Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D03
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: 50986338
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 218898 characters in sequence are not A, C, G, or T
File 20 of 170
Found at i:5298801 original size:25 final size:25
Alignment explanation
Indices: 5298737--5298794 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
5298727 CGAACACACC
* * *
5298737 ATAGCTCGTAAGAGCATCCCGTTAT
1 ATAGCTCTTATGAGCATCCCGATAT
*
5298762 TTAGCTCTTATGAGCATCCCGATAT
1 ATAGCTCTTATGAGCATCCCGATAT
*
5298787 ATGGCTCT
1 ATAGCTCT
5298795 CTTGAGCTTC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (25 bp):
ATAGCTCTTATGAGCATCCCGATAT
Found at i:5298859 original size:25 final size:25
Alignment explanation
Indices: 5298765--5298954 Score: 104
Period size: 25 Copynumber: 7.7 Consensus size: 25
5298755 CCGTTATTTA
* *
5298765 GCTCTTATGAGCATCCCGAT-ATATG
1 GCTCTCATGAGCTTCCCGATAAT-TG
* * * *
5298790 GCTCTCTTGAGCTTCCTGCTATTTG
1 GCTCTCATGAGCTTCCCGATAATTG
* * **
5298815 GCTTTCACGAGCTTTTCGATAATTG
1 GCTCTCATGAGCTTCCCGATAATTG
*
5298840 GTTCTCATGAGCTTCCCGATTAA-TG
1 GCTCTCATGAGCTTCCCGA-TAATTG
* *
5298865 ACTCTC-TGAAGCTTCCAGAT-ATTG
1 GCTCTCATG-AGCTTCCCGATAATTG
* ** *
5298889 GCTCGCATGAGCTTCCTAATTA-TG
1 GCTCTCATGAGCTTCCCGATAATTG
* * * *
5298913 GCTTTTATGAGCTTTCCGTTACA-TG
1 GCTCTCATGAGCTTCCCGATA-ATTG
*
5298938 GCTCACATGAGCTTCCC
1 GCTCTCATGAGCTTCCC
5298955 ATTTCATGGC
Statistics
Matches: 120, Mismatches: 38, Indels: 14
0.70 0.22 0.08
Matches are distributed among these distances:
23 1 0.01
24 33 0.28
25 82 0.68
26 4 0.03
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.36
Consensus pattern (25 bp):
GCTCTCATGAGCTTCCCGATAATTG
Found at i:5298962 original size:25 final size:25
Alignment explanation
Indices: 5298887--5298966 Score: 72
Period size: 25 Copynumber: 3.2 Consensus size: 25
5298877 TTCCAGATAT
* * *
5298887 TGGCTCGCATGAGCTTCCTAATT-A
1 TGGCTCACATGAGCTTCCCATTTCA
*** * * *
5298911 TGGCTTTTATGAGCTTTCCGTTACA
1 TGGCTCACATGAGCTTCCCATTTCA
5298936 TGGCTCACATGAGCTTCCCATTTCA
1 TGGCTCACATGAGCTTCCCATTTCA
5298961 TGGCTC
1 TGGCTC
5298967 GAAAAAGCTT
Statistics
Matches: 41, Mismatches: 14, Indels: 1
0.73 0.25 0.02
Matches are distributed among these distances:
24 15 0.37
25 26 0.63
ACGTcount: A:0.17, C:0.26, G:0.20, T:0.36
Consensus pattern (25 bp):
TGGCTCACATGAGCTTCCCATTTCA
Found at i:5302154 original size:50 final size:50
Alignment explanation
Indices: 5302049--5302173 Score: 142
Period size: 50 Copynumber: 2.5 Consensus size: 50
5302039 TTATTGAGGT
* * * *
5302049 TATGAGAGGTCCCACGTAAGACCATGTCTAGGACATGACGTTGGTACTGA
1 TATGAGAGGTCCCACGTAAGACCATGTCTAGGACATGACATGGGCACCGA
* * * *
5302099 GATGAGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGA
1 TATGAGAGGTCCCACGTAAGACCATGTCTAGGACATGACATGGGCACCGA
** * *
5302149 TATGAGAACTCTCATGTAAGACCAT
1 TATGAGAGGTCCCACGTAAGACCAT
5302174 ATTTGGGATA
Statistics
Matches: 61, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
50 61 1.00
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22
Consensus pattern (50 bp):
TATGAGAGGTCCCACGTAAGACCATGTCTAGGACATGACATGGGCACCGA
Found at i:5302471 original size:20 final size:20
Alignment explanation
Indices: 5302446--5302484 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
5302436 TGTGTTGTTT
5302446 AAGTAAGCA-AGTAAGTAAAC
1 AAGTAAG-AGAGTAAGTAAAC
5302466 AAGTAAGAGAGTAAGTAAA
1 AAGTAAGAGAGTAAGTAAA
5302485 GAAGAAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.56, C:0.05, G:0.23, T:0.15
Consensus pattern (20 bp):
AAGTAAGAGAGTAAGTAAAC
Found at i:5302761 original size:17 final size:17
Alignment explanation
Indices: 5302735--5302767 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5302725 ATAGAAAGTC
5302735 AAAGAAATGGGTATCAG
1 AAAGAAATGGGTATCAG
*
5302752 AAAGATATGGGTATCA
1 AAAGAAATGGGTATCA
5302768 AAATATGAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.06, G:0.27, T:0.21
Consensus pattern (17 bp):
AAAGAAATGGGTATCAG
Found at i:5307354 original size:17 final size:17
Alignment explanation
Indices: 5307332--5307374 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
5307322 ATAGAAAGTC
5307332 AAAGATATGGGTATCAG
1 AAAGATATGGGTATCAG
*
5307349 AAAGATATGGGTATCGG
1 AAAGATATGGGTATCAG
5307366 AAAGATATG
1 AAAGATATG
5307375 AGAATCAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.42, C:0.05, G:0.30, T:0.23
Consensus pattern (17 bp):
AAAGATATGGGTATCAG
Found at i:5309910 original size:146 final size:146
Alignment explanation
Indices: 5309646--5309925 Score: 551
Period size: 146 Copynumber: 1.9 Consensus size: 146
5309636 CAAGACTCAA
*
5309646 AAACAATTTATCCTTGATTAAAATCATGTTGGTGGAAAGGGATGATCATGATCATTAACTCCCAC
1 AAACAATTTATCCTTGATTAAAATCATGTTAGTGGAAAGGGATGATCATGATCATTAACTCCCAC
5309711 TAAGTATGTCTTAAATAAATGTTAACCATTGATTTAGTTTCTAATTAAGCTTAATTTAGTTTTAT
66 TAAGTATGTCTTAAATAAATGTTAACCATTGATTTAGTTTCTAATTAAGCTTAATTTAGTTTTAT
5309776 CCACTAAGTATGTCTT
131 CCACTAAGTATGTCTT
5309792 AAACAATTTATCCTTGATTAAAATCATGTTAGTGGAAAGGGATGATCATGATCATTAACTCCCAC
1 AAACAATTTATCCTTGATTAAAATCATGTTAGTGGAAAGGGATGATCATGATCATTAACTCCCAC
5309857 TAAGTATGTCTTAAATAAATGTTAACCATTGATTTAGTTTCTAATTAAGCTTAATTTAGTTTTAT
66 TAAGTATGTCTTAAATAAATGTTAACCATTGATTTAGTTTCTAATTAAGCTTAATTTAGTTTTAT
5309922 CCAC
131 CCAC
5309926 ATGTGTATAT
Statistics
Matches: 133, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
146 133 1.00
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.39
Consensus pattern (146 bp):
AAACAATTTATCCTTGATTAAAATCATGTTAGTGGAAAGGGATGATCATGATCATTAACTCCCAC
TAAGTATGTCTTAAATAAATGTTAACCATTGATTTAGTTTCTAATTAAGCTTAATTTAGTTTTAT
CCACTAAGTATGTCTT
Found at i:5318119 original size:50 final size:50
Alignment explanation
Indices: 5317991--5318287 Score: 245
Period size: 50 Copynumber: 5.8 Consensus size: 50
5317981 GAATATAACA
* * * ** * * * *
5317991 TGCCAAAGCTATGTCCCAGACATAGTCTTACATGGGATGTTTCTTGTA-C
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAGG
* * * * * **
5318040 TGCCAATGTCATATCCTAGATATGGTCTTACATTGGAGTTCTCATATAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAGG
* ** * *
5318090 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAGG
* ** * *
5318140 TGCCCACACCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAGG
* * * * *
5318190 TGCCAACGTCATGTCCCAAACATGGTCTTACATGAGACCTCTCATAATCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--T--A-GG
*
5318246 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGTCCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
5318288 TTACCCAAAT
Statistics
Matches: 198, Mismatches: 43, Indels: 7
0.80 0.17 0.03
Matches are distributed among these distances:
49 35 0.18
50 124 0.63
53 1 0.01
56 38 0.19
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAGG
Found at i:5334692 original size:43 final size:43
Alignment explanation
Indices: 5334639--5334725 Score: 156
Period size: 43 Copynumber: 2.0 Consensus size: 43
5334629 AACAAGACGA
* *
5334639 TCGCCTTCATCTTTAGACAAAGCTGATGACCTAATCATTGGTG
1 TCGCCCTCATCTTTAGAAAAAGCTGATGACCTAATCATTGGTG
5334682 TCGCCCTCATCTTTAGAAAAAGCTGATGACCTAATCATTGGTG
1 TCGCCCTCATCTTTAGAAAAAGCTGATGACCTAATCATTGGTG
5334725 T
1 T
5334726 GTGGACACTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.32
Consensus pattern (43 bp):
TCGCCCTCATCTTTAGAAAAAGCTGATGACCTAATCATTGGTG
Found at i:5339153 original size:16 final size:16
Alignment explanation
Indices: 5339132--5339167 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
5339122 TTTGGTTCGC
5339132 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
5339148 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
5339164 TGTA
1 TGTA
5339168 ATAGCAAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.36, T:0.39
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:5339496 original size:61 final size:61
Alignment explanation
Indices: 5339431--5339617 Score: 190
Period size: 61 Copynumber: 3.1 Consensus size: 61
5339421 ATAGAATTTA
*
5339431 ATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATAATAATATATGATACT
1 ATAAAATTATTAATAATCAATATTCTTATATGAATTTACTCAAATAATAATATATGATACT
* * * * * * *
5339492 ATAAAA-TATAAATTAA-C-ATAATTATTAT-TAAATATA-TTATAATTAA-AATATATAAT-TT
1 ATAAAATTATTAA-TAATCAAT-ATTCTTATATGAATTTACTCA-AA-TAATAATATATGATACT
* *
5339550 AATAAAATTATTAATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACT
1 -ATAAAATTATTAATAATCAATATTCTTATATGAATTTACTCAAATAATAATATATGATACT
5339612 ATAAAA
1 ATAAAA
5339618 GATAATTTGA
Statistics
Matches: 97, Mismatches: 17, Indels: 24
0.70 0.12 0.17
Matches are distributed among these distances:
58 3 0.03
59 28 0.29
60 29 0.30
61 34 0.35
62 3 0.03
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.41
Consensus pattern (61 bp):
ATAAAATTATTAATAATCAATATTCTTATATGAATTTACTCAAATAATAATATATGATACT
Found at i:5339544 original size:18 final size:18
Alignment explanation
Indices: 5339523--5339570 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
5339513 TTATTATTAA
5339523 ATATATTATAATTAAAAT
1 ATATATTATAATTAAAAT
5339541 ATATAATT-TAA-TAAAAT
1 ATAT-ATTATAATTAAAAT
*
5339558 -TAT-TAATAATTAA
1 ATATATTATAATTAA
5339571 TATTCTTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
14 1 0.04
15 3 0.12
16 6 0.23
17 6 0.23
18 7 0.27
19 3 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATATATTATAATTAAAAT
Found at i:5339551 original size:14 final size:15
Alignment explanation
Indices: 5339502--5339553 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
5339492 ATAAAATATA
5339502 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
5339517 TATTAAATATATTAT
1 AATTAAATATATTAT
5339532 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
