Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold209
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: 944012
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 59703 characters in sequence are not A, C, G, or T
File 3 of 4
Found at i:577558 original size:224 final size:224
Alignment explanation
Indices: 577179--577640 Score: 762
Period size: 224 Copynumber: 2.1 Consensus size: 224
577169 CACGGCTTGG
*
577179 CACATGGGTGTGTGGTTTGGCCGTGTGTCCCCTAGACCTTAAAATTTCAAACAGAATGCCCAGGT
1 CACATGGGCGTGTGGTTTGGCCGTGTGTCCCCTAGACCTTAAAATTTCAAACAGAATGCCCAGGT
* * * * *
577244 TTTTACACACGGCCTAGCACACGGGCTTGTGGCTTGGCCGTGTGACCCCTGCACTTAAATGTATT
66 TTTTACACACGGCCTAGCACACGGGCGTATAGCTCGGCCGTGTAACCCCTGCACTTAAATGTATT
* * * *
577309 GCAAGTTAGAGAGTTACATGGGCTGGGGACACGACCGTGTACCCTACTTCAAATACCACATGGCC
131 GCAAGTCAGAGAGTTACACGGGCTGGGGACACCACCGTGTACCCTACTTCAAATACCACATGACC
*
577374 TAAGACATGGGTGTGCTCACACGGCCAGC
196 TAAGACACGGGTGTGCTCACACGGCCAGC
* *
577403 CACATGTGCGTGTGGTTTGGCCGTGTGTCCCCTATACCTTAAAATTTCAAACAGAATGCCCAGGT
1 CACATGGGCGTGTGGTTTGGCCGTGTGTCCCCTAGACCTTAAAATTTCAAACAGAATGCCCAGGT
**
577468 TTTTACATGCGGCCTAGCACACGGGCGTATAGCTCGGCCGTGTAACCCCTGCACTTAAATGTATT
66 TTTTACACACGGCCTAGCACACGGGCGTATAGCTCGGCCGTGTAACCCCTGCACTTAAATGTATT
*
577533 GCAAGTCAGAGAGTTACACGGGCTGGGGACGCCACCGTGTACCCTACTTCAAATACCACATGACC
131 GCAAGTCAGAGAGTTACACGGGCTGGGGACACCACCGTGTACCCTACTTCAAATACCACATGACC
577598 TAAGACACGGGTGTGCTCACACGGCCAGC
196 TAAGACACGGGTGTGCTCACACGGCCAGC
* *
577627 CACACGGGTGTGTG
1 CACATGGGCGTGTG
577641 TCCCCTGCTT
Statistics
Matches: 219, Mismatches: 19, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
224 219 1.00
ACGTcount: A:0.23, C:0.27, G:0.26, T:0.24
Consensus pattern (224 bp):
CACATGGGCGTGTGGTTTGGCCGTGTGTCCCCTAGACCTTAAAATTTCAAACAGAATGCCCAGGT
TTTTACACACGGCCTAGCACACGGGCGTATAGCTCGGCCGTGTAACCCCTGCACTTAAATGTATT
GCAAGTCAGAGAGTTACACGGGCTGGGGACACCACCGTGTACCCTACTTCAAATACCACATGACC
TAAGACACGGGTGTGCTCACACGGCCAGC
Found at i:580856 original size:14 final size:15
Alignment explanation
Indices: 580834--580910 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
580824 CAATCAAACA
580834 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
580848 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
* *
580863 ACAGAAAAGTAAAATATTTT
1 CCAGAAAA-T----CATTTT
580883 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
*
580897 CCGGAAAA-CATTTT
1 CCAGAAAATCATTTT
580911 ACTGTCAATG
Statistics
Matches: 49, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
14 22 0.45
15 14 0.29
16 1 0.02
18 1 0.02
19 3 0.06
20 8 0.16
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.34
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:585063 original size:17 final size:18
Alignment explanation
Indices: 585028--585064 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
585018 ATCCGATGAG
585028 TAAGCTCGTAAATTTTAT
1 TAAGCTCGTAAATTTTAT
585046 TAAGCTCGTAAA-TTTAT
1 TAAGCTCGTAAATTTTAT
585063 TA
1 TA
585065 TTTAGTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.43
Consensus pattern (18 bp):
TAAGCTCGTAAATTTTAT
Found at i:585408 original size:20 final size:20
Alignment explanation
Indices: 585383--585447 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 20
585373 AATGGAAAGG
*
585383 AATCAAAGGATTGAGAATCA
1 AATCAAAGGATTGAGAATAA
* * *
585403 AATCAATGTAATG-GAA-AGA
1 AATCAAAGGATTGAGAATA-A
*
585422 AATCAAAAGATTGAGAATAA
1 AATCAAAGGATTGAGAATAA
585442 AATCAA
1 AATCAA
585448 TGTAAACAAG
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
19 13 0.38
20 20 0.59
21 1 0.03
ACGTcount: A:0.55, C:0.08, G:0.17, T:0.20
Consensus pattern (20 bp):
AATCAAAGGATTGAGAATAA
Found at i:585415 original size:39 final size:39
Alignment explanation
Indices: 585372--585452 Score: 135
Period size: 39 Copynumber: 2.1 Consensus size: 39
585362 AGCAAAACAA
* * *
585372 TAATGGAAAGGAATCAAAGGATTGAGAATCAAATCAATG
1 TAATGGAAAGAAATCAAAAGATTGAGAATAAAATCAATG
585411 TAATGGAAAGAAATCAAAAGATTGAGAATAAAATCAATG
1 TAATGGAAAGAAATCAAAAGATTGAGAATAAAATCAATG
585450 TAA
1 TAA
585453 ACAAGATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.53, C:0.06, G:0.20, T:0.21
Consensus pattern (39 bp):
TAATGGAAAGAAATCAAAAGATTGAGAATAAAATCAATG
Found at i:586334 original size:26 final size:27
Alignment explanation
Indices: 586305--586356 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
586295 TTTTATAATC
*
586305 TATATATGTATATAAT-TATTTTTTTA
1 TATATATGTACATAATATATTTTTTTA
*
586331 TATATATGTACATATTATATTTTTTT
1 TATATATGTACATAATATATTTTTTT
586357 CAATTAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 14 0.61
27 9 0.39
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.62
Consensus pattern (27 bp):
TATATATGTACATAATATATTTTTTTA
Found at i:586820 original size:11 final size:11
Alignment explanation
Indices: 586776--586818 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 11
586766 ATGTCATGGA
586776 TTATTTTTT-T
1 TTATTTTTTAT
586786 TTATTTCGTTTAT
1 TTATTT--TTTAT
586799 TTATTTTTTAT
1 TTATTTTTTAT
586810 ATTATTTTT
1 -TTATTTTT
586819 ATGCCATTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
10 6 0.21
11 5 0.17
12 11 0.38
13 7 0.24
ACGTcount: A:0.16, C:0.02, G:0.02, T:0.79
Consensus pattern (11 bp):
TTATTTTTTAT
Found at i:589081 original size:5 final size:5
Alignment explanation
Indices: 589071--589114 Score: 88
Period size: 5 Copynumber: 8.8 Consensus size: 5
589061 AACATTTAAG
589071 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATA
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATA
589115 ATAAAACAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 39 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:589664 original size:277 final size:283
Alignment explanation
Indices: 589180--589688 Score: 782
Period size: 279 Copynumber: 1.8 Consensus size: 283
589170 AAAGAGAGAA
* * * * *
589180 AAAGGAAAGAAAGAAGGAGAAAGGAGAAATTAGGGTTTCAAAGTTTCAAGTTCAATTGGTTAGTC
1 AAAGAAAAGAAAGAAGGAGAAAGGAAAAATTAGGGTTTCAAAGTTCCAAGCTCAAATGGTTAGTC
* ** * *
589245 AATTTAGTCTATTTTTCTTATAATTTTATGTTTTTGGAATCTTAGTGTTAAAATACTATCCGACT
66 AATTTAGTCTACTTTTCTTATAATTTTATGTTTTTGGAATCCCAGTATTAAAATACTACCCGACT
* *
589310 CATGTCAAAATTTTAGATATTATTGAGTTTTTAAGTGTTGTTTATGTTAAATAATTTTAGTATTA
131 CATGTCAAAATTTTAGAAATTATTAAGTTTTTAAGTGTTGTTTATGTTAAATAATTTTAGTATTA
* *
589375 GAGGTTAAATTGATAGATTTTTAGGTTAGAAA-GAAATAGAAAAGAAAGAAAGAAACAGAGAAAG
196 GAGATTAAATTGATAGATTTTTAAGTTAGAAACGAAATAGAAAAGAAAGAAAGAAACAGAGAAAG
589439 CCAAACGAAACAGGGAGAAAAAT
261 CCAAACGAAACAGGGAGAAAAAT
589462 AAAGAAAAGAAAGAA-G-G-AAGGAAAAATTAGGGTTTCAAAGTTCCAAGCTCAAATGGTTAGTC
1 AAAGAAAAGAAAGAAGGAGAAAGGAAAAATTAGGGTTTCAAAGTTCCAAGCTCAAATGGTTAGTC
* *
589524 AATTTAGTCT-CTTTTCTTGTAATTTTTATGTTTTTGGAATCCCGGTATT-AAATACTACCCGAA
66 AATTTAGTCTACTTTTCTTATAA-TTTTATGTTTTTGGAATCCCAGTATTAAAATACTACCCG-A
* *
589587 C-CATGTCAAAATTTTAGAAATTATTAAG-TTTTACGTGTTGTTTATGTTGAATAATTTTAGTAT
129 CTCATGTCAAAATTTTAGAAATTATTAAGTTTTTAAGTGTTGTTTATGTTAAATAATTTTAGTAT
589650 TAGAGATTAAATTGATAGATTTTTAAGTTAGAAACGAAA
194 TAGAGATTAAATTGATAGATTTTTAAGTTAGAAACGAAA
589689 AATGATTAAA
Statistics
Matches: 206, Mismatches: 18, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
277 65 0.32
278 50 0.24
279 75 0.36
280 1 0.00
281 1 0.00
282 14 0.07
ACGTcount: A:0.39, C:0.08, G:0.18, T:0.35
Consensus pattern (283 bp):
AAAGAAAAGAAAGAAGGAGAAAGGAAAAATTAGGGTTTCAAAGTTCCAAGCTCAAATGGTTAGTC
AATTTAGTCTACTTTTCTTATAATTTTATGTTTTTGGAATCCCAGTATTAAAATACTACCCGACT
CATGTCAAAATTTTAGAAATTATTAAGTTTTTAAGTGTTGTTTATGTTAAATAATTTTAGTATTA
GAGATTAAATTGATAGATTTTTAAGTTAGAAACGAAATAGAAAAGAAAGAAAGAAACAGAGAAAG
CCAAACGAAACAGGGAGAAAAAT
Found at i:593972 original size:41 final size:40
Alignment explanation
Indices: 593925--594040 Score: 121
Period size: 37 Copynumber: 2.9 Consensus size: 40
593915 GACTTTGAGT
**
593925 CAATGAGACACTGGGTGTCAATTTACTACTTCGGATTAATT
1 CAATGAGACACTGGGTGTCAATTTA-TACTTCGGATTAAAC
* * * * *
593966 CGATGAGGCACTGGATGCCAA-TT-TACTTC-GATAAAAC
1 CAATGAGACACTGGGTGTCAATTTATACTTCGGATTAAAC
*
594003 CAATGAGACACTGGGTGTCAATTTATTACTTCGAATTA
1 CAATGAGACACTGGGTGTCAATTTA-TACTTCGGATTA
594041 TCTGATGAGG
Statistics
Matches: 58, Mismatches: 13, Indels: 8
0.73 0.16 0.10
Matches are distributed among these distances:
37 22 0.38
38 8 0.14
40 8 0.14
41 20 0.34
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (40 bp):
CAATGAGACACTGGGTGTCAATTTATACTTCGGATTAAAC
Found at i:595900 original size:11 final size:12
Alignment explanation
Indices: 595884--595915 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
595874 AGTGGAAGTG
595884 TTAGGTTTT-TT
1 TTAGGTTTTATT
595895 TTAGGTTTTATT
1 TTAGGTTTTATT
595907 TT-GGTTTTA
1 TTAGGTTTTA
595916 AACACGGGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 16 0.80
12 4 0.20
ACGTcount: A:0.12, C:0.00, G:0.19, T:0.69
Consensus pattern (12 bp):
TTAGGTTTTATT
Found at i:596763 original size:20 final size:22
Alignment explanation
Indices: 596715--596766 Score: 76
Period size: 20 Copynumber: 2.5 Consensus size: 22
596705 AAAAATACAT
596715 TATT-TTTTAAATTATTATCAA
1 TATTGTTTTAAATTATTATCAA
596736 TA-TGTTTTAAA-T-TTATCAA
1 TATTGTTTTAAATTATTATCAA
596755 TATTGTTTTAAA
1 TATTGTTTTAAA
596767 AAATATATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.31
20 11 0.38
21 9 0.31
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.56
Consensus pattern (22 bp):
TATTGTTTTAAATTATTATCAA
Found at i:601949 original size:24 final size:24
Alignment explanation
Indices: 601922--601967 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
601912 TAATAGGAGT
*
601922 GTAGTAAGATTGAAACACCTTAGA
1 GTAGTAAGATTAAAACACCTTAGA
601946 GTAGTAAGATTAAAACACCTTA
1 GTAGTAAGATTAAAACACCTTA
601968 TTCTAATCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.26
Consensus pattern (24 bp):
GTAGTAAGATTAAAACACCTTAGA
Found at i:604900 original size:33 final size:33
Alignment explanation
Indices: 604834--604931 Score: 126
Period size: 33 Copynumber: 3.0 Consensus size: 33
604824 TTTTTTTTAA
* * * *
604834 AATTAAATTACGTTTTAGGGGTTTTAAATAAATT
1 AATTAAATTAGGGTTT-GGGGTTTTTAAGAAATT
604868 AATTAAATTAGGGTTTGGGGTTTTTAAGAAATT
1 AATTAAATTAGGGTTTGGGGTTTTTAAGAAATT
* *
604901 AATTAAATTAGGGTTT-AGTTTTTTAAGAAAT
