Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr2
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: 41236440
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2030548 characters in sequence are not A, C, G, or T
File 84 of 106
Found at i:31884803 original size:56 final size:56
Alignment explanation
Indices: 31884696--31884829 Score: 160
Period size: 56 Copynumber: 2.4 Consensus size: 56
31884686 CTTTTAGCCT
* * *
31884696 TCAAAAATCAGTAGCTAAAGCTACTAATCTCACCTTCAAAATCAACGGCCAAAACC
1 TCAAAAATCAGCAGCTAAAGCTACTAATCTCACCCTCAAAATCAACAGCCAAAACC
* * * *** *
31884752 TCAAAAATCAACAGCTAAAGCTACTTATCTCACCCTCGAAATCGGTAGCCAAAGCC
1 TCAAAAATCAGCAGCTAAAGCTACTAATCTCACCCTCAAAATCAACAGCCAAAACC
* *
31884808 TAAAAAATTAGCAGCTAAAGCT
1 TCAAAAATCAGCAGCTAAAGCT
31884830 GCTCCTTTCA
Statistics
Matches: 65, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
56 65 1.00
ACGTcount: A:0.42, C:0.27, G:0.11, T:0.20
Consensus pattern (56 bp):
TCAAAAATCAGCAGCTAAAGCTACTAATCTCACCCTCAAAATCAACAGCCAAAACC
Found at i:31884804 original size:148 final size:148
Alignment explanation
Indices: 31884604--31884885 Score: 366
Period size: 148 Copynumber: 1.9 Consensus size: 148
31884594 CTTTCAGCCT
* * * * *
31884604 TCAAAAATCAGCAGCTAAAGCTACTCATCTGATCCTCAAAATCGATAACCAAAACCTCAACAATC
1 TCAAAAATCAACAGCTAAAGCTACTCATCTCACCCTCAAAATCGATAACCAAAACCTAAAAAATC
* * * * ** *
31884669 AGTAGCAAAAGGTGCTTCTTTTAGCCTTCAAAAATCAGTAGCTAAAGCTACTAATCTCACCTTCA
66 AGCAGCAAAAGCTGCTCCTTTCAGCCTTCAAAAATCAACAGCTAAAGCTACTAATCTCACCCTCA
31884734 AAATCAACGGCCAAAACC
131 AAATCAACGGCCAAAACC
* * * * * *
31884752 TCAAAAATCAACAGCTAAAGCTACTTATCTCACCCTCGAAATCGGTAGCCAAAGCCTAAAAAATT
1 TCAAAAATCAACAGCTAAAGCTACTCATCTCACCCTCAAAATCGATAACCAAAACCTAAAAAATC
* * * *
31884817 AGCAGCTAAAGCTGCTCCTTTCAGCTTTCAAAAATCAACAGCTAAAGCTGCTCATCTCACCCTCA
66 AGCAGCAAAAGCTGCTCCTTTCAGCCTTCAAAAATCAACAGCTAAAGCTACTAATCTCACCCTCA
31884882 AAAT
131 AAAT
31884886 TGACAGAAAA
Statistics
Matches: 112, Mismatches: 22, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
148 112 1.00
ACGTcount: A:0.39, C:0.28, G:0.11, T:0.23
Consensus pattern (148 bp):
TCAAAAATCAACAGCTAAAGCTACTCATCTCACCCTCAAAATCGATAACCAAAACCTAAAAAATC
AGCAGCAAAAGCTGCTCCTTTCAGCCTTCAAAAATCAACAGCTAAAGCTACTAATCTCACCCTCA
AAATCAACGGCCAAAACC
Found at i:31884990 original size:18 final size:18
Alignment explanation
Indices: 31884967--31885053 Score: 67
Period size: 18 Copynumber: 5.1 Consensus size: 18
31884957 TTGACTTTTC
31884967 TCTTCTTTTTCTTTCCTT
1 TCTTCTTTTTCTTTCCTT
*
31884985 TCTTCTTTCTCTTT-C--
1 TCTTCTTTTTCTTTCCTT
* *** *
31885000 TCTTCCTAGGCTGTT--TC
1 TCTTCTTTTTCT-TTCCTT
31885017 TCTTCTTTTTCTTTCCTT
1 TCTTCTTTTTCTTTCCTT
*
31885035 TCTTCTTTTGCTTTCCTT
1 TCTTCTTTTTCTTTCCTT
31885053 T
1 T
31885054 TGCTCTCTCT
Statistics
Matches: 53, Mismatches: 11, Indels: 10
0.72 0.15 0.14
Matches are distributed among these distances:
15 8 0.15
16 4 0.08
17 9 0.17
18 32 0.60
ACGTcount: A:0.01, C:0.29, G:0.05, T:0.66
Consensus pattern (18 bp):
TCTTCTTTTTCTTTCCTT
Found at i:31884990 original size:23 final size:23
Alignment explanation
Indices: 31884964--31885040 Score: 77
Period size: 23 Copynumber: 3.2 Consensus size: 23
31884954 CGTTTGACTT
31884964 TTCTCTTCTTTTTCTTTCCTTTC
1 TTCTCTTCTTTTTCTTTCCTTTC
*
31884987 TTCT-TTCTCTTTCTCTTCCTAGGCTGT-
1 TTCTCTTCTTTTTCT-TTCCT----T-TC
31885014 TTCTCTTCTTTTTCTTTCCTTTC
1 TTCTCTTCTTTTTCTTTCCTTTC
31885037 TTCT
1 TTCT
31885041 TTTGCTTTCC
Statistics
Matches: 44, Mismatches: 2, Indels: 16
0.71 0.03 0.26
Matches are distributed among these distances:
22 10 0.23
23 14 0.32
27 10 0.23
28 10 0.23
ACGTcount: A:0.01, C:0.30, G:0.04, T:0.65
Consensus pattern (23 bp):
TTCTCTTCTTTTTCTTTCCTTTC
Found at i:31889336 original size:19 final size:20
Alignment explanation
Indices: 31889307--31889346 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
31889297 TCACTTCTAA
31889307 ACTTCAAATCATACTCCAAT
1 ACTTCAAATCATACTCCAAT
31889327 ACTT-AAATCATACTCCAAT
1 ACTTCAAATCATACTCCAAT
31889346 A
1 A
31889347 AGTCAAATGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.42, C:0.28, G:0.00, T:0.30
Consensus pattern (20 bp):
ACTTCAAATCATACTCCAAT
Found at i:31895688 original size:13 final size:13
Alignment explanation