5339545 AATTTAATA
1 AATTAAATA
5339554 AAATTATTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:5339555 original size:59 final size:58
Alignment explanation
Indices: 5339386--5339682 Score: 173
Period size: 59 Copynumber: 5.0 Consensus size: 58
5339376 ATCATATTTA
* * *
5339386 AACATAATTATTATTAGATATATTATAATTAAAATATA-GAATTTAATAAAATTCTTAAT
1 AACATAATTATTATTAAATATATTATAATTAAAATATATG-ATTTAATAAAA-TATAAAT
* * * * *
5339445 AATCA-ATATTCTTATATGAATTTACTCA-AA-TAATAATATATGATACT-ATAAAATATAAATT
1 AA-CATA-ATTATTAT-TAAATATA-TTATAATTAA-AATATATGAT-TTAATAAAATATAAA-T
* *
5339506 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAAT
1 AACATAATTATTATTAAATATATTATAATTAAAATATATGATTTAATAAAA-TATAAAT
* * * * * * * *
5339565 AA-TTAA-TATTCTTATATGA-ATTTACTCAAATCATAATATATGATACT-ATAAAAGATAATTT
1 AACATAATTATTATTAAAT-ATA-TTA-T--AATTAAAATATATGAT-TTAATAAAATATAA-AT
* * *
5339626 GAA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTTAAA
1 -AACATAATTATTATTAAATATATTATAATTAAAATATATGATTTAATAAAATATAAA
5339683 ATAATTATAA
Statistics
Matches: 178, Mismatches: 36, Indels: 49
0.68 0.14 0.19
Matches are distributed among these distances:
57 10 0.06
58 11 0.06
59 53 0.30
60 36 0.20
61 46 0.26
62 13 0.07
63 9 0.05
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (58 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATGATTTAATAAAATATAAAT
Found at i:5339559 original size:44 final size:43
Alignment explanation
Indices: 5339479--5339562 Score: 107
Period size: 43 Copynumber: 1.9 Consensus size: 43
5339469 CTCAAATAAT
* *
5339479 AATATATGATACTATAAAATATAAATTAACATAATTATTATTA
1 AATATATGATAATATAAAATATAAATTAACAAAATTATTATTA
* *
5339522 AATATATTATAAT-TAAAATATATAATTTAATAAAATTATTA
1 AATATATGATAATATAAAATATA-AA-TTAACAAAATTATTA
5339563 ATAATTAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
42 9 0.26
43 13 0.37
44 13 0.37
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (43 bp):
AATATATGATAATATAAAATATAAATTAACAAAATTATTATTA
Found at i:5339601 original size:120 final size:121
Alignment explanation
Indices: 5339386--5339678 Score: 482
Period size: 120 Copynumber: 2.4 Consensus size: 121
5339376 ATCATATTTA
* * *
5339386 AACATAATTATTATTAGATATATTATAATTAAAATATAGAATTTAATAAAATTCTTAATAATCAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAATAATCAA
*
5339451 TATTCTTATATGAATTTACTCAAATAATAATATATGATACTATAAAATATAAATT-
66 TATTCTTATATGAATTTACTCAAATAATAATATATGATACTATAAAAGATAAATTG
*
5339506 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAATAATCAA
* *
5339571 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTTG
66 TATTCTTATATGAATTTACTCAAATAATAATATATGATACTATAAAAGATAAATTG
* * *
5339627 AA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
5339679 TAAAATAATT
Statistics
Matches: 162, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
120 160 0.99
121 2 0.01
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (121 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAATAATCAA
TATTCTTATATGAATTTACTCAAATAATAATATATGATACTATAAAAGATAAATTG
Found at i:5342534 original size:8 final size:8
Alignment explanation
Indices: 5342521--5342555 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
5342511 TAAAGATTCT
5342521 AAAAAAGA
1 AAAAAAGA
5342529 AAAAAAGA
1 AAAAAAGA
*
5342537 AACAAAG-
1 AAAAAAGA
5342544 AAAAAAGA
1 AAAAAAGA
5342552 AAAA
1 AAAA
5342556 GTAGAATACC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 6 0.25
8 18 0.75
ACGTcount: A:0.86, C:0.03, G:0.11, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:5342549 original size:15 final size:16
Alignment explanation
Indices: 5342524--5342553 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5342514 AGATTCTAAA
5342524 AAAGAAAAAAAGAAAC
1 AAAGAAAAAAAGAAAC
5342540 AAAG-AAAAAAGAAA
1 AAAGAAAAAAAGAAA
5342554 AAGTAGAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.83, C:0.03, G:0.13, T:0.00
Consensus pattern (16 bp):
AAAGAAAAAAAGAAAC
Found at i:5345062 original size:14 final size:12
Alignment explanation
Indices: 5345017--5345087 Score: 54
Period size: 13 Copynumber: 5.4 Consensus size: 12
5345007 CTTAACAAAT
5345017 ATTTTAATTA-A
1 ATTTTAATTATA
*
5345028 ATATTTAATAATAA
1 AT-TTTAATTAT-A
5345042 ATTTTAATTGATA
1 ATTTTAATT-ATA
5345055 ATTCTTAAATTATTA
1 ATT-TT-AATTA-TA
*
5345070 TTTTTAATTTATA
1 ATTTTAA-TTATA
5345083 ATTTT
1 ATTTT
5345088 GATTGGTACA
Statistics
Matches: 48, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
11 2 0.04
12 7 0.15
13 18 0.38
14 13 0.27
15 8 0.17
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (12 bp):
ATTTTAATTATA
Found at i:5353281 original size:20 final size:20
Alignment explanation
Indices: 5353224--5353282 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
5353214 TTTTTTAAAA
* * *
5353224 ATTAAAGTTTTAAAAAATATT
1 ATTAAAATTATAAAAAA-AGT
* **
5353245 ATAAAAATTATTTAAAAAGT
1 ATTAAAATTATAAAAAAAGT
5353265 ATTAAAATTATAAAAAAA
1 ATTAAAATTATAAAAAAA
5353283 TATATTTTTA
Statistics
Matches: 29, Mismatches: 9, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (20 bp):
ATTAAAATTATAAAAAAAGT
Found at i:5359112 original size:2 final size:2
Alignment explanation
Indices: 5359107--5359137 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
5359097 TGAAACCAAA
*
5359107 AC AC AC AC AC AC AC AG AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
5359138 AAGAAACAGC
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:0.45, G:0.03, T:0.00
Consensus pattern (2 bp):
AC
Found at i:5360695 original size:3 final size:3
Alignment explanation
Indices: 5360689--5360716 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
5360679 CGTTGTTGCA
5360689 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
5360717 AGTCTTCACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:5365569 original size:46 final size:47
Alignment explanation
Indices: 5365502--5365594 Score: 116
Period size: 46 Copynumber: 2.0 Consensus size: 47
5365492 GCTGTCAAAT
* * * *
5365502 CAGATGTATGTGATCAAGCCACTATG-TTGTAGCCAAGTTGCTAGAA
1 CAGATGTATGTGATCAAGCCACCATGATTGTAGACAAGCTGCCAGAA
* **
5365548 CAGATGTATGTGGTTGAGCCACCATGATTGTAGACAAGCTGCCAGAA
1 CAGATGTATGTGATCAAGCCACCATGATTGTAGACAAGCTGCCAGAA
5365595 AGAATTGTAG
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
46 22 0.56
47 17 0.44
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (47 bp):
CAGATGTATGTGATCAAGCCACCATGATTGTAGACAAGCTGCCAGAA
Found at i:5366312 original size:12 final size:12
Alignment explanation
Indices: 5366297--5366334 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
5366287 TGGCACACGG
*
5366297 CCTAACACATGC
1 CCTAACACAAGC
5366309 CCTAACACAAGC
1 CCTAACACAAGC
5366321 CCTAACACAAGC
1 CCTAACACAAGC
5366333 CC
1 CC
5366335 GTGTGACTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.37, C:0.45, G:0.08, T:0.11
Consensus pattern (12 bp):
CCTAACACAAGC
Found at i:5371349 original size:6 final size:6
Alignment explanation
Indices: 5371330--5371390 Score: 104
Period size: 6 Copynumber: 10.0 Consensus size: 6
5371320 TTTAAATGAA
5371330 TTCATT TCTCATT TTCATT TTCATT TTCATT TTCATT TTCATT TTCATT
1 TTCATT T-TCATT TTCATT TTCATT TTCATT TTCATT TTCATT TTCATT
*
5371379 TTCATT TCCATT
1 TTCATT TTCATT
5371391 GAGAAAACCA
Statistics
Matches: 53, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
6 47 0.89
7 6 0.11
ACGTcount: A:0.16, C:0.20, G:0.00, T:0.64
Consensus pattern (6 bp):
TTCATT
Found at i:5374486 original size:28 final size:30
Alignment explanation
Indices: 5374455--5374518 Score: 87
Period size: 28 Copynumber: 2.2 Consensus size: 30
5374445 GCTTTTCATA
5374455 TTTTTATTTTGACTTTGA-TTGATTTT-AT
1 TTTTTATTTTGACTTTGATTTGATTTTGAT
**
5374483 TTTTGCTTTTGACTTTGATTTTGATTTTGAT
1 TTTTTATTTTGACTTTGA-TTTGATTTTGAT
5374514 TTTTT
1 TTTTT
5374519 TCTTCTTCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 16 0.53
30 8 0.27
31 6 0.20
ACGTcount: A:0.14, C:0.05, G:0.12, T:0.69
Consensus pattern (30 bp):
TTTTTATTTTGACTTTGATTTGATTTTGAT
Found at i:5374492 original size:6 final size:6
Alignment explanation
Indices: 5374454--5374516 Score: 60
Period size: 6 Copynumber: 10.8 Consensus size: 6
5374444 CGCTTTTCAT
* * * *
5374454 ATTTTT ATTTTG ACTTTG A--TTG ATTTT- ATTTTTG CTTTTG ACTTTG
1 ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG A-TTTTG ATTTTG ATTTTG
5374500 ATTTTG ATTTTG ATTTT
1 ATTTTG ATTTTG ATTTT
5374517 TTTCTTCTTC
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
4 4 0.09
5 1 0.02
6 42 0.89
ACGTcount: A:0.16, C:0.05, G:0.13, T:0.67
Consensus pattern (6 bp):
ATTTTG
Found at i:5374541 original size:11 final size:11
Alignment explanation
Indices: 5374513--5374550 Score: 58
Period size: 11 Copynumber: 3.3 Consensus size: 11
5374503 TTGATTTTGA
5374513 TTTTTTTCTTCT
1 TTTTTTTCTT-T
5374525 TCTTTTTTCTTT
1 T-TTTTTTCTTT
5374537 TTTTTTTCTTT
1 TTTTTTTCTTT
5374548 TTT
1 TTT
5374551 GAAATTGGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 13 0.52
12 3 0.12
13 9 0.36
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:5379802 original size:3 final size:3
Alignment explanation
Indices: 5379796--5379829 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
5379786 AAAAAGAGAC
*
5379796 TAA TAA TAA TAA TAA TAA TAA CTAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA
5379830 AAACAATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:5379822 original size:22 final size:22
Alignment explanation
Indices: 5379794--5379838 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
5379784 TAAAAAAGAG
* * *
5379794 ACTAATAATAATAATAATAATA
1 ACTAATAAAAATAAAAACAATA
5379816 ACTAATAAAAATAAAAACAATA
1 ACTAATAAAAATAAAAACAATA
5379838 A
1 A