1 AATTAAATTAGGGTTTGGGGTTTTTAAGAAAT
604932 AACTCTGTGT
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
32 13 0.22
33 31 0.53
34 14 0.24
ACGTcount: A:0.37, C:0.01, G:0.18, T:0.44
Consensus pattern (33 bp):
AATTAAATTAGGGTTTGGGGTTTTTAAGAAATT
Found at i:605197 original size:124 final size:124
Alignment explanation
Indices: 605019--605506 Score: 712
Period size: 126 Copynumber: 3.9 Consensus size: 124
605009 TATTCAATTT
* * *
605019 ATTTTGAGAAGACAGTTCTGAACAAACAGTGTAAAAAACGCTTCAAACAGGATGCACTGTCAGCA
1 ATTTTGAGAAGACAGTTCTGAACAAATAG-GTCAAAAACGCTTCAAGCAGGATGCACTGTCAGCA
* * *
605084 AAATTGATGAAAAAAGCTCCCACATGGACACTCTTTTTCTACAGTAGTTCCTAAAAAAATA
65 AAATTGATGAAAAAAGCTCCCACGTGGACGCTATTTTTCTACAGTAGTTCCT-AAAAAATA
* *
605145 ATTCTGAGAAGACAGTTATGAACAAATA-GTCAAAAACGCTTCAAGCAGGATGCACTGTCAGCAA
1 ATTTTGAGAAGACAGTTCTGAACAAATAGGTCAAAAACGCTTCAAGCAGGATGCACTGTCAGCAA
* *
605209 AATCGATG-AAAAAGCTCCCACGTGGGCGCTATTTTTCTACAGTAGTTCCTAAAAAATA
66 AATTGATGAAAAAAGCTCCCACGTGGACGCTATTTTTCTACAGTAGTTCCTAAAAAATA
* *
605267 GTTTTGAGAAGACGGTTCTGAACAAATAGTGTCAAAAACGCTTCAAGCAGGATGCACTGTCAGCA
1 ATTTTGAGAAGACAGTTCTGAACAAATAG-GTCAAAAACGCTTCAAGCAGGATGCACTGTCAGCA
* * *
605332 AAAATGATGAAAAAAGCTCCCACGTGGACGCTATTTTTCTACAGTAGTTCTTGAAAAATAA
65 AAATTGATGAAAAAAGCTCCCACGTGGACGCTATTTTTCTACAGTAGTTCCTAAAAAAT-A
* * *
605393 ATTTTGAGAAGACGGTTTTGAACAAATAGTGTCAAAAACGCTTCAAGCAGGATGTACTGTCAGCA
1 ATTTTGAGAAGACAGTTCTGAACAAATAG-GTCAAAAACGCTTCAAGCAGGATGCACTGTCAGCA
* * *
605458 AAATTGAT-AAAACAAGCTCCCACGTGGATGGTCTTTTTCTACAGTAGTT
65 AAATTGATGAAAA-AAGCTCCCACGTGGACGCTATTTTTCTACAGTAGTT
605507 GCTGTTTGGC
Statistics
Matches: 331, Mismatches: 26, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
122 32 0.10
123 38 0.11
124 83 0.25
125 50 0.15
126 128 0.39
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.26
Consensus pattern (124 bp):
ATTTTGAGAAGACAGTTCTGAACAAATAGGTCAAAAACGCTTCAAGCAGGATGCACTGTCAGCAA
AATTGATGAAAAAAGCTCCCACGTGGACGCTATTTTTCTACAGTAGTTCCTAAAAAATA
Found at i:605882 original size:17 final size:17
Alignment explanation
Indices: 605860--605893 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
605850 GGTGGTTGTA
605860 GCTTGGAGGCGATGGTG
1 GCTTGGAGGCGATGGTG
605877 GCTTGGAGGCGATGGTG
1 GCTTGGAGGCGATGGTG
605894 CAGACTCATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.12, C:0.12, G:0.53, T:0.24
Consensus pattern (17 bp):
GCTTGGAGGCGATGGTG
Found at i:608687 original size:56 final size:56
Alignment explanation
Indices: 608585--608692 Score: 132
Period size: 56 Copynumber: 1.9 Consensus size: 56
608575 AGAACTTCTA
*
608585 TTTTATAAAATAAAAATATAAAAATAATTTACTATTAAAATATTAAAAAAATTTAT
1 TTTTATAAAATAAAAATATAAAAATAATTTACTATCAAAATATTAAAAAAATTTAT
* * *
608641 TTTTATTAAATGAACAATATAAAAA-AGTTTAC-A-CAAATATATTTAAAAAAAT
1 TTTTATAAAAT-AAAAATATAAAAATAATTTACTATCAAA-ATA-TTAAAAAAAT
608693 CAATGTATGT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
54 3 0.07
55 4 0.09
56 26 0.58
57 12 0.27
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (56 bp):
TTTTATAAAATAAAAATATAAAAATAATTTACTATCAAAATATTAAAAAAATTTAT
Found at i:609670 original size:7 final size:7
Alignment explanation
Indices: 609660--609684 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
609650 TTCTATACAT
609660 AATACTA
1 AATACTA
609667 AATACTA
1 AATACTA
609674 AATACTA
1 AATACTA
609681 AATA
1 AATA
609685 TGAAATGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:611162 original size:29 final size:30
Alignment explanation
Indices: 611114--611175 Score: 99
Period size: 29 Copynumber: 2.1 Consensus size: 30
611104 TAAAGAAAGC
*
611114 TTTGAGAAATTTAAGCAG-AATTTGAGAGT
1 TTTGAGAAATTTAAGAAGAAATTTGAGAGT
*
611143 TTTGAGAAATTTAGGAAGAAATTTGAGAGT
1 TTTGAGAAATTTAAGAAGAAATTTGAGAGT
611173 TTT
1 TTT
611176 TTTGCCAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 16 0.53
30 14 0.47
ACGTcount: A:0.37, C:0.02, G:0.24, T:0.37
Consensus pattern (30 bp):
TTTGAGAAATTTAAGAAGAAATTTGAGAGT
Found at i:613798 original size:53 final size:53
Alignment explanation
Indices: 613718--613875 Score: 271
Period size: 53 Copynumber: 3.0 Consensus size: 53
613708 ATCACCGTCG
*
613718 TTGATTTTCTAACCATTGAGACCAACGGCTATTTAGACCAACGGTCACATTTC
1 TTGATTTTCTAACCGTTGAGACCAACGGCTATTTAGACCAACGGTCACATTTC
*
613771 TTGATTTTCTAACCGTTGAGACCAACGGCTATTTAGACCAACGGTCAGATTTC
1 TTGATTTTCTAACCGTTGAGACCAACGGCTATTTAGACCAACGGTCACATTTC
* * *
613824 TTGATTTTCTAACCGTTGAGACCAACGGCTAATTAGACCAATGATCACATTT
1 TTGATTTTCTAACCGTTGAGACCAACGGCTATTTAGACCAACGGTCACATTT
613876 TTCCAATGGT
Statistics
Matches: 99, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 99 1.00
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.32
Consensus pattern (53 bp):
TTGATTTTCTAACCGTTGAGACCAACGGCTATTTAGACCAACGGTCACATTTC
Found at i:613892 original size:16 final size:17
Alignment explanation
Indices: 613861--613893 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
613851 GCTAATTAGA
613861 CCAATGATCACATTTTT
1 CCAATGATCACATTTTT
*
613878 CCAATGGTC-CATTTTT
1 CCAATGATCACATTTTT
613894 TTTCTATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.24, C:0.24, G:0.09, T:0.42
Consensus pattern (17 bp):
CCAATGATCACATTTTT
Found at i:625896 original size:9 final size:9
Alignment explanation
Indices: 625884--625921 Score: 58
Period size: 9 Copynumber: 4.1 Consensus size: 9
625874 TAATTAATTT
625884 TTTAAAAAA
1 TTTAAAAAA
*
625893 TTTAAAAAT
1 TTTAAAAAA
625902 TTTAAAAAA
1 TTTAAAAAA
625911 TTATAAAAAA
1 TT-TAAAAAA
625921 T
1 T
625922 ATTTTTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
9 18 0.69
10 8 0.31
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (9 bp):
TTTAAAAAA
Found at i:625906 original size:18 final size:19
Alignment explanation
Indices: 625883--625919 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
625873 TTAATTAATT
625883 TTTTAAAAAATT-TAAAAA
1 TTTTAAAAAATTATAAAAA
625901 TTTTAAAAAATTATAAAAA
1 TTTTAAAAAATTATAAAAA
625920 ATATTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TTTTAAAAAATTATAAAAA
Found at i:625909 original size:10 final size:10
Alignment explanation
Indices: 625883--625921 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
625873 TTAATTAATT
625883 TTTTAAAAAA
1 TTTTAAAAAA
625893 -TTT-AAAAA
1 TTTTAAAAAA
625901 TTTTAAAAAA
1 TTTTAAAAAA
*
625911 TTATAAAAAA
1 TTTTAAAAAA
625921 T
1 T
625922 ATTTTTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
8 5 0.19
9 6 0.23
10 15 0.58
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
TTTTAAAAAA
Found at i:626453 original size:27 final size:27
Alignment explanation
Indices: 626391--626456 Score: 71
Period size: 29 Copynumber: 2.4 Consensus size: 27
626381 TATTATTTTG
*
626391 AAATTAGAAATATATAAAATCTAAAAA
1 AAATTATAAATATATAAAATCTAAAAA
* *
626418 AAACTTTATAAATGTA-AAAATCTATAAAT
1 AAA--TTATAAATATATAAAATCTA-AAAA
626447 AAATTATAAA
1 AAATTATAAA
626457 AATTGATTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
27 10 0.30
28 8 0.24
29 15 0.45
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (27 bp):
AAATTATAAATATATAAAATCTAAAAA
Found at i:626682 original size:19 final size:19
Alignment explanation
Indices: 626639--626683 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
626629 TCTTTTAAAG
* **
626639 AAAATTTTAGATTTTTTTC
1 AAAATTTTAGAATTTTTAA
*
626658 ATAATTTTAGAATTTTTAA
1 AAAATTTTAGAATTTTTAA
626677 AAAATTT
1 AAAATTT
626684 GCAATTTTTG
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53
Consensus pattern (19 bp):
AAAATTTTAGAATTTTTAA
Found at i:628123 original size:114 final size:115
Alignment explanation
Indices: 627924--628155 Score: 385
Period size: 114 Copynumber: 2.0 Consensus size: 115
627914 GGCTATGTCT
*
627924 AAAAATAAGTTTTTTAGGGCTAGTTCAACATCTATGTGTGCTAAGTTTAGTTATATATGGCACTA
1 AAAAATAAGTTTTTTAGGGCTAGTTCAACAGCTATGTGTGCTAAGTTTAGTTATATATGGCACTA
* * * *
627989 TTAAGTTTTTCGCACTCATTAGAATCAGGGTAATTATTATTGAATGCTTA
66 TCAAATTTTTCGCACTCATTAGAATCAGGGTAATTAATATTAAATGCTTA
* *
628039 AAAAATACG-TTTTTAGGGCTAGTTCAACAGCTATGTGTGCTAAGTTTAGTTATATATGGCGCTA
1 AAAAATAAGTTTTTTAGGGCTAGTTCAACAGCTATGTGTGCTAAGTTTAGTTATATATGGCACTA
*
628103 TCAAATTTTTCGCACTCATTAGAATCGGGGTAATTAATATTAAATGCTTA
66 TCAAATTTTTCGCACTCATTAGAATCAGGGTAATTAATATTAAATGCTTA
628153 AAA
1 AAA
628156 GGATCTCAAT
Statistics
Matches: 109, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
114 101 0.93
115 8 0.07
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (115 bp):
AAAAATAAGTTTTTTAGGGCTAGTTCAACAGCTATGTGTGCTAAGTTTAGTTATATATGGCACTA
TCAAATTTTTCGCACTCATTAGAATCAGGGTAATTAATATTAAATGCTTA
Found at i:629810 original size:3 final size:3
Alignment explanation
Indices: 629802--629839 Score: 60
Period size: 3 Copynumber: 12.7 Consensus size: 3
629792 TTATTTTTTG
629802 TAT TAT TAT TAT TAT TAT TAT TAGT TAT TAT T-T TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TA
629840 CGCATATGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:631746 original size:15 final size:15
Alignment explanation
Indices: 631726--631756 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
631716 AATCATTGCT
631726 CAGTTAACCTGGAAA
1 CAGTTAACCTGGAAA
631741 CAGTTAACCTGGAAA
1 CAGTTAACCTGGAAA
631756 C
1 C
631757 CAACCAACCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.19
Consensus pattern (15 bp):
CAGTTAACCTGGAAA
Found at i:637230 original size:42 final size:42
Alignment explanation
Indices: 637169--637280 Score: 179
Period size: 42 Copynumber: 2.7 Consensus size: 42
637159 GAAAAGGCCG
* *
637169 GCTCAAATATTGATTAGAATGGGGCATGTGATTATCGGAGTA
1 GCTCAAATACTGATTAGAATGGGGCATGAGATTATCGGAGTA
**
637211 GCTCAAATACTGAACAGAATGGGGCATGAGATTATCGGAGTA
1 GCTCAAATACTGATTAGAATGGGGCATGAGATTATCGGAGTA
*
637253 GCTCAAATACTGATTAGAGTGGGGCATG
1 GCTCAAATACTGATTAGAATGGGGCATG
637281 CAGTGGTCTT
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.32, C:0.12, G:0.29, T:0.26
Consensus pattern (42 bp):
GCTCAAATACTGATTAGAATGGGGCATGAGATTATCGGAGTA
Found at i:638506 original size:44 final size:44
Alignment explanation
Indices: 638438--638900 Score: 148
Period size: 44 Copynumber: 10.5 Consensus size: 44
638428 GTAGAGCAGG
* * ** * *
638438 TTGAAGATTACAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGA
1 TTGAAGATGACAGATTTTACCTCCCTAGGCAGTAGTGGAGTAGA