Indices: 31895670--31895694 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31895660 ATTTGTAAAA
31895670 ATTTTATAAAATT
1 ATTTTATAAAATT
31895683 ATTTTATAAAAT
1 ATTTTATAAAAT
31895695 CTCATTTTCC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATTTTATAAAATT
Found at i:31896821 original size:19 final size:20
Alignment explanation
Indices: 31896785--31896824 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
31896775 TCACTTATAA
*
31896785 ACTTCAAATCATACTCCAAT
1 ACTTCAAATAATACTCCAAT
*
31896805 ACTT-AAATAATAGTCCAAT
1 ACTTCAAATAATACTCCAAT
31896824 A
1 A
31896825 AGCCAAATGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.45, C:0.23, G:0.03, T:0.30
Consensus pattern (20 bp):
ACTTCAAATAATACTCCAAT
Found at i:31907392 original size:17 final size:18
Alignment explanation
Indices: 31907358--31907392 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
31907348 AGAAAAATGT
*
31907358 CTAACCGAAGTAATTATA
1 CTAACCGAACTAATTATA
31907376 CTAACCGAACT-ATTATA
1 CTAACCGAACTAATTATA
31907393 ACCGAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.43, C:0.20, G:0.09, T:0.29
Consensus pattern (18 bp):
CTAACCGAACTAATTATA
Found at i:31908631 original size:46 final size:46
Alignment explanation
Indices: 31908578--31908670 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
31908568 AAAATGTAGG
31908578 TTTTGGTTTTGTTTTGGTACACTCAATTGCACCAAGGTAAAGTTAC
1 TTTTGGTTTTGTTTTGGTACACTCAATTGCACCAAGGTAAAGTTAC
31908624 TTTTGGTTTTGTTTTGGTACACTCAATTGCACCAAGGTAAAGTTAC
1 TTTTGGTTTTGTTTTGGTACACTCAATTGCACCAAGGTAAAGTTAC
31908670 T
1 T
31908671 CTAGACTCTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.24, C:0.15, G:0.19, T:0.42
Consensus pattern (46 bp):
TTTTGGTTTTGTTTTGGTACACTCAATTGCACCAAGGTAAAGTTAC
Found at i:31925319 original size:16 final size:16
Alignment explanation
Indices: 31925298--31925383 Score: 52
Period size: 16 Copynumber: 5.4 Consensus size: 16
31925288 GTATGTATGT
31925298 ATGTATATACATGTAC
1 ATGTATATACATGTAC
* * *
31925314 ATGTATATATATATATAT
1 ATG--TATATACATGTAC
*
31925332 ATGTATA-ATATGT--
1 ATGTATATACATGTAC
* *
31925345 ATATAAATACATGTAC
1 ATGTATATACATGTAC
* **
31925361 ATATATATACACATAC
1 ATGTATATACATGTAC
31925377 ATGTATA
1 ATGTATA
31925384 ATATGTATAT
Statistics
Matches: 54, Mismatches: 11, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
13 5 0.09
14 5 0.09
15 5 0.09
16 26 0.48
18 13 0.24
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (16 bp):
ATGTATATACATGTAC
Found at i:31925322 original size:2 final size:2
Alignment explanation
Indices: 31925317--31925444 Score: 84
Period size: 2 Copynumber: 66.0 Consensus size: 2
31925307 CATGTACATG
* * * * *
31925317 TA TA TA TA TA TA TA TA TG TA TA -A TA TG TA TA TA AA TA CA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * * *
31925358 TA CA TA TA TA TA CA CA TA CA TG TA TA -A TA TG TA TA TA AA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
31925399 TA TA TA TA TA TA TA CA TA CA TA CA TA CA TA TA TA T- TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
31925439 TA TA TA
1 TA TA TA
31925445 AAACTTGAAT
Statistics
Matches: 92, Mismatches: 30, Indels: 8
0.71 0.23 0.06
Matches are distributed among these distances:
1 4 0.04
2 88 0.96
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (2 bp):
TA
Found at i:31925381 original size:45 final size:45
Alignment explanation
Indices: 31925274--31925423 Score: 167
Period size: 45 Copynumber: 3.3 Consensus size: 45
31925264 ATTGAATTTG
* * * * *
31925274 ATATATGCATATATGTAT-GTATGTATGTATATACATGTACATGTAT
1 ATATATACATACATGTATAATATGTATATAAATACATGTACA--TAT
* *
31925320 ATATATATATATATGTATAATATGTATATAAATACATGTACATAT
1 ATATATACATACATGTATAATATGTATATAAATACATGTACATAT
* * * *
31925365 ATATACACATACATGTATAATATGTATATAAATATATATATATAT
1 ATATATACATACATGTATAATATGTATATAAATACATGTACATAT
*
31925410 ATACATACATACAT
1 ATATATACATACAT
31925424 ACATATATAT
Statistics
Matches: 90, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
45 54 0.60
46 16 0.18
47 20 0.22
ACGTcount: A:0.44, C:0.07, G:0.08, T:0.41
Consensus pattern (45 bp):
ATATATACATACATGTATAATATGTATATAAATACATGTACATAT
Found at i:31925438 original size:45 final size:45
Alignment explanation
Indices: 31925336--31925438 Score: 127
Period size: 45 Copynumber: 2.3 Consensus size: 45
31925326 ATATATATGT