5379839 ATCAATTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (22 bp):
ACTAATAAAAATAAAAACAATA
Found at i:5382177 original size:22 final size:23
Alignment explanation
Indices: 5382129--5382177 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
5382119 TATTGGTATG
5382129 ATTAATGTGTCCTAATAAGTCGT
1 ATTAATGTGTCCTAATAAGTCGT
* *
5382152 -TTAATGTGTCTTAATAGGT-GT
1 ATTAATGTGTCCTAATAAGTCGT
5382173 ATTAA
1 ATTAA
5382178 AGAAGCTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.31, C:0.08, G:0.18, T:0.43
Consensus pattern (23 bp):
ATTAATGTGTCCTAATAAGTCGT
Found at i:5385113 original size:2 final size:2
Alignment explanation
Indices: 5385077--5385105 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
5385067 TATGGTTGTA
5385077 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5385106 GGATATATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:5386429 original size:17 final size:18
Alignment explanation
Indices: 5386392--5386429 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
5386382 TGTTTTAAAG
5386392 AATATTTTTAATATTACAA
1 AATATTTTT-ATATTACAA
*
5386411 AATATTTTT-TATTAGAA
1 AATATTTTTATATTACAA
5386428 AA
1 AA
5386430 AAAATTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 9 0.50
19 9 0.50
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (18 bp):
AATATTTTTATATTACAA
Found at i:5386624 original size:20 final size:19
Alignment explanation
Indices: 5386599--5386651 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
5386589 CTATTTTTTA
*
5386599 ACTTATTAATTTTTTAGTTG
1 ACTTATTAATTTTGTA-TTG
* *
5386619 ACTTATTATATATTGTATTT
1 ACTTATTA-ATTTTGTATTG
5386639 ACTTATTAATTTT
1 ACTTATTAATTTT
5386652 ATTATGTATG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 4 0.14
20 18 0.64
21 6 0.21
ACGTcount: A:0.28, C:0.06, G:0.06, T:0.60
Consensus pattern (19 bp):
ACTTATTAATTTTGTATTG
Found at i:5390000 original size:13 final size:13
Alignment explanation
Indices: 5389982--5390006 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5389972 TAAAACCAAA
5389982 AAATGTTTAGTTG
1 AAATGTTTAGTTG
5389995 AAATGTTTAGTT
1 AAATGTTTAGTT
5390007 TGAATCATAT
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:0.00, G:0.20, T:0.48
Consensus pattern (13 bp):
AAATGTTTAGTTG
Found at i:5393059 original size:12 final size:11
Alignment explanation
Indices: 5393024--5393075 Score: 54
Period size: 11 Copynumber: 4.6 Consensus size: 11
5393014 ATTTAGCAAG
5393024 TATAAAAAAA-
1 TATAAAAAAAT
*
5393034 TATAAAAATAT
1 TATAAAAAAAT
5393045 TATAAAAAAAGT
1 TATAAAAAAA-T
5393057 TATAGAAAATAA-
1 TATA-AAAA-AAT
5393069 TATAAAA
1 TATAAAA
5393076 TTATTCAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
10 9 0.25
11 12 0.33
12 9 0.25
13 4 0.11
14 2 0.06
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (11 bp):
TATAAAAAAAT
Found at i:5403014 original size:26 final size:29
Alignment explanation
Indices: 5402961--5403020 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 29
5402951 ATGGATTTAA
5402961 ATTACTTATTATTTAAGTAAATAGATATTT
1 ATTACTTATTATTTAAGTAAATA-ATATTT
*
5402991 ATTATTTATTA-TTAAGT-AAT-ATATTT
1 ATTACTTATTATTTAAGTAAATAATATTT
5403017 ATTA
1 ATTA
5403021 ATTAAATAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 10 0.34
28 3 0.10
29 6 0.21
30 10 0.34
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (29 bp):
ATTACTTATTATTTAAGTAAATAATATTT
Found at i:5403017 original size:19 final size:21
Alignment explanation
Indices: 5402993--5403036 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 21
5402983 AGATATTTAT
*
5402993 TATTTATT-ATTAAGTAA-TA
1 TATTTATTAATTAAATAATTA
5403012 TATTTATTAATTAAATAATTA
1 TATTTATTAATTAAATAATTA
5403033 TATT
1 TATT
5403037 ATAAGATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 8 0.36
20 8 0.36
21 6 0.27
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (21 bp):
TATTTATTAATTAAATAATTA
Found at i:5403038 original size:20 final size:19
Alignment explanation
Indices: 5402991--5403038 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
5402981 ATAGATATTT
*
5402991 ATTAT-TTATTATTAAGTA
1 ATTATATTATTATTAAATA
5403009 A-TATATTTATTAATTAAATA
1 ATTATA-TTATT-ATTAAATA
5403029 ATTATATTAT
1 ATTATATTAT
5403039 AAGATTTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
17 3 0.12
18 1 0.04
19 5 0.20
20 12 0.48
21 4 0.16
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (19 bp):
ATTATATTATTATTAAATA
Found at i:5403683 original size:17 final size:18
Alignment explanation
Indices: 5403661--5403696 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
5403651 TAAATGAGTC
5403661 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
5403678 AATTAGGGTATAAATTGG
1 AATTAGGATATAAATTGG
5403696 A
1 A
5403697 TAAAAATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:5414036 original size:6 final size:6
Alignment explanation
Indices: 5414027--5414051 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
5414017 TGATAATTCG
5414027 AATTTA AATTTA AATTTA AATTTA A
1 AATTTA AATTTA AATTTA AATTTA A
5414052 TTTTTTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
AATTTA
Found at i:5420385 original size:85 final size:85
Alignment explanation
Indices: 5420243--5420416 Score: 276
Period size: 85 Copynumber: 2.0 Consensus size: 85
5420233 GGGTTTTAAT
* * *
5420243 TTTTTTTGTAGTATTATTTATTTGTATGTTTGTAACTTAATTAGTATAAAAAAACTAAATAAATA
1 TTTTTTTGAAGTATTATTTATTTGTATGCTTCTAACTTAATTAGTATAAAAAAACTAAATAAATA
5420308 CTGAAATGGTATATTTGAGA
66 CTGAAATGGTATATTTGAGA
* * *
5420328 TTTTTTTGAATTATTATTTATTTGTATGCTTCTTACTTAATTAGTATAAAAAAACTAATTAAATA
1 TTTTTTTGAAGTATTATTTATTTGTATGCTTCTAACTTAATTAGTATAAAAAAACTAAATAAATA
* *
5420393 CTGAAATGGTATGTTTGAGG
66 CTGAAATGGTATATTTGAGA
5420413 TTTT
1 TTTT
5420417 CAAGGGTTTT
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
85 81 1.00
ACGTcount: A:0.35, C:0.05, G:0.13, T:0.48
Consensus pattern (85 bp):
TTTTTTTGAAGTATTATTTATTTGTATGCTTCTAACTTAATTAGTATAAAAAAACTAAATAAATA
CTGAAATGGTATATTTGAGA
Found at i:5429836 original size:8 final size:8
Alignment explanation
Indices: 5429822--5429851 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
5429812 CCCGCTTTCC
5429822 CAAAAAAA
1 CAAAAAAA
*
5429830 AAAAAAAA
1 CAAAAAAA
5429838 CAAAAAAA
1 CAAAAAAA
5429846 CAAAAA
1 CAAAAA
5429852 GCTTTGAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (8 bp):
CAAAAAAA
Found at i:5430490 original size:27 final size:27
Alignment explanation
Indices: 5430452--5430534 Score: 157
Period size: 27 Copynumber: 3.1 Consensus size: 27
5430442 ATTAATTTAT
5430452 TTTGTAAAGTAATTATTTATTTTGAAC
1 TTTGTAAAGTAATTATTTATTTTGAAC
*
5430479 TTTGTGAAGTAATTATTTATTTTGAAC
1 TTTGTAAAGTAATTATTTATTTTGAAC
5430506 TTTGTAAAGTAATTATTTATTTTGAAC
1 TTTGTAAAGTAATTATTTATTTTGAAC
5430533 TT
1 TT
5430535 AGCAAATAGA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 54 1.00
ACGTcount: A:0.31, C:0.04, G:0.12, T:0.53
Consensus pattern (27 bp):
TTTGTAAAGTAATTATTTATTTTGAAC
Found at i:5436898 original size:40 final size:42
Alignment explanation
Indices: 5436843--5436920 Score: 115
Period size: 41 Copynumber: 1.9 Consensus size: 42
5436833 ATAATTCATA
* *
5436843 AATTTTTTT-TAAAAAATAATAAAAATATTTA-AAAATCAAC
1 AATTTTTTTAAAAAAAATAATAAAAAAATTTAGAAAATCAAC
*
5436883 AATTTTTTTAAAAAAAATCATAAAAAAATTTAGAAAAT
1 AATTTTTTTAAAAAAAATAATAAAAAAATTTAGAAAAT
5436921 TTATCTATGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 9 0.27
41 19 0.58
42 5 0.15
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.36
Consensus pattern (42 bp):
AATTTTTTTAAAAAAAATAATAAAAAAATTTAGAAAATCAAC
Found at i:5438226 original size:14 final size:14
Alignment explanation
Indices: 5438207--5438233 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5438197 AACACAAAAT
5438207 ATTAGACATTGGAC
1 ATTAGACATTGGAC
5438221 ATTAGACATTGGA
1 ATTAGACATTGGA
5438234 ATTTTGAAAA
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:0.37, C:0.11, G:0.22, T:0.30
Consensus pattern (14 bp):
ATTAGACATTGGAC
Found at i:5441070 original size:21 final size:21
Alignment explanation
Indices: 5441022--5441165 Score: 91
Period size: 21 Copynumber: 7.0 Consensus size: 21
5441012 CGGGTGGATC
* *
5441022 AGCTCTTACGAGCTTCTTTTTT
1 AGCTCTTATGAGCTTC-TGTTT
* *
5441044 AACTCTTTTGAGCTTCTGTTT
1 AGCTCTTATGAGCTTCTGTTT
*
5441065 AGCTCTTATAAGCTTCTG-TT
1 AGCTCTTATGAGCTTCTGTTT
* * * * * *
5441085 GGCATGATT-TG-G-GT-GGATC
1 AGC-T-CTTATGAGCTTCTGTTT
* *
5441104 AGCTCTTACGAGCTTCTGTTC
1 AGCTCTTATGAGCTTCTGTTT
* *
5441125 AGCTCTTACGAGCTTCTATTT
1 AGCTCTTATGAGCTTCTGTTT
5441146 AGCTCTTATGAGCTTCTGTT
1 AGCTCTTATGAGCTTCTGTT
5441166 GGCATGTTCG
Statistics
Matches: 92, Mismatches: 23, Indels: 15
0.71 0.18 0.12
Matches are distributed among these distances:
17 2 0.02
18 3 0.03
19 5 0.05
20 6 0.07
21 61 0.66
22 15 0.16
ACGTcount: A:0.16, C:0.21, G:0.19, T:0.44
Consensus pattern (21 bp):
AGCTCTTATGAGCTTCTGTTT
Found at i:5441161 original size:81 final size:81
Alignment explanation
Indices: 5440995--5441203 Score: 276
Period size: 81 Copynumber: 2.6 Consensus size: 81
5440985 GCGTTTTACT
* * * **
5440995 TTCTGTGTGGCGTGATTCGGGTGGATCAGCTCTTACGAGCTTCTTTTTTAACTCTTTTGAGCTTC
1 TTCTGT-TGGCATGATTCGGGTGGATCAGCTCTTACGAGCTTC-TGTTCAACTCTTACGAGCTTC
*
5441060 TGTTTAGCTCTTATAAGC
64 TATTTAGCTCTTATAAGC
* *
5441078 TTCTGTTGGCATGATTTGGGTGGATCAGCTCTTACGAGCTTCTGTTCAGCTCTTACGAGCTTCTA
1 TTCTGTTGGCATGATTCGGGTGGATCAGCTCTTACGAGCTTCTGTTCAACTCTTACGAGCTTCTA
*
5441143 TTTAGCTCTTATGAGC
66 TTTAGCTCTTATAAGC
** * *
5441159 TTCTGTTGGCATG-TTCGGAAGGACCAGCTCTTATGAGCTTCTGTT
1 TTCTGTTGGCATGATTCGGGTGGATCAGCTCTTACGAGCTTCTGTT
5441204 GACGATGTAC
Statistics
Matches: 112, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
