTGGCAGATAACCCTTCTCGACTTAAG
676260 CTATGCTGCAAATGATGTGCCTTGGAGCTGAACGTAGTCGAACTCGAAGGTCTTTTGGTGACAGA
1 CTATGCTGCAAATGATGTGCCTTGGAGCTGAACGTAGTCGAACTCGAAGGTC-TTTGGTGACAGA
*
676325 TAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTACCCTCGAAGCTGAGTGTAATCGAACTC
65 TAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTC
* **
676390 GAGGGTC-T-TTGGCAGATAGTCCTTCTCGACTTAAG
130 GAAGGTCTTGTTGGCAGATAACCCTTCTCGACTTAAG
* * *
676425 CTATGTTGCAAATGATGTTCCTTGGAGCTGAACGTAGTCAAACTCGAAGGTCTTTTGGTGACAGA
1 CTATGCTGCAAATGATGTGCCTTGGAGCTGAACGTAGTCGAACTCGAAGGTC-TTTGGTGACAGA
* * * * * * *
676490 TAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATG-CCTTGGAGCTTAGCGTAGTCAAACTC
65 TAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTC
*
676554 GAAGGTCTTTGGTTGGCAGATAACCTTTCTCGACTTAAG
130 GAAGGTC-TT-GTTGGCAGATAACCCTTCTCGACTTAAG
* * * * * ** * **
676593 TTATGCTGCAAATGACGTACCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTT-G-GA-AGA
1 CTATGCTGCAAATGATGT-GCCTTGGAGCTGAACGTAGTCGAACTCGAAGGTCTTTGGTGACAGA
* * * * * * * * *
676655 TAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGTCATTG-AGCTGAGTGTAATCGAACTC
65 TAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTC
* * * * *
676719 AAAGGTCATGAGTTGGCAGACAACCCTTATAGACTTAAG
130 GAAGGTC-T-TGTTGGCAGATAACCCTTCTCGACTTAAG
* * * * *
676758 TTGTGCTGTAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGAT
1 CTATGCTGCAAATGATGTGCCTTGGAGCTGAACGTAGTCGAACTCGAAGGTCTTTGGTGACAGAT
* *
676823 AACCCTTCTAGCCTTGAGTTATGTTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCG
66 AACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCG
* * *
676888 AATGACTTTTGTTAGCAGATAACCCTTCTCGACTTAAG
131 AA-G-GTCTTGTTGGCAGATAACCCTTCTCGACTTAAG
* *
676926 TTATACTGCAAATG
1 CTATGCTGCAAATG
676940 TTGTATTAAA
Statistics
Matches: 575, Mismatches: 90, Indels: 30
0.83 0.13 0.04
Matches are distributed among these distances:
164 56 0.10
165 219 0.38
166 9 0.02
167 38 0.07
168 143 0.25
169 109 0.19
170 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.30
Consensus pattern (166 bp):
CTATGCTGCAAATGATGTGCCTTGGAGCTGAACGTAGTCGAACTCGAAGGTCTTTGGTGACAGAT
AACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCG
AAGGTCTTGTTGGCAGATAACCCTTCTCGACTTAAG
Found at i:676492 original size:249 final size:247
Alignment explanation
Indices: 676153--676939 Score: 984
Period size: 249 Copynumber: 3.1 Consensus size: 247
676143 CTTTGGTGGC
* * * * * * * * ** *
676153 AGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAA
1 AGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGTCATTG-AGCTGAACGTAATCAAA
* * * *
676218 CTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTT
65 CTCGAAGGTCTTTGG-TGGCAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATGATATGCCTT
*
676283 GGAGCTGAACGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTAT
129 GGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTGACAGATAACCCTTCTAGCCTTGAGTTAT
*
676348 GCTGTAAATGATGTACCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGC
193 GCTGTAAATGATGTACCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGA
* * * *
676403 AGATAGTCCTTCTCGACTTAAGCTATGTTGCAAATGATGT-TCCTTGGAGCTGAACGTAGTCAAA
1 AGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGTCATT-GAGCTGAACGTAATCAAA
* * *
676467 CTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCTT
65 CTCGAAGGTC-TTTGGTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATGATATGCCTT
* * * * * * *
676532 GGAGCTTAGCGTAGTCAAACTCGAAGGTCTTTGGTTGGCAGATAACCTTTCTCGACTTAAGTTAT
129 GGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-TGACAGATAACCCTTCTAGCCTTGAGTTAT
* * *
676597 GCTGCAAATGACGTACCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGA
193 GCTGTAAATGATGTACCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGA
** *
676652 AGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGTCATTGAGCTGAGTGTAATCGAAC
1 AGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGTCATTGAGCTGAACGTAATCAAAC
* * * * *
676717 TCAAAGGTC-ATGAGTTGGCAGACAACCCTTATAGACTTAAGTTGTGCTGTAAATGATATGCCTT
66 TCGAAGGTCTTTG-G-TGGCAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATGATATGCCTT
676781 GGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATG
129 GGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATG
* * * ** * *
676846 TTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGAATGACTTTTGTTAGC
194 CTGTAAATGATGTACCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTC-TTTG---GA
* * *
676904 AGATAACCCTTCTCGACTTAAGTTATACTGCAAATG
1 AGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATG
676940 TTGTATTAAA
Statistics
Matches: 460, Mismatches: 67, Indels: 18
0.84 0.12 0.03
Matches are distributed among these distances:
247 2 0.00
248 71 0.15
249 310 0.67
250 43 0.09
252 34 0.07
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (247 bp):
AGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGTCATTGAGCTGAACGTAATCAAAC
TCGAAGGTCTTTGGTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATGATATGCCTTGG
AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCT
GTAAATGATGTACCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGA
Found at i:676737 original size:333 final size:333
Alignment explanation
Indices: 676092--676939 Score: 1066
Period size: 333 Copynumber: 2.5 Consensus size: 333
676082 ATGCATTGAA
* * * *
676092 CTATGCTGCAAATGGTGTGT-CTTGGAGCT-AAGCGTAAT-AGAACTCAAAGGTCTTTGGTGGCA
1 CTATGCTGCAAATGATGT-TCCTTGGAGCTGAA-CGTAGTCA-AACTCGAAGGTCTTTGGTGACA
* *
676154 GATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAAC
63 GATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAAC
* * * *
676219 TCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTG
128 TCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGACGTCCCTCG
* * * * *
676284 GAGCTGAACGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATG
193 AAGCTGAACGTAATCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGACTTAAGCTATG
* * * * * **
676349 CTGTAAATGATGTACCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGTCCTT
258 CTGCAAATGATGTACCATCGAAGCTGAGTGTAATCGAACTCAAAGGTCTTTGGCAGACAACCCTT
* *
676414 CTCGACTTAAG
323 ATAGACTTAAG
*
676425 CTATGTTGCAAATGATGTTCCTTGGAGCTGAACGTAGTCAAACTCGAAGGTCTTTTGGTGACAGA
1 CTATGCTGCAAATGATGTTCCTTGGAGCTGAACGTAGTCAAACTCGAAGGTC-TTTGGTGACAGA
* * * * * *
676490 TAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATG-CCTTGGAGCTTAGCGTAGTCAAACTC
65 TAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTC
*
676554 GAAGGTCTTTGGTTGGCAGATAACCTTTCTCGACTTAAGTTATGCTGCAAATGACGTACCCTCGA
130 GAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGACGT-CCCTCGA
** ** * *
676619 AGCTGAGTGTAATCGAACTCGGGGGTC-TTT-G-GA-AGATAGCCCTTCTCGACTTAAGCTATGC
194 AGCTGAACGTAATCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGACTTAAGCTATGC
** *
676680 TGCAAATGATGTGTCATTG-AGCTGAGTGTAATCGAACTCAAAGGTCATGAGTTGGCAGACAACC
259 TGCAAATGATGTACCATCGAAGCTGAGTGTAATCGAACTCAAAGGTC-T---TTGGCAGACAACC
676744 CTTATAGACTTAAG
320 CTTATAGACTTAAG
* * * * * * *
676758 TTGTGCTGTAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGAT
1 CTATGCTGCAAATGATGTTCCTTGGAGCTGAACGTAGTCAAACTCGAAGGTCTTTGGTGACAGAT
*
676823 AACCCTTCTAGCCTTGAGTTATGTTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCG
66 AACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCG
* * * * *
676888 AATGACTTTTGTTAGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATG
131 AAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATG
676940 TTGTATTAAA
Statistics
Matches: 443, Mismatches: 62, Indels: 20
0.84 0.12 0.04
Matches are distributed among these distances:
329 25 0.06
330 38 0.09
331 2 0.00
332 51 0.12
333 251 0.57
334 76 0.17
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.30
Consensus pattern (333 bp):
CTATGCTGCAAATGATGTTCCTTGGAGCTGAACGTAGTCAAACTCGAAGGTCTTTGGTGACAGAT
AACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCG
AAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGACGTCCCTCGAAG
CTGAACGTAATCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGACTTAAGCTATGCTG
CAAATGATGTACCATCGAAGCTGAGTGTAATCGAACTCAAAGGTCTTTGGCAGACAACCCTTATA
GACTTAAG
Found at i:682219 original size:24 final size:25
Alignment explanation
Indices: 682168--682223 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 25
682158 AAAAATATTT
682168 AAATAAATAAAAAAACATAAGAACA
1 AAATAAATAAAAAAACATAAGAACA
*
682193 AAATAAGATAAAAACAA-A-AAGAAAA
1 AAATAA-ATAAAAA-AACATAAGAACA
682218 AAATAA
1 AAATAA
682224 TAATAATTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 18 0.64
26 8 0.29
27 2 0.07
ACGTcount: A:0.79, C:0.05, G:0.05, T:0.11
Consensus pattern (25 bp):
AAATAAATAAAAAAACATAAGAACA
Found at i:682303 original size:46 final size:48
Alignment explanation
Indices: 682214--682305 Score: 111
Period size: 46 Copynumber: 1.9 Consensus size: 48
682204 AAACAAAAAG
*
682214 AAAAAAATAATAATAATTAAATAAATCAAAAGGGAAAATAAGAAAAACA
1 AAAAAAATAATAATAATTAAATAAATCAAAA-GGAAAAAAAGAAAAACA
*
682263 AAAAAAAT-AT-AT-ATTAAGTAAATCAAAA-GAAATGAAAAGAAAA
1 AAAAAAATAATAATAATTAAATAAATCAAAAGGAAA--AAAAGAAAA
682306 TGTAAAAGTA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
44 4 0.10
46 23 0.59
47 2 0.05
48 2 0.05
49 8 0.21
ACGTcount: A:0.71, C:0.03, G:0.09, T:0.17
Consensus pattern (48 bp):
AAAAAAATAATAATAATTAAATAAATCAAAAGGAAAAAAAGAAAAACA
Found at i:682411 original size:11 final size:11
Alignment explanation
Indices: 682397--682472 Score: 82
Period size: 11 Copynumber: 6.9 Consensus size: 11
682387 CAGAATAAAT
682397 AAAAAAAATAA
1 AAAAAAAATAA
*
682408 AAAAAACA-AA
1 AAAAAAAATAA
*
682418 AAACAAAATAA
1 AAAAAAAATAA
*
682429 AAGAAAAATAA
1 AAAAAAAATAA
* *
682440 ATAAAAAACAA
1 AAAAAAAATAA
682451 AAAACAAAATAA
1 AAAA-AAAATAA
*
682463 AACAAAAATA
1 AAAAAAAATA
682473 TACATATATA
Statistics
Matches: 52, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
10 8 0.15
11 35 0.67
12 9 0.17
ACGTcount: A:0.84, C:0.07, G:0.01, T:0.08
Consensus pattern (11 bp):
AAAAAAAATAA
Found at i:682420 original size:17 final size:17
Alignment explanation
Indices: 682406--682470 Score: 78
Period size: 17 Copynumber: 3.8 Consensus size: 17
682396 TAAAAAAAAT
682406 AAAAAAAACAAAAAACA
1 AAAAAAAACAAAAAACA
* *
682423 AAATAAAAGAAAAATA-A
1 AAAAAAAACAAAAA-ACA
*
682440 ATAAAAAACAAAAAACA
1 AAAAAAAACAAAAAACA
*
682457 AAATAAAACAAAAA
1 AAAAAAAACAAAAA
682471 TATACATATA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
16 1 0.03
17 37 0.95
18 1 0.03
ACGTcount: A:0.85, C:0.08, G:0.02, T:0.06
Consensus pattern (17 bp):
AAAAAAAACAAAAAACA
Found at i:682436 original size:34 final size:33
Alignment explanation
Indices: 682390--682472 Score: 114
Period size: 34 Copynumber: 2.4 Consensus size: 33
682380 ACAAATGCAG
682390 AATAAATAAAAAA-AATAAAAAAAACAAAAAACAA
1 AATAAA-AAAAAATAA-AAAAAAAACAAAAAACAA
*
682424 AATAAAAGAAAAATAAATAAAAAACAAAAAACAA
1 AATAAAA-AAAAATAAAAAAAAAACAAAAAACAA
682458 AATAAAACAAAAATA
1 AATAAAA-AAAAATA
682473 TACATATATA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
33 1 0.02
34 42 0.93
35 2 0.04
ACGTcount: A:0.83, C:0.06, G:0.01, T:0.10
Consensus pattern (33 bp):
AATAAAAAAAAATAAAAAAAAAACAAAAAACAA
Found at i:682445 original size:27 final size:25
Alignment explanation
Indices: 682397--682470 Score: 87
Period size: 27 Copynumber: 2.9 Consensus size: 25
682387 CAGAATAAAT
*
682397 AAAAAAAATAAAAAAAACAAAAAAC
1 AAAAAAAAGAAAAAAAACAAAAAAC
*
682422 AAAATAAAAGAAAAATAAATAAAAAAC
1 AAAA-AAAAGAAAAA-AAACAAAAAAC
* *
682449 AAAAAACA-AAATAAAACAAAAA
1 AAAAAAAAGAAAAAAAACAAAAA
682471 TATACATATA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
24 8 0.19
25 8 0.19
26 12 0.29
27 14 0.33
ACGTcount: A:0.85, C:0.07, G:0.01, T:0.07
Consensus pattern (25 bp):
AAAAAAAAGAAAAAAAACAAAAAAC
Found at i:682483 original size:2 final size:2
Alignment explanation
Indices: 682470--682500 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
682460 TAAAACAAAA
*
682470 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
682501 AATTAAAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:687001 original size:2 final size:2
Alignment explanation
Indices: 686994--687019 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
686984 AGGAAATACG
686994 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
687020 GCCAGAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:689108 original size:29 final size:28
Alignment explanation
Indices: 689075--689299 Score: 161
Period size: 29 Copynumber: 7.7 Consensus size: 28
689065 AATATAAAAC
689075 TACAATAAAAAGCAAAACTTTTTGAAATT
1 TACAATAAAAA-CAAAACTTTTTGAAATT
* ** *
689104 TACAATAAAGAAAAAAACTAATTGTAA-T
1 TACAATAAA-AACAAAACTTTTTGAAATT
* *
689132 TACAATAAAGGAA-AAAACATTTTGGAATT
1 TACAATAAA--AACAAAACTTTTTGAAATT
*
689161 TACAA-AAAAGGACAAAACTTTTTGGAATT
1 TACAATAAAA--ACAAAACTTTTTGAAATT
* *
689190 TACAATAAAATACTAAACTTTTTGAAACT
1 TACAATAAAA-ACAAAACTTTTTGAAATT
* *
689219 TACAATAAAGTACAAAACTTTTTTGGAATT
1 TACAATAAA-AACAAAAC-TTTTTGAAATT
* * *
689249 TACAGTAAAAAGCATAAAATATTTT-ATAAAT
1 TACAATAAAAA-CA-AAACT-TTTTGA-AATT
*
689280 TACAATAAAATAAAAAACTT
1 TACAATAAAA-ACAAAACTT
689300 CATAAGAATT
Statistics
Matches: 157, Mismatches: 25, Indels: 28
0.75 0.12 0.13
Matches are distributed among these distances:
26 1 0.01
28 24 0.15
29 81 0.52
30 30 0.19
31 20 0.13
32 1 0.01
ACGTcount: A:0.52, C:0.09, G:0.08, T:0.30
Consensus pattern (28 bp):
TACAATAAAAACAAAACTTTTTGAAATT
Found at i:689213 original size:58 final size:57
Alignment explanation
Indices: 689075--689259 Score: 203
Period size: 57 Copynumber: 3.2 Consensus size: 57
689065 AATATAAAAC
* ** *
689075 TACAATAAAAAGCAAAACTTTTTGAAATTTACAATAAAGAAAAAAACTAATTGTAA-T