* * **
31925336 ATAATATGTATATAAATACATGTACATATATATACACATACATGT
1 ATAATATGTATATAAATACATATACATATATACACACATACATAC
* * *
31925381 ATAATATGTATATAAATATATATATATATATACATACATACATAC
1 ATAATATGTATATAAATACATATACATATATACACACATACATAC
31925426 ATATATAT-TATAT
1 ATA-ATATGTATAT
31925439 TATATAAAAC
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
45 46 0.92
46 4 0.08
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.39
Consensus pattern (45 bp):
ATAATATGTATATAAATACATATACATATATACACACATACATAC
Found at i:31928735 original size:2 final size:2
Alignment explanation
Indices: 31928728--31928812 Score: 161
Period size: 2 Copynumber: 42.0 Consensus size: 2
31928718 TTTGATACAA
31928728 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31928770 NAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31928813 TCATCACCAT
Statistics
Matches: 82, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
2 80 0.98
3 2 0.02
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:31940259 original size:73 final size:73
Alignment explanation
Indices: 31940166--31940320 Score: 249
Period size: 73 Copynumber: 2.1 Consensus size: 73
31940156 AATGGGCTAG
*
31940166 TCGACTAAGAGTCTACTGCCAAAAATTTGGACTTCAAGATAGAACCAACTTAATCGACGAAGAA-
1 TCGACTAAGAGTCTACTGCCAAAAATTTGGACTTCAAGATAGAAACAACTTAATCGACGAAGAAG
31940230 GATAGTTAC
66 GA-AGTTAC
* * *
31940239 TCGACTAAGAGTCTATTGCCAGAAATTTGGACTTCAAGATAGAAACAACTTAATCGACTAAGAAG
1 TCGACTAAGAGTCTACTGCCAAAAATTTGGACTTCAAGATAGAAACAACTTAATCGACGAAGAAG
*
31940304 GAAGTTAG
66 GAAGTTAC
31940312 TCGACTAAG
1 TCGACTAAG
31940321 TGCTCACTGC
Statistics
Matches: 76, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
73 74 0.97
74 2 0.03
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.24
Consensus pattern (73 bp):
TCGACTAAGAGTCTACTGCCAAAAATTTGGACTTCAAGATAGAAACAACTTAATCGACGAAGAAG
GAAGTTAC
Found at i:31954839 original size:86 final size:85
Alignment explanation
Indices: 31954683--31954839 Score: 224
Period size: 86 Copynumber: 1.8 Consensus size: 85
31954673 CAGCAACGTT
* * * *
31954683 GAAGGGAGAGGGAAGCAAAGAAATACGGGCGGCAAACCCAAAGAACAAAAAACAAAAGAAGAAGA
1 GAAGGCAGAGGGAAGCAAAGAAACACGGGCGACAAACCCAAAGAACAAAAAACAAAAGAAGAAAA
*
31954748 TAGATGCAAAAAATAAAAAA
66 AAGATGCAAAAAATAAAAAA
* * * *
31954768 GAAGGCAGAGGGAAGCAAGGAAAACACGGGCGACAAGCCCAAAGAACAAAAAACAAAATAGGAAA
1 GAAGGCAGAGGGAAGCAAAG-AAACACGGGCGACAAACCCAAAGAACAAAAAACAAAAGAAGAAA
31954833 AAAGATG
65 AAAGATG
31954840 TGAAAAGTCC
Statistics
Matches: 62, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
85 18 0.29
86 44 0.71
ACGTcount: A:0.57, C:0.13, G:0.26, T:0.04
Consensus pattern (85 bp):
GAAGGCAGAGGGAAGCAAAGAAACACGGGCGACAAACCCAAAGAACAAAAAACAAAAGAAGAAAA
AAGATGCAAAAAATAAAAAA
Found at i:31965067 original size:21 final size:21
Alignment explanation
Indices: 31965043--31965083 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
31965033 TAATTTATCT
*
31965043 AATATATATGTGTATATATAC
1 AATATATATATGTATATATAC
*
31965064 AATATATGTATGTATATATA
1 AATATATATATGTATATATA
31965084 TATATTTTAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.44
Consensus pattern (21 bp):
AATATATATATGTATATATAC
Found at i:31965745 original size:17 final size:17
Alignment explanation
Indices: 31965723--31965756 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
31965713 CTTCTCAGCT
31965723 CTCCTTCCTCTTGCGCC
1 CTCCTTCCTCTTGCGCC
31965740 CTCCTTCCTCTTGCGCC
1 CTCCTTCCTCTTGCGCC
31965757 GGCAGATCGC
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:0.00, C:0.53, G:0.12, T:0.35
Consensus pattern (17 bp):
CTCCTTCCTCTTGCGCC
Found at i:31965798 original size:84 final size:86
Alignment explanation
Indices: 31965654--31965823 Score: 272
Period size: 84 Copynumber: 2.0 Consensus size: 86
31965644 CACTCAGCTT
* * *
31965654 TCCTTCCTCTTGCGCCGGCAGCAGATCATGGCTCCGCCTCTCCCTCCTTCTCTATTCCTCTTCTC
1 TCCTTCCTCTTGCGCCGG-AGCAGATCACGGCTCCGCCTCTCCCTCATTCTCTATTCCTCTGCTC
31965719 AGCTCTCCTTCCTCTTGCGCCC
65 AGCTCTCCTTCCTCTTGCGCCC
*
31965741 TCCTTCCTCTTGCGCC-G-GCAGATCGCGGCTCCGCCTCTCCCTCATTCTCTATTCCTCTGCTCA
1 TCCTTCCTCTTGCGCCGGAGCAGATCACGGCTCCGCCTCTCCCTCATTCTCTATTCCTCTGCTCA
*
31965804 TCTCTCCTTCCTCTTGCGCC
66 GCTCTCCTTCCTCTTGCGCC
31965824 GGCAGCAGAT
Statistics
Matches: 78, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