80 27 0.24
81 45 0.40
82 34 0.30
83 6 0.05
ACGTcount: A:0.15, C:0.20, G:0.24, T:0.41
Consensus pattern (81 bp):
TTCTGTTGGCATGATTCGGGTGGATCAGCTCTTACGAGCTTCTGTTCAACTCTTACGAGCTTCTA
TTTAGCTCTTATAAGC
Found at i:5449650 original size:40 final size:40
Alignment explanation
Indices: 5449560--5449779 Score: 241
Period size: 40 Copynumber: 5.5 Consensus size: 40
5449550 ACCCAAGTAT
* ** * *
5449560 CTTCGGGATTTAG-CCGGATATAACCACTCGCAC-AAGGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* * *
5449598 CTTCGGGTCTTAGCCCGGATATGGTCACTAGCATAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
5449638 CTTTGGGACTTAGCCCGGATATAGTCGCTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
5449678 CTTCGGGTCTTAGCCCGGATATAG-CAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
** * * *
5449718 CTTC-GGATCTTAGTTCGGATATAGTGACTAGCATAAAAGC
1 CTTCGGGA-CTTAGCCCGGATATAGTCACTAGCACAAATGC
5449758 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
5449780 CATTCGAATA
Statistics
Matches: 150, Mismatches: 26, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
38 11 0.07
39 18 0.12
40 118 0.79
41 3 0.02
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.25
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:5456260 original size:25 final size:24
Alignment explanation
Indices: 5456222--5456274 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 24
5456212 AAGTTCAAGC
5456222 GAGCCATATCAGGAAGCTCACAAA
1 GAGCCATATCAGGAAGCTCACAAA
* * *
5456246 GAGCCTATATTAGGATGCTCATAAA
1 GAGCC-ATATCAGGAAGCTCACAAA
5456271 GAGC
1 GAGC
5456275 TACGGTATGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.38, C:0.21, G:0.23, T:0.19
Consensus pattern (24 bp):
GAGCCATATCAGGAAGCTCACAAA
Found at i:5472486 original size:19 final size:19
Alignment explanation
Indices: 5472462--5472509 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
5472452 CTTTCTGTCC
*
5472462 CCGTCTCCACC-CACTCCTA
1 CCGTCTCCACCAC-CGCCTA
5472481 CCGTCTCGCACCACCGCCTA
1 CCGTCTC-CACCACCGCCTA
5472501 CCGTCTCCA
1 CCGTCTCCA
5472510 TTCACGTACG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 9 0.35
20 16 0.62
21 1 0.04
ACGTcount: A:0.15, C:0.56, G:0.10, T:0.19
Consensus pattern (19 bp):
CCGTCTCCACCACCGCCTA
Found at i:5479642 original size:81 final size:81
Alignment explanation
Indices: 5479521--5479670 Score: 221
Period size: 81 Copynumber: 1.9 Consensus size: 81
5479511 TAGAGCACTC
* *
5479521 GCAAGGCATGGTATACTTCATCCATCGTTGAGACCTGTAGCAAATCATAGTAATACAATGACCAA
1 GCAAGGCATGGTATACTTCATCCATCGTCGAGACCTGTAGCAAATCATAGTAATACAACGACCAA
5479586 CCTCTACTAAGCATTT
66 CCTCTACTAAGCATTT
* * * * *
5479602 GCAAGGCATGGTATACTTCATTCTTCGTCGAGA-TTAGTAGCAGATCATAGTAATACAACGAGCA
1 GCAAGGCATGGTATACTTCATCCATCGTCGAGACCT-GTAGCAAATCATAGTAATACAACGACCA
5479666 ACCTC
65 ACCTC
5479671 CACCAAGACA
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
80 1 0.02
81 60 0.98
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.27
Consensus pattern (81 bp):
GCAAGGCATGGTATACTTCATCCATCGTCGAGACCTGTAGCAAATCATAGTAATACAACGACCAA
CCTCTACTAAGCATTT
Found at i:5481069 original size:16 final size:18
Alignment explanation
Indices: 5481048--5481080 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
5481038 AAGTTAATTA
5481048 TAATT-AATTA-ATAAAC
1 TAATTAAATTATATAAAC
5481064 TAATTAAATTATATAAA
1 TAATTAAATTATATAAA
5481081 ATTCATGTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 5 0.33
18 5 0.33
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
TAATTAAATTATATAAAC
Found at i:5483251 original size:50 final size:50
Alignment explanation
Indices: 5483127--5483375 Score: 284
Period size: 50 Copynumber: 4.8 Consensus size: 50
5483117 GATAATAACA
* * ** * *
5483127 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
5483178 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
5483228 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
5483278 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
5483333 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
5483376 TTACCCAAAT
Statistics
Matches: 170, Mismatches: 21, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
49 1 0.01
50 92 0.54
51 33 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:5483305 original size:100 final size:104
Alignment explanation
Indices: 5483126--5483375 Score: 357
Period size: 100 Copynumber: 2.4 Consensus size: 104
5483116 TGATAATAAC
**
5483126 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
5483191 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
5483228 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
5483291 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
5483333 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
5483376 TTACCCAAAT
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 50 0.38
101 36 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:5483491 original size:13 final size:13
Alignment explanation
Indices: 5483470--5483501 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
5483460 GCTTGGATCA
*
5483470 TCATCAAATAAAT
1 TCATAAAATAAAT
5483483 TCATAAAATAAAT
1 TCATAAAATAAAT
5483496 TCATAA
1 TCATAA
5483502 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:5483749 original size:30 final size:30
Alignment explanation
Indices: 5483713--5483770 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
5483703 CCTCGACTCT
*
5483713 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
5483743 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
5483771 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:5484480 original size:18 final size:18
Alignment explanation
Indices: 5484459--5484495 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
5484449 AATTTCCCTT
* *
5484459 TTTCTTTTCTTTTCTTTC
1 TTTCTTTCCTTTCCTTTC
5484477 TTTCTTTCCTTTCCTTTC
1 TTTCTTTCCTTTCCTTTC
5484495 T
1 T
5484496 CTCTCTGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTCTTTCCTTTCCTTTC
Found at i:5484506 original size:17 final size:17
Alignment explanation
Indices: 5484486--5484533 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
5484476 CTTTCTTTCC
5484486 TTTCCTTTCTCTCTCTG
1 TTTCCTTTCTCTCTCTG
*
5484503 TTTCGTTT-TGCTCTCTG
1 TTTCCTTTCT-CTCTCTG
*
5484520 TTT-CTTTCTTTCTC
1 TTTCCTTTCTCTCTC
5484534 CCTTCTCTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
16 8 0.31
17 18 0.69
ACGTcount: A:0.00, C:0.29, G:0.08, T:0.62
Consensus pattern (17 bp):
TTTCCTTTCTCTCTCTG
Found at i:5484551 original size:40 final size:41
Alignment explanation
Indices: 5484497--5484573 Score: 138
Period size: 40 Copynumber: 1.9 Consensus size: 41
5484487 TTCCTTTCTC
5484497 TCTCTGTTTCGTTTTGCTCTCTGTTTC-TTTCTTTCTCCCT
1 TCTCTGTTTCGTTTTGCTCTCTGTTTCTTTTCTTTCTCCCT
*
5484537 TCTCTGTTTTGTTTTGCTCTCTGTTTCTTTTCTTTCT
1 TCTCTGTTTCGTTTTGCTCTCTGTTTCTTTTCTTTCT
5484574 TTCTTTGTCA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
40 26 0.74
41 9 0.26
ACGTcount: A:0.00, C:0.26, G:0.10, T:0.64
Consensus pattern (41 bp):
TCTCTGTTTCGTTTTGCTCTCTGTTTCTTTTCTTTCTCCCT
Found at i:5484559 original size:17 final size:17
Alignment explanation
Indices: 5484496--5484562 Score: 53
Period size: 17 Copynumber: 3.6 Consensus size: 17
5484486 TTTCCTTTCT
*
5484496 CTCTCTGTTTCGTTTTG
1 CTCTCTGTTTTGTTTTG
* *
5484513 CTCTCTGTTTCTTTCTTTCTCC
1 CTCTCTG--T-TTTGTTT-T-G
5484535 CTTCTCTGTTTTGTTTTG
1 C-TCTCTGTTTTGTTTTG
5484553 CTCTCTGTTT
1 CTCTCTGTTT
5484563 CTTTTCTTTC
Statistics
Matches: 39, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
17 16 0.41
18 1 0.03
19 2 0.05
20 11 0.28
21 2 0.05
22 1 0.03
23 6 0.15
ACGTcount: A:0.00, C:0.27, G:0.12, T:0.61
Consensus pattern (17 bp):
CTCTCTGTTTTGTTTTG
Found at i:5484606 original size:14 final size:14
Alignment explanation
Indices: 5484587--5484639 Score: 70
Period size: 14 Copynumber: 3.6 Consensus size: 14
5484577 TTTGTCATAT
5484587 ATATAATAATAATA
1 ATATAATAATAATA
5484601 ATATAATATATATATAA
1 ATATAATA-ATA-AT-A
*
5484618 ATATATTAATAATA
1 ATATAATAATAATA
5484632 ATATAATA
1 ATATAATA
5484640 TAAAAACATA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
14 16 0.47
15 5 0.15
16 5 0.15
17 8 0.24
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
ATATAATAATAATA
Found at i:5484608 original size:11 final size:11
Alignment explanation
Indices: 5484592--5484639 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
5484582 CATATATATA
5484592 ATAATAATAAT
1 ATAATAATAAT
5484603 ATAAT-AT-AT
1 ATAATAATAAT
5484612 AT-ATAA-ATAT
1 ATAATAATA-AT
5484622 ATTAATAATAAT
1 A-TAATAATAAT
5484634 ATAATA
1 ATAATA
5484640 TAAAAACATA
Statistics
Matches: 31, Mismatches: 0, Indels: 12
0.72 0.00 0.28
Matches are distributed among these distances:
8 2 0.06
9 5 0.16
10 5 0.16
11 11 0.35
12 7 0.23
13 1 0.03
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
ATAATAATAAT
Found at i:5484616 original size:25 final size:26
Alignment explanation
Indices: 5484583--5484643 Score: 83
Period size: 25 Copynumber: 2.4 Consensus size: 26
5484573 TTTCTTTGTC
5484583 ATATATAT-AATAATAATAAT-ATAAT
1 ATATATATAAAT-ATAATAATAATAAT
*
5484608 ATATATATAAATATATTAATAATAAT
1 ATATATATAAATATAATAATAATAAT
5484634 ATA-ATATAAA
1 ATATATATAAA
5484644 AACATAATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
25 22 0.67
26 11 0.33
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (26 bp):
ATATATATAAATATAATAATAATAAT
Found at i:5484656 original size:31 final size:31
Alignment explanation
Indices: 5484587--5484656 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
5484577 TTTGTCATAT
* * * *
5484587 ATATAATAATAATAATATAATATATATATAA
1 ATATATTAATAATAATATAATATAAAAACAA
5484618 ATATATTAATAATAATATAATATAAAAACATA