** ** * *
638482 TCAAAGATGACAGATTTTACCTCCCTGAGGTTGCAGTGGAGTATA
1 TTGAAGATGACAGATTTTACCTCCCT-AGGCAGTAGTGGAGTAGA
*** * * * * * *
638527 TTGAAGCCAATA-ATTCTACTTCCCTGGGCAGCAGTGGAATAGA
1 TTGAAGATGACAGATTTTACCTCCCTAGGCAGTAGTGGAGTAGA
** * ** * *
638570 TTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGA
1 TTGAAGATGACAGATTTTACCTCCCTAGGCAGTAGTGGAGTAGA
** * ** *
638614 TCAAAGATGGA-AAATTTTACCTCCCTGAGGTTGTAGTGGAGTACA
1 TTGAAGAT-GACAGATTTTACCTCCCT-AGGCAGTAGTGGAGTAGA
*** * * * * *
638659 TTGAAGCCAATA-ATTCTACTTCCCTAGGTAGTAGTGGAATAGA
1 TTGAAGATGACAGATTTTACCTCCCTAGGCAGTAGTGGAGTAGA
** * ** * * *
638702 TTGAAGATTTCAGATATTGTCTCCCCAAGCAGTAGTGGAGCAGA
1 TTGAAGATGACAGATTTTACCTCCCTAGGCAGTAGTGGAGTAGA
** * ** * *
638746 TCAAAGATGGCAGATTTTACCTCCCTGAGGTTGCAGTGGAGTACA
1 TTGAAGATGACAGATTTTACCTCCCT-AGGCAGTAGTGGAGTAGA
* * * * * *
638791 TTG-A-A-GCCAGTAATTCTACTTCCCTGGGCAGCAGTGGAATAGA
1 TTGAAGATGACAG--ATTTTACCTCCCTAGGCAGTAGTGGAGTAGA
** * ** * * *
638834 TTGAAGATTTCAGATCTTGTCTCCCCAAGCAGTAGTGGAGCAGA
1 TTGAAGATGACAGATTTTACCTCCCTAGGCAGTAGTGGAGTAGA
** *
638878 TCAAAGATGGA-GGATTTTACCTC
1 TTGAAGAT-GACAGATTTTACCTC
638901 TTCGTGGTTA
Statistics
Matches: 283, Mismatches: 123, Indels: 26
0.66 0.28 0.06
Matches are distributed among these distances:
42 4 0.01
43 59 0.21
44 167 0.59
45 50 0.18
46 3 0.01
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (44 bp):
TTGAAGATGACAGATTTTACCTCCCTAGGCAGTAGTGGAGTAGA
Found at i:638596 original size:132 final size:132
Alignment explanation
Indices: 638438--639101 Score: 1037
Period size: 132 Copynumber: 5.0 Consensus size: 132
638428 GTAGAGCAGG
*
638438 TTGAAGATTACAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGACAGATTTTACC
1 TTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGACAGATTTTACC
* *
638503 TCCCTGAGGTTGCAGTGGAGTATATTGAAGCCAATAATTCTACTTCCCTGGGCAGCAGTGGAATA
66 TCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGAATA
638568 GA
131 GA
*
638570 TTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGA-AAATTTTAC
1 TTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAT-GACAGATTTTAC
* * * * *
638634 CTCCCTGAGGTTGTAGTGGAGTACATTGAAGCCAATAATTCTACTTCCCTAGGTAGTAGTGGAAT
65 CTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGAAT
638699 AGA
130 AGA
* * *
638702 TTGAAGATTTCAGATATTGTCTCCCCAAGCAGTAGTGGAGCAGATCAAAGATGGCAGATTTTACC
1 TTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGACAGATTTTACC
638767 TCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGAATA
66 TCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGAATA
638832 GA
131 GA
* *
638834 TTGAAGATTTCAGATCTTGTCTCCCCAAGCAGTAGTGGAGCAGATCAAAGATGGA-GGATTTTAC
1 TTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAT-GACAGATTTTAC
* * ** * * * *
638898 CT-CTTCGTGGTTATAGTGAAGTACATTGAAGCTAGTAATTCTATTTCCCTGGGCAACAGTGGAA
65 CTCCCT-GAGGTTGCAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGAA
638962 TAGA
129 TAGA
* *
638966 TTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCATATTTTACC
1 TTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGACAGATTTTACC
* * *
639031 TCCCTGTGGTTACAGTGGAGTATATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGAATA
66 TCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGAATA
639096 GA
131 GA
639098 TTGA
1 TTGA
639102 NNNNNNNNNN
Statistics
Matches: 488, Mismatches: 38, Indels: 12
0.91 0.07 0.02
Matches are distributed among these distances:
131 4 0.01
132 479 0.98
133 5 0.01
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (132 bp):
TTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGACAGATTTTACC
TCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGAATA
GA
Found at i:639776 original size:12 final size:12
Alignment explanation
Indices: 639759--639786 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
639749 AGTCCAACAC
639759 TAGCAGGCCCAA
1 TAGCAGGCCCAA
639771 TAGCAGGCCCAA
1 TAGCAGGCCCAA
639783 TAGC
1 TAGC
639787 CAATTTTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.32, C:0.32, G:0.25, T:0.11
Consensus pattern (12 bp):
TAGCAGGCCCAA
Found at i:640711 original size:3 final size:3
Alignment explanation
Indices: 640703--640740 Score: 60
Period size: 3 Copynumber: 12.7 Consensus size: 3
640693 TTATTTTTTG
640703 TAT TAT TAT TAT TAT TAT TAT TAGT TAT TAT T-T TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TA
640741 CGCATATGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:646545 original size:32 final size:31
Alignment explanation
Indices: 646456--646562 Score: 99
Period size: 32 Copynumber: 3.4 Consensus size: 31
646446 CCTTAGAGAA
* * *
646456 AGGCGACACACCACTGGCAATGCCCATTTCAC
1 AGGCGGCACACCACTGTC-ATGCCCATTCCAC
* ***
646488 AGGCGGCA-TCGGTTGGTCATGCCCATTCCAC
1 AGGCGGCACACCACT-GTCATGCCCATTCCAC
646519 AGGCGGCACACCACTGATCATGCCCATTCCAC
1 AGGCGGCACACCACTG-TCATGCCCATTCCAC
* *
646551 AAGTGGCACACC
1 AGGCGGCACACC
646563 TTTGACTTGT
Statistics
Matches: 59, Mismatches: 13, Indels: 6
0.76 0.17 0.08
Matches are distributed among these distances:
31 23 0.39
32 36 0.61
ACGTcount: A:0.24, C:0.36, G:0.22, T:0.17
Consensus pattern (31 bp):
AGGCGGCACACCACTGTCATGCCCATTCCAC
Found at i:646688 original size:3 final size:3
Alignment explanation
Indices: 646675--646705 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
646665 AAAGAAATTT
646675 GAA GAA G-A GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
646706 GAGCGGGAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:649449 original size:22 final size:22
Alignment explanation
Indices: 649403--649446 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
649393 TTTTTTTTCC
*
649403 CTTTCTCTCTTCTCTTCTCTTT
1 CTTTCTCTCTTCTCCTCTCTTT
*
649425 CTTTCTTTCTTCTCCCTCTCTT
1 CTTTCTCTCTTCT-CCTCTCTT
649447 CTTCCTTATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (22 bp):
CTTTCTCTCTTCTCCTCTCTTT
Found at i:651786 original size:19 final size:19
Alignment explanation
Indices: 651764--651806 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
651754 ATAATTTATT
* *
651764 TAAAAATATTTAAAAGTTG
1 TAAAAATACTTAAAAATTG
*
651783 TAAAAATCCTTAAAAATTG
1 TAAAAATACTTAAAAATTG
651802 TAAAA
1 TAAAA
651807 TTTATTATAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.33
Consensus pattern (19 bp):
TAAAAATACTTAAAAATTG
Found at i:657600 original size:23 final size:22
Alignment explanation
Indices: 657573--657620 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
657563 TTTTAAAAGG
657573 AAAAATGAAAACAAATGAAAAGAC
1 AAAAA-GAAAACAAATGAAAA-AC
**
657597 AAAAAGAAAGGAAATGAAAAAC
1 AAAAAGAAAACAAATGAAAAAC
657619 AA
1 AA
657621 TGAAAAGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 4 0.18
23 13 0.59
24 5 0.23
ACGTcount: A:0.73, C:0.06, G:0.15, T:0.06
Consensus pattern (22 bp):
AAAAAGAAAACAAATGAAAAAC
Found at i:658881 original size:64 final size:64
Alignment explanation
Indices: 658785--658921 Score: 152
Period size: 64 Copynumber: 2.2 Consensus size: 64
658775 CCTCAAATTC
* *** * * * *
658785 TTTTCCCCAAATCAGTTCCTCCTCTTTTTGAAATCCTTAATTTTTTTTC-CTAAACCTCTTTCTT
1 TTTTCCCCAAATCAGTTCCCCCTCTCCCTGAAATCCCTAAGTTTCTTTCAC-AAACCCCTTTCTT
* * *
658849 TTTTTCCCAAATCGGTTCCCCCTCTCCCTGAAATCCCTAAGTTTCTTTCACAGACCCCTTTC-T
1 TTTTCCCCAAATCAGTTCCCCCTCTCCCTGAAATCCCTAAGTTTCTTTCACAAACCCCTTTCTT
658912 TTTTCCCCAA
1 TTTTCCCCAA
658922 TTTCTTTTCC
Statistics
Matches: 60, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
63 10 0.17
64 49 0.82
65 1 0.02
ACGTcount: A:0.18, C:0.34, G:0.05, T:0.43
Consensus pattern (64 bp):
TTTTCCCCAAATCAGTTCCCCCTCTCCCTGAAATCCCTAAGTTTCTTTCACAAACCCCTTTCTT
Found at i:658938 original size:15 final size:15
Alignment explanation
Indices: 658907--658935 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
658897 CACAGACCCC
658907 TTTCTTTTTCCCCAA
1 TTTCTTTTTCCCCAA
658922 TTTC-TTTTCCCCAA
1 TTTCTTTTTCCCCAA
658936 ATTAATTCCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.14, C:0.34, G:0.00, T:0.52
Consensus pattern (15 bp):
TTTCTTTTTCCCCAA
Found at i:658990 original size:75 final size:78
Alignment explanation
Indices: 658849--659028 Score: 212
Period size: 76 Copynumber: 2.4 Consensus size: 78
658839 CCTCTTTCTT
* ** *
658849 TTTTTCCCAAATCGGTTCCCCCTCTCCCTGAAATCCCTAAGTTTCTTTCACAGACCCCTTTC-TT
1 TTTTCCCCAAATCAATTCCCCCTCTCCCTGAAATCCCTAAGTTTCTTTCACAAACCCCTTTCTTT
*
658913 TTTCCCCAATTTC
66 TTTCCCAAATTTC
* * *
658926 TTTTCCCCAAATTAATTCCCCCT-TCTC-GAAATCCCTAA-TTT-TTTC-CTAAATCCCTTTCTT
1 TTTTCCCCAAATCAATTCCCCCTCTCCCTGAAATCCCTAAGTTTCTTTCAC-AAACCCCTTTC--
658986 TTTTTTCCCAAATTTC
63 TTTTTTCCCAAATTTC
659002 TTTTCCCCAAATCAATTCCCCC-CTCCC
1 TTTTCCCCAAATCAATTCCCCCTCTCCC
659029 CAATATATGT
Statistics
Matches: 88, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
72 1 0.01
73 13 0.15
74 3 0.03
75 11 0.12
76 41 0.47
77 19 0.22
ACGTcount: A:0.19, C:0.37, G:0.03, T:0.41
Consensus pattern (78 bp):
TTTTCCCCAAATCAATTCCCCCTCTCCCTGAAATCCCTAAGTTTCTTTCACAAACCCCTTTCTTT
TTTCCCAAATTTC
Found at i:667010 original size:45 final size:43
Alignment explanation
Indices: 666891--667010 Score: 114
Period size: 45 Copynumber: 2.7 Consensus size: 43
666881 GAGAAAAGTA
* * * * * *
666891 CCGCTAAAGATCATATTCTGTAGCGGCGTTTTTAGTAAAAGCG
1 CCGCTAAAGGTCATGTTCTATAGCGGCATTTTTAGAAAAAACG
* * * * *
666934 ACGCTAAAGGTCGTGTTTTTTAGCGGGATTTTTAGAAAAAAAACG
1 CCGCTAAAGGTCATGTTCTATAGCGGCATTTTTAG--AAAAAACG
*
666979 CCGCTAAAGGTCATGTTCTATAACGGCATTTT
1 CCGCTAAAGGTCATGTTCTATAGCGGCATTTT
667011 CATACATAAA
Statistics
Matches: 59, Mismatches: 16, Indels: 2
0.77 0.21 0.03
Matches are distributed among these distances:
43 27 0.46
45 32 0.54
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.32
Consensus pattern (43 bp):
CCGCTAAAGGTCATGTTCTATAGCGGCATTTTTAGAAAAAACG
Found at i:668347 original size:16 final size:17
Alignment explanation
Indices: 668321--668352 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
668311 TAAAAACTAT
668321 AAATTTAAAAATATTTC
1 AAATTTAAAAATATTTC
668338 AAATTT-AAAATATTT
1 AAATTTAAAAATATTT
668353 TTTAAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
AAATTTAAAAATATTTC
Found at i:668476 original size:17 final size:19
Alignment explanation
Indices: 668451--668487 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
668441 AAAATAATAT