84 61 0.78
86 1 0.01
87 16 0.21
ACGTcount: A:0.06, C:0.46, G:0.14, T:0.34
Consensus pattern (86 bp):
TCCTTCCTCTTGCGCCGGAGCAGATCACGGCTCCGCCTCTCCCTCATTCTCTATTCCTCTGCTCA
GCTCTCCTTCCTCTTGCGCCC
Found at i:31965849 original size:70 final size:70
Alignment explanation
Indices: 31965740--31966083 Score: 604
Period size: 70 Copynumber: 5.0 Consensus size: 70
31965730 CTCTTGCGCC
*
31965740 CTCCTTCCTCTTGCGCC-G--GCAGATCGCGGCTCCGCCTCTCCCTCATTCTCTATTCCTCTGCT
1 CTCCTTCCTCTTGCGCCGGCAGCAGATCGCGGCTCCGCCTCTCCCTCCTTCTCTATTCCTCTGCT
*
31965802 CATCT
66 CAGCT
31965807 CTCCTTCCTCTTGCGCCGGCAGCAGATCGCGGCTCCGCCTCTCCCTCCTTCTCTATTCCTCTGCT
1 CTCCTTCCTCTTGCGCCGGCAGCAGATCGCGGCTCCGCCTCTCCCTCCTTCTCTATTCCTCTGCT
31965872 CAGCT
66 CAGCT
*
31965877 CTCCTTCCCCTTGCGCCGGCAGCAGATCGCGGCTCCGCCTCTCCCTCCTTCTCTATTCCTCTGCT
1 CTCCTTCCTCTTGCGCCGGCAGCAGATCGCGGCTCCGCCTCTCCCTCCTTCTCTATTCCTCTGCT
31965942 CAGCT
66 CAGCT
*
31965947 CTCCTTCCCCTTGCGCCGGCAGCAGATCGCGGCTCCGCCTCTCCCTCCTTCTCTATTCCTCTGCT
1 CTCCTTCCTCTTGCGCCGGCAGCAGATCGCGGCTCCGCCTCTCCCTCCTTCTCTATTCCTCTGCT
31966012 CAGCT
66 CAGCT
* * *
31966017 CTCCTTCCTCTTGCGTCGGCAGTAGATCGCGGCTCCGCCTCTCCCACCTTCTCTATTCCTCTGCT
1 CTCCTTCCTCTTGCGCCGGCAGCAGATCGCGGCTCCGCCTCTCCCTCCTTCTCTATTCCTCTGCT
31966082 CA
66 CA
31966084 AAATCCCAAA
Statistics
Matches: 267, Mismatches: 7, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
67 17 0.06
68 1 0.00
70 249 0.93
ACGTcount: A:0.08, C:0.46, G:0.17, T:0.30
Consensus pattern (70 bp):
CTCCTTCCTCTTGCGCCGGCAGCAGATCGCGGCTCCGCCTCTCCCTCCTTCTCTATTCCTCTGCT
CAGCT
Found at i:31979840 original size:2 final size:2
Alignment explanation
Indices: 31979833--31979870 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
31979823 AGCTGTCATT
31979833 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
31979871 CNNNNNNCCG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:31979909 original size:2 final size:2
Alignment explanation
Indices: 31979902--31979941 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
31979892 CTGTCATTCT
31979902 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC -C TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
31979942 GTGTACATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:31985544 original size:16 final size:17
Alignment explanation
Indices: 31985513--31985546 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
31985503 TTATTTGTTA
31985513 AAATAATACATTTAATT
1 AAATAATACATTTAATT
*
31985530 AAATAATA-TTTTAATT
1 AAATAATACATTTAATT
31985546 A
1 A
31985547 TGCTTAACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
AAATAATACATTTAATT
Found at i:31985685 original size:21 final size:21
Alignment explanation
Indices: 31985655--31985694 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
31985645 GACTTAGAAC
*
31985655 TTTAATCAAGATCCATGCAAT
1 TTTAACCAAGATCCATGCAAT
31985676 TTTAACCAAGATCCATGCA
1 TTTAACCAAGATCCATGCA
31985695 TCGCTTAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.23, G:0.10, T:0.30
Consensus pattern (21 bp):
TTTAACCAAGATCCATGCAAT
Found at i:31986054 original size:3 final size:3
Alignment explanation
Indices: 31986046--31986070 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
31986036 TGCAAGTAAA
31986046 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
31986071 TGTAGATATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:31991204 original size:60 final size:60
Alignment explanation
Indices: 31991137--31991266 Score: 251
Period size: 60 Copynumber: 2.2 Consensus size: 60
31991127 GTTGGGTTAG
31991137 GGGTGTGAGTCAACGAAACAGGGTTCTGCTGGTTTGCTGCGAATTGAATTGCTGGGATTT
1 GGGTGTGAGTCAACGAAACAGGGTTCTGCTGGTTTGCTGCGAATTGAATTGCTGGGATTT
*
31991197 GGGTGTGAGTCAACGACACAGGGTTCTGCTGGTTTGCTGCGAATTGAATTGCTGGGATTT
1 GGGTGTGAGTCAACGAAACAGGGTTCTGCTGGTTTGCTGCGAATTGAATTGCTGGGATTT
31991257 GGGTGTGAGT
1 GGGTGTGAGT
31991267 AGCTGTTTGG
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
60 69 1.00
ACGTcount: A:0.18, C:0.13, G:0.37, T:0.32
Consensus pattern (60 bp):
GGGTGTGAGTCAACGAAACAGGGTTCTGCTGGTTTGCTGCGAATTGAATTGCTGGGATTT
Found at i:31998209 original size:23 final size:22
Alignment explanation
Indices: 31998169--31998215 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
31998159 ATTAGCTTAC