1 ATATATTAATAATAATATAATATAAAAACA-A
5484650 AT-TATTA
1 ATATATTA
5484657 CTTACGCATG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 31 0.91
32 3 0.09
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (31 bp):
ATATATTAATAATAATATAATATAAAAACAA
Found at i:5486629 original size:13 final size:13
Alignment explanation
Indices: 5486611--5486638 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
5486601 GATAAAAGAG
5486611 CATATAGAATACC
1 CATATAGAATACC
5486624 CATATAGAATACC
1 CATATAGAATACC
5486637 CA
1 CA
5486639 GAAGAGATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.25, G:0.07, T:0.21
Consensus pattern (13 bp):
CATATAGAATACC
Found at i:5489202 original size:50 final size:50
Alignment explanation
Indices: 5489112--5489309 Score: 247
Period size: 50 Copynumber: 3.9 Consensus size: 50
5489102 TTCTCGTGAT
* *
5489112 GGTGCCCATGCCATGTCCCA-A-ATGGTCTTATAGGGGACCTCTCATCTC
1 GGTGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTC
* * *
5489160 GGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTC
1 GGTGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTC
* *
5489210 GGTGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAA
1 GGTGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-C
* *
5489265 GGATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 GG-TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
5489310 TTACCCAAAT
Statistics
Matches: 129, Mismatches: 13, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
48 18 0.14
49 1 0.01
50 66 0.51
53 2 0.02
54 1 0.01
55 2 0.02
56 39 0.30
ACGTcount: A:0.20, C:0.30, G:0.24, T:0.26
Consensus pattern (50 bp):
GGTGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTC
Found at i:5489291 original size:106 final size:98
Alignment explanation
Indices: 5489112--5489309 Score: 288
Period size: 106 Copynumber: 1.9 Consensus size: 98
5489102 TTCTCGTGAT
* *
5489112 GGTGCCCATGCCATGTCCCAAATGGTCTTATAGGGGACCTCTCATCTCGGTGCCAACGCCATGTC
1 GGTGCCCATGCCATGTCCCAAATGGTCTTACAGGGGACCTCTCATCTAGGTGCCAACGCCATGTC
5489177 CCAGACATGGTCTTACATGGGACCTCTCGTCTC
66 CCAGACATGGTCTTACATGGGACCTCTCGTCTC
*
5489210 GGTGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGGATGCCAAT
1 GGTGCCCATGCCATGTCCCA-A-ATGGTCTTACAGGGGACCTCTC---ATC-T-AGG-TGCCAAC
*
5489275 GCCATGTCCCAGACATGGTCTTACATGGGATCTCT
58 GCCATGTCCCAGACATGGTCTTACATGGGACCTCT
5489310 TTACCCAAAT
Statistics
Matches: 88, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
98 20 0.23
99 1 0.01
100 21 0.24
103 3 0.03
104 1 0.01
105 2 0.02
106 40 0.45
ACGTcount: A:0.20, C:0.30, G:0.24, T:0.26
Consensus pattern (98 bp):
GGTGCCCATGCCATGTCCCAAATGGTCTTACAGGGGACCTCTCATCTAGGTGCCAACGCCATGTC
CCAGACATGGTCTTACATGGGACCTCTCGTCTC
Found at i:5489425 original size:13 final size:13
Alignment explanation
Indices: 5489404--5489435 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
5489394 GCTTGGATCA
*
5489404 TCATCAAATAAAT
1 TCATAAAATAAAT
5489417 TCATAAAATAAAT
1 TCATAAAATAAAT
5489430 TCATAA
1 TCATAA
5489436 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:5489682 original size:30 final size:31
Alignment explanation
Indices: 5489646--5489704 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
5489636 CCTCGACTCT
5489646 AACTTTTT-CAAAATTACAATTTTGCCCCTA
1 AACTTTTTACAAAATTACAATTTTGCCCCTA
* *
5489676 AACTTTTTACATAATTACATTTTTGCCCC
1 AACTTTTTACAAAATTACAATTTTGCCCC
5489705 AAGGCTCGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 8 0.31
31 18 0.69
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.42
Consensus pattern (31 bp):
AACTTTTTACAAAATTACAATTTTGCCCCTA
Found at i:5490415 original size:17 final size:18
Alignment explanation
Indices: 5490388--5490462 Score: 59
Period size: 17 Copynumber: 4.3 Consensus size: 18
5490378 AATTTCCCTT
5490388 TTTCTTTTCT-TTTCTTTC
1 TTTC-TTTCTGTTTCTTTC
*
5490406 TTTCTTTC--TTTCCTTC
1 TTTCTTTCTGTTTCTTTC
* *
5490422 CTTCTTCTCTGTTTCGTT-
1 TTTCTT-TCTGTTTCTTTC
* *
5490440 TTGCTCTCTGTTTCTTTC
1 TTTCTTTCTGTTTCTTTC
5490458 TTTCT
1 TTTCT
5490463 CCCTTCTCTG
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
16 12 0.27
17 16 0.36
18 11 0.24
19 6 0.13
ACGTcount: A:0.00, C:0.27, G:0.05, T:0.68
Consensus pattern (18 bp):
TTTCTTTCTGTTTCTTTC
Found at i:5490469 original size:40 final size:43
Alignment explanation
Indices: 5490406--5490505 Score: 134
Period size: 42 Copynumber: 2.3 Consensus size: 43
5490396 CTTTTCTTTC
5490406 TTTCTTTCTTTCCTTCCTTCTTCTCTG-TTT-CGTTTTGCTCTCTG
1 TTTCTTTCTTT-C-TCC-TCTTCTCTGTTTTGCGTTTTGCTCTCTG
*
5490450 TTTCTTTCTTTCTCC-CTTCTCTGTTTTGTGTTTTGCTCTCTG
1 TTTCTTTCTTTCTCCTCTTCTCTGTTTTGCGTTTTGCTCTCTG
5490492 TTTCTTTTCTTTCT
1 TTTC-TTTCTTTCT
5490506 TTCTTTGTCA
Statistics
Matches: 52, Mismatches: 1, Indels: 7
0.87 0.02 0.12
Matches are distributed among these distances:
40 8 0.15
41 3 0.06
42 20 0.38
43 10 0.19
44 11 0.21
ACGTcount: A:0.00, C:0.27, G:0.09, T:0.64
Consensus pattern (43 bp):
TTTCTTTCTTTCTCCTCTTCTCTGTTTTGCGTTTTGCTCTCTG
Found at i:5490522 original size:2 final size:2
Alignment explanation
Indices: 5490515--5490572 Score: 53
Period size: 2 Copynumber: 33.5 Consensus size: 2
5490505 TTTCTTTGTC
5490515 AT AT AT AT AT A- AT AT AT AT A- AT AT A- AT A- AT A- 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
5490552 AT AT AT -T A- AT A- AT A- AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
5490573 AAACATAATT
Statistics
Matches: 47, Mismatches: 0, Indels: 18
0.72 0.00 0.28
Matches are distributed among these distances:
1 9 0.19
2 38 0.81
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:5490546 original size:20 final size:20
Alignment explanation
Indices: 5490523--5490572 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
5490513 TCATATATAT
5490523 ATAATATATATA-ATATAATA
1 ATAATATATATATAT-TAATA
5490543 ATAATATATATATATTAATA
1 ATAATATATATATATTAATA
5490563 ATAATATATA
1 ATAATATATA
5490573 AAACATAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 27 0.93
21 2 0.07
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
ATAATATATATATATTAATA
Found at i:5490580 original size:14 final size:14
Alignment explanation
Indices: 5490521--5490581 Score: 56
Period size: 14 Copynumber: 4.5 Consensus size: 14
5490511 TGTCATATAT
*
5490521 ATATAATATATATA
1 ATATAATATATAAA
*
5490535 ATATAATA-ATAAT
1 ATATAATATATAAA
*
5490548 ATAT-ATATAT-TA
1 ATATAATATATAAA
5490560 ATAATAATATATAAA
1 AT-ATAATATATAAA
*
5490575 ACATAAT
1 ATATAAT
5490582 TATTACTTAC
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
12 5 0.14
13 11 0.30
14 19 0.51
15 2 0.05
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (14 bp):
ATATAATATATAAA
Found at i:5490581 original size:20 final size:19
Alignment explanation
Indices: 5490523--5490581 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 19
5490513 TCATATATAT
*
5490523 ATAATATATATAATATAATA
1 ATAATATATA-AAAATAATA
* *
5490543 ATAATATATATATATTAATA
1 ATAATATATA-AAAATAATA
5490563 ATAATATATAAAACATAAT
1 ATAATATATAAAA-ATAAT
5490582 TATTACTTAC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
19 2 0.06
20 31 0.94
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (19 bp):
ATAATATATAAAAATAATA
Found at i:5491891 original size:45 final size:45
Alignment explanation
Indices: 5491842--5491927 Score: 118
Period size: 45 Copynumber: 1.9 Consensus size: 45
5491832 ATCTTTTTAC
* *
5491842 CATGATGTCATAGCGTCATTCATCCATGGTCTTACTCATTTCCAT
1 CATGATGTCATAGCATCATTCAACCATGGTCTTACTCATTTCCAT
** * *
5491887 CATGATGTCATAGCATTTTTCAACTATGGTCTTACTTATTT
1 CATGATGTCATAGCATCATTCAACCATGGTCTTACTCATTT
5491928 TAGGTATAGC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 35 1.00
ACGTcount: A:0.23, C:0.22, G:0.13, T:0.42
Consensus pattern (45 bp):
CATGATGTCATAGCATCATTCAACCATGGTCTTACTCATTTCCAT
Found at i:5495847 original size:27 final size:27
Alignment explanation
Indices: 5495809--5495873 Score: 103
Period size: 27 Copynumber: 2.4 Consensus size: 27
5495799 TTTATCGAGG
* *
5495809 TTATTAGTTTATCGTTAAATAAATATT
1 TTATTAATTTATCGATAAATAAATATT
*
5495836 TTATTAATTTATCGATAAATTAATATT
1 TTATTAATTTATCGATAAATAAATATT
5495863 TTATTAATTTA
1 TTATTAATTTA
5495874 GAGAATATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (27 bp):
TTATTAATTTATCGATAAATAAATATT
Found at i:5497501 original size:3 final size:3
Alignment explanation
Indices: 5497483--5497539 Score: 60
Period size: 3 Copynumber: 19.0 Consensus size: 3
5497473 ATAATAAATG
* * ***
5497483 TAA TAA CAA GAA TAA TAA TAA TAA TAA TAA GCT TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
5497531 TAA CAA TAA
1 TAA TAA TAA
5497540 CAGGATTAGA
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.63, C:0.05, G:0.04, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:5498814 original size:38 final size:33
Alignment explanation
Indices: 5498748--5498819 Score: 90
Period size: 33 Copynumber: 2.0 Consensus size: 33
5498738 TAGATCAAAG
*
5498748 TTAATTGGTTCATGTAACAAAAAAAAGAGTTAA
1 TTAATTGGTTCATGTAAAAAAAAAAAGAGTTAA
5498781 TTAATTGGTTCATGTAGCCAAAAAGAATAAAGAGTTAA
1 TTAATTGGTTCATGTA---AAAAA-AA-AAAGAGTTAA
5498819 T
1 T
5498820 GGTTTCAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
33 16 0.48
36 4 0.12
37 2 0.06
38 11 0.33
ACGTcount: A:0.46, C:0.07, G:0.17, T:0.31
Consensus pattern (33 bp):
TTAATTGGTTCATGTAAAAAAAAAAAGAGTTAA
Found at i:5500226 original size:14 final size:15
Alignment explanation
Indices: 5500202--5500230 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5500192 TTTTTCTGTG
5500202 TTTATTATGTGTGAA
1 TTTATTATGTGTGAA
5500217 TTTA-TATGTGTGAA
1 TTTATTATGTGTGAA
5500231 AGTTTCGTGA
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:0.28, C:0.00, G:0.21, T:0.52