1 TACAATAAAAA-CAAAACTTTTTGAAATTTACAATAAAGAACAAAACTTTTTGGAATT
* * * *
689132 TACAATAAAGGAA-AAAACATTTTGGAATTTACAAAAAAGGACAAAACTTTTTGGAATT
1 TACAATAAA--AACAAAACTTTTTGAAATTTACAATAAAGAACAAAACTTTTTGGAATT
* * *
689190 TACAATAAAATACTAAACTTTTTGAAACTTACAATAAAGTACAAAACTTTTTTGGAATT
1 TACAATAAAA-ACAAAACTTTTTGAAATTTACAATAAAGAACAAAAC-TTTTTGGAATT
*
689249 TACAGTAAAAA
1 TACAATAAAAA
689260 GCATAAAATA
Statistics
Matches: 107, Mismatches: 15, Indels: 11
0.80 0.11 0.08
Matches are distributed among these distances:
56 1 0.01
57 45 0.42
58 39 0.36
59 22 0.21
ACGTcount: A:0.51, C:0.10, G:0.09, T:0.30
Consensus pattern (57 bp):
TACAATAAAAACAAAACTTTTTGAAATTTACAATAAAGAACAAAACTTTTTGGAATT
Found at i:689312 original size:90 final size:87
Alignment explanation
Indices: 689087--689316 Score: 211
Period size: 90 Copynumber: 2.6 Consensus size: 87
689077 CAATAAAAAG
* *
689087 CAAAACTTTTT-GAAATTTACAATAAAGA-AAAAAAC-TAATTG-TAATTACAATAAAGGAAAAA
1 CAAAACTTTTTAGAAA-TTACAATAAA-ATAAAAAACTTCA-TGAAAATTACAATAAAGGAAAAA
*
689148 ACATTTTGGAATTTACAAAAAAGGA
63 ACATTTTGGAATTTACAAAAAAGCA
* * ** ** * * *
689173 CAAAACTTTTTGGAATTTACAATAAAATACTAAACTTTTTGAAACTTACAATAAAGTACAAAACT
1 CAAAACTTTTTAGAAATTACAATAAAATAAAAAACTTCATGAAAATTACAATAAAGGAAAAAAC-
*
689238 TTTTTGGAATTTACAGTAAAAAGCA
65 ATTTTGGAATTTACA--AAAAAGCA
* *
689263 TAAAA-TATTTTATAAATTACAATAAAATAAAAAACTTCAT-AAGAATTACAATAA
1 CAAAACT-TTTTAGAAATTACAATAAAATAAAAAACTTCATGAA-AATTACAATAA
689317 TGACATTTCT
Statistics
Matches: 115, Mismatches: 20, Indels: 14
0.77 0.13 0.09
Matches are distributed among these distances:
85 1 0.01
86 28 0.24
87 22 0.19
88 14 0.12
89 3 0.03
90 47 0.41
ACGTcount: A:0.52, C:0.10, G:0.08, T:0.30
Consensus pattern (87 bp):
CAAAACTTTTTAGAAATTACAATAAAATAAAAAACTTCATGAAAATTACAATAAAGGAAAAAACA
TTTTGGAATTTACAAAAAAGCA
Found at i:692210 original size:14 final size:13
Alignment explanation
Indices: 692192--692216 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
692182 TAAAAGTTTT
692192 TTTTTTCAAAATG
1 TTTTTTCAAAATG
692205 TTTTTTCAAAAT
1 TTTTTTCAAAAT
692217 TTTAATATTA
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:0.32, C:0.08, G:0.04, T:0.56
Consensus pattern (13 bp):
TTTTTTCAAAATG
Found at i:692964 original size:25 final size:25
Alignment explanation
Indices: 692927--692998 Score: 87
Period size: 23 Copynumber: 2.9 Consensus size: 25
692917 TTAATTTCAC
692927 AATATTTTATATATATTAACTTAAAA
1 AATATTTT-TATATATTAACTTAAAA
**
692953 AATA-TTTT-TATATTAACTTATTA
1 AATATTTTTATATATTAACTTAAAA
692976 AATATATTTTAT-TATTAACTTAA
1 AATAT-TTTTATATATTAACTTAA
692999 TTTAAAAATA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
23 17 0.43
24 1 0.03
25 17 0.43
26 5 0.12
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.51
Consensus pattern (25 bp):
AATATTTTTATATATTAACTTAAAA
Found at i:692968 original size:23 final size:24
Alignment explanation
Indices: 692938--692998 Score: 88
Period size: 23 Copynumber: 2.5 Consensus size: 24
692928 ATATTTTATA
692938 TATATTAACTTAAAAAATAT-TTT
1 TATATTAACTTAAAAAATATATTT
**
692961 TATATTAACTTATTAAATATATTT
1 TATATTAACTTAAAAAATATATTT
692985 TATTATTAACTTAA
1 TA-TATTAACTTAA
692999 TTTAAAAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 18 0.55
24 5 0.15
25 10 0.30
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (24 bp):
TATATTAACTTAAAAAATATATTT
Found at i:692990 original size:27 final size:27
Alignment explanation
Indices: 692927--693012 Score: 94
Period size: 25 Copynumber: 3.3 Consensus size: 27
692917 TTAATTTCAC
692927 AATATTTTATATATATTAACTTA--AAA
1 AATATTTTAT-TATATTAACTTATTAAA
692953 AATA-TTT-TTATATTAACTTATTAAA
1 AATATTTTATTATATTAACTTATTAAA
*
692978 TATATTTTA-T-TATTAACTTAATTTAAA
1 AATATTTTATTATATTAACTT-A-TTAAA
693005 AATATTTT
1 AATATTTT
693013 TATTTTTATT
Statistics
Matches: 52, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
23 12 0.23
24 1 0.02
25 18 0.35
26 9 0.17
27 12 0.23
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.52
Consensus pattern (27 bp):
AATATTTTATTATATTAACTTATTAAA
Found at i:693016 original size:25 final size:26
Alignment explanation
Indices: 692915--693013 Score: 89
Period size: 25 Copynumber: 3.8 Consensus size: 26
692905 GTGTATAAAT
* * *
692915 ACTTAATTTCACAATATTTTATA-TA
1 ACTTAATTTAAAAATATTTTTTATTA
*
692940 TA-TTAACTTAAAAAATATTTTTATATTA
1 -ACTTAA-TTTAAAAATATTTTT-TATTA
*
692968 ACTT-A-TTAAATATATTTTATTATTA
1 ACTTAATTTAAAAATATTTT-TTATTA
692993 ACTTAATTTAAAAATATTTTT
1 ACTTAATTTAAAAATATTTTT
693014 ATTTTTATTT
Statistics
Matches: 59, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
25 24 0.41
26 15 0.25
27 16 0.27
28 4 0.07
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (26 bp):
ACTTAATTTAAAAATATTTTTTATTA
Found at i:693033 original size:27 final size:29
Alignment explanation
Indices: 692950--693045 Score: 98
Period size: 28 Copynumber: 3.5 Consensus size: 29
692940 TATTAACTTA
692950 AAAAATAT-TTTTA-TATTAACTT-A-TT
1 AAAAATATATTTTATTATTAACTTAATTT
692975 --AAATATATTTTATTATTAACTTAATTT
1 AAAAATATATTTTATTATTAACTTAATTT
* ** *
693002 AAAAATAT-TTTTATTTTTATTTTCATTT
1 AAAAATATATTTTATTATTAACTTAATTT
693030 AAAATATATATTTTAT
1 AAAA-ATATATTTTAT
693046 GTTAAAATTT
Statistics
Matches: 59, Mismatches: 4, Indels: 11
0.80 0.05 0.15
Matches are distributed among these distances:
23 6 0.10
24 5 0.08
25 9 0.15
26 1 0.02
27 2 0.03
28 20 0.34
29 10 0.17
30 6 0.10
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (29 bp):
AAAAATATATTTTATTATTAACTTAATTT
Found at i:694829 original size:19 final size:18
Alignment explanation
Indices: 694807--694842 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
694797 TTCTTCCAAA
694807 AAAATAAAAATAATAAAAG
1 AAAATAAAAATAA-AAAAG
694826 AAAATAAAAATAAAAAA
1 AAAATAAAAATAAAAAA
694843 TGGGAGGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.14
Consensus pattern (18 bp):
AAAATAAAAATAAAAAAG
Found at i:698572 original size:20 final size:20
Alignment explanation
Indices: 698547--698596 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
698537 CTTACCTTTG
698547 GTATCGGTACCATATGAACA
1 GTATCGGTACCATATGAACA
698567 GTATCGGTACCATATGAACA
1 GTATCGGTACCATATGAACA
698587 GTATCGGTAC
1 GTATCGGTAC
698597 TGTTCATGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (20 bp):
GTATCGGTACCATATGAACA
Found at i:707661 original size:25 final size:27
Alignment explanation
Indices: 707615--707667 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
707605 GAGTTGGTCC
707615 ACACCATTTCATAATTGCAGA-TATTTT
1 ACACCATTTCA-AATTGCAGATTATTTT
707642 ACACCATTTC-AATT-CAAGATTATTTT
1 ACACCATTTCAAATTGC-AGATTATTTT
707668 TAAAATCCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
24 1 0.04
25 7 0.29
26 6 0.25
27 10 0.42
ACGTcount: A:0.34, C:0.19, G:0.06, T:0.42
Consensus pattern (27 bp):
ACACCATTTCAAATTGCAGATTATTTT
Found at i:709962 original size:17 final size:16