31998169 TTAATCAAACTTATTAAATTGAA
1 TTAATCAAACTTATTAAATT-AA
*
31998192 TTAATCAAATTTCA-TAAATTAA
1 TTAATCAAACTT-ATTAAATTAA
31998214 TT
1 TT
31998216 TGGTTAAGTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 4 0.18
23 17 0.77
24 1 0.05
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.43
Consensus pattern (22 bp):
TTAATCAAACTTATTAAATTAA
Found at i:32012428 original size:20 final size:20
Alignment explanation
Indices: 32012403--32012441 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
32012393 TGTCAAAACT
32012403 GATGAACTTT-GTTGGTAATG
1 GATGAA-TTTCGTTGGTAATG
32012423 GATGAATTTCGTTGGTAAT
1 GATGAATTTCGTTGGTAAT
32012442 AACTACAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.26, C:0.05, G:0.28, T:0.41
Consensus pattern (20 bp):
GATGAATTTCGTTGGTAATG
Found at i:32021591 original size:2 final size:2
Alignment explanation
Indices: 32021584--32021609 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
32021574 ATACAAATGG
32021584 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
32021610 ACACACGCAT
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:32027391 original size:199 final size:194
Alignment explanation
Indices: 32027040--32027419 Score: 571
Period size: 199 Copynumber: 1.9 Consensus size: 194
32027030 TTCAAAACTC
* *
32027040 GCAAGACTATCCTACTAATCGTCAAACTGAAGTAGTAAATCACTGTTTAGGGAATCTGTTGCATT
1 GCAAGAATATCCTACTAATCGTCAAACTGAAGTAGGAAATCACTGTTTAGGGAATCTGTTGCATT
** *
32027105 GTGTTGTAGGAGAGAAGCAAGCTAATTGGCATTTATTTGGTTTATTTTGTTGTACTTTATTTGTT
66 ACGTTGTAGGAGAGAACCAAGCTAATTGGCATTTATTTGGTTTATTTTGTTGTACTTTATTTGTT
* * *
32027170 AGTTAGGTAAGCTTTATTCTCTATAGGCTTAAAACCTAGGTTGATGAAGTTAATCCATGTATAT
131 AGTTAGGTAAGCTTTATTCTCTATAAGCATAAAACCTAGGTTAATGAAGTTAATCCATGTATAT
* * * * *
32027234 GCAAGAATGTCCTACTAATGGTCAAACTGCAGTAGGGAATCACTGTTTGGGGAATCTGCTGTGTT
1 GCAAGAATATCCTACTAATCGTCAAACTGAAGTAGGAAATCACTGTTTAGGGAA--T-C--TGTT
*
32027299 GCATTACGTTGTAGGAGAGAACCAAGGTAATTGGCATTTATTTGGTTTATTTTGTTGTACTTTAT
61 GCATTACGTTGTAGGAGAGAACCAAGCTAATTGGCATTTATTTGGTTTATTTTGTTGTACTTTAT
* *
32027364 TTGTTTGTTAGGTAAGCTTTGTTCTCTATAAGCATAAAACCTAGGTTAATGAAGTT
126 TTGTTAGTTAGGTAAGCTTTATTCTCTATAAGCATAAAACCTAGGTTAATGAAGTT
32027420 TATATATATA
Statistics
Matches: 165, Mismatches: 16, Indels: 5
0.89 0.09 0.03
Matches are distributed among these distances:
194 47 0.28
196 1 0.01
197 1 0.01
199 116 0.70
ACGTcount: A:0.27, C:0.12, G:0.22, T:0.38
Consensus pattern (194 bp):
GCAAGAATATCCTACTAATCGTCAAACTGAAGTAGGAAATCACTGTTTAGGGAATCTGTTGCATT
ACGTTGTAGGAGAGAACCAAGCTAATTGGCATTTATTTGGTTTATTTTGTTGTACTTTATTTGTT
AGTTAGGTAAGCTTTATTCTCTATAAGCATAAAACCTAGGTTAATGAAGTTAATCCATGTATAT
Found at i:32034787 original size:91 final size:89
Alignment explanation
Indices: 32034673--32034869 Score: 252
Period size: 91 Copynumber: 2.2 Consensus size: 89
32034663 TAAATTTATC
*
32034673 ACTA-AAATATTAATAATTTAAAATGTTAATGATTCAATTATAAATAAAATATTAATATCTAAAT
1 ACTATAAATATTAAT-ATTTAAAATGTTAATGATTAAATTATAAATAAAATATTAATATCTAAAT
* * * * *
32034737 TATCGATTATTAATATTTTCATTAA
65 GATCAATTATAAATATTTTAAATAA
* * * *
32034762 ACTATAAAGTATTAATATTTAAAAATGTTAATGATTAAATTGTAAATAAAATATTGATTTTTAAA
1 ACTATAAA-TATTAATATTT-AAAATGTTAATGATTAAATTATAAATAAAATATTAATATCTAAA
32034827 TGATCAATTATAAATATTTTAAATAA
64 TGATCAATTATAAATATTTTAAATAA
* *
32034853 ATTATAAATTTTAATAT
1 ACTATAAATATTAATAT
32034870 AAAAACAAAA
Statistics
Matches: 93, Mismatches: 12, Indels: 5
0.85 0.11 0.05
Matches are distributed among these distances:
89 4 0.04
90 15 0.16
91 74 0.80
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.43
Consensus pattern (89 bp):
ACTATAAATATTAATATTTAAAATGTTAATGATTAAATTATAAATAAAATATTAATATCTAAATG
ATCAATTATAAATATTTTAAATAA
Found at i:32035007 original size:42 final size:42
Alignment explanation
Indices: 32034910--32035010 Score: 123
Period size: 42 Copynumber: 2.4 Consensus size: 42
32034900 AAAATAACAT
* * *
32034910 TTAAATTTATAAATAAACTATTAATATTTCAAAATGTTAATGA
1 TTAAATTT-TAAATAAAATATTAATATTTCAAAATATCAATGA
* * *
32034953 TTAAATTATAAATAAAATATTAATATTT-AAATTATCAATTA
1 TTAAATTTTAAATAAAATATTAATATTTCAAAATATCAATGA
32034994 TTAATATTTTAAATAAA
1 TTAA-ATTTTAAATAAA
32035011 TTATAAATTA
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
41 13 0.26
42 30 0.60
43 7 0.14