668451 AAATATATAA-ATTTAAAA
1 AAATATATAATATTTAAAA
*
668469 AAAT-TATAATTTTTAAAA
1 AAATATATAATATTTAAAA
668487 A
1 A
668488 TCTTAAATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AAATATATAATATTTAAAA
Found at i:670750 original size:6 final size:6
Alignment explanation
Indices: 670735--670765 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
670725 TGCATTTGTG
670735 AAAATAA AAAATA AAAATA AAAATA AAAATA
1 AAAAT-A AAAATA AAAATA AAAATA AAAATA
670766 TACATATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.79
7 5 0.21
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:671460 original size:12 final size:11
Alignment explanation
Indices: 671436--671470 Score: 52
Period size: 12 Copynumber: 3.0 Consensus size: 11
671426 CGTTCTCCCT
671436 TTTTTTTTATTC
1 TTTTTTTT-TTC
671448 TTTTCTTTTTTC
1 TTTT-TTTTTTC
671460 TTTTTTTTTTC
1 TTTTTTTTTTC
671471 GACAATGAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 7 0.32
12 11 0.50
13 4 0.18
ACGTcount: A:0.03, C:0.11, G:0.00, T:0.86
Consensus pattern (11 bp):
TTTTTTTTTTC
Found at i:671599 original size:22 final size:21
Alignment explanation
Indices: 671564--671640 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 21
671554 AAAAGGTATC
* *
671564 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCTAAGAT
671585 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
* *
671608 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
671627 TATATATCATATCT
1 TACAAATCATATCT
671641 AAGATTGCAT
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
19 17 0.37
21 4 0.09
22 15 0.33
23 10 0.22
ACGTcount: A:0.42, C:0.16, G:0.05, T:0.38
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:671607 original size:23 final size:22
Alignment explanation
Indices: 671564--671621 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
671554 AAAAGGTATC
* *
671564 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
671585 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
671608 TGCATATCATATCT
1 TACAAATCATATCT
671622 AAGATTATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:671624 original size:19 final size:19
Alignment explanation
Indices: 671600--671653 Score: 90
Period size: 19 Copynumber: 2.8 Consensus size: 19
671590 AATCATATCT
671600 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
**
671619 TCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATA
671638 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
671654 CTTGAATATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.39
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:672267 original size:45 final size:43
Alignment explanation
Indices: 672202--673411 Score: 341
Period size: 44 Copynumber: 27.8 Consensus size: 43
672192 TTATCGGCTC
* *
672202 TAATCTGCTCCACTGTAACTTCAGGGAGATAAGA-TT-TTCCATCT
1 TAATCTCCT-CACTGCAACTTCAGGGAGATAAGACTTGTT-CA-CT
* *
672246 TCAGTCTACCTCACTGCAACTTCA-GGAGGATAAGACTTGTTTACT
1 T-AATCT-CCTCACTGCAACTTCAGGGA-GATAAGACTTGTTCACT
* * *
672291 TAATCTGCTCTACTGCAACTTCAGGGAGATAAGACTAG---ACC
1 TAATCTCCTC-ACTGCAACTTCAGGGAGATAAGACTTGTTCACT
** * * * **
672332 CGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCCAAGGTT---T
1 TAATCTCCTCACTGCAACTTCAGGGAGATAAGA--C-TTGTTCACT
* * * * * *
672375 TGATC-CGCTCCACTGCAACTTTAGGCAGATAGGA-TT-ATCGGCT
1 TAATCTC-CT-CACTGCAACTTCAGGGAGATAAGACTTGTTC-ACT
* *
672418 CTAATCTGCTCCACTGTAACTTCAGGGAGATAAGA-TT-TTCCATCT
1 -TAATCTCCT-CACTGCAACTTCAGGGAGATAAGACTTGTT-CA-CT
* *
672463 TCAGTCTACCTCACTGCAACTTCA-GGAGGATAAGACTTGTTTACT
1 T-AATCT-CCTCACTGCAACTTCAGGGA-GATAAGACTTGTTCACT
* * *
672508 TAATCTGCTCTACTGCAACTTCAGGGAGATAAGACTAG---ACC
1 TAATCTCCTC-ACTGCAACTTCAGGGAGATAAGACTTGTTCACT
** * * * **
672549 CGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCCAAGGTT---T
1 TAATCTCCTCACTGCAACTTCAGGGAGATAAGA--C-TTGTTCACT
* * * * * *
672592 TGATC-CGCTCCACTGCAACTTTAGGCAGATAGGA-TT-ATCGGCT
1 TAATCTC-CT-CACTGCAACTTCAGGGAGATAAGACTTGTTC-ACT
* *
672635 CTAATCTGCTCCACTGTAACTTCAGGGAGATAAGA-TT-TTCCATCT
1 -TAATCTCCT-CACTGCAACTTCAGGGAGATAAGACTTGTT-CA-CT
* *
672680 TCAGTCTACCTCACTGCAACTTCA-GGAGGATAAGACTTGTTTACT
1 T-AATCT-CCTCACTGCAACTTCAGGGA-GATAAGACTTGTTCACT
* * *
672725 TAATCTGCTCTACTGCAACTTCAGGGAGATAAGACTAG---ACC
1 TAATCTCCTC-ACTGCAACTTCAGGGAGATAAGACTTGTTCACT
** * * * **
672766 CGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCCAAGGTT---T
1 TAATCTCCTCACTGCAACTTCAGGGAGATAAGA--C-TTGTTCACT
* * * * * *
672809 TGATC-CGCTCCACTGCAACTTTAGGCAGATAGGA-TT-ATCGGCT
1 TAATCTC-CT-CACTGCAACTTCAGGGAGATAAGACTTGTTC-ACT
* *
672852 CTAATCTGCTCCACTGTAACTTCAGGGAGATAAGA-TT-TTCCATCT
1 -TAATCTCCT-CACTGCAACTTCAGGGAGATAAGACTTGTT-CA-CT
* *
672897 TCAGTCTACCTCACTGCAACTTCA-GGAGGATAAGACTTGTTTACT
1 T-AATCT-CCTCACTGCAACTTCAGGGA-GATAAGACTTGTTCACT
* * *
672942 TAATCTGCTCTACTGCAACTTCAGGGAGATAAGACTAG---ACC
1 TAATCTCCTC-ACTGCAACTTCAGGGAGATAAGACTTGTTCACT
** * * * **
672983 CGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCCAAGGTT---T
1 TAATCTCCTCACTGCAACTTCAGGGAGATAAGA--C-TTGTTCACT
* * * * * *
673026 TGATC-CGCTCCACTGCAACTTTAGGCAGATAGGA-TT-ATCGGCT
1 TAATCTC-CT-CACTGCAACTTCAGGGAGATAAGACTTGTTC-ACT
* *
673069 CTAATCTGCTCCACTGTAACTTCAGGGAGATAAGA-TT-TTCCATCT
1 -TAATCTCCT-CACTGCAACTTCAGGGAGATAAGACTTGTT-CA-CT
* *
673114 TCAGTCTACCTCACTGCAACTTCA-GGAGGATAAGACTTGTTTACT
1 T-AATCT-CCTCACTGCAACTTCAGGGA-GATAAGACTTGTTCACT
* * *
673159 TAATCTGCTCTACTGCAACTTCAGGGAGATAAGACTAG---ACC
1 TAATCTCCTC-ACTGCAACTTCAGGGAGATAAGACTTGTTCACT
** * * * **
673200 CGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCCAAGGTT---T
1 TAATCTCCTCACTGCAACTTCAGGGAGATAAGA--C-TTGTTCACT
* * * * * *
673243 TGATC-CGCTCCACTGCAACTTTAGGCAGATAGGA-TT-ATCGGCT
1 TAATCTC-CT-CACTGCAACTTCAGGGAGATAAGACTTGTTC-ACT
* *
673286 CTAATCTGCTCCACTGTAACTTCAGGGAGATAAGA-TT-TTCCATCT
1 -TAATCTCCT-CACTGCAACTTCAGGGAGATAAGACTTGTT-CA-CT
* *
673331 TCAGTCTACCTCACTGCAACTTCA-GGAGGATAAGACTTGTTTACT
1 T-AATCT-CCTCACTGCAACTTCAGGGA-GATAAGACTTGTTCACT
*
673376 TAATCTGCTCTACTGCAACTTCAGGGAGATAAGACT
1 TAATCTCCTC-ACTGCAACTTCAGGGAGATAAGACT
673412 AGACCCGATC
Statistics
Matches: 878, Mismatches: 171, Indels: 234
0.68 0.13 0.18
Matches are distributed among these distances:
39 5 0.01
40 105 0.12
41 50 0.06
42 5 0.01
43 58 0.07
44 424 0.48
45 189 0.22
46 30 0.03
47 12 0.01
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.29
Consensus pattern (43 bp):
TAATCTCCTCACTGCAACTTCAGGGAGATAAGACTTGTTCACT
Found at i:672306 original size:217 final size:217
Alignment explanation
Indices: 672031--673591 Score: 3113
Period size: 217 Copynumber: 7.2 Consensus size: 217
672021 TTGTTTATTT
*
672031 AGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGTTTACTTAATCTGCTCTACTGCAACTTC
1 AGTCTACCTCACTGCAACTTCAGGAGGATAAGACTTGTTTACTTAATCTGCTCTACTGCAACTTC
672096 AGGGAGATAAGACTAGACCCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCCAAGGTTTTGA
66 AGGGAGATAAGACTAGACCCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCCAAGGTTTTGA
672161 TCCGCTCCACTGCAACTTTAGGCAGATAGGATTATCGGCTCTAATCTGCTCCACTGTAACTTCAG
131 TCCGCTCCACTGCAACTTTAGGCAGATAGGATTATCGGCTCTAATCTGCTCCACTGTAACTTCAG
672226 GGAGATAAGATTTTCCATCTTC
196 GGAGATAAGATTTTCCATCTTC
672248 AGTCTACCTCACTGCAACTTCAGGAGGATAAGACTTGTTTACTTAATCTGCTCTACTGCAACTTC
1 AGTCTACCTCACTGCAACTTCAGGAGGATAAGACTTGTTTACTTAATCTGCTCTACTGCAACTTC
672313 AGGGAGATAAGACTAGACCCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCCAAGGTTTTGA
66 AGGGAGATAAGACTAGACCCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCCAAGGTTTTGA
672378 TCCGCTCCACTGCAACTTTAGGCAGATAGGATTATCGGCTCTAATCTGCTCCACTGTAACTTCAG
131 TCCGCTCCACTGCAACTTTAGGCAGATAGGATTATCGGCTCTAATCTGCTCCACTGTAACTTCAG
672443 GGAGATAAGATTTTCCATCTTC
196 GGAGATAAGATTTTCCATCTTC
672465 AGTCTACCTCACTGCAACTTCAGGAGGATAAGACTTGTTTACTTAATCTGCTCTACTGCAACTTC
1 AGTCTACCTCACTGCAACTTCAGGAGGATAAGACTTGTTTACTTAATCTGCTCTACTGCAACTTC
672530 AGGGAGATAAGACTAGACCCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCCAAGGTTTTGA
66 AGGGAGATAAGACTAGACCCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCCAAGGTTTTGA
672595 TCCGCTCCACTGCAACTTTAGGCAGATAGGATTATCGGCTCTAATCTGCTCCACTGTAACTTCAG
131 TCCGCTCCACTGCAACTTTAGGCAGATAGGATTATCGGCTCTAATCTGCTCCACTGTAACTTCAG
672660 GGAGATAAGATTTTCCATCTTC
196 GGAGATAAGATTTTCCATCTTC
672682 AGTCTACCTCACTGCAACTTCAGGAGGATAAGACTTGTTTACTTAATCTGCTCTACTGCAACTTC
1 AGTCTACCTCACTGCAACTTCAGGAGGATAAGACTTGTTTACTTAATCTGCTCTACTGCAACTTC
672747 AGGGAGATAAGACTAGACCCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCCAAGGTTTTGA
66 AGGGAGATAAGACTAGACCCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCCAAGGTTTTGA
672812 TCCGCTCCACTGCAACTTTAGGCAGATAGGATTATCGGCTCTAATCTGCTCCACTGTAACTTCAG
131 TCCGCTCCACTGCAACTTTAGGCAGATAGGATTATCGGCTCTAATCTGCTCCACTGTAACTTCAG
672877 GGAGATAAGATTTTCCATCTTC
196 GGAGATAAGATTTTCCATCTTC
672899 AGTCTACCTCACTGCAACTTCAGGAGGATAAGACTTGTTTACTTAATCTGCTCTACTGCAACTTC
1 AGTCTACCTCACTGCAACTTCAGGAGGATAAGACTTGTTTACTTAATCTGCTCTACTGCAACTTC
672964 AGGGAGATAAGACTAGACCCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCCAAGGTTTTGA
66 AGGGAGATAAGACTAGACCCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCCAAGGTTTTGA
673029 TCCGCTCCACTGCAACTTTAGGCAGATAGGATTATCGGCTCTAATCTGCTCCACTGTAACTTCAG
131 TCCGCTCCACTGCAACTTTAGGCAGATAGGATTATCGGCTCTAATCTGCTCCACTGTAACTTCAG
673094 GGAGATAAGATTTTCCATCTTC
196 GGAGATAAGATTTTCCATCTTC
673116 AGTCTACCTCACTGCAACTTCAGGAGGATAAGACTTGTTTACTTAATCTGCTCTACTGCAACTTC
1 AGTCTACCTCACTGCAACTTCAGGAGGATAAGACTTGTTTACTTAATCTGCTCTACTGCAACTTC
673181 AGGGAGATAAGACTAGACCCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCCAAGGTTTTGA
66 AGGGAGATAAGACTAGACCCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCCAAGGTTTTGA
673246 TCCGCTCCACTGCAACTTTAGGCAGATAGGATTATCGGCTCTAATCTGCTCCACTGTAACTTCAG
131 TCCGCTCCACTGCAACTTTAGGCAGATAGGATTATCGGCTCTAATCTGCTCCACTGTAACTTCAG
673311 GGAGATAAGATTTTCCATCTTC
196 GGAGATAAGATTTTCCATCTTC
673333 AGTCTACCTCACTGCAACTTCAGGAGGATAAGACTTGTTTACTTAATCTGCTCTACTGCAACTTC
1 AGTCTACCTCACTGCAACTTCAGGAGGATAAGACTTGTTTACTTAATCTGCTCTACTGCAACTTC
673398 AGGGAGATAAGACTAGACCCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCCAAGGTTTTGA
66 AGGGAGATAAGACTAGACCCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCCAAGGTTTTGA
673463 TCCGCTCCACTGCAACTTTAGGCAGATAGGATTATCGGCTCTAATCTGCTCCACTGTAACTTCAG