Alignment explanation
Indices: 709931--709964 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
709921 ATGTCATTTC
709931 ATATTTTTCTAATAAA
1 ATATTTTTCTAATAAA
*
709947 ATATTATTTTTAATAAA
1 ATATT-TTTCTAATAAA
709964 A
1 A
709965 CCATCTTGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (16 bp):
ATATTTTTCTAATAAA
Found at i:720097 original size:18 final size:18
Alignment explanation
Indices: 720063--720098 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
720053 AGTTTTTGGG
* *
720063 TAAGAGTATCGATACTTT
1 TAAGAGTATCAAAACTTT
720081 TAAGAGTATCAAAACTTT
1 TAAGAGTATCAAAACTTT
720099 GAGTCACAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (18 bp):
TAAGAGTATCAAAACTTT
Found at i:723460 original size:20 final size:21
Alignment explanation
Indices: 723415--723465 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
723405 GAGCCAACCC
723415 ATTT-TATTTTATGTTTTCTT
1 ATTTCTATTTTATGTTTTCTT
723435 ATTTTCTATTTTAT-TTTGT-TT
1 A-TTTCTATTTTATGTTT-TCTT
723456 ATTTC-ATTTT
1 ATTTCTATTTT
723466 TCTATGCATT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
19 5 0.18
20 5 0.18
21 9 0.32
22 9 0.32
ACGTcount: A:0.16, C:0.06, G:0.04, T:0.75
Consensus pattern (21 bp):
ATTTCTATTTTATGTTTTCTT
Found at i:726493 original size:4 final size:4
Alignment explanation
Indices: 726484--726525 Score: 50
Period size: 4 Copynumber: 10.5 Consensus size: 4
726474 TATTCTTGCA
**
726484 TTAT TTAT TTAT TTAT TTAT TT-T CAAT TTAT TTAAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT-AT TTAT TT
726526 TGTTAAACCC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
3 1 0.03
4 27 0.84
5 4 0.12
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.71
Consensus pattern (4 bp):
TTAT
Found at i:736530 original size:2 final size:2
Alignment explanation
Indices: 736523--736547 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
736513 CCAAATTGGT
736523 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
736548 GTGTGTGTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:751628 original size:165 final size:168
Alignment explanation
Indices: 751434--751738 Score: 395
Period size: 165 Copynumber: 1.8 Consensus size: 168
751424 TAATAGAGTG
* ** * * *
751434 GTAATTTAGCGGCATTTATAGCTCAAACGCCAG-AATATAGTTGTTCATAGTGGCGTTTTTTCAA
1 GTAATTTAGCGGCACTTATAGAACAAACGCC-GTAATAGAGTTGTTCATAGTGGCGTTTGTGCAA
** * * *
751498 AAAACGT-C-GTAATAGAGTAGTAATTTAGCGGTGTTTTT-ATACAAATGCCGCAATAGGATTGT
65 AAAAAATGCTGTAATAGAGTAATAATTTAACGGCGTTTTTCATACAAATGCCGCAATAGGATTGT
*
751560 TTATAGTGGCGTTTGTCTAACAAACGATGCTATATATAA
130 TTACAGTGGCGTTTGTCTAACAAACGATGCTATATATAA
*
751599 GTAATTTAGCGGCACTTATCA-AACAAACGCCGTAATAGAGTTGTTTATAGTGGCGTTTGTGCAA
1 GTAATTTAGCGGCACTTAT-AGAACAAACGCCGTAATAGAGTTGTTCATAGTGGCGTTTGTGCAA
* * * * *
751663 AAAAAATGCTGTAATAGAGTAATAATTTAACGGCGTTTTTCTTACAAATGCTGTAATATGTTTGT
65 AAAAAATGCTGTAATAGAGTAATAATTTAACGGCGTTTTTCATACAAATGCCGCAATAGGATTGT
751728 TTACAGTGGCG
130 TTACAGTGGCG
751739 CTTTTATAAA
Statistics
Matches: 117, Mismatches: 18, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
164 1 0.01
165 58 0.50
166 2 0.02
167 27 0.23
168 29 0.25
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.34
Consensus pattern (168 bp):
GTAATTTAGCGGCACTTATAGAACAAACGCCGTAATAGAGTTGTTCATAGTGGCGTTTGTGCAAA
AAAAATGCTGTAATAGAGTAATAATTTAACGGCGTTTTTCATACAAATGCCGCAATAGGATTGTT
TACAGTGGCGTTTGTCTAACAAACGATGCTATATATAA
Found at i:751728 original size:85 final size:82
Alignment explanation
Indices: 751470--751738 Score: 235
Period size: 85 Copynumber: 3.2 Consensus size: 82
751460 ACGCCAGAAT
* * ** * *
751470 ATAG-TTGTTCATAGTGGCGTTTTTTCAAAAAACGT-CGTAATAGAGTAGTAATTTAGCGGTGTT
1 ATAGATTGTTTATAGTGGCG-TTTGTCAAAAAAAATGCGTAATAGAGTAATAATTTAGCGGCGTT
*
751533 TTT-ATACAAATGCCGCA
65 TTTCATACAAATGCCGTA
** *
751550 ATAGGATTGTTTATAGTGGCGTTTGTCTAACAAACGATGC-T-ATATA-TAAGTAATTTAGCGGC
1 ATA-GATTGTTTATAGTGGCGTTTGTC-AA-AAAAAATGCGTAATAGAGTAA-TAATTTAGCGGC
** * * *
751612 ACTTATCAAACAAACGCCGTA
62 GTTTTTCATACAAATGCCGTA
*
751633 ATAGAGTTGTTTATAGTGGCGTTTGTGCAAAAAAAATGCTGTAATAGAGTAATAATTTAACGGCG
1 ATAGA-TTGTTTATAGTGGCGTTTGT-CAAAAAAAATGC-GTAATAGAGTAATAATTTAGCGGCG
* *
751698 TTTTTCTTACAAATGCTGTA
63 TTTTTCATACAAATGCCGTA
* *
751718 ATATGTTTGTTTACAGTGGCG
1 ATA-GATTGTTTATAGTGGCG
751739 CTTTTATAAA
Statistics
Matches: 148, Mismatches: 27, Indels: 23
0.75 0.14 0.12
Matches are distributed among these distances:
80 3 0.02
81 8 0.05
82 43 0.29
83 41 0.28
84 3 0.02
85 46 0.31
86 4 0.03
ACGTcount: A:0.31, C:0.12, G:0.21, T:0.35
Consensus pattern (82 bp):
ATAGATTGTTTATAGTGGCGTTTGTCAAAAAAAATGCGTAATAGAGTAATAATTTAGCGGCGTTT
TTCATACAAATGCCGTA
Found at i:755495 original size:21 final size:21
Alignment explanation
Indices: 755434--755496 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
755424 AATGAAGCAG
* *
755434 GGAAACAGAGAGAGCAGCAGC
1 GGAAGCAGAGAGAGCAGCAAC
**
755455 GGAAGCAGCTAGAGCAGCAAC
1 GGAAGCAGAGAGAGCAGCAAC
*
755476 GGAAGCAGAGAGAGAAGCAAC
1 GGAAGCAGAGAGAGCAGCAAC
755497 ATATCAGCAG
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.43, C:0.19, G:0.37, T:0.02
Consensus pattern (21 bp):
GGAAGCAGAGAGAGCAGCAAC
Found at i:755894 original size:44 final size:44
Alignment explanation
Indices: 755812--756014 Score: 200
Period size: 44 Copynumber: 4.7 Consensus size: 44
755802 TTCTGTGTTA
* * * *
755812 TTTAGCGGCGTTTGTAACA-AAAAACACTGCAATATACCATACA
1 TTTAGCGGCGTTTGTATCATAAAAACGCCGCAATATACCATACC
* * *
755855 TTTAGCGGCATTTGTATCATAAAAACGCCGCTATATACCAGACC
1 TTTAGCGGCGTTTGTATCATAAAAACGCCGCAATATACCATACC
* * *
755899 TTTAGCGGCGTTTGTATCCTAAAAACGCCGCTATATACCACACC
1 TTTAGCGGCGTTTGTATCATAAAAACGCCGCAATATACCATACC
* * * * *
755943 TTCAGCGGCGTTTGTAT-AAAAAAACACCGCAAAATATCAATACC
1 TTTAGCGGCGTTTGTATCATAAAAACGCCGCAATATA-CCATACC
* *
755987 TGTT-GCGGC-ATT-TATGATAAAAACGCCG
1 T-TTAGCGGCGTTTGTATCATAAAAACGCCG
756015 TTAAATCTCA
Statistics
Matches: 134, Mismatches: 22, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
42 3 0.02
43 43 0.32
44 87 0.65
45 1 0.01
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (44 bp):
TTTAGCGGCGTTTGTATCATAAAAACGCCGCAATATACCATACC
Found at i:756009 original size:43 final size:43
Alignment explanation
Indices: 755948--756128 Score: 184
Period size: 43 Copynumber: 4.2 Consensus size: 43
755938 ACACCTTCAG
* * * * *
755948 CGGCGTTTGTATAAAAAAACACCGCAAAATATCAATACCTGTTG
1 CGGCGTTTGT-GAAAAAAACACCGCTAAATATCAACACCTATTA
* * * * * *
755992 CGGCATTTATGATAAAAACGCCGTTAAATCTCAACACCTATTA
1 CGGCGTTTGTGAAAAAAACACCGCTAAATATCAACACCTATTA
*
756035 CGGCGTTTGTGAAAAAAAACACCGCTAAACATCAACACCTATTA
1 CGGCGTTTGTG-AAAAAAACACCGCTAAATATCAACACCTATTA
* * * *
756079 CGGCGTTTGT-AAAACAAACGCCGCTAAATATTAATACCTATTG
1 CGGCGTTTGTGAAAA-AAACACCGCTAAATATCAACACCTATTA
756122 CGGCGTT
1 CGGCGTT
756129 GCTATATATC
Statistics
Matches: 112, Mismatches: 23, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