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (42 bp):
TTAAATTTTAAATAAAATATTAATATTTCAAAATATCAATGA
Found at i:32035114 original size:156 final size:156
Alignment explanation
Indices: 32034765--32035143 Score: 557
Period size: 156 Copynumber: 2.4 Consensus size: 156
32034755 TCATTAAACT
* * * *
32034765 ATAAAGTATTAATATTTAAAAATGTTAATGATTAAATTGTAAATAAAATATTGATTTTTAAATGA
1 ATAAACTATTAATATTTAAAAATGTTAATGATTAAATTATAAATAAAATATTAATTTTTAAATTA
32034830 TCAATTATAAATATTTTAAATAAATTATAAATTTTAATATAAAAACAAAATAAAATAAAAACAAA
66 TCAATTATAAATATTTTAAATAAATTATAAA-TTTAATATAAAAACAAAATAAAATAAAAACAAA
32034895 TAATCAAAATAACATTTAAATTTATAA
130 TAATCAAAATAACATTTAAATTTATAA
* *
32034922 ATAAACTATTAATATTTCAAAATGTTAATGATTAAATTATAAATAAAATATTAATATTTAAATTA
1 ATAAACTATTAATATTTAAAAATGTTAATGATTAAATTATAAATAAAATATTAATTTTTAAATTA
* *** *
32034987 TCAATTATTAATATTTTAAATAAATTATAAA-TTAATA-ACATTTCAAAAATAAAATAAAAATAA
66 TCAATTATAAATATTTTAAATAAATTATAAATTTAATATA-AAAAC-AAAATAAAATAAAAACAA
* *
32035050 ATAATCATAATAACATTTGAATTTATAA
129 ATAATCAAAATAACATTTAAATTTATAA
* * *
32035078 ATGAAA-TATTAATATTTTAGAATGTTAATGATTAAATTATAAATAAATTATTAATTTTTAAATT
1 AT-AAACTATTAATATTTAAAAATGTTAATGATTAAATTATAAATAAAATATTAATTTTTAAATT
32035142 AT
65 AT
32035144 TAACTTTTAA
Statistics
Matches: 202, Mismatches: 17, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
154 1 0.00
155 8 0.04
156 101 0.50
157 92 0.46
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (156 bp):
ATAAACTATTAATATTTAAAAATGTTAATGATTAAATTATAAATAAAATATTAATTTTTAAATTA
TCAATTATAAATATTTTAAATAAATTATAAATTTAATATAAAAACAAAATAAAATAAAAACAAAT
AATCAAAATAACATTTAAATTTATAA
Found at i:32035119 original size:42 final size:41
Alignment explanation
Indices: 32035072--32035287 Score: 142
Period size: 42 Copynumber: 5.2 Consensus size: 41
32035062 ACATTTGAAT
*
32035072 TTATAAATGAAATATTAATATTTTAGAATGTTAATGATTAAA
1 TTATAAATAAAATATTAATATTTTA-AATGTTAATGATTAAA
* * *
32035114 TTATAAATAAATTATTAAT-TTTTAAATTATTAACT-TTTAAA
1 TTATAAATAAAATATTAATATTTTAAA-TGTTAA-TGATTAAA
** * * * *
32035155 AAATAAAATAAAATA-AAAAATAATTATAA---TAA-CATTTAAA
1 TTAT-AAATAAAATATTAATAT-TTTA-AATGTTAATGA-TTAAA
* * *
32035195 TTATAAATAAAATATTATTATTTTAAAATGTTAATGACTGAA
1 TTATAAATAAAATATTAATATTTT-AAATGTTAATGATTAAA
* * *
32035237 TTATAAATAAAATATTAATA-TTTAAATGATCAATTATTATA
1 TTATAAATAAAATATTAATATTTTAAATG-TTAATGATTAAA
*
32035278 TTTTAAATAA
1 TTATAAATAA
32035288 TTATATATTA
Statistics
Matches: 132, Mismatches: 27, Indels: 31
0.69 0.14 0.16
Matches are distributed among these distances:
39 14 0.11
40 21 0.16
41 38 0.29
42 53 0.40
43 4 0.03
44 2 0.02
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (41 bp):
TTATAAATAAAATATTAATATTTTAAATGTTAATGATTAAA
Found at i:32035141 original size:15 final size:15
Alignment explanation
Indices: 32035121--32035154 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
32035111 AAATTATAAA
*
32035121 TAAATTATTAATTTT
1 TAAATTATTAACTTT
32035136 TAAATTATTAACTTT
1 TAAATTATTAACTTT
32035151 TAAA
1 TAAA
32035155 AAATAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (15 bp):
TAAATTATTAACTTT
Found at i:32035208 original size:156 final size:154
Alignment explanation
Indices: 32034765--32035208 Score: 475
Period size: 156 Copynumber: 2.8 Consensus size: 154
32034755 TCATTAAACT
* * * *
32034765 ATAAAGTATTAATATTTAAAAATGTTAATGATTAAATTGTAAATAAAATATTGATTTTTAAATGA
1 ATAAACTATTAATATTTAAAAATGTTAATGATTAAATTATAAATAAAATATTAATTTTTAAATTA
* ** * *
32034830 TCAATTATAAATATTTTAAATAAATTATAAATTTTAA-TATAAAAACAAAATAAA-ATAAAAACA
66 TCAATTTTAAA-ATTTTAAATAAA--ATAAAAATTAATTATAATAAC-AAATAAATATAAATA-A
32034893 AATAATCAAAATAACATTTAAATTTATAA
126 AATAATCAAAATAACATTTAAATTTATAA
* *
32034922 ATAAACTATTAATATTTCAAAATGTTAATGATTAAATTATAAATAAAATATTAATATTTAAATTA
1 ATAAACTATTAATATTTAAAAATGTTAATGATTAAATTATAAATAAAATATTAATTTTTAAATTA
* * * * * * *
32034987 TCAATTATTAATATTTTAAATAAATTATAAATTAATAACATTTCAA-AAATAAA-ATAAAAATAA
66 TCAATT-TTAAAATTTTAAATAAAATAAAAATTAATTATA-AT-AACAAATAAATATAAATA-AA
* *
32035050 ATAATCATAATAACATTTGAATTTATAA
127 ATAATCAAAATAACATTTAAATTTATAA
* * *
32035078 ATGAAA-TATTAATATTTTAGAATGTTAATGATTAAATTATAAATAAATTATTAATTTTTAAATT
1 AT-AAACTATTAATATTTAAAAATGTTAATGATTAAATTATAAATAAAATATTAATTTTTAAATT
* ** * * **
32035142 ATTAACTTTTAAAAAATAAAATAAAATAAAAAATAATTATAATAACATTTAAATTATAAATAAAA