Consensus pattern (15 bp):
TTTATTATGTGTGAA
Found at i:5500469 original size:28 final size:29
Alignment explanation
Indices: 5500424--5500482 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 29
5500414 CAGTTTTTAT
5500424 AATAATTATAAAGGTTATAATAATAA-AA
1 AATAATTATAAAGGTTATAATAATAATAA
*
5500452 AATATATTATAAA-GTTATTATAATAATAA
1 AATA-ATTATAAAGGTTATAATAATAATAA
5500481 AA
1 AA
5500483 AAACATAAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 16 0.57
29 12 0.43
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (29 bp):
AATAATTATAAAGGTTATAATAATAATAA
Found at i:5501634 original size:64 final size:64
Alignment explanation
Indices: 5501549--5501724 Score: 227
Period size: 64 Copynumber: 2.8 Consensus size: 64
5501539 ATATATATTT
* * *
5501549 AAAGTTCTTGAGTTGTATTTAATGTATGAATTTTATATACATATGTGGTTCAAATATAGGTTAC
1 AAAGTTTTTGAGCTGAATTTAATGTATGAATTTTATATACATATGTGGTTCAAATATAGGTTAC
* *
5501613 AAAGTTTTTGAGCTGAATTTAATGTATGAATTTTACATACATATGTGGTTCGAATATAGGTTAC
1 AAAGTTTTTGAGCTGAATTTAATGTATGAATTTTATATACATATGTGGTTCAAATATAGGTTAC
* * *
5501677 AAA-TCTTTGAGCTAAATTTTAATGT-TGTAA--AT-TATACATATGTGGTTC
1 AAAGTTTTTGAGCTGAA-TTTAATGTATG-AATTTTATATACATATGTGGTTC
5501725 GAATGTTTGT
Statistics
Matches: 101, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
61 15 0.15
62 1 0.01
63 13 0.13
64 72 0.71
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (64 bp):
AAAGTTTTTGAGCTGAATTTAATGTATGAATTTTATATACATATGTGGTTCAAATATAGGTTAC
Found at i:5501903 original size:41 final size:41
Alignment explanation
Indices: 5501844--5501946 Score: 179
Period size: 41 Copynumber: 2.5 Consensus size: 41
5501834 ATCTGATATT
* * *
5501844 TTCAGGCTTAATGCCTAGCAGACTTGATGTCGGTGAATTAC
1 TTCAGACTTTATGTCTAGCAGACTTGATGTCGGTGAATTAC
5501885 TTCAGACTTTATGTCTAGCAGACTTGATGTCGGTGAATTAC
1 TTCAGACTTTATGTCTAGCAGACTTGATGTCGGTGAATTAC
5501926 TTCAGACTTTATGTCTAGCAG
1 TTCAGACTTTATGTCTAGCAG
5501947 GCTTTGTGCC
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 59 1.00
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35
Consensus pattern (41 bp):
TTCAGACTTTATGTCTAGCAGACTTGATGTCGGTGAATTAC
Found at i:5501962 original size:41 final size:41
Alignment explanation
Indices: 5501844--5501962 Score: 150
Period size: 41 Copynumber: 2.9 Consensus size: 41
5501834 ATCTGATATT
* * * * *
5501844 TTCAGGCTTAATGCCTAGCAGACTTGATGTCGGTGAATTAC
1 TTCAGACTTTATGTCTAGCAGACTTGATGCCAGTGAATTAC
* *
5501885 TTCAGACTTTATGTCTAGCAGACTTGATGTCGGTGAATTAC
1 TTCAGACTTTATGTCTAGCAGACTTGATGCCAGTGAATTAC
*
5501926 TTCAGACTTTATGTCTAGCAGGCTTTG-TGCCAGTGAA
1 TTCAGACTTTATGTCTAGCAGAC-TTGATGCCAGTGAA
5501963 ATGTTTCAGG
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
41 68 0.96
42 3 0.04
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (41 bp):
TTCAGACTTTATGTCTAGCAGACTTGATGCCAGTGAATTAC
Found at i:5501971 original size:41 final size:41
Alignment explanation
Indices: 5501876--5501997 Score: 120
Period size: 41 Copynumber: 3.0 Consensus size: 41
5501866 CTTGATGTCG
* * * *
5501876 GTGAATTACTTCAGACTTTATGTCTAGCAGAC-TTGATGTCG
1 GTGAAATACTTCAGACTTTATGTCTAGCAGGCTTTG-TGCCA
*
5501917 GTGAATTACTTCAGACTTTATGTCTAGCAGGCTTTGTGCCA
1 GTGAAATACTTCAGACTTTATGTCTAGCAGGCTTTGTGCCA
** * * * * *
5501958 GTGAAATGTTTCAGGCTTTGTGCCTAGCCGGCTTTATGCC
1 GTGAAATACTTCAGACTTTATGTCTAGCAGGCTTTGTGCC
5501998 GATGTTTTAA
Statistics
Matches: 69, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
41 66 0.96
42 3 0.04
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (41 bp):
GTGAAATACTTCAGACTTTATGTCTAGCAGGCTTTGTGCCA
Found at i:5508311 original size:14 final size:15
Alignment explanation
Indices: 5508287--5508315 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5508277 TTTTTCTGTG
5508287 TTTATTATGTGTGAA
1 TTTATTATGTGTGAA
5508302 TTTA-TATGTGTGAA
1 TTTATTATGTGTGAA
5508316 AGTTTCGTGA
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:0.28, C:0.00, G:0.21, T:0.52
Consensus pattern (15 bp):
TTTATTATGTGTGAA
Found at i:5508553 original size:28 final size:28
Alignment explanation
Indices: 5508507--5508563 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
5508497 TATAGTTTTT
5508507 ATAATAATTATAAAGGTTATAATAATAA
1 ATAATAATTATAAAGGTTATAATAATAA
* *
5508535 ATAATATATTCTAAA-GTTATTATAATAA
1 ATAATA-ATTATAAAGGTTATAATAATAA
5508563 A
1 A
5508564 AAAACAAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 19 0.73
29 7 0.27
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.39
Consensus pattern (28 bp):
ATAATAATTATAAAGGTTATAATAATAA
Found at i:5509548 original size:21 final size:22
Alignment explanation
Indices: 5509522--5509564 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
5509512 GAGTTGAAAT
5509522 TAAAGTTATGAAT-TAT-ATATA
1 TAAAGTT-TGAATGTATGATATA
5509543 TAAAGTTTGAATGTATGATATA
1 TAAAGTTTGAATGTATGATATA
5509565 AGTTCTTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 5 0.25
21 10 0.50
22 5 0.25
ACGTcount: A:0.44, C:0.00, G:0.14, T:0.42
Consensus pattern (22 bp):
TAAAGTTTGAATGTATGATATA
Found at i:5509563 original size:20 final size:21
Alignment explanation
Indices: 5509522--5509565 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
5509512 GAGTTGAAAT
*
5509522 TAAAGTTATGAATTATATATA
1 TAAAGTTATGAATTATAGATA
5509543 TAAAGTT-TGAATGTAT-GATA
1 TAAAGTTATGAAT-TATAGATA
5509563 TAA
1 TAA
5509566 GTTCTTTGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.45, C:0.00, G:0.14, T:0.41
Consensus pattern (21 bp):
TAAAGTTATGAATTATAGATA
Found at i:5509571 original size:60 final size:61
Alignment explanation
Indices: 5509486--5509605 Score: 165
Period size: 61 Copynumber: 2.0 Consensus size: 61
5509476 ATGGATAAGT
* *
5509486 AGTTCGAATGTAAGATTTAATTTC-TTGAGTTGAA-ATTAA-AGTTATGAATTATATATATAA
1 AGTTCGAATGTAAGATATAAGTTCTTTGAGTTGAACA-TAATA-TTATGAATTATATATATAA
* *
5509546 AGTTTGAATGTATGATATAAGTTCTTTGAGTTGAACATAATATTATGAATTATATATATA
1 AGTTCGAATGTAAGATATAAGTTCTTTGAGTTGAACATAATATTATGAATTATATATATA
5509606 TATGCACATA
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
60 20 0.38
61 31 0.58
62 2 0.04
ACGTcount: A:0.39, C:0.03, G:0.15, T:0.42
Consensus pattern (61 bp):
AGTTCGAATGTAAGATATAAGTTCTTTGAGTTGAACATAATATTATGAATTATATATATAA
Found at i:5509711 original size:64 final size:64
Alignment explanation
Indices: 5509636--5509783 Score: 226
Period size: 64 Copynumber: 2.3 Consensus size: 64
5509626 ATATATATTT
* * * *
5509636 AAAGTTCTTGAGTTGTATTTAATATATGAATTTTATATACATATGTGGTTCAAATATAGGTTAC
1 AAAGTTTTTGAGCTGAATTTAATATATGAATTTTACATACATATGTGGTTCAAATATAGGTTAC
* *
5509700 AAAGTTTTTGAGCTGAATTTAATGTATGAATTTTACATACATATGTGGTTCGAATATAGGTTAC
1 AAAGTTTTTGAGCTGAATTTAATATATGAATTTTACATACATATGTGGTTCAAATATAGGTTAC
5509764 AAA-TTCTTTGAGCTGAATTT
1 AAAGTT-TTTGAGCTGAATTT
5509784 TAATGTTGTA
Statistics
Matches: 77, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
63 2 0.03
64 75 0.97
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (64 bp):
AAAGTTTTTGAGCTGAATTTAATATATGAATTTTACATACATATGTGGTTCAAATATAGGTTAC
Found at i:5510974 original size:15 final size:16
Alignment explanation
Indices: 5510951--5511006 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 16
5510941 TTTTTATGTT
*
5510951 TTATATATATTATTTTA
1 TTATATATA-TATTATA
*
5510968 TTATATAATATAATATA
1 TTATAT-ATATATTATA
*
5510985 TTATAT-TGTATTATA
1 TTATATATATATTATA
5511000 TTATATA
1 TTATATA
5511007 AATTAAATAG
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
15 13 0.39
17 17 0.52
18 3 0.09
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (16 bp):
TTATATATATATTATA
Found at i:5510990 original size:5 final size:5
Alignment explanation
Indices: 5510951--5511005 Score: 53
Period size: 5 Copynumber: 11.2 Consensus size: 5
5510941 TTTTTATGTT
* *
5510951 TTATA -TATA TTAT- TT-TA TTATA TAATATA ATATA TTATA TTGTA TTATA
1 TTATA TTATA TTATA TTATA TTATA T--TATA TTATA TTATA TTATA TTATA
5511000 TTATA T
1 TTATA T
5511006 AAATTAAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
3 1 0.02
4 8 0.20
5 28 0.68
7 4 0.10
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (5 bp):
TTATA
Found at i:5510991 original size:27 final size:29
Alignment explanation
Indices: 5510952--5511007 Score: 80
Period size: 27 Copynumber: 2.0 Consensus size: 29
5510942 TTTTATGTTT
*
5510952 TATATATATTATTTTATTATATAATATAA
1 TATATATATTATTGTATTATATAATATAA
*
5510981 TATAT-TA-TATTGTATTATATTATATAA
1 TATATATATTATTGTATTATATAATATAA
5511008 ATTAAATAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 18 0.72
28 2 0.08
29 5 0.20
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (29 bp):
TATATATATTATTGTATTATATAATATAA
Found at i:5511197 original size:19 final size:19
Alignment explanation
Indices: 5511161--5511196 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
5511151 TAAAAGAAAT
5511161 AAAGTAAAGTAAATAAAAG
1 AAAGTAAAGTAAATAAAAG
5511180 AAAGTAAAG-AAATAAAA
1 AAAGTAAAGTAAATAAAA
5511197 ACAAAACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.72, C:0.00, G:0.14, T:0.14
Consensus pattern (19 bp):
AAAGTAAAGTAAATAAAAG
Found at i:5511240 original size:15 final size:17
Alignment explanation
Indices: 5511222--5511253 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5511212 CAGAATAGAA
5511222 AGAA-CAAA-GAAACAG
1 AGAAGCAAACGAAACAG
5511237 AGAAGCAAACGAAACAG
1 AGAAGCAAACGAAACAG
5511254 GGGAAGAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.27
16 4 0.27
17 7 0.47
ACGTcount: A:0.62, C:0.16, G:0.22, T:0.00
Consensus pattern (17 bp):
AGAAGCAAACGAAACAG
Found at i:5511933 original size:12 final size:12
Alignment explanation
Indices: 5511916--5511958 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
5511906 ATGTGAAGTA
5511916 AGTATTAATATT