42 4 0.04
43 63 0.56
44 45 0.40
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.25
Consensus pattern (43 bp):
CGGCGTTTGTGAAAAAAACACCGCTAAATATCAACACCTATTA
Found at i:756039 original size:87 final size:87
Alignment explanation
Indices: 755921--756128 Score: 217
Period size: 87 Copynumber: 2.4 Consensus size: 87
755911 TGTATCCTAA
* * * *
755921 AAACGCCGCTATATA-CCACACCT-TCAGCGGCGTTTGT-ATAAAAAAACACCGCAAAATATCAA
1 AAACGCCGCTAAATATCAACACCTATTA-CGGCGTTTGTGA-AAAAAAACACCGCAAAACATCAA
* * * *
755983 TACCTGTTGCGGCATTTATGATAA-
64 CACCTATTACGGCATTTAT-AAAAC
* * *
756007 AAACGCCGTTAAATCTCAACACCTATTACGGCGTTTGTGAAAAAAAACACCGCTAAACATCAACA
1 AAACGCCGCTAAATATCAACACCTATTACGGCGTTTGTGAAAAAAAACACCGCAAAACATCAACA
* *
756072 CCTATTACGGCGTTTGTAAAAC
66 CCTATTACGGCATTTATAAAAC
* * *
756094 AAACGCCGCTAAATATTAATACCTATTGCGGCGTT
1 AAACGCCGCTAAATATCAACACCTATTACGGCGTT
756129 GCTATATATC
Statistics
Matches: 100, Mismatches: 18, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
86 15 0.15
87 82 0.82
88 3 0.03
ACGTcount: A:0.36, C:0.25, G:0.15, T:0.25
Consensus pattern (87 bp):
AAACGCCGCTAAATATCAACACCTATTACGGCGTTTGTGAAAAAAAACACCGCAAAACATCAACA
CCTATTACGGCATTTATAAAAC
Found at i:756484 original size:7 final size:7
Alignment explanation
Indices: 756472--756512 Score: 55
Period size: 7 Copynumber: 5.6 Consensus size: 7
756462 TCTAAACGTC
*
756472 TATAATG
1 TATAATA
756479 TATAATA
1 TATAATA
756486 TATAAATA
1 TAT-AATA
756494 TATAAATA
1 TAT-AATA
756502 TATAATA
1 TATAATA
756509 TATA
1 TATA
756513 TTCATATCTG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
7 17 0.53
8 15 0.47
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (7 bp):
TATAATA
Found at i:756495 original size:8 final size:8
Alignment explanation
Indices: 756482--756512 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
756472 TATAATGTAT
756482 AATATATA
1 AATATATA
756490 AATATATA
1 AATATATA
756498 AATATAT-
1 AATATATA
756505 AATATATA
1 AATATATA
756513 TTCATATCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 7 0.32
8 15 0.68
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
AATATATA
Found at i:757176 original size:3 final size:3
Alignment explanation
Indices: 757163--757211 Score: 89
Period size: 3 Copynumber: 16.0 Consensus size: 3
757153 GAGTATGTGG
757163 AGA AGGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA A-GA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
757209 AGA
1 AGA
757212 TATCAGGTAT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 42 0.93
4 3 0.07
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:759251 original size:21 final size:21
Alignment explanation
Indices: 759227--759266 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
759217 AATATTATTA
*
759227 TTTCTATCATTTTTGTTATAT
1 TTTCTATCAGTTTTGTTATAT
759248 TTTCTATCAGTTTTGTTAT
1 TTTCTATCAGTTTTGTTAT
759267 TATTGGGCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.10, G:0.07, T:0.65
Consensus pattern (21 bp):
TTTCTATCAGTTTTGTTATAT
Found at i:762394 original size:13 final size:13
Alignment explanation
Indices: 762376--762402 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
762366 AAATTTATTA
762376 ATTTTAATAATTT
1 ATTTTAATAATTT
762389 ATTTTAATAATTT
1 ATTTTAATAATTT
762402 A
1 A
762403 AAATAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
ATTTTAATAATTT
Found at i:762444 original size:32 final size:29
Alignment explanation
Indices: 762384--762444 Score: 68
Period size: 29 Copynumber: 2.0 Consensus size: 29
762374 TAATTTTAAT
*
762384 AATTTATTTTAATAATTTAAAATAAATAA
1 AATTTATTTTAATAATTGAAAATAAATAA
* *
762413 AATTTATTATTTATATATTGAAATATTAATAA
1 AATTTATT-TTAATA-ATTGAAA-ATAAATAA
762445 TGAGTTATAC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
29 8 0.31
30 5 0.19
31 6 0.23
32 7 0.27
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (29 bp):
AATTTATTTTAATAATTGAAAATAAATAA
Found at i:763733 original size:3 final size:3
Alignment explanation
Indices: 763725--763789 Score: 123
Period size: 3 Copynumber: 22.0 Consensus size: 3
763715 TGCACAAGTT
763725 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
763773 TTA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA
763790 ATAAATAAAA
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 59 0.97
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:765998 original size:28 final size:27
Alignment explanation
Indices: 765963--766037 Score: 73
Period size: 28 Copynumber: 2.7 Consensus size: 27
765953 CATAATTCCT
765963 TCCTGATTCTGCATGTGAATATAT-CC-
1 TCCTGATTCTGCATG-GAATATATCCCA
* * *
765989 TGCCTTGATTGTACATGGGATTATATCCCA
1 T-CC-TGATTCTGCAT-GGAATATATCCCA
766019 TCCTGATTCTGCATGGAAT
1 TCCTGATTCTGCATGGAAT
766038 CCTCTACGGA
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
26 1 0.03
27 6 0.16
28 25 0.66
29 5 0.13
30 1 0.03
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.37
Consensus pattern (27 bp):
TCCTGATTCTGCATGGAATATATCCCA
Found at i:766775 original size:19 final size:19
Alignment explanation
Indices: 766751--766800 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
766741 TTTTAAAAAA
766751 TTTAATTTAATATATATTT
1 TTTAATTTAATATATATTT
*
766770 TTTAATTTAATCTATATTT
1 TTTAATTTAATATATATTT
* *
766789 ATTAATATAATA
1 TTTAATTTAATA
766801 AAAATAAAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTAATTTAATATATATTT
Found at i:767556 original size:11 final size:11
Alignment explanation
Indices: 767524--767548 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
767514 TATTATTAAA
767524 AAAAATATTTT
1 AAAAATATTTT
767535 AAAAATATTTT
1 AAAAATATTTT
767546 AAA
1 AAA
767549 TGTATTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:768462 original size:2 final size:2
Alignment explanation
Indices: 768455--768488 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
768445 TGTCATGTTC
*
768455 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
768489 TCTCGCTAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:771430 original size:18 final size:19
Alignment explanation
Indices: 771397--771432 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
771387 GTAAGAAACC
771397 AATTTGATTAAAAGTAGAA
1 AATTTGATTAAAAGTAGAA
*
771416 AATTTTATT-AAAGTAGA
1 AATTTGATTAAAAGTAGA
771433 TTTCTATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (19 bp):
AATTTGATTAAAAGTAGAA
Found at i:774791 original size:52 final size:52
Alignment explanation
Indices: 774708--774814 Score: 144
Period size: 52 Copynumber: 2.1 Consensus size: 52
774698 GATGCGTTGT
* * * *
774708 AATTTTGATTTCTTACATTATTAATAAAATCTTGTTACCAT-TGTTAAAATAA
1 AATTCTGATTTCTTACACTATTAATAAAATCTCGTTACCATGT-TTAAAAGAA
* *
774760 AATTCTGATTTCTTTCACTATTAATAAAATCTCGTTGCCATGTTTAAAAGAA
1 AATTCTGATTTCTTACACTATTAATAAAATCTCGTTACCATGTTTAAAAGAA
774812 AAT
1 AAT