65 ATCAA-TTTTAAAATTTTAAATAAAATAAAAATTAATTATAATAACAAATAAA-TATAAATAAAA
32035207 TA
128 TA
32035209 TTATTATTTT
Statistics
Matches: 241, Mismatches: 37, Indels: 19
0.81 0.12 0.06
Matches are distributed among these distances:
154 2 0.01
155 13 0.05
156 133 0.55
157 88 0.37
158 5 0.02
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (154 bp):
ATAAACTATTAATATTTAAAAATGTTAATGATTAAATTATAAATAAAATATTAATTTTTAAATTA
TCAATTTTAAAATTTTAAATAAAATAAAAATTAATTATAATAACAAATAAATATAAATAAAATAA
TCAAAATAACATTTAAATTTATAA
Found at i:32035211 original size:123 final size:122
Alignment explanation
Indices: 32035014--32035263 Score: 358
Period size: 123 Copynumber: 2.0 Consensus size: 122
32035004 AAATAAATTA
* * *
32035014 TAAATTAATAACATTTCAAAAATAAAATAAAAATAAATAATCATAATAACATTTGAATTTATAAA
1 TAAATTAATAACATTTAAAAAATAAAATAAAAAAAAATAATCATAATAACATTTGAAATTATAAA
* * * * *
32035079 TGAAATATTAATATTTTAGAATGTTAATGATTAAATTATAAATAAATTATTAATTTT
66 TAAAATATTAATATTTTAAAATGTTAATGACTAAATTATAAATAAAATATTAATATT
* * *
32035136 TAAATTATTAACTTTTAAAAAATAAAATAAAATAAAAAATAATTATAATAACATTT-AAATTATA
1 TAAATTAATAACATTTAAAAAATAAAAT-AAA-AAAAAATAATCATAATAACATTTGAAATTATA
* *
32035200 AATAAAATATTATTATTTTAAAATGTTAATGACTGAATTATAAATAAAATATTAATATT
64 AATAAAATATTAATATTTTAAAATGTTAATGACTAAATTATAAATAAAATATTAATATT
32035259 TAAAT
1 TAAAT
32035264 GATCAATTAT
Statistics
Matches: 113, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
122 25 0.22
123 67 0.59
124 21 0.19
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (122 bp):
TAAATTAATAACATTTAAAAAATAAAATAAAAAAAAATAATCATAATAACATTTGAAATTATAAA
TAAAATATTAATATTTTAAAATGTTAATGACTAAATTATAAATAAAATATTAATATT
Found at i:32035307 original size:25 final size:22
Alignment explanation
Indices: 32035249--32035309 Score: 61
Period size: 22 Copynumber: 2.6 Consensus size: 22
32035239 ATAAATAAAA
*
32035249 TATTAATATTTAAATGATCAAT
1 TATTAATATTTAAATAATCAAT
*
32035271 TATT-ATATTTTAAATAATTATATAT
1 TATTAATA-TTTAAATAA-T-CA-AT
32035296 TATTAATATTTAAA
1 TATTAATATTTAAA
32035310 AAATAGAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
21 3 0.09
22 12 0.38
23 1 0.03
24 1 0.03
25 12 0.38
26 3 0.09
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (22 bp):
TATTAATATTTAAATAATCAAT
Found at i:32048078 original size:20 final size:20
Alignment explanation
Indices: 32048019--32048078 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
32048009 TGGTAAGGTG
32048019 AAATGGCA-TGGGAGCATGA
1 AAATGGCATTGGGAGCATGA
* * **
32048038 AAATGGCGTTGGGTGGGTGA
1 AAATGGCATTGGGAGCATGA
32048058 AAATGGCATTGGGAGCATGA
1 AAATGGCATTGGGAGCATGA
32048078 A
1 A
32048079 GGTGGAGGAG
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
19 7 0.22
20 25 0.78
ACGTcount: A:0.32, C:0.08, G:0.40, T:0.20
Consensus pattern (20 bp):
AAATGGCATTGGGAGCATGA
Found at i:32050036 original size:13 final size:13
Alignment explanation
Indices: 32050018--32050042 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
32050008 TTCCAAAAAA
32050018 TTTATAAAATCAT
1 TTTATAAAATCAT
32050031 TTTATAAAATCA
1 TTTATAAAATCA
32050043 CAATTTCTCC
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:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:32051291 original size:19 final size:19
Alignment explanation
Indices: 32051267--32051304 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
32051257 ACTTCTAAAC
*
32051267 CTCAAATTATACTCCAATA
1 CTCAAATCATACTCCAATA
32051286 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
32051305 AGTCAAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:32054630 original size:13 final size:13
Alignment explanation
Indices: 32054612--32054637 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
32054602 TTTCAAAAAA
32054612 TTTATAAAATCAT
1 TTTATAAAATCAT
32054625 TTTATAAAATCAT
1 TTTATAAAATCAT
32054638 AATTTCTCCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:32060453 original size:25 final size:24
Alignment explanation
Indices: 32060391--32060450 Score: 77
Period size: 25 Copynumber: 2.5 Consensus size: 24
32060381 ATTTGAGGAG
*
32060391 TGTCTTTATTTATTTTTAAGTTGT
1 TGTCTTTATTTATCTTTAAGTTGT
*
32060415 TGGTCTTTATTTATCTTT-ATTTGCT
1 T-GTCTTTATTTATCTTTAAGTTG-T
32060440 TGTCTTTATTT
1 TGTCTTTATTT
32060451 TATTATTTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