1 AGTATTAATATT
*
5511928 AGTATTAATATA
1 AGTATTAATATT
* *
5511940 ATTATTAGTATT
1 AGTATTAATATT
*
5511952 ATTATTA
1 AGTATTA
5511959 TTATGAGTGG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (12 bp):
AGTATTAATATT
Found at i:5511947 original size:18 final size:18
Alignment explanation
Indices: 5511924--5511962 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
5511914 TAAGTATTAA
5511924 TATTAGTATTAATATAAT
1 TATTAGTATTAATATAAT
* *
5511942 TATTAGTATTATTATTAT
1 TATTAGTATTAATATAAT
5511960 TAT
1 TAT
5511963 GAGTGGGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (18 bp):
TATTAGTATTAATATAAT
Found at i:5514945 original size:31 final size:31
Alignment explanation
Indices: 5514908--5514972 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
5514898 TATAATTATA
5514908 TTTAATTGCTTTATGTACTCAAATTATAATC
1 TTTAATTGCTTTATGTACTCAAATTATAATC
*
5514939 TTTAATTTCTTTATGTACTCAAATTATAATC
1 TTTAATTGCTTTATGTACTCAAATTATAATC
5514970 TTT
1 TTT
5514973 GTGTAAGTGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.31, C:0.12, G:0.05, T:0.52
Consensus pattern (31 bp):
TTTAATTGCTTTATGTACTCAAATTATAATC
Found at i:5519317 original size:19 final size:18
Alignment explanation
Indices: 5519293--5519338 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
5519283 GAAATAAATT
*
5519293 TATAAAAATCGTAAAAAAA
1 TATAAAAATAG-AAAAAAA
*
5519312 TATAAAATATAGAAAAAAT
1 TATAAAA-ATAGAAAAAAA
5519331 TATAAAAA
1 TATAAAAA
5519339 ATTATGAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 1 0.04
19 20 0.83
20 3 0.12
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.24
Consensus pattern (18 bp):
TATAAAAATAGAAAAAAA
Found at i:5519373 original size:20 final size:19
Alignment explanation
Indices: 5519350--5519405 Score: 51
Period size: 20 Copynumber: 2.8 Consensus size: 19
5519340 TTATGAAGTC
5519350 GTAATAAAATTATAAAAAAG
1 GTAA-AAAATTATAAAAAAG
***
5519370 GTAAAGAAA-TATAAAATTT
1 GTAAA-AAATTATAAAAAAG
5519389 GTAAAAAAATTATAAAA
1 GT-AAAAAATTATAAAA
5519406 GTTATCATAC
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
19 13 0.43
20 17 0.57
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.27
Consensus pattern (19 bp):
GTAAAAAATTATAAAAAAG
Found at i:5519640 original size:29 final size:30
Alignment explanation
Indices: 5519589--5519645 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
5519579 TTTGATGCAT
*
5519589 TTTATAATTTTTTAATGA-TTTTTACAAAA
1 TTTACAATTTTTTAATGATTTTTTACAAAA
5519618 TTTACAATTTTTT-ATGATTTTTTTACAA
1 TTTACAATTTTTTAATGA-TTTTTTACAA
5519646 TTTTTATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 4 0.16
29 12 0.48
30 9 0.36
ACGTcount: A:0.33, C:0.05, G:0.04, T:0.58
Consensus pattern (30 bp):
TTTACAATTTTTTAATGATTTTTTACAAAA
Found at i:5519644 original size:21 final size:19
Alignment explanation
Indices: 5519618--5519659 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 19
5519608 TTTTACAAAA
5519618 TTTACAATTTTTTATGATTTT
1 TTTACAA-TTTTTAT-ATTTT
5519639 TTTACAATTTTTATATTTT
1 TTTACAATTTTTATATTTT
5519658 TT
1 TT
5519660 CTAATTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 7 0.33
20 7 0.33
21 7 0.33
ACGTcount: A:0.24, C:0.05, G:0.02, T:0.69
Consensus pattern (19 bp):
TTTACAATTTTTATATTTT
Found at i:5519656 original size:29 final size:29
Alignment explanation
Indices: 5519587--5519668 Score: 78
Period size: 29 Copynumber: 2.8 Consensus size: 29
5519577 TTTTTGATGC
5519587 ATTTTATAATTTTTTAATGA--TTTTTACAA
1 ATTTTAT-ATTTTTT-ATGATTTTTTTACAA
* *
5519616 AATTTACAATTTTTTATGATTTTTTTACAA
1 ATTTTA-TATTTTTTATGATTTTTTTACAA
* * *
5519646 TTTTTATATTTTTTCTAATTTTT
1 ATTTTATATTTTTTATGATTTTT
5519669 AATAAATTAT
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
28 4 0.09
29 26 0.60
30 13 0.30
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (29 bp):
ATTTTATATTTTTTATGATTTTTTTACAA
Found at i:5522421 original size:34 final size:34
Alignment explanation
Indices: 5522373--5522437 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
5522363 AACCACTACC
* *
5522373 ATAAATATATTAAATATTTTATTATATTAAAAAA
1 ATAAATAAAATAAATATTTTATTATATTAAAAAA
* *
5522407 ATAAATAAAATAAATGTTTTATTGTATTAAA
1 ATAAATAAAATAAATATTTTATTATATTAAA
5522438 TATAATATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (34 bp):
ATAAATAAAATAAATATTTTATTATATTAAAAAA
Found at i:5522938 original size:32 final size:32
Alignment explanation
Indices: 5522897--5522962 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
5522887 AGTAGGAGTT
5522897 GGATTGCATTTTGCTCATCTACTTAAAAAATG
1 GGATTGCATTTTGCTCATCTACTTAAAAAATG
5522929 GGATTGCATTTTGCTCATCTACTTAAAAAATG
1 GGATTGCATTTTGCTCATCTACTTAAAAAATG
5522961 GG
1 GG
5522963 CAATTAGTCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.36
Consensus pattern (32 bp):
GGATTGCATTTTGCTCATCTACTTAAAAAATG
Found at i:5524289 original size:42 final size:42
Alignment explanation
Indices: 5524243--5524363 Score: 154
Period size: 42 Copynumber: 2.9 Consensus size: 42
5524233 GACATGGGCA
*
5524243 TGTGCCCAGGCCGTGTGAGTCACACGGGTAAGGACATAGGTG
1 TGTGCCCAGGCCGTGTGAGTCACACGGGTAAGGACATAGATG
* * *
5524285 TGTGCCCAAGCCGTATGA-TCCTCACGGGTAAGGACATAGATG
1 TGTGCCCAGGCCGTGTGAGT-CACACGGGTAAGGACATAGATG
* * * *
5524327 TGTGCCCAGGCCATGTGAGCCACATGGGCAAGGACAT
1 TGTGCCCAGGCCGTGTGAGTCACACGGGTAAGGACAT
5524364 GTGCATGTGT
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 1 0.02
42 65 0.98
ACGTcount: A:0.24, C:0.24, G:0.33, T:0.19
Consensus pattern (42 bp):
TGTGCCCAGGCCGTGTGAGTCACACGGGTAAGGACATAGATG
Found at i:5527471 original size:21 final size:21
Alignment explanation
Indices: 5527447--5527511 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
5527437 AACTTAAAAT
5527447 AGAGGCAGCAACGAGAGAAGC
1 AGAGGCAGCAACGAGAGAAGC
* *
5527468 AGAGGCTGCAGCGAGAGAAGC
1 AGAGGCAGCAACGAGAGAAGC
*
5527489 AGAGGCTA-CAACGCGAGAAGC
1 AGAGGC-AGCAACGAGAGAAGC
5527510 AG
1 AG
5527512 CGAGAGAAGC
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.38, C:0.20, G:0.38, T:0.03
Consensus pattern (21 bp):
AGAGGCAGCAACGAGAGAAGC
Found at i:5528014 original size:42 final size:42
Alignment explanation
Indices: 5527949--5528082 Score: 135
Period size: 42 Copynumber: 3.1 Consensus size: 42
5527939 TAACAGAAAA
**
5527949 AAACGCCGTTAAAG-ATCATGATCTTTAACGGCGTCTTTTTTT
1 AAACGCCACTAAAGAAT-ATGATCTTTAACGGCGTCTTTTTTT
* ** * **
5527991 AAGCGCTGCTAAAGAATATGATCTTTAGCGGTATCTTTTTTT
1 AAACGCCACTAAAGAATATGATCTTTAACGGCGTCTTTTTTT
* * *
5528033 AAATGCCACTAAAGAACATGATCTTTAACGGCGTTTTTTTCTGT
1 AAACGCCACTAAAGAATATGATCTTTAACGGCGTCTTTTT-T-T
5528077 AAACGC
1 AAACGC
5528083 TGCAAAAGTT
Statistics
Matches: 73, Mismatches: 16, Indels: 4
0.78 0.17 0.04
Matches are distributed among these distances:
42 64 0.88
43 3 0.04
44 6 0.08
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.37
Consensus pattern (42 bp):
AAACGCCACTAAAGAATATGATCTTTAACGGCGTCTTTTTTT
Found at i:5530421 original size:5 final size:5
Alignment explanation
Indices: 5530411--5530442 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
5530401 AAATGATGAA
5530411 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TT
5530443 GTTAACATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:5534124 original size:9 final size:9
Alignment explanation
Indices: 5534110--5534151 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
5534100 TGTGAAGGTT
5534110 AAAAATAAA
1 AAAAATAAA
5534119 AAAAATAAA
1 AAAAATAAA
5534128 AAAAA-ACAA
1 AAAAATA-AA
*
5534137 AACATATAAA
1 AA-AAATAAA
5534147 AAAAA
1 AAAAA
5534152 CGCACGAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
8 1 0.04
9 20 0.71
10 6 0.21
11 1 0.04
ACGTcount: A:0.86, C:0.05, G:0.00, T:0.10
Consensus pattern (9 bp):
AAAAATAAA
Found at i:5534138 original size:17 final size:18
Alignment explanation
Indices: 5534109--5534152 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
5534099 ATGTGAAGGT
*
5534109 TAAAAATAA-AAAAAATA
1 TAAAAAAAACAAAAAATA
*
5534126 -AAAAAAAACAAAACATA
1 TAAAAAAAACAAAAAATA
5534143 TAAAAAAAAC
1 TAAAAAAAAC
5534153 GCACGAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 7 0.30
17 7 0.30
18 9 0.39
ACGTcount: A:0.82, C:0.07, G:0.00, T:0.11
Consensus pattern (18 bp):
TAAAAAAAACAAAAAATA
Found at i:5534138 original size:19 final size:19
Alignment explanation
Indices: 5534110--5534151 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
5534100 TGTGAAGGTT
*
5534110 AAAAATAAAAAAAATAAAA
1 AAAAACAAAAAAAATAAAA
* *
5534129 AAAAACAAAACATATAAAA
1 AAAAACAAAAAAAATAAAA
5534148 AAAA
1 AAAA
5534152 CGCACGAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.86, C:0.05, G:0.00, T:0.10
Consensus pattern (19 bp):
AAAAACAAAAAAAATAAAA
Found at i:5534152 original size:18 final size:17
Alignment explanation
Indices: 5534109--5534152 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
5534099 ATGTGAAGGT
5534109 TAAAAATAAA-AAAAATA
1 TAAAAA-AAACAAAAATA
5534126 -AAAAAAAACAAAACATA
1 TAAAAAAAACAAAA-ATA
5534143 TAAAAAAAAC
1 TAAAAAAAAC
5534153 GCACGAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 3 0.12
16 9 0.38
17 3 0.12
18 9 0.38
ACGTcount: A:0.82, C:0.07, G:0.00, T:0.11
Consensus pattern (17 bp):
TAAAAAAAACAAAAATA
Found at i:5534240 original size:23 final size:25
Alignment explanation
Indices: 5534196--5534249 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
5534186 CTTATGAACA
** *
5534196 TATATATTTTATATAAAGAAATATG
1 TATATATACTATATAAAGAAATACG
*
5534221 TATATATACTATAT-AA-AAATGCG
1 TATATATACTATATAAAGAAATACG
5534244 TATATA
1 TATATA
5534250 AGTTTAGAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
23 11 0.44
24 2 0.08
25 12 0.48
ACGTcount: A:0.48, C:0.04, G:0.07, T:0.41
Consensus pattern (25 bp):
TATATATACTATATAAAGAAATACG