131 TCCGCTCCACTGCAACTTTAGGCAGATAGGATTATCGGCTCTAATCTGCTCCACTGTAACTTCAG
673528 GGAGATAAGATTTTCCATCTTC
196 GGAGATAAGATTTTCCATCTTC
673550 AGTCTACCTCACTGCAACTTCAGGAGGATAAGACTTGTTTAC
1 AGTCTACCTCACTGCAACTTCAGGAGGATAAGACTTGTTTAC
673592 AGATCTACAA
Statistics
Matches: 1343, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
217 1343 1.00
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.29
Consensus pattern (217 bp):
AGTCTACCTCACTGCAACTTCAGGAGGATAAGACTTGTTTACTTAATCTGCTCTACTGCAACTTC
AGGGAGATAAGACTAGACCCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCCAAGGTTTTGA
TCCGCTCCACTGCAACTTTAGGCAGATAGGATTATCGGCTCTAATCTGCTCCACTGTAACTTCAG
GGAGATAAGATTTTCCATCTTC
Found at i:674875 original size:14 final size:15
Alignment explanation
Indices: 674852--674898 Score: 80
Period size: 14 Copynumber: 3.3 Consensus size: 15
674842 AGCCTCTCCA
674852 TTTT-ACTTTTTCAT
1 TTTTCACTTTTTCAT
674866 TTTTCA-TTTTTCAT
1 TTTTCACTTTTTCAT
674880 TTTTCACTTTTTCAT
1 TTTTCACTTTTTCAT
674895 TTTT
1 TTTT
674899 TTCATTTTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
14 18 0.58
15 13 0.42
ACGTcount: A:0.13, C:0.15, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTTCACTTTTTCAT
Found at i:674911 original size:8 final size:7
Alignment explanation
Indices: 674858--674898 Score: 73
Period size: 7 Copynumber: 5.7 Consensus size: 7
674848 TCCATTTTAC
674858 TTTTTCA
1 TTTTTCA
674865 TTTTTCA
1 TTTTTCA
674872 TTTTTCA
1 TTTTTCA
674879 TTTTTCA
1 TTTTTCA
674886 CTTTTTCA
1 -TTTTTCA
674894 TTTTT
1 TTTTT
674899 TTCATTTTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 26 0.79
8 7 0.21
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTTTCA
Found at i:680630 original size:24 final size:22
Alignment explanation
Indices: 680602--680653 Score: 72
Period size: 21 Copynumber: 2.4 Consensus size: 22
680592 ATATTACAAA
680602 ATCATATCTTCTAAGATTGCAT
1 ATCATATCTTCTAAGATTGCAT
*
680624 AT-ATCAT-ATCTAAGATTGCAT
1 ATCAT-ATCTTCTAAGATTGCAT
680645 ATCATATCT
1 ATCATATCT
680654 AATATTGCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
21 19 0.76
22 6 0.24
ACGTcount: A:0.35, C:0.17, G:0.08, T:0.40
Consensus pattern (22 bp):
ATCATATCTTCTAAGATTGCAT
Found at i:680637 original size:21 final size:21
Alignment explanation
Indices: 680611--680665 Score: 87
Period size: 19 Copynumber: 2.7 Consensus size: 21
680601 AATCATATCT
680611 TCTAAGATTGCATATATCATA
1 TCTAAGATTGCATATATCATA
680632 TCTAAGATTGC--ATATCATA
1 TCTAAGATTGCATATATCATA
*
680651 TCTAATATTGCATAT
1 TCTAAGATTGCATAT
680666 CCTCGAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 18 0.58
21 13 0.42
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (21 bp):
TCTAAGATTGCATATATCATA
Found at i:682531 original size:6 final size:6
Alignment explanation
Indices: 682520--682545 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
682510 AAAATATTAA
682520 TTTATT TTTATT TTTATT TTTATT TT
1 TTTATT TTTATT TTTATT TTTATT TT
682546 CTTGCTAGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTATT
Found at i:683830 original size:23 final size:23
Alignment explanation
Indices: 683800--683847 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
683790 TATCATCACT
683800 GGATAGTCGATCTAGGAGAACTA
1 GGATAGTCGATCTAGGAGAACTA
683823 GGATAGTCGATCTAGGAGAACTA
1 GGATAGTCGATCTAGGAGAACTA
683846 GG
1 GG
683848 TTGACACAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.33, C:0.12, G:0.33, T:0.21
Consensus pattern (23 bp):
GGATAGTCGATCTAGGAGAACTA
Found at i:688862 original size:9 final size:9
Alignment explanation
Indices: 688848--688878 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
688838 GTTAAACGAA
688848 TCGAGTTAT
1 TCGAGTTAT
*
688857 TCGAGTTAA
1 TCGAGTTAT
688866 TCGAGTTAT
1 TCGAGTTAT
688875 TCGA
1 TCGA
688879 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:689508 original size:41 final size:39
Alignment explanation
Indices: 689446--689578 Score: 198
Period size: 41 Copynumber: 3.3 Consensus size: 39
689436 ATTTTTATTA
*
689446 TTTTTT-ATTTTTTAATTTTAAAATACTTTTAAAATACTT
1 TTTTTTAATTTTTTAATTTTAAAATATTTTTAAAATAC-T
689485 TTTTTTAATTTTTTAAATTTTAAAATATTTTTAAAATAC-
1 TTTTTTAATTTTTT-AATTTTAAAATATTTTTAAAATACT
689524 TTTTTTAAGTTTTTTTAATTTTAAAAATATTTTTAAAATACT
1 TTTTTTAA--TTTTTTAATTTT-AAAATATTTTTAAAATACT
689566 TTTTTTAATTTTT
1 TTTTTTAATTTTT
689579 GTTTTAATTT
Statistics
Matches: 87, Mismatches: 1, Indels: 11
0.88 0.01 0.11
Matches are distributed among these distances:
39 14 0.16
40 18 0.21
41 47 0.54
42 8 0.09
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (39 bp):
TTTTTTAATTTTTTAATTTTAAAATATTTTTAAAATACT
Found at i:689568 original size:12 final size:11
Alignment explanation
Indices: 689461--689569 Score: 56
Period size: 11 Copynumber: 10.4 Consensus size: 11
689451 TATTTTTTAA
*
689461 TTTTAAAATAC
1 TTTTAAAATAT
689472 TTTTAAAATACTT
1 TTTTAAAATA--T
**
689485 TTTTTTAAT-T
1 TTTTAAAATAT
689495 TTTT--AA-A-
1 TTTTAAAATAT
689502 TTTTAAAATAT
1 TTTTAAAATAT
689513 TTTTAAAATACT
1 TTTTAAAATA-T
* *
689525 TTTTTAAGT-T
1 TTTTAAAATAT
*
689535 TTTT--TA-AT
1 TTTTAAAATAT
*
689543 TTTAAAAATAT
1 TTTTAAAATAT
689554 TTTTAAAATACT
1 TTTTAAAATA-T
689566 TTTT
1 TTTT
689570 TTAATTTTTG
Statistics
Matches: 75, Mismatches: 10, Indels: 25
0.68 0.09 0.23
Matches are distributed among these distances:
7 4 0.05
8 6 0.08
9 2 0.03
10 12 0.16
11 31 0.41
12 13 0.17
13 7 0.09
ACGTcount: A:0.37, C:0.04, G:0.01, T:0.59
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:698724 original size:15 final size:15
Alignment explanation
Indices: 698704--698736 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
698694 GTTCTGAATT
698704 AGGCGTCATAGATGG
1 AGGCGTCATAGATGG
*
698719 AGGCGTCATAGGTGG
1 AGGCGTCATAGATGG
698734 AGG
1 AGG
698737 TGCCGGTGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.45, T:0.18
Consensus pattern (15 bp):
AGGCGTCATAGATGG
Found at i:706856 original size:168 final size:167
Alignment explanation
Indices: 706571--706907 Score: 566
Period size: 168 Copynumber: 2.0 Consensus size: 167
706561 TAAAAATTAC
*
706571 TCATTTATTAGCATATATTTCATTTCTAATTCATTATACAATTAATACCCTTTTATTTTTGAATT
1 TCATTTATTAGCATATATTTCATTTCCAATTCATTATACAATTAATACCCTTTTATTTTTGAATT
* *
706636 TACACAATTACCCCAAACTTTTGCAATTTTGGCAATTTAATCCTTTAATTAGTTAATCTATCAAA
66 TACACAATTACCCCAAACTTTTGCAATTTTGACAATTTAATCCCTTAATTAGTTAATCTATCAAA
* * *
706701 TTAACTAATTTCCTCAATCACTAATCTATCCAAATAT
131 TAAACTAATTTCCTCAATAAATAATCTATCCAAATAT
*
706738 TCATTTATTAGCATATATTTCATTTCCAATTCATTTTACAATTAATACCCTTTTATTTTTTGAAT
1 TCATTTATTAGCATATATTTCATTTCCAATTCATTATACAATTAATACCCTTTTA-TTTTTGAAT
** *
706803 TTATGCAATTACCCCAAACTTTTGCAATTTTTACAATTTAATCCCTTAATTAGTTAATCTATCAA
65 TTACACAATTACCCCAAACTTTTGCAATTTTGACAATTTAATCCCTTAATTAGTTAATCTATCAA
*
706868 ATAAACTAATTTTCTCAATAAATAATCTATCCAAATAT
130 ATAAACTAATTTCCTCAATAAATAATCTATCCAAATAT
706906 TC
1 TC
706908 TAGGCCTTAA
Statistics
Matches: 158, Mismatches: 11, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
167 53 0.34
168 105 0.66
ACGTcount: A:0.34, C:0.18, G:0.03, T:0.44
Consensus pattern (167 bp):
TCATTTATTAGCATATATTTCATTTCCAATTCATTATACAATTAATACCCTTTTATTTTTGAATT
TACACAATTACCCCAAACTTTTGCAATTTTGACAATTTAATCCCTTAATTAGTTAATCTATCAAA
TAAACTAATTTCCTCAATAAATAATCTATCCAAATAT
Found at i:706904 original size:17 final size:18
Alignment explanation
Indices: 706857--706904 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
706847 CTTAATTAGT
706857 TAATCTAT-CAAATAAAC
1 TAATCTATCCAAATAAAC
*
706874 TAAT-TTTCTC-AATAAA-
1 TAATCTATC-CAAATAAAC
706890 TAATCTATCCAAATA
1 TAATCTATCCAAATA
706905 TTCTAGGCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 8
0.71 0.06 0.23
Matches are distributed among these distances:
16 7 0.28
17 17 0.68
18 1 0.04
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.35
Consensus pattern (18 bp):
TAATCTATCCAAATAAAC
Found at i:709797 original size:30 final size:30
Alignment explanation
Indices: 709761--709828 Score: 95
Period size: 29 Copynumber: 2.3 Consensus size: 30
709751 AGATTCCTGG
*
709761 GATATTTTTTTTAGAA-CTCATCTCGTCAAA
1 GATATTTTTTTCAGAACCT-ATCTCGTCAAA
709791 GATA-TTTTTTCAGAACCTATCTCGTCAAA
1 GATATTTTTTTCAGAACCTATCTCGTCAAA
*
709820 AATATTTTT
1 GATATTTTT
709829 CAGTACACCG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 24 0.71
30 10 0.29
ACGTcount: A:0.31, C:0.16, G:0.09, T:0.44
Consensus pattern (30 bp):
GATATTTTTTTCAGAACCTATCTCGTCAAA
Found at i:716278 original size:13 final size:13
Alignment explanation
Indices: 716260--716294 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
716250 CGCCACCACC
716260 TTTTTTTATAATA
1 TTTTTTTATAATA
*
716273 TTTTTTTAAAATA
1 TTTTTTTATAATA
*
716286 TTATTTTAT
1 TTTTTTTAT
716295 TGGTGGCGCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTTTTATAATA
Found at i:716635 original size:99 final size:99
Alignment explanation
Indices: 716490--716780 Score: 355
Period size: 99 Copynumber: 2.9 Consensus size: 99
716480 AATCACATTA
* *
716490 TAAAAA-AGTTTACATTAATAAAAAATCACAAAACACTAAACTAAACACTAACAATTTATATAAC
1 TAAAAAGAATTTACATTACTAAAAAATCACAAAAC-CTAAACTAAACACTAACAATTTATA-AA-
* *
716554 CTAATCATAAATTACTAACAAAAAAATTATAATTTTT
63 CTAATCATAAATTACTAACAAAATAACTATAATTTTT
*** *
716591 T-TTTA-AA-TTACATTACTAAAAAATCACAAAACCCTAAACTAAACACTAACAATTTATAAATT
1 TAAAAAGAATTTACATTACTAAAAAATCACAAAA-CCTAAACTAAACACTAACAATTTATAAACT
*
716653 AATCACAAATTACTAACAAAATAACTATAACATTTTT
65 AATCATAAATTACTAACAAAATAACTAT-A-ATTTTT
* *
716690 TAAAAAAGAATTTACATTACTAATAAATCACAAAA-C---ACAAAACACTAACAATTTATAAACT
1 T-AAAAAGAATTTACATTACTAAAAAATCACAAAACCTAAACTAAACACTAACAATTTATAAACT
*
716751 AATCATAAATTACTTACAAAATAACTATAA
65 AATCATAAATTACTAACAAAATAACTATAA
716781 AAATATTTTT
Statistics
Matches: 166, Mismatches: 17, Indels: 19
0.82 0.08 0.09
Matches are distributed among these distances:
96 1 0.01
97 27 0.16
98 52 0.31
99 55 0.33
100 3 0.02
101 3 0.02
102 2 0.01
103 23 0.14
ACGTcount: A:0.55, C:0.15, G:0.01, T:0.29
Consensus pattern (99 bp):
TAAAAAGAATTTACATTACTAAAAAATCACAAAACCTAAACTAAACACTAACAATTTATAAACTA
ATCATAAATTACTAACAAAATAACTATAATTTTT
Found at i:716754 original size:98 final size:97
Alignment explanation
Indices: 716490--716781 Score: 319