774815 ATTATGTATA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
52 47 0.98
53 1 0.02
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.43
Consensus pattern (52 bp):
AATTCTGATTTCTTACACTATTAATAAAATCTCGTTACCATGTTTAAAAGAA
Found at i:775297 original size:23 final size:23
Alignment explanation
Indices: 775271--775315 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
775261 GTTCGTTTAT
775271 TTCACAAATATATT-TATTTAACG
1 TTCACAAATATATTCT-TTTAACG
775294 TTCACAAATATATTCTTTTAAC
1 TTCACAAATATATTCTTTTAAC
775316 ATTTGTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 20 0.95
24 1 0.05
ACGTcount: A:0.38, C:0.16, G:0.02, T:0.44
Consensus pattern (23 bp):
TTCACAAATATATTCTTTTAACG
Found at i:779808 original size:37 final size:37
Alignment explanation
Indices: 779732--779808 Score: 95
Period size: 36 Copynumber: 2.1 Consensus size: 37
779722 TTTTTATATT
*
779732 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* *
779769 TTTAATTTT-TAAAGAAAA-TATATAAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATAT-AAATATTAT-CAA
779806 TTT
1 TTT
779809 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
35 5 0.14
36 16 0.46
37 14 0.40
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.45
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:791736 original size:22 final size:22
Alignment explanation
Indices: 791695--791761 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
791685 CTCGTATAAA
791695 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
791718 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
791740 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
791762 GATGTCCATA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 31 0.72
23 12 0.28
ACGTcount: A:0.25, C:0.28, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:793482 original size:21 final size:21
Alignment explanation
Indices: 793458--793502 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
793448 TCTTGTTCGT
* *
793458 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
793479 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
793500 TTG
1 TTG
793503 CCCAGAAATC
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:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:796680 original size:22 final size:22
Alignment explanation
Indices: 796639--796705 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
796629 CTCGTATAAA
796639 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
796662 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
796684 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
796706 GATGTCCATA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 31 0.72
23 12 0.28
ACGTcount: A:0.25, C:0.28, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:798426 original size:21 final size:21
Alignment explanation
Indices: 798402--798446 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
798392 TCTTGTTCGT
*
798402 TTGAAGGGGTATC-GGTTCCCC
1 TTGAAGGGGTA-CAGATTCCCC
*
798423 TTGAATGGGTACAGATTCCCC
1 TTGAAGGGGTACAGATTCCCC
798444 TTG
1 TTG
798447 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.18, C:0.22, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACAGATTCCCC
Found at i:799591 original size:42 final size:42
Alignment explanation
Indices: 799544--799642 Score: 162
Period size: 42 Copynumber: 2.3 Consensus size: 42
799534 CAATAGTGAT
*
799544 AAAAATTATTATCGTCACAAATCATCAACTAAGACCAGTAAC
1 AAAAATTATTATCATCACAAATCATCAACTAAGACCAGTAAC
*
799586 AAAAATAATTATCATCACAAATCATCAACTAAGACCAGTAAC
1 AAAAATTATTATCATCACAAATCATCAACTAAGACCAGTAAC
*
799628 AAAATATTTTTATCA
1 AAAA-ATTATTATCA
799643 CAATTATGAA
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
42 44 0.85
43 8 0.15
ACGTcount: A:0.49, C:0.19, G:0.05, T:0.26
Consensus pattern (42 bp):
AAAAATTATTATCATCACAAATCATCAACTAAGACCAGTAAC
Found at i:799944 original size:2 final size:2
Alignment explanation
Indices: 799937--799976 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
799927 TCTGTAGTGA
799937 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
799977 TGTCTCTAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:812320 original size:14 final size:14
Alignment explanation
Indices: 812298--812331 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
812288 CGTTGGGCAT
*
812298 CCGAAGGCATCCGA
1 CCGAGGGCATCCGA
812312 CCGAGGGCATCCGA
1 CCGAGGGCATCCGA
812326 CCGAGG
1 CCGAGG
812332 CCATTCGAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.35, G:0.35, T:0.06
Consensus pattern (14 bp):
CCGAGGGCATCCGA
Found at i:812344 original size:14 final size:14
Alignment explanation
Indices: 812305--812335 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
812295 CATCCGAAGG
*
812305 CATCCGACCGAGGG
1 CATCCGACCGAGGC
812319 CATCCGACCGAGGC
1 CATCCGACCGAGGC
812333 CAT
1 CAT
812336 TCGAGCGAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.39, G:0.29, T:0.10
Consensus pattern (14 bp):
CATCCGACCGAGGC
Found at i:812432 original size:29 final size:29
Alignment explanation
Indices: 812391--812467 Score: 145
Period size: 29 Copynumber: 2.7 Consensus size: 29
812381 GAGGAGCAGG
812391 AGGAGTGCATGGCGACCTACAAGGTCGCC
1 AGGAGTGCATGGCGACCTACAAGGTCGCC
812420 AGGAGTGCATGGCGACCTACAAGGTCGCC
1 AGGAGTGCATGGCGACCTACAAGGTCGCC
*
812449 CGGAGTGCATGGCGACCTA
1 AGGAGTGCATGGCGACCTA
812468 TGCTGGGAAG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.23, C:0.27, G:0.35, T:0.14
Consensus pattern (29 bp):
AGGAGTGCATGGCGACCTACAAGGTCGCC
Found at i:813090 original size:33 final size:33
Alignment explanation
Indices: 813025--813095 Score: 97
Period size: 33 Copynumber: 2.2 Consensus size: 33
813015 CCGGTGGGGT
* *
813025 TTAATATATTGATTAGCAATGACAATTCTGAAA
1 TTAATATATTGATTAGCAATGACAAATATGAAA
* *
813058 TTAATATATTGATTAGTAATGATAAATATGAAA
1 TTAATATATTGATTAGCAATGACAAATATGAAA
*
813091 ATAAT
1 TTAAT
813096 GACATTTTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.46, C:0.04, G:0.11, T:0.38
Consensus pattern (33 bp):
TTAATATATTGATTAGCAATGACAAATATGAAA
Found at i:813848 original size:28 final size:29
Alignment explanation
Indices: 813817--813881 Score: 89
Period size: 28 Copynumber: 2.3 Consensus size: 29
813807 ATTTAAAGAT
**
813817 AAATATAAATT-ATTAATAAAAATATAAA
1 AAATATAAATTAACAAATAAAAATATAAA
*
813845 AAAT-TATATTAACAAATAAAAATATAAA
1 AAATATAAATTAACAAATAAAAATATAAA
813873 AAATATAAA
1 AAATATAAA
813882 ATAATTTTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
27 5 0.16
28 23 0.74
29 3 0.10
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (29 bp):
AAATATAAATTAACAAATAAAAATATAAA
Found at i:813850 original size:19 final size:19
Alignment explanation
Indices: 813817--813887 Score: 51
Period size: 19 Copynumber: 3.7 Consensus size: 19
813807 ATTTAAAGAT
**
813817 AAATATAAATTATTAATAA
1 AAATATAAAAAATTAATAA