Found at i:5535826 original size:50 final size:50
Alignment explanation
Indices: 5535747--5536713 Score: 561
Period size: 50 Copynumber: 19.3 Consensus size: 50
5535737 AATTGTAATA
* * * * * * *
5535747 TTCAATTTGTTCAACTGCAATGTCGGGGAAACCAGATCCGCCGTCGTAGC
1 TTCAATCTGTTCCATTGCACTGTCAGGGAAACAAGATCCGCCGTTGTAGC
** * ** * *
5535797 TTCAATCTGTTCCACCGCACCGTCAGGGAAGTAAGATCTGCCGTTGTGGC
1 TTCAATCTGTTCCATTGCACTGTCAGGGAAACAAGATCCGCCGTTGTAGC
* ** * * *
5535847 TTCAATCTTTTAAATTGCAATGTCA-GGAATACTAGATCCGCCGTCGTAGC
1 TTCAATCTGTTCCATTGCACTGTCAGGGAA-ACAAGATCCGCCGTTGTAGC
* * * * ** * *
5535897 TTCAATCTATTCTATTGTACTG-CTAAGGAAGTAAGATCCGCCGTTGTGGT
1 TTCAATCTGTTCCATTGCACTGTC-AGGGAAACAAGATCCGCCGTTGTAGC
* ** * * * **
5535947 TTCAATCTTTTTTATTGCAATATCAGGGAAACCAGATCTACCGTTGTAGC
1 TTCAATCTGTTCCATTGCACTGTCAGGGAAACAAGATCCGCCGTTGTAGC
* * ** *
5535997 TTCAATCTGTTCCACTGCACTG-CTAAGGAAGTAAGATCCGCCGTTGTGGC
1 TTCAATCTGTTCCATTGCACTGTC-AGGGAAACAAGATCCGCCGTTGTAGC
* ** * * * *
5536047 TTCAATCTTTTTGATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGC
1 TTCAATCTGTTCCATTGCACTGTCAGGGAAACAAGATCCGCCGTTGTAGC
* * ** * * * *
5536097 TTCAATCTGTTCCACTGCACTGTTAAAGAAGCAAGATCTGCCGTTATGGC
1 TTCAATCTGTTCCATTGCACTGTCAGGGAAACAAGATCCGCCGTTGTAGC
** * * *
5536147 TTCAATCT-TTTTATTGCAATATCAGGGAAACCAGATCCGCC-TTCGTAGC
1 TTCAATCTGTTCCATTGCACTGTCAGGGAAACAAGATCCGCCGTT-GTAGC
* ** ** *
5536196 TTCAATCTGTTCCACTGCACTG-CTAAAGAAGTAAGATCCGCCGTTGTGGC
1 TTCAATCTGTTCCATTGCACTGTC-AGGGAAACAAGATCCGCCGTTGTAGC
* ** * * * *
5536246 TTCAATCTTTTTGATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGC
1 TTCAATCTGTTCCATTGCACTGTCAGGGAAACAAGATCCGCCGTTGTAGC
* * * ** *
5536296 TTTAATCTGTTCCACTGCACTG-CTAAGGAAGTAAGATCCGCCGTTGTGGC
1 TTCAATCTGTTCCATTGCACTGTC-AGGGAAACAAGATCCGCCGTTGTAGC
* ** * * * *
5536346 TTCAATCTTTTTGATTGCAATATCAGGGAAACTAGATCCGCCGTCGTAGC
1 TTCAATCTGTTCCATTGCACTGTCAGGGAAACAAGATCCGCCGTTGTAGC
* * * ** * *
5536396 TTCAATCTGTTCTACTGCGCTG-CTA-ATAAAGTAAGATCCGCCGTTGTGGC
1 TTCAATCTGTTCCATTGCACTGTC-AGGGAAA-CAAGATCCGCCGTTGTAGC
* ** * * * *
5536446 TTCAAT-TTTTTGATTGCAATATCAAGGAAACCAGATCCGCCGTTGTAGC
1 TTCAATCTGTTCCATTGCACTGTCAGGGAAACAAGATCCGCCGTTGTAGC
* * ** *
5536495 TTCAATCTGTTCCACTGCACTG-CTAAGGAAGTAAGATCCGCCGTTGTGGC
1 TTCAATCTGTTCCATTGCACTGTC-AGGGAAACAAGATCCGCCGTTGTAGC
* ** * * * * *
5536545 TTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCATCGTAGC
1 TTCAATCTGTTCCATTGCACTGTCAGGGAAACAAGATCCGCCGTTGTAGC
* * * ** *
5536595 TTTAATCTGTTCCACTGCACTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGC
1 TTCAATCTGTTCCATTGCACTG---T-C-AGGGAAACAAGATCCGCCGTTGTAGC
* * ** * * * * * *
5536650 TTCAATATTTTTAATTGTAATATCAGGGAAACCAGATCCACCGTCGTAGC
1 TTCAATCTGTTCCATTGCACTGTCAGGGAAACAAGATCCGCCGTTGTAGC
5536700 TTCAATCTGTTCCA
1 TTCAATCTGTTCCA
5536714 CTGCTGCCCA
Statistics
Matches: 658, Mismatches: 234, Indels: 50
0.70 0.25 0.05
Matches are distributed among these distances:
48 2 0.00
49 77 0.12
50 532 0.81
51 12 0.02
52 1 0.00
53 1 0.00
54 1 0.00
55 32 0.05
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (50 bp):
TTCAATCTGTTCCATTGCACTGTCAGGGAAACAAGATCCGCCGTTGTAGC
Found at i:5535927 original size:100 final size:100
Alignment explanation
Indices: 5535762--5536717 Score: 1452
Period size: 100 Copynumber: 9.5 Consensus size: 100
5535752 TTTGTTCAAC
* * * * *
5535762 TGCAATGTCGGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACCGCACCG-TCAGGGA
1 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCT-AAGGA
* **
5535826 AGTAAGATCTGCCGTTGTGGCTTCAATCTTTTAAAT
65 AGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTGAT
* * * * * *
5535862 TGCAATGTCA-GGAATACTAGATCCGCCGTCGTAGCTTCAATCTATTCTATTGTACTGCTAAGGA
1 TGCAATATCAGGGAA-ACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGA
* *
5535926 AGTAAGATCCGCCGTTGTGGTTTCAATCTTTTTTAT
65 AGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTGAT
** *
5535962 TGCAATATCAGGGAAACCAGATCTACCGTTGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAA
1 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAA
5536027 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTGAT
66 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTGAT
* *
5536062 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGTTAAAGAA
1 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAA
* * *
5536127 GCAAGATCTGCCGTTATGGCTTCAATCTTTTT-AT
66 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTGAT
* *
5536161 TGCAATATCAGGGAAACCAGATCCGCCTTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAAGAA
1 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAA
5536226 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTGAT
66 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTGAT
*
5536261 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTTAATCTGTTCCACTGCACTGCTAAGGAA
1 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAA
5536326 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTGAT
66 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTGAT
* * * **
5536361 TGCAATATCAGGGAAACTAGATCCGCCGTCGTAGCTTCAATCTGTTCTACTGCGCTGCTAATAAA
1 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAA
5536426 GTAAGATCCGCCGTTGTGGCTTCAAT-TTTTTGAT
66 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTGAT
* *
5536460 TGCAATATCAAGGAAACCAGATCCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAA
1 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAA
*
5536525 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAAT
66 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTGAT
* *
5536560 TGCAATATCAGGGAAACCAGATCCGCCATCGTAGCTTTAATCTGTTCCACTGCACTGCACTGCTA
1 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTT---C--CACTGCACTGCTA
* *
5536625 AGGAAGTAAGATCCGCCGTTGTGGCTTCAATATTTTTAAT
61 AGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTGAT
* *
5536665 TGTAATATCAGGGAAACCAGATCCACCGTCGTAGCTTCAATCTGTTCCACTGC
1 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGC
5536718 TGCCCAGAGA
Statistics
Matches: 783, Mismatches: 63, Indels: 20
0.90 0.07 0.02
Matches are distributed among these distances:
99 190 0.24
100 492 0.63
101 5 0.01
102 1 0.00
103 1 0.00
105 94 0.12
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (100 bp):
TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAA
GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTGAT
Found at i:5536311 original size:299 final size:298
Alignment explanation
Indices: 5535762--5536717 Score: 1468
Period size: 299 Copynumber: 3.2 Consensus size: 298
5535752 TTTGTTCAAC
* * * * * **
5535762 TGCAATGTCGGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACCGCACCGTCAGGGAA
1 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGTTAAAGAA
* * * *
5535827 GTAAGATCTGCCGTTGTGGCTTCAATCTTTTAAATTGCAATGTCAGGAATACTAGATCCGCCGTC
66 GTAAGATCTGCCGTTGTGGCTTCAATCTTTT-TATTGCAATATCAGGAA-ACCAGATCCGCCTTC
* * * * *
5535892 GTAGCTTCAATCTATTCTATTGTACTGCTAAGGAAGTAAGATCCGCCGTTGTGGTTTCAATCTTT
129 GTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTT
* ** * *
5535957 TTTATTGCAATATCAGGGAAACCAGATCTACCGTTGTAGCTTCAATCTGTTCCACTGCACTGCTA
194 TTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTTAATCTGTTCCACTGCACTGCTA
5536022 AGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTGAT
259 AGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTGAT
5536062 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGTTAAAGAA
1 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGTTAAAGAA
* *
5536127 GCAAGATCTGCCGTTATGGCTTCAATCTTTTTATTGCAATATCAGGGAAACCAGATCCGCCTTCG
66 GTAAGATCTGCCGTTGTGGCTTCAATCTTTTTATTGCAATATCA-GGAAACCAGATCCGCCTTCG
*
5536192 TAGCTTCAATCTGTTCCACTGCACTGCTAAAGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTT
130 TAGCTTCAATCTGTTCCACTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTT
*
5536257 TGATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTTAATCTGTTCCACTGCACTGCTAA
195 TAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTTAATCTGTTCCACTGCACTGCTAA
5536322 GGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTGAT
260 GGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTGAT
* * * *
5536361 TGCAATATCAGGGAAACTAGATCCGCCGTCGTAGCTTCAATCTGTTCTACTGCGCTGCTAATA-A
1 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGTTAA-AGA
*
5536425 AGTAAGATCCGCCGTTGTGGCTTCAAT-TTTTTGATTGCAATATCAAGGAAACCAGATCCGCCGT
65 AGTAAGATCTGCCGTTGTGGCTTCAATCTTTTT-ATTGCAATATC-AGGAAACCAGATCCGCC-T
5536489 T-GTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCT
127 TCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCT
*
5536553 TTTTAATTGCAATATCAGGGAAACCAGATCCGCCATCGTAGCTTTAATCTGTTCCACTGCACTGC
192 TTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTTAATCTGTT---C--CACTGC
* *
5536618 ACTGCTAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATATTTTTAAT
252 ACTGCTAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTGAT
* *
5536665 TGTAATATCAGGGAAACCAGATCCACCGTCGTAGCTTCAATCTGTTCCACTGC
1 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGC
5536718 TGCCCAGAGA
Statistics
Matches: 606, Mismatches: 40, Indels: 16
0.92 0.06 0.02
Matches are distributed among these distances:
298 5 0.01
299 405 0.67
300 95 0.16
302 1 0.00
304 100 0.17
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (298 bp):
TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGTTAAAGAA
GTAAGATCTGCCGTTGTGGCTTCAATCTTTTTATTGCAATATCAGGAAACCAGATCCGCCTTCGT
AGCTTCAATCTGTTCCACTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTT
AATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTTAATCTGTTCCACTGCACTGCTAAG
GAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTGAT
Done.