Period size: 98 Copynumber: 2.9 Consensus size: 97
716480 AATCACATTA
*
716490 TAAAAAAG--TTTACATTAATAAAAAATCACAAAACACTAAACTAAACACTAACAATTTATATAA
1 TAAAAAAGAATTTACATTACTAAAAAATCACAAAACAC---A--AAACACTAACAATTTATA-AA
* *
716553 CCTAATCATAAATTACTAACAAAAAAATTAT-AATTTTT
60 -CTAATCATAAATTACTAACAAAATAACTATAAATTTTT
*** * *
716591 T--TTTA-AA-TTACATTACTAAAAAATCACAAAACCCTAAACTAAACACTAACAATTTATAAAT
1 TAAAAAAGAATTTACATTACTAAAAAATCACAAAA--C---ACAAAACACTAACAATTTATAAAC
*
716652 TAATCACAAATTACTAACAAAATAACTATAACATTTTT
61 TAATCATAAATTACTAACAAAATAACTATAA-ATTTTT
*
716690 TAAAAAAGAATTTACATTACTAATAAATCACAAAACACAAAACACTAACAATTTATAAACTAATC
1 TAAAAAAGAATTTACATTACTAAAAAATCACAAAACACAAAACACTAACAATTTATAAACTAATC
*
716755 ATAAATTACTTACAAAATAACTATAAA
66 ATAAATTACTAACAAAATAACTATAAA
716782 AATATTTTTT
Statistics
Matches: 161, Mismatches: 17, Indels: 30
0.77 0.08 0.14
Matches are distributed among these distances:
97 27 0.17
98 54 0.34
99 49 0.30
101 4 0.02
102 2 0.01
103 23 0.14
104 2 0.01
ACGTcount: A:0.55, C:0.15, G:0.01, T:0.29
Consensus pattern (97 bp):
TAAAAAAGAATTTACATTACTAAAAAATCACAAAACACAAAACACTAACAATTTATAAACTAATC
ATAAATTACTAACAAAATAACTATAAATTTTT
Found at i:716898 original size:60 final size:59
Alignment explanation
Indices: 716766--716901 Score: 148
Period size: 60 Copynumber: 2.3 Consensus size: 59
716756 TAAATTACTT
* ** * *
716766 ACAAAATAACTATA-AAAATATTTTTTTATAAACAAAAAATCACAAAACACAAAATACTA
1 ACAAAATAACTA-ACAAAATAGTTTTACATAAACAAAAAATCACAAAAAACAAAACACTA
* * * * *
716825 ACATTAGTTACTAACAAAATAGTTTTACATTAATAAAAAATCACAAAAAAACAAAACACTA
1 ACA-AAATAACTAACAAAATAGTTTTACATAAACAAAAAATCAC-AAAAAACAAAACACTA
716886 ACAAAATAACTAACAA
1 ACAAAATAACTAACAA
716902 TTTATAACAA
Statistics
Matches: 61, Mismatches: 13, Indels: 5
0.77 0.16 0.06
Matches are distributed among these distances:
59 4 0.07
60 40 0.66
61 17 0.28
ACGTcount: A:0.60, C:0.15, G:0.01, T:0.24
Consensus pattern (59 bp):
ACAAAATAACTAACAAAATAGTTTTACATAAACAAAAAATCACAAAAAACAAAACACTA
Found at i:723025 original size:45 final size:48
Alignment explanation
Indices: 722943--723040 Score: 139
Period size: 51 Copynumber: 2.0 Consensus size: 48
722933 ATTTATTATT
722943 TATATTAATAATCTTATTAAAATTTAATAACAATAACAATAATTATCTACC
1 TATATTAATAATCTTATTAAAATTT-AT-A-AATAACAATAATTATCTACC
*
722994 TATATTAATAATCTTATTAAAA-TT-T-AATAACAATAATTATTTACC
1 TATATTAATAATCTTATTAAAATTTATAAATAACAATAATTATCTACC
723039 TA
1 TA
723041 AAAAAATTCT
Statistics
Matches: 46, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
45 21 0.46
48 1 0.02
50 2 0.04
51 22 0.48
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (48 bp):
TATATTAATAATCTTATTAAAATTTATAAATAACAATAATTATCTACC
Found at i:731377 original size:15 final size:17
Alignment explanation
Indices: 731352--731383 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
731342 GCTAATCTGA
731352 TATCATTTTTCT-TTTT
1 TATCATTTTTCTCTTTT
731368 TATC-TTTTTCTCTTTT
1 TATCATTTTTCTCTTTT
731384 GCCTTGGAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.09, C:0.16, G:0.00, T:0.75
Consensus pattern (17 bp):
TATCATTTTTCTCTTTT
Found at i:733076 original size:19 final size:20
Alignment explanation
Indices: 733052--733089 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
733042 CTTTTATTAT
733052 TATTATTAT-CACACTTTAA
1 TATTATTATGCACACTTTAA
*
733071 TATTATTATGTACACTTTA
1 TATTATTATGCACACTTTA
733090 TTACCTCTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.34, C:0.13, G:0.03, T:0.50
Consensus pattern (20 bp):
TATTATTATGCACACTTTAA
Found at i:736532 original size:50 final size:50
Alignment explanation
Indices: 736453--736635 Score: 249
Period size: 50 Copynumber: 3.7 Consensus size: 50
736443 NNNNNNNNNN
736453 ATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCC
1 ATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCC
* * *
736503 ATGTAAGACCATGTCTAGGACATGACGTTGGCACCAAGATGAGAGGTCCC
1 ATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCC
** * * * **
736553 CCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAACTCCC
1 ATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCC
* * *
736603 ATGTAAGACCATATCTGGGATATGGCATTGGCA
1 ATGTAAGACCATGTCTGGGACATGGCGTTGGCA
736636 GTACAGAAAA
Statistics
Matches: 115, Mismatches: 18, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 115 1.00
ACGTcount: A:0.27, C:0.22, G:0.30, T:0.21
Consensus pattern (50 bp):
ATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCC
Found at i:742590 original size:25 final size:25
Alignment explanation
Indices: 742542--742590 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
742532 CATAATTGAA
* * *
742542 ATGAAATGGATTGATTTTGTATATT
1 ATGAAATAGATTGATTATGAATATT
*
742567 ATGAAATATATTGATTATGAATAT
1 ATGAAATAGATTGATTATGAATAT
742591 ATGTTTATTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (25 bp):
ATGAAATAGATTGATTATGAATATT
Found at i:744440 original size:49 final size:49
Alignment explanation
Indices: 744368--744464 Score: 149
Period size: 49 Copynumber: 2.0 Consensus size: 49
744358 TCTAGAAGGG
* * * *
744368 ATAAATAGTGATAAGAGTGTAGACAGTGGGAGACTAAATTTAGCAATGT
1 ATAAATAGTGATAAGAGTGTAGACAATGGAAGACCAAATTTAGAAATGT
*
744417 ATAAATAGTGATAAGAGTGTAGACAATGGAAGACCAAGTTTAGAAATG
1 ATAAATAGTGATAAGAGTGTAGACAATGGAAGACCAAATTTAGAAATG
744465 CATAGCATAA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
49 43 1.00
ACGTcount: A:0.43, C:0.06, G:0.26, T:0.25
Consensus pattern (49 bp):
ATAAATAGTGATAAGAGTGTAGACAATGGAAGACCAAATTTAGAAATGT
Found at i:749633 original size:17 final size:16
Alignment explanation
Indices: 749613--749654 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 16
749603 AGTATAGAAG
749613 ATTTT-GTTTATCATTTT
1 ATTTTAGTTTAT--TTTT
749630 ATTTCTAGTTTATTTTT
1 ATTT-TAGTTTATTTTT
749647 ATTTTAGT
1 ATTTTAGT
749655 GGTGGGAGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 4 0.17
17 12 0.52
18 1 0.04
19 6 0.26
ACGTcount: A:0.19, C:0.05, G:0.07, T:0.69
Consensus pattern (16 bp):
ATTTTAGTTTATTTTT
Found at i:754736 original size:15 final size:15
Alignment explanation
Indices: 754716--754747 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
754706 ACCCATTAGG
754716 GCACATAATCAGGAA
1 GCACATAATCAGGAA
754731 GCACATAATCAGGAA
1 GCACATAATCAGGAA
754746 GC
1 GC
754748 TTCGGATAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (15 bp):
GCACATAATCAGGAA
Found at i:757296 original size:9 final size:9
Alignment explanation
Indices: 757252--757296 Score: 58
Period size: 9 Copynumber: 5.1 Consensus size: 9
757242 CATTTAAATA
757252 AATAATTAT
1 AATAATTAT
757261 AATAATTAT
1 AATAATTAT
757270 AATAATTAT
1 AATAATTAT
757279 -ATACA-TAT
1 AATA-ATTAT
*
757287 AATATTTAT
1 AATAATTAT
757296 A
1 A
757297 TATATCTTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
8 6 0.19
9 26 0.81
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (9 bp):
AATAATTAT
Found at i:759253 original size:16 final size:18
Alignment explanation
Indices: 759221--759253 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
759211 CATATATTTA
759221 TATATATTTTTATAAATT
1 TATATATTTTTATAAATT
759239 TATAT-TTTTTA-AAAT
1 TATATATTTTTATAAAT
759254 AATAATAACC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 6 0.40
18 5 0.33
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TATATATTTTTATAAATT
Found at i:769790 original size:53 final size:53
Alignment explanation
Indices: 769727--769833 Score: 214
Period size: 53 Copynumber: 2.0 Consensus size: 53
769717 TGTGACTCTC
769727 TTTCCAACCCTCGTCACGATGTTGAGGAACCTACGTCGCGACATGACCCTTGT
1 TTTCCAACCCTCGTCACGATGTTGAGGAACCTACGTCGCGACATGACCCTTGT
769780 TTTCCAACCCTCGTCACGATGTTGAGGAACCTACGTCGCGACATGACCCTTGT
1 TTTCCAACCCTCGTCACGATGTTGAGGAACCTACGTCGCGACATGACCCTTGT
769833 T
1 T
769834 CTATACAAAG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.21, C:0.32, G:0.21, T:0.27
Consensus pattern (53 bp):
TTTCCAACCCTCGTCACGATGTTGAGGAACCTACGTCGCGACATGACCCTTGT
Found at i:770474 original size:20 final size:20
Alignment explanation
Indices: 770449--770520 Score: 90
Period size: 20 Copynumber: 3.5 Consensus size: 20
770439 ACCGAATCTA
770449 AAATCATAATACTCAAATCC
1 AAATCATAATACTCAAATCC
* *
770469 AAATCATAATACCCAATCATCTA
1 AAATCATAATACTCAA--ATC-C
*
770492 AAATCATAATACTCATATCC
1 AAATCATAATACTCAAATCC
770512 AAATCATAA
1 AAATCATAA
770521 CCATGAATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
20 24 0.55
21 3 0.07
22 3 0.07
23 14 0.32
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (20 bp):
AAATCATAATACTCAAATCC
Found at i:770606 original size:28 final size:28
Alignment explanation
Indices: 770574--770629 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
770564 TCTCGAAACA
770574 TAATTTTATAAATATTAACTAAATTATT
1 TAATTTTATAAATATTAACTAAATTATT
770602 TAATTTTATAAATATTAACTAAATTATT
1 TAATTTTATAAATATTAACTAAATTATT
770630 CAAACTCATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (28 bp):
TAATTTTATAAATATTAACTAAATTATT
Found at i:770658 original size:5 final size:5
Alignment explanation
Indices: 770648--770677 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
770638 TCCAAAACTC
770648 ATAAA ATAAA ATAAA ATAAA ATAAA TATAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA -ATAA
770678 CTAGTCATAG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 20 0.83
6 4 0.17
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (5 bp):
ATAAA
Found at i:776290 original size:34 final size:34
Alignment explanation
Indices: 776247--776347 Score: 184
Period size: 34 Copynumber: 3.0 Consensus size: 34
776237 ATGTCAGAAC
*
776247 TCCATGTAACCTCACAATCTCTAACACATATAAT
1 TCCATGTAACCTCACAATCTCTGACACATATAAT
776281 TCCATGTAACCTCACAATCTCTGACACATATAAT
1 TCCATGTAACCTCACAATCTCTGACACATATAAT
*
776315 TCCATGTAATCTCACAATCTCTGACACATATAA
1 TCCATGTAACCTCACAATCTCTGACACATATAA
776348 ATCATAACAT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 65 1.00
ACGTcount: A:0.37, C:0.29, G:0.05, T:0.30
Consensus pattern (34 bp):
TCCATGTAACCTCACAATCTCTGACACATATAAT
Found at i:781388 original size:23 final size:23
Alignment explanation
Indices: 781362--781436 Score: 123
Period size: 23 Copynumber: 3.3 Consensus size: 23
781352 ATAAGTGCAA
*
781362 CACTGATATGTAGCCGAAGCTAC
1 CACTGAAATGTAGCCGAAGCTAC
*
781385 CACTGAAATGTAGCCGAAGCTAA