813836 AAATATAAAAAATTATATTAA
1 AAATATAAAAAATTA-A-TAA
*
813857 CAA-AT-AAAAA-T-ATAAA
1 AAATATAAAAAATTAAT-AA
813873 AAATATAAAATAATT
1 AAATATAAAA-AATT
813888 TTATAATATA
Statistics
Matches: 41, Mismatches: 4, Indels: 13
0.71 0.07 0.22
Matches are distributed among these distances:
15 1 0.02
16 5 0.12
17 2 0.05
18 4 0.10
19 20 0.49
20 4 0.10
21 5 0.12
ACGTcount: A:0.68, C:0.01, G:0.00, T:0.31
Consensus pattern (19 bp):
AAATATAAAAAATTAATAA
Found at i:813861 original size:22 final size:21
Alignment explanation
Indices: 813823--813866 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
813813 AGATAAATAT
813823 AAATTATTAATAAAAATATAAA
1 AAATTATTAATAAAAATA-AAA
*
813845 AAATTA-TATTAACAAATAAAA
1 AAATTATTAATAA-AAATAAAA
813866 A
1 A
813867 TATAAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (21 bp):
AAATTATTAATAAAAATAAAA
Found at i:814240 original size:2 final size:2
Alignment explanation
Indices: 814233--814319 Score: 174
Period size: 2 Copynumber: 43.5 Consensus size: 2
814223 TCTTGCACGA
814233 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
814275 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
814317 AT A
1 AT A
814320 ATTTCTAACC
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 85 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:817426 original size:16 final size:16
Alignment explanation
Indices: 817405--817455 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 16
817395 AGGTCAGTAT
817405 ATAAATAAATACATAC
1 ATAAATAAATACATAC
**
817421 ATAAATACGTACATAC
1 ATAAATAAATACATAC
* *
817437 ATACATATATACATAC
1 ATAAATAAATACATAC
817453 ATA
1 ATA
817456 CGTACGTACA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.55, C:0.16, G:0.02, T:0.27
Consensus pattern (16 bp):
ATAAATAAATACATAC
Found at i:817437 original size:4 final size:4
Alignment explanation
Indices: 817413--817466 Score: 63
Period size: 4 Copynumber: 13.5 Consensus size: 4
817403 ATATAAATAA
* * * *
817413 ATAC ATAC ATAA ATAC GTAC ATAC ATAC ATAT ATAC ATAC ATAC GTAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
*
817461 GTAC AT
1 ATAC AT
817467 TGTGCAGAAG
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 42 1.00
ACGTcount: A:0.46, C:0.20, G:0.06, T:0.28
Consensus pattern (4 bp):
ATAC
Found at i:817465 original size:16 final size:16
Alignment explanation
Indices: 817414--817466 Score: 70
Period size: 16 Copynumber: 3.3 Consensus size: 16
817404 TATAAATAAA
*
817414 TACATACATAAATACG
1 TACATACATACATACG
**
817430 TACATACATACATATA
1 TACATACATACATACG
*
817446 TACATACATACGTACG
1 TACATACATACATACG
817462 TACAT
1 TACAT
817467 TGTGCAGAAG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.45, C:0.21, G:0.06, T:0.28
Consensus pattern (16 bp):
TACATACATACATACG
Found at i:824739 original size:21 final size:22
Alignment explanation
Indices: 824713--824757 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
824703 GAATTCAAAT
824713 AGGGAATCG-GTACCCTGCTAC
1 AGGGAATCGAGTACCCTGCTAC
* *
824734 AGGGAATCGATTCCCCTGCTAC
1 AGGGAATCGAGTACCCTGCTAC
824756 AG
1 AG
824758 TATTGCTACA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.24, C:0.29, G:0.27, T:0.20
Consensus pattern (22 bp):
AGGGAATCGAGTACCCTGCTAC
Found at i:825388 original size:23 final size:23
Alignment explanation
Indices: 825323--825405 Score: 82
Period size: 23 Copynumber: 3.6 Consensus size: 23
825313 TATAAATTTT
825323 CACCGAAGTGCCACGTAGAATTTG
1 CACCGAAGTGCCACGTAGAA-TTG
* *
825347 TC-CCAAAG-GACCGCGTAGAGA-TG
1 -CACCGAAGTG-CCACGTAGA-ATTG
825370 CACCGAAGTGCCACGTAGAATTG
1 CACCGAAGTGCCACGTAGAATTG
*
825393 CACCGTAGTGCCA
1 CACCGAAGTGCCA
825406 TATAATATGT
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
22 2 0.04
23 30 0.62
24 14 0.29
25 2 0.04
ACGTcount: A:0.29, C:0.28, G:0.27, T:0.17
Consensus pattern (23 bp):
CACCGAAGTGCCACGTAGAATTG
Found at i:832466 original size:24 final size:24
Alignment explanation
Indices: 832439--832509 Score: 69
Period size: 24 Copynumber: 3.0 Consensus size: 24
832429 AGCTCATATA
832439 AATTTGCACCGAAGTGCCACGTAG
1 AATTTGCACCGAAGTGCCACGTAG
* *
832463 AATTTG-TCCGAAAG-GACCGCGTAG
1 AATTTGCACCG-AAGTG-CCACGTAG
832487 AGA--TGCACCGAAGTGCCACGTAG
1 A-ATTTGCACCGAAGTGCCACGTAG
832510 TGCCATATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 11
0.72 0.08 0.21
Matches are distributed among these distances:
23 16 0.42
24 21 0.55
25 1 0.03
ACGTcount: A:0.30, C:0.24, G:0.28, T:0.18
Consensus pattern (24 bp):
AATTTGCACCGAAGTGCCACGTAG
Found at i:837792 original size:20 final size:20
Alignment explanation
Indices: 837748--837799 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
837738 CTCTTGCAAT
*
837748 TGGTATCAATATTGTAGGTG
1 TGGTATCAATATAGTAGGTG
*
837768 AGGTATCAATACTAGTAGG-G
1 TGGTATCAATA-TAGTAGGTG
*
837788 TGGTATCGATAT
1 TGGTATCAATAT
837800 GGAGTTCACT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 1 0.04
20 20 0.74
21 6 0.22
ACGTcount: A:0.29, C:0.08, G:0.29, T:0.35
Consensus pattern (20 bp):
TGGTATCAATATAGTAGGTG
Found at i:849523 original size:5 final size:5
Alignment explanation
Indices: 849518--849555 Score: 67
Period size: 5 Copynumber: 7.6 Consensus size: 5
849508 GCTCTCCGAC
*
849518 GAGAC GAGAG GAGAG GAGAG GAGAG GAGAG GAGAG GAG
1 GAGAG GAGAG GAGAG GAGAG GAGAG GAGAG GAGAG GAG
849556 GAGAGAAAGG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.39, C:0.03, G:0.58, T:0.00
Consensus pattern (5 bp):
GAGAG
Found at i:850420 original size:4 final size:4
Alignment explanation
Indices: 850411--850457 Score: 94
Period size: 4 Copynumber: 11.8 Consensus size: 4
850401 ACATATTCTT
850411 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA
850458 CTAAGGGTTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.23, T:0.26
Consensus pattern (4 bp):
ATAG
Found at i:851017 original size:43 final size:42
Alignment explanation
Indices: 850930--851009 Score: 108
Period size: 43 Copynumber: 1.9 Consensus size: 42
850920 AGAAAAGTGT
* * *
850930 TTTATTCTGTGGGCATAACATATTTGAGAATAAAAAAAAGAG
1 TTTATTCTATGGGCATAACAGATTCGAGAATAAAAAAAAGAG
*
850972 TTTAGTTCTATGGGCATAATAGATTCGAGAA-AAAAAAA
1 TTTA-TTCTATGGGCATAACAGATTCGAGAATAAAAAAA
851010 TTTAGTTTCA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 11 0.33
43 22 0.67
ACGTcount: A:0.44, C:0.07, G:0.19, T:0.30
Consensus pattern (42 bp):
TTTATTCTATGGGCATAACAGATTCGAGAATAAAAAAAAGAG
Found at i:851431 original size:19 final size:19
Alignment explanation
Indices: 851407--851450 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
851397 ATCTAGTTTA
*
851407 ATTAAAAGTAGATAACTTT
1 ATTAAAAGTAGAGAACTTT
*
851426 ATT-AAAGTAGAGAATTTT
1 ATTAAAAGTAGAGAACTTT
851444 ATTAAAA
1 ATTAAAA
851451 TAGCTTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.36
Consensus pattern (19 bp):
ATTAAAAGTAGAGAACTTT
Found at i:859698 original size:14 final size:15
Alignment explanation
Indices: 859679--859707 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
859669 TGTGGTTATC
859679 TTATAACA-TCAACA
1 TTATAACAGTCAACA
859693 TTATAACAGTCAACA
1 TTATAACAGTCAACA
859708 ATGAAAATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.48, C:0.21, G:0.03, T:0.28
Consensus pattern (15 bp):
TTATAACAGTCAACA
Found at i:860157 original size:20 final size:21
Alignment explanation
Indices: 860134--860182 Score: 73
Period size: 20 Copynumber: 2.3 Consensus size: 21
860124 TTAGTTAATT
860134 AAAATATGTTTAAAG-TGTTA
1 AAAATATGTTTAAAGATGTTA
*
860154 AAAATATGTTTAAAGATTTTA
1 AAAATATGTTTAAAGATGTTA
860175 AAATATAT
1 AAA-ATAT
860183 TCAATCTCCA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 15 0.58
21 7 0.27
22 4 0.15
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (21 bp):
AAAATATGTTTAAAGATGTTA
Found at i:878345 original size:2 final size:2
Alignment explanation
Indices: 878329--878374 Score: 53
Period size: 2 Copynumber: 24.0 Consensus size: 2
878319 TAGGTTTAAG
*
878329 AT AT -T AT AT -T AT AT AT AT AT AT AT AT AT AT AT -T AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
878368 ACT AT AT
1 A-T AT AT
878375 GACAAGTAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
1 3 0.08
2 33 0.87
3 2 0.05
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (2 bp):
AT
Found at i:878602 original size:24 final size:26
Alignment explanation
Indices: 878575--878626 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
878565 ATAAATTACC
*
878575 TTAGTT-AAAAA-AGTTGAGTATATT
1 TTAGTTAAAAAACAGTTGAATATATT
878599 TTAGTTACAAAAACAGTTGAATATATT
1 TTAGTTA-AAAAACAGTTGAATATATT
878626 T
1 T
878627 ACTTTGGCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 6 0.25
26 5 0.21
27 13 0.54
ACGTcount: A:0.42, C:0.04, G:0.13, T:0.40
Consensus pattern (26 bp):
TTAGTTAAAAAACAGTTGAATATATT
Found at i:879088 original size:7 final size:8
Alignment explanation
Indices: 879062--879115 Score: 51
Period size: 8 Copynumber: 6.8 Consensus size: 8
879052 ATAATTTGTG
879062 ATATTTTA
1 ATATTTTA
879070 ATATTATTTA
1 ATA-T-TTTA
879080 AT-TTTTA
1 ATATTTTA
879087 ATAATTTT-
1 AT-ATTTTA
879095 -TATTTTA
1 ATATTTTA
879102 ATATTTTA
1 ATATTTTA
*
879110 AAATTT
1 ATATTT
879116 ATTTAATATA
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
6 5 0.13
7 7 0.18
8 16 0.41
9 5 0.13
10 6 0.15
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (8 bp):
ATATTTTA
Found at i:879100 original size:15 final size:15
Alignment explanation
Indices: 879045--879141 Score: 56
Period size: 17 Copynumber: 6.1 Consensus size: 15
879035 TTATAATTCA
879045 TTATTTT-ATAATTT
1 TTATTTTAATAATTT
879059 GTGATATTTTAAT-ATTAT
1 -T--TATTTTAATAATT-T
879077 TTAATTTTTAATAATTT
1 TT-A-TTTTAATAATTT
879094 TTATTTTAAT-ATTT
1 TTATTTTAATAATTT
* * * *
879108 TAAAATTTATTTAATAT
1 T-TATTTTA-ATAATTT
*
879125 ATATTTTAATAATTT
1 TTATTTTAATAATTT
879140 TT
1 TT
879142 TAAATAATTT
Statistics
Matches: 62, Mismatches: 10, Indels: 20
0.67 0.11 0.22
Matches are distributed among these distances:
14 5 0.08
15 20 0.32
16 8 0.13
17 23 0.37
18 6 0.10
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (15 bp):
TTATTTTAATAATTT
Found at i:879115 original size:32 final size:30
Alignment explanation
Indices: 879062--879140 Score: 79
Period size: 32 Copynumber: 2.5 Consensus size: 30
879052 ATAATTTGTG
* *
879062 ATATTTTAATATTATTTAATTT-TTAATAATTT
1 ATATTTTAATATT-TTAAATTTATT--TAATAT
*
879094 TTATTTTAATATTTTAAAATTTATTTAATAT
1 ATATTTTAATATTTT-AAATTTATTTAATAT
879125 ATATTTTAATAATTTT
1 ATATTTTAAT-ATTTT
879141 TTAAATAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
31 16 0.40
32 22 0.55
33 2 0.05
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (30 bp):
ATATTTTAATATTTTAAATTTATTTAATAT
Found at i:879118 original size:12 final size:13
Alignment explanation
Indices: 879103--879157 Score: 55
Period size: 12 Copynumber: 4.5 Consensus size: 13
879093 TTTATTTTAA
879103 TATTTTAA-AATT
1 TATTTTAATAATT
*
879115 TA-TTTAAT-ATA
1 TATTTTAATAATT
879126 TATTTTAATAATT
1 TATTTTAATAATT
*
879139 T-TTTAAATAATT
1 TATTTTAATAATT
*
879151 TTTTTTA
1 TATTTTA
879158 TTTTTAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
11 9 0.26
12 19 0.54
13 7 0.20
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TATTTTAATAATT
Found at i:879154 original size:23 final size:23
Alignment explanation
Indices: 879078--879154 Score: 72
Period size: 23 Copynumber: 3.4 Consensus size: 23
879068 TAATATTATT
**
879078 TAAT-TTTTAATAA-TTTTTATTT
1 TAATATTTTAATAATTTTTTA-AA
879100 TAATATTTTAA-AATTTATTT-AA
1 TAATATTTTAATAATTT-TTTAAA
879122 TATATATTTTAATAATTTTTTAAA
1 TA-ATATTTTAATAATTTTTTAAA
*
879146 TAATTTTTT
1 TAATATTTT
879155 TTATTTTTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
22 8 0.17
23 26 0.57
24 12 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
TAATATTTTAATAATTTTTTAAA
Found at i:887774 original size:32 final size:32
Alignment explanation
Indices: 887719--887779 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
887709 ATAACATGGT
*
887719 ATATACCATATCATCACTTATATACACGTACC
1 ATATACCATATCATCACTCATATACACGTACC
* * *
887751 ATATACCATGTTATTACTCATATACACGT
1 ATATACCATATCATCACTCATATACACGT
887780 GATATATACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.34
Consensus pattern (32 bp):
ATATACCATATCATCACTCATATACACGTACC
Found at i:887787 original size:32 final size:32
Alignment explanation
Indices: 887718--887788 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
887708 GATAACATGG
*
887718 TATATACCATATCATCACTTATATACACGTAC
1 TATATACCATATCATCACTCATATACACGTAC
* * * *
887750 CATATACCATGTTATTACTCATATACACGTGA-
1 TATATACCATATCATCACTCATATACACGT-AC
887782 TATATAC
1 TATATAC
887789 TACATTATCA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
32 31 0.97
33 1 0.03
ACGTcount: A:0.37, C:0.23, G:0.06, T:0.35
Consensus pattern (32 bp):
TATATACCATATCATCACTCATATACACGTAC
Found at i:894417 original size:7 final size:7
Alignment explanation
Indices: 894405--894442 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
894395 TTTAATTGGG
894405 AAAATTT
1 AAAATTT
894412 AAAATTT
1 AAAATTT
894419 -AAATTT
1 AAAATTT
894425 AAAATTT
1 AAAATTT
894432 -AAATTT
1 AAAATTT
894438 AAAAT
1 AAAAT
894443 ATTCAATTCG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 12 0.41
7 17 0.59
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
AAAATTT
Found at i:894424 original size:6 final size:6
Alignment explanation
Indices: 894406--894440 Score: 52
Period size: 6 Copynumber: 5.5 Consensus size: 6
894396 TTAATTGGGA
894406 AAATTT AAAATTT AAATTT AAAATTT AAATTT AAA
1 AAATTT -AAATTT AAATTT -AAATTT AAATTT AAA
894441 ATATTCAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 15 0.56
7 12 0.44
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (6 bp):
AAATTT
Done.