1 CACTGAAATGTAGCCGAAGCTAC
*
781408 CACTGAAACGTAGCCGAAGCTAC
1 CACTGAAATGTAGCCGAAGCTAC
781431 CACTGA
1 CACTGA
781437 TCAATAACAC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.35, C:0.27, G:0.21, T:0.17
Consensus pattern (23 bp):
CACTGAAATGTAGCCGAAGCTAC
Found at i:794170 original size:2 final size:2
Alignment explanation
Indices: 794163--794188 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
794153 ATATCAAACT
794163 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
794189 AGTATAACGC
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):
TA
Found at i:796009 original size:27 final size:27
Alignment explanation
Indices: 795979--796034 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
795969 ATAAAAAATT
*
795979 TATTTAAAATTAAAAAAATTAGAAAAA
1 TATTAAAAATTAAAAAAATTAGAAAAA
* ** *
796006 TATTAAAAATTCATTAAATTATAAAAA
1 TATTAAAAATTAAAAAAATTAGAAAAA
796033 TA
1 TA
796035 GATAAATCCC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (27 bp):
TATTAAAAATTAAAAAAATTAGAAAAA
Found at i:796354 original size:29 final size:30
Alignment explanation
Indices: 796317--796378 Score: 72
Period size: 31 Copynumber: 2.1 Consensus size: 30
796307 GTTTCACGTG
*
796317 TATAATTA-CACCAAATTAAAATTCATGTA
1 TATAATTACCACCAAATCAAAATTCATGTA
* * *
796346 TATAGTTACGCACTAAATCAAAATTTATGTA
1 TATAATTAC-CACCAAATCAAAATTCATGTA
796377 TA
1 TA
796379 ATTTTAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 7 0.26
31 20 0.74
ACGTcount: A:0.45, C:0.13, G:0.06, T:0.35
Consensus pattern (30 bp):
TATAATTACCACCAAATCAAAATTCATGTA
Found at i:797025 original size:31 final size:31
Alignment explanation
Indices: 796987--797049 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
796977 TTTTTAATGC
* *
796987 AATAGTTGAAACAGTAATTTGTTGTATAAAG
1 AATAGTTGAAACAGCAAATTGTTGTATAAAG
*
797018 AATAGTTGAAAGAGCAAATTGTTGTATAAAG
1 AATAGTTGAAACAGCAAATTGTTGTATAAAG
797049 A
1 A
797050 GATTTAAGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.44, C:0.03, G:0.21, T:0.32
Consensus pattern (31 bp):
AATAGTTGAAACAGCAAATTGTTGTATAAAG
Found at i:797103 original size:9 final size:10
Alignment explanation
Indices: 797088--797122 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
797078 AGTGATTGAT
*
797088 TTTTTTTTAA
1 TTTTTTATAA
*
797098 TTTTTTATAT
1 TTTTTTATAA
797108 TTTTTTATAA
1 TTTTTTATAA
797118 TTTTT
1 TTTTT
797123 GAATTTCTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTTTTATAA
Found at i:797128 original size:19 final size:20
Alignment explanation
Indices: 797083--797133 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 20
797073 AATGTAGTGA
797083 TTGAT-TTTTTTT-TAATTT
1 TTGATATTTTTTTATAATTT
*
797101 TTTATATTTTTTTATAATTT
1 TTGATATTTTTTTATAATTT
*
797121 TTGA-ATTTCTTTA
1 TTGATATTTTTTTA
797134 AAAAATTAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 4 0.14
19 15 0.54
20 9 0.32
ACGTcount: A:0.22, C:0.02, G:0.04, T:0.73
Consensus pattern (20 bp):
TTGATATTTTTTTATAATTT
Found at i:809824 original size:21 final size:21
Alignment explanation
Indices: 809800--809847 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
809790 AGTAACGGTA
*
809800 AGATTAGTTAATGTAGCGATG
1 AGATTAGATAATGTAGCGATG
* *
809821 AGATTAGATATTGTAGCGGTG
1 AGATTAGATAATGTAGCGATG
809842 AGATTA
1 AGATTA
809848 AAAATAATGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.33, C:0.04, G:0.29, T:0.33
Consensus pattern (21 bp):
AGATTAGATAATGTAGCGATG
Found at i:836835 original size:12 final size:12
Alignment explanation
Indices: 836806--836892 Score: 70
Period size: 12 Copynumber: 7.2 Consensus size: 12
836796 AAAAATGAAA
*
836806 TGATTAAAAACT
1 TGATGAAAAACT
* *
836818 AGATGAAAAATT
1 TGATGAAAAACT
*
836830 TTATGAAAAGACT
1 TGATGAAAA-ACT
836843 TGATGAAAAACT
1 TGATGAAAAACT
836855 T--TGAAAAGAACT
1 TGATG-AAA-AACT
* *
836867 TGCTGCAAAACT
1 TGATGAAAAACT
*
836879 TGATAAAAAACT
1 TGATGAAAAACT
836891 TG
1 TG
836893 GTAATTAAAA
Statistics
Matches: 59, Mismatches: 11, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
10 2 0.03
11 3 0.05
12 40 0.68
13 12 0.20
14 2 0.03
ACGTcount: A:0.48, C:0.09, G:0.15, T:0.28
Consensus pattern (12 bp):
TGATGAAAAACT
Found at i:838380 original size:21 final size:21
Alignment explanation
Indices: 838356--838416 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
838346 AAGAGGGGGG
*
838356 AAACCAGCAAAAACGAGGGAC
1 AAACCAGCAAGAACGAGGGAC
* * * *
838377 AAACTAACAAGAACAAGGGAG
1 AAACCAGCAAGAACGAGGGAC
*
838398 AAACCAGCAAGAATGAGGG
1 AAACCAGCAAGAACGAGGG
838417 GAGAAACTGC
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.52, C:0.18, G:0.26, T:0.03
Consensus pattern (21 bp):
AAACCAGCAAGAACGAGGGAC
Found at i:838421 original size:22 final size:21
Alignment explanation
Indices: 838343--838423 Score: 65
Period size: 21 Copynumber: 3.8 Consensus size: 21
838333 GAACAAAGCA
*
838343 AAAAAGAGGGGGGAAACCAGC
1 AAAAAGAGGGGAGAAACCAGC
* * *
838364 AAAAACGA-GGGACAAACTAAC
1 AAAAA-GAGGGGAGAAACCAGC
* * *
838385 AAGAACAAGGGAGAAACCAGC
1 AAAAAGAGGGGAGAAACCAGC
*
838406 AAGAATGAGGGGAGAAAC
1 AA-AAAGAGGGGAGAAAC
838424 TGCTGTTTTG
Statistics
Matches: 44, Mismatches: 13, Indels: 5
0.71 0.21 0.08
Matches are distributed among these distances:
20 1 0.02
21 30 0.68
22 13 0.30
ACGTcount: A:0.52, C:0.15, G:0.31, T:0.02
Consensus pattern (21 bp):
AAAAAGAGGGGAGAAACCAGC
Found at i:849955 original size:41 final size:41
Alignment explanation
Indices: 849891--849978 Score: 131
Period size: 41 Copynumber: 2.1 Consensus size: 41
849881 AACAAGTCTT
* **
849891 TTGGCTTGTGAATGGATTACTTAGAGTCTGAGTAAGCTTGAA
1 TTGG-TTGTGAATGGATTACTTAGAGCCCAAGTAAGCTTGAA
*
849933 TTGGTTGTGAATGGATTCCTTAGAGCCCAAGTAAGCTTGAA
1 TTGGTTGTGAATGGATTACTTAGAGCCCAAGTAAGCTTGAA
849974 TTGGT
1 TTGGT
849979 AAACTTGTTG
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
41 38 0.90
42 4 0.10
ACGTcount: A:0.25, C:0.11, G:0.28, T:0.35
Consensus pattern (41 bp):
TTGGTTGTGAATGGATTACTTAGAGCCCAAGTAAGCTTGAA
Found at i:870390 original size:4 final size:4
Alignment explanation
Indices: 870383--870495 Score: 77
Period size: 4 Copynumber: 26.0 Consensus size: 4
870373 TTTCTCCTTC
* *
870383 CTTT CTTT CCTTT -TTT TTTT CTTT CTTCT CCTTC CTTT CTTT CCTTT
1 CTTT CTTT -CTTT CTTT CTTT CTTT CTT-T -CTTT CTTT CTTT -CTTT
*
870430 -TTT TTTT CTTT CTTT CTTT CTGTTT CGTTT CGTTT CGTTT CGTTT CGTTT
1 CTTT CTTT CTTT CTTT CTTT C--TTT C-TTT C-TTT C-TTT C-TTT C-TTT
*
870480 CTAT CTTT CTTT CTTT
1 CTTT CTTT CTTT CTTT
870496 TTATTTATTC
Statistics
Matches: 95, Mismatches: 6, Indels: 16
0.81 0.05 0.14
Matches are distributed among these distances:
3 6 0.06
4 48 0.51
5 34 0.36
6 7 0.07
ACGTcount: A:0.01, C:0.24, G:0.05, T:0.70
Consensus pattern (4 bp):
CTTT
Found at i:870447 original size:38 final size:34
Alignment explanation
Indices: 870374--870443 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
870364 GGCCGTGGCT
870374 TTCTCCTTCCTTTCTTTCCTTTTTTTTTTCTTTC
1 TTCTCCTTCCTTTCTTTCCTTTTTTTTTTCTTTC
870408 TTCTCCTTCCTTTCTTTCCTTTTTTTTTTCTTTC
1 TTCTCCTTCCTTTCTTTCCTTTTTTTTTTCTTTC
870442 TT
1 TT
870444 TCTTTCTGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (34 bp):
TTCTCCTTCCTTTCTTTCCTTTTTTTTTTCTTTC
Found at i:870461 original size:5 final size:5
Alignment explanation
Indices: 870434--870480 Score: 64
Period size: 5 Copynumber: 9.8 Consensus size: 5
870424 TCCTTTTTTT
870434 TTTC- TTTC- TTTC- TTTCTG TTTCG TTTCG TTTCG TTTCG TTTCG TTTC
1 TTTCG TTTCG TTTCG TTTC-G TTTCG TTTCG TTTCG TTTCG TTTCG TTTC
870481 TATCTTTCTT
Statistics
Matches: 41, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
4 12 0.29
5 25 0.61
6 4 0.10
ACGTcount: A:0.00, C:0.21, G:0.13, T:0.66
Consensus pattern (5 bp):
TTTCG
Found at i:870538 original size:5 final size:5
Alignment explanation
Indices: 870530--870568 Score: 78
Period size: 5 Copynumber: 7.8 Consensus size: 5
870520 TTTATTATGT
870530 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATA
870569 TACTTAATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TATAA
Found at i:871925 original size:20 final size:20
Alignment explanation
Indices: 871900--871951 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 20
871890 TTTAAAATAC
*
871900 TTTAAAAATATTTTTTTATT
1 TTTAAAAATATTTTTGTATT
*
871920 TTTAAAATATTATTTTTGTGTT
1 TTTAAAA-A-TATTTTTGTATT
871942 TATTAAAAAT
1 T-TTAAAAAT
871952 GGGGCCGGGC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 7 0.26
21 2 0.07
22 12 0.44
23 6 0.22
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.60
Consensus pattern (20 bp):
TTTAAAAATATTTTTGTATT
Found at i:874044 original size:2 final size:2
Alignment explanation
Indices: 874037--874061 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
874027 TGTAAGGTGT
874037 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
874062 TCATATTTTT
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:874942 original size:22 final size:22
Alignment explanation
Indices: 874917--874960 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
874907 CATACAAATC
*
874917 ACATTCTCTGTTACCAATTTAG
1 ACATTCTCTCTTACCAATTTAG
874939 ACATTCTCTCTTACCAATTTAG
1 ACATTCTCTCTTACCAATTTAG
874961 TGTTTTAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.27, C:0.25, G:0.07, T:0.41
Consensus pattern (22 bp):
ACATTCTCTCTTACCAATTTAG
Found at i:875425 original size:23 final size:23
Alignment explanation
Indices: 875393--875436 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
875383 ACTACCATTT
875393 TCTAAATAAAATAATAATAAATA
1 TCTAAATAAAATAATAATAAATA
* *
875416 TCTAAGTAAAATATTAATAAA
1 TCTAAATAAAATAATAATAAA
875437 ATAATATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (23 bp):
TCTAAATAAAATAATAATAAATA
Found at i:875429 original size:13 final size:11
Alignment explanation
Indices: 875397--875439 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
875387 CCATTTTCTA
*
875397 AATAAAATAAT
1 AATAAAATATT
875408 AAT-AAATATCT
1 AATAAAATAT-T
875419 AAGTAAAATATT
1 AA-TAAAATATT
875431 AATAAAATA
1 AATAAAATA
875440 ATATTTAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 5 0.18
11 13 0.46
12 4 0.14
13 6 0.21
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (11 bp):
AATAAAATATT
Found at i:878621 original size:189 final size:189
Alignment explanation
Indices: 878282--878664 Score: 601
Period size: 189 Copynumber: 2.0 Consensus size: 189
878272 CGGCAGGGTG
* *
878282 GCTGCACCAATCACTAGACCAAGTGAGCAAGCACAAGGACTGGTAGTATCCGAGTCTGAAAACCC
1 GCTGCACCAATCACTAGACCAAGTGAGCAAGCACAAGGACAGGCAGTATCCGAGTCTGAAAACCC
* *
878347 AGCATCATTGCCTGATTCTGTAGAGAGAGTTCAGTGTGAAACAAAGGTTTCAGAAGAATCTGAAA
66 AGCATCATTGCCTGATTCTGTAGAAAGAGTTCAGTGTGAAACAAAGGTTTCAGAAGAATCAGAAA
*
878412 ATGCGACTAGTTCAGTAAATGAAGTTTCTGGTTC-GCAGAAGGATTTGCCTGAGGAGAAT
131 ATGCGACGAGTTCAGTAAATGAAGTTTCTGGTTCAG-AGAAGGATTTGCCTGAGGAGAAT
* * *
878471 GCTGCATCAATCACTAGACCAAGTGAGCAAGCACAAGGGCAGGCAGTATCTGAGTCTGAAAACCC
1 GCTGCACCAATCACTAGACCAAGTGAGCAAGCACAAGGACAGGCAGTATCCGAGTCTGAAAACCC
* * *
878536 AGCATCATTGCCTGATTGTGTAGATAAG-GTTCAGTGTGAAACAAAGTTTTCAGGAGAATCCAG-
66 AGCATCATTGCCTGATTCTGTAGA-AAGAGTTCAGTGTGAAACAAAGGTTTCAGAAGAAT-CAGA
* *
878599 AATTGCGACGAGTTCGGTAAATGAAGTTTCTGGTTCAGAGAAGGATTTGCCTGAGGAGAAT
129 AAATGCGACGAGTTCAGTAAATGAAGTTTCTGGTTCAGAGAAGGATTTGCCTGAGGAGAAT
878660 GCTGC
1 GCTGC
878665 TATTTCTGAA
Statistics
Matches: 178, Mismatches: 13, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
189 173 0.97
190 5 0.03
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.23
Consensus pattern (189 bp):
GCTGCACCAATCACTAGACCAAGTGAGCAAGCACAAGGACAGGCAGTATCCGAGTCTGAAAACCC
AGCATCATTGCCTGATTCTGTAGAAAGAGTTCAGTGTGAAACAAAGGTTTCAGAAGAATCAGAAA
ATGCGACGAGTTCAGTAAATGAAGTTTCTGGTTCAGAGAAGGATTTGCCTGAGGAGAAT
Found at i:881691 original size:113 final size:113
Alignment explanation
Indices: 881509--881735 Score: 436
Period size: 113 Copynumber: 2.0 Consensus size: 113
881499 TTTTTTGCAG
881509 GCATTTGAATATTCAGAGGCTTTACTATAAGCAAGCTTCTTGTTGGTGTTCAAATTTTGTGCTTG
1 GCATTTGAATATTCAGAGGCTTTACTATAAGCAAGCTTCTTGTTGGTGTTCAAATTTTGTGCTTG
881574 AAAAGACCAGATCGATCATCCATGCCATCAATTGCTGGGATCAATTTT
66 AAAAGACCAGATCGATCATCCATGCCATCAATTGCTGGGATCAATTTT
* *
881622 GCATTTGAATATTCAGAGGCTTTACTATGAGTAAGCTTCTTGTTGGTGTTCAAATTTTGTGCTTG
1 GCATTTGAATATTCAGAGGCTTTACTATAAGCAAGCTTCTTGTTGGTGTTCAAATTTTGTGCTTG
881687 AAAAGACCAGATCGATCATCCATGCCATCAATTGCTGGGATCAATTTT
66 AAAAGACCAGATCGATCATCCATGCCATCAATTGCTGGGATCAATTTT
881735 G
1 G
881736 AGGAAACGGT
Statistics
Matches: 112, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
113 112 1.00
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (113 bp):
GCATTTGAATATTCAGAGGCTTTACTATAAGCAAGCTTCTTGTTGGTGTTCAAATTTTGTGCTTG
AAAAGACCAGATCGATCATCCATGCCATCAATTGCTGGGATCAATTTT
Found at i:886670 original size:32 final size:32
Alignment explanation
Indices: 886634--886697 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
886624 CAAATACTTT
886634 TCTAGGTTATTTGAGTATCTCACTCCCATATC
1 TCTAGGTTATTTGAGTATCTCACTCCCATATC
*
886666 TCTAGGTTATTTGAGTATCTCACTGCCATATC
1 TCTAGGTTATTTGAGTATCTCACTCCCATATC
886698 GTTGGATAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.22, C:0.23, G:0.14, T:0.41
Consensus pattern (32 bp):
TCTAGGTTATTTGAGTATCTCACTCCCATATC
Found at i:886988 original size:17 final size:17
Alignment explanation
Indices: 886966--886999 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
886956 TAAACCTTCA
886966 TTGCTAATCAGAAAGAG
1 TTGCTAATCAGAAAGAG
886983 TTGCTAATCAGAAAGAG
1 TTGCTAATCAGAAAGAG
887000 AAAATGGCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.12, G:0.24, T:0.24
Consensus pattern (17 bp):
TTGCTAATCAGAAAGAG
Found at i:888912 original size:14 final size:14
Alignment explanation
Indices: 888876--888902 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
888866 TTTTAATTTA
888876 AATATACTAATCTG
1 AATATACTAATCTG
888890 AATATACTAATCT
1 AATATACTAATCT
888903 AATTTAACTA
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:0.15, G:0.04, T:0.37
Consensus pattern (14 bp):
AATATACTAATCTG
Found at i:890211 original size:10 final size:10
Alignment explanation
Indices: 890196--890223 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
890186 TTTAACTCAA
890196 AATCGACAAG
1 AATCGACAAG
890206 AATCGACAAG
1 AATCGACAAG
890216 AATCGACA
1 AATCGACA
890224 TCCTCACTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.50, C:0.21, G:0.18, T:0.11
Consensus pattern (10 bp):
AATCGACAAG
Found at i:892384 original size:49 final size:49
Alignment explanation
Indices: 892312--892413 Score: 186
Period size: 49 Copynumber: 2.1 Consensus size: 49
892302 AATTAATCAT
*
892312 TCAAAAATGTATTAAAAATGTGATTAAAATATGTTAGTTTTATAGCTTA
1 TCAAAAATGTATTAAAAATGTGATTAAAATATGTTACTTTTATAGCTTA
*
892361 TCAAAAATGTATTAAGAATGTGATTAAAATATGTTACTTTTATAGCTTA
1 TCAAAAATGTATTAAAAATGTGATTAAAATATGTTACTTTTATAGCTTA
892410 TCAA
1 TCAA
892414 TAAACCACAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.42, C:0.06, G:0.12, T:0.40
Consensus pattern (49 bp):
TCAAAAATGTATTAAAAATGTGATTAAAATATGTTACTTTTATAGCTTA
Found at i:894092 original size:22 final size:23
Alignment explanation
Indices: 894067--894110 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
894057 AGTACTGTAA
*
894067 AATTTTTTA-ATGAATTTTAAAT
1 AATTTATTATATGAATTTTAAAT
894089 AATTTATTATATGAATTTTAAA
1 AATTTATTATATGAATTTTAAA
894111 CAAATCATCC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (23 bp):
AATTTATTATATGAATTTTAAAT
Found at i:909966 original size:18 final size:18
Alignment explanation
Indices: 909945--909982 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
909935 AGGGAAAAGG
*
909945 AGAAAAGAATGAAAAA-AA
1 AGAAAA-AAAGAAAAAGAA
909963 AGAAAAAAAGAAAAAGAA
1 AGAAAAAAAGAAAAAGAA
909981 AG
1 AG
909983 TTTAAAGAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (18 bp):
AGAAAAAAAGAAAAAGAA
Found at i:910586 original size:10 final size:10
Alignment explanation
Indices: 910571--910687 Score: 70
Period size: 10 Copynumber: 12.4 Consensus size: 10
910561 CATGTGGCCA
910571 AAAAAATTAT
1 AAAAAATTAT
910581 AAAAAA-TAT
1 AAAAAATTAT
*
910590 AAATAA--AT
1 AAAAAATTAT
**
910598 -AAAAGGTAT
1 AAAAAATTAT
910607 --AAAATTAT
1 AAAAAATTAT
* *
910615 TAAAATTTA-
1 AAAAAATTAT
*
910624 ATAAAAACTAT
1 A-AAAAATTAT
*
910635 AAAAAATTGT
1 AAAAAATTAT
*
910645 AAAAAATTGT
1 AAAAAATTAT
**
910655 AAAATTTTAT
1 AAAAAATTAT
*
910665 -AAAAATCAT
1 AAAAAATTAT
910674 AAAAAATTAT
1 AAAAAATTAT
910684 AAAA
1 AAAA
910688 TGTGTAACAT
Statistics
Matches: 82, Mismatches: 18, Indels: 14
0.72 0.16 0.12
Matches are distributed among these distances:
7 3 0.04
8 8 0.10
9 16 0.20
10 54 0.66
11 1 0.01
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.30
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:910676 original size:19 final size:19
Alignment explanation
Indices: 910615--910687 Score: 51
Period size: 19 Copynumber: 3.8 Consensus size: 19
910605 ATAAAATTAT
*
910615 TAAAATTTAATAAAAA-CTA
1 TAAAATTTTATAAAAATC-A
* **
910634 TAAAAAATTGTA-AAAAATTG
1 T--AAAATTTTATAAAAATCA
910654 TAAAATTTTATAAAAATCA
1 TAAAATTTTATAAAAATCA
**
910673 TAAAAAATTATAAAA
1 TAAAATTTTATAAAA
910688 TGTGTAACAT
Statistics
Matches: 41, Mismatches: 9, Indels: 8
0.71 0.16 0.14
Matches are distributed among these distances:
18 8 0.20
19 20 0.49
20 6 0.15
21 7 0.17
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.32
Consensus pattern (19 bp):
TAAAATTTTATAAAAATCA
Found at i:910720 original size:10 final size:10
Alignment explanation
Indices: 910705--910822 Score: 63
Period size: 10 Copynumber: 12.4 Consensus size: 10
910695 CATGTGGCCA
910705 AAAAAATTAT
1 AAAAAATTAT
910715 AAAAAA-TAT
1 AAAAAATTAT
*
910724 AAATAA--AT
1 AAAAAATTAT
**
910732 -AAAAGGTAT
1 AAAAAATTAT
910741 --AAAATTAT
1 AAAAAATTAT
* *
910749 TAAAATTTA-
1 AAAAAATTAT
*
910758 ATAAAAACTAT
1 A-AAAAATTAT
*
910769 AAAAAATTGT
1 AAAAAATTAT
*
910779 AAAAAATTGT
1 AAAAAATTAT
**
910789 AAAATTTTAT
1 AAAAAATTAT
*
910799 -AAAAATCAT
1 AAAAAATTAT
910808 AAAAAAATTAT
1 -AAAAAATTAT
910819 AAAA
1 AAAA
910823 TGCATCAAAA
Statistics
Matches: 82, Mismatches: 18, Indels: 16
0.71 0.16 0.14
Matches are distributed among these distances:
7 3 0.04
8 8 0.10
9 16 0.20
10 46 0.56
11 9 0.11
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.30
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:910795 original size:134 final size:135
Alignment explanation
Indices: 910555--910824 Score: 533
Period size: 134 Copynumber: 2.0 Consensus size: 135
910545 AGCTTTAACA
910555 GTGTAACATGTGGCCAAAAAAATTATAAAAAATATAAATAAATAAAAGGTATAAAATTATTAAAA
1 GTGTAACATGTGGCCAAAAAAATTATAAAAAATATAAATAAATAAAAGGTATAAAATTATTAAAA
910620 TTTAATAAAAACTATAAAAAATTGTAAAAAATTGTAAAATTTTATAAAAATCAT-AAAAAATTAT
66 TTTAATAAAAACTATAAAAAATTGTAAAAAATTGTAAAATTTTATAAAAATCATAAAAAAATTAT
910684 AAAAT
131 AAAAT
910689 GTGTAACATGTGGCCAAAAAAATTATAAAAAATATAAATAAATAAAAGGTATAAAATTATTAAAA
1 GTGTAACATGTGGCCAAAAAAATTATAAAAAATATAAATAAATAAAAGGTATAAAATTATTAAAA
910754 TTTAATAAAAACTATAAAAAATTGTAAAAAATTGTAAAATTTTATAAAAATCATAAAAAAATTAT
66 TTTAATAAAAACTATAAAAAATTGTAAAAAATTGTAAAATTTTATAAAAATCATAAAAAAATTAT
910819 AAAAT
131 AAAAT
910824 G
1 G
910825 CATCAAAAAG
Statistics
Matches: 135, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
134 119 0.88
135 16 0.12
ACGTcount: A:0.60, C:0.04, G:0.07, T:0.30
Consensus pattern (135 bp):
GTGTAACATGTGGCCAAAAAAATTATAAAAAATATAAATAAATAAAAGGTATAAAATTATTAAAA
TTTAATAAAAACTATAAAAAATTGTAAAAAATTGTAAAATTTTATAAAAATCATAAAAAAATTAT
AAAAT
Found at i:911324 original size:28 final size:26
Alignment explanation
Indices: 911280--911332 Score: 63
Period size: 28 Copynumber: 2.0 Consensus size: 26
911270 GGAGAATGGA
*
911280 AAATTTGCAAAGATAAGGATGAAAAGTC
1 AAATTTGAAAAGATAAGG--GAAAAGTC
911308 AAATTTGTAAAAG-TAAGGGAAAAGT
1 AAATTTG-AAAAGATAAGGGAAAAGT
911333 GAGGAAATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 7 0.30
28 12 0.52
29 4 0.17
ACGTcount: A:0.51, C:0.04, G:0.23, T:0.23
Consensus pattern (26 bp):
AAATTTGAAAAGATAAGGGAAAAGTC
Found at i:917927 original size:20 final size:20
Alignment explanation
Indices: 917885--917927 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
917875 CCTACCCACC
*
917885 TCATGGCTGAGCAACTGTTT
1 TCATGGCTGAGCAACTGTCT
*
917905 TCATGGCTGAAGC-ATTGTCT
1 TCATGGCTG-AGCAACTGTCT
917925 TCA
1 TCA
917928 ATCTTTGCGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 17 0.85
21 3 0.15
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.35
Consensus pattern (20 bp):
TCATGGCTGAGCAACTGTCT
Done.