24 15 0.47
25 17 0.53
ACGTcount: A:0.13, C:0.08, G:0.12, T:0.67
Consensus pattern (24 bp):
TGTCTTTATTTATCTTTAAGTTGT
Found at i:32063767 original size:43 final size:43
Alignment explanation
Indices: 32063706--32063900 Score: 201
Period size: 43 Copynumber: 4.5 Consensus size: 43
32063696 ATTAAGGATG
* * **
32063706 CCTTTTAAAGTTACGTAACTTTATTCTAGATGGGGAGCTTATT
1 CCTTTTAAAGTTACGTAACCTTATTCCAGATGAAGAGCTTATT
*
32063749 CCTTTTAAAGTTACGTAACCTCATTCCAGATGAAGAGCTTATT
1 CCTTTTAAAGTTACGTAACCTTATTCCAGATGAAGAGCTTATT
* * *
32063792 CTTTTTAAAGTTACGTAACCTTATTCCAAATGAGGAGCTTATT
1 CCTTTTAAAGTTACGTAACCTTATTCCAGATGAAGAGCTTATT
* * ** * * ** ** *
32063835 CATTTTAAATTTATATAGCTTTATTTTAGATGAAGAATTTCTT
1 CCTTTTAAAGTTACGTAACCTTATTCCAGATGAAGAGCTTATT
32063878 CCTACTTTAAAGTTACGTAACCT
1 CCT--TTTAAAGTTACGTAACCT
32063901 CATTTCAATT
Statistics
Matches: 122, Mismatches: 28, Indels: 2
0.80 0.18 0.01
Matches are distributed among these distances:
43 109 0.89
45 13 0.11
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.41
Consensus pattern (43 bp):
CCTTTTAAAGTTACGTAACCTTATTCCAGATGAAGAGCTTATT
Found at i:32064554 original size:5 final size:5
Alignment explanation
Indices: 32064544--32064609 Score: 51
Period size: 5 Copynumber: 11.8 Consensus size: 5
32064534 TGAGTTTCTT
* *
32064544 TTTTA TTTTA TTTTTTA TTCTAA TTTTTA TTTTTA TTTTTA TCTTA TTTTA
1 TTTTA TTTTA --TTTTA TT-TTA -TTTTA -TTTTA -TTTTA TTTTA TTTTA
32064595 TTTTA TTTTAA TTTT
1 TTTTA TTTT-A TTTT
32064610 TAAGACATTT
Statistics
Matches: 52, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
5 24 0.46
6 21 0.40
7 7 0.13
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:32064558 original size:6 final size:6
Alignment explanation
Indices: 32064543--32064611 Score: 65
Period size: 6 Copynumber: 12.0 Consensus size: 6
32064533 GTGAGTTTCT
* * *
32064543 TTTTTA -TTTTA TTTTTTA TTCTAA TTTTTA TTTTTA TTTTTA -TCTTA
1 TTTTTA TTTTTA -TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
*
32064590 -TTTTA -TTTTA TTTTAA TTTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA
32064612 AGACATTTAA
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
5 18 0.35
6 29 0.56
7 5 0.10
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (6 bp):
TTTTTA
Found at i:32064917 original size:163 final size:163
Alignment explanation
Indices: 32064639--32064936 Score: 404
Period size: 163 Copynumber: 1.8 Consensus size: 163
32064629 GGATTTACAT
* *
32064639 TAAATAAATAAAAATTCTCCAATGATGGATTCAAAAAGGTTATGAATAATAGCTTCTTGAAAATT
1 TAAACAAATAAAAATTCTCCAATGATGGATTCAAAAAGGTTATGAATAATAGCTTCCTGAAAATT
* * * * * *
32064704 TCTAAATGAGAGATTTTTCTTAAATTCTATCATAATTGTTCAAGTTTTCAAGGAATATTTCAATA
66 TCTAAACGAAAGATTTTTCTTAAATGCTATCATAAGTGTTCAAATTTTCAACGAATATTTCAATA
32064769 -CCAAAGAATTTTTGTTTATTTCAATCACATAG
131 TCCAAAGAATTTTTGTTTATTTCAATCACATAG
* * *
32064801 TAAACAAATAAAAATTC-CCTACTGATGGAATTTCAAGAA-GTTATGAATAATTGCTTCCTGAAA
1 TAAACAAATAAAAATTCTCC-AATGATGG-A-TTCAAAAAGGTTATGAATAATAGCTTCCTGAAA
** * * *
32064864 ATTTCTAGGCGAAAGATTTTTCTTGAATGCTATCATAAGTGTTGAAATTTTCAACGAATGTTTCA
63 ATTTCTAAACGAAAGATTTTTCTTAAATGCTATCATAAGTGTTCAAATTTTCAACGAATATTTCA
32064929 ATATCCAA
128 ATATCCAA
32064937 TAGTTTTTTT
Statistics
Matches: 116, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
161 2 0.02
162 23 0.20
163 80 0.69
164 11 0.09
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (163 bp):
TAAACAAATAAAAATTCTCCAATGATGGATTCAAAAAGGTTATGAATAATAGCTTCCTGAAAATT
TCTAAACGAAAGATTTTTCTTAAATGCTATCATAAGTGTTCAAATTTTCAACGAATATTTCAATA
TCCAAAGAATTTTTGTTTATTTCAATCACATAG
Found at i:32091584 original size:13 final size:13
Alignment explanation
Indices: 32091566--32091590 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
32091556 AGAGAAATTG
32091566 TGATTTTATAAAA
1 TGATTTTATAAAA
32091579 TGATTTTATAAA
1 TGATTTTATAAA
32091591 TTTTTTGGAA
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:32104338 original size:21 final size:21
Alignment explanation
Indices: 32104287--32104353 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 21
32104277 ATTTTTTAAA
** *
32104287 ATTACGTGACTAGTTTTTAGAC
1 ATTACGTGACT-GACTTGAGAC
* *
32104309 ATTATGTGATTGACTTTGAG-C
1 ATTACGTGACTGAC-TTGAGAC
32104330 ATTACGTGACTGACTTGAGAC
1 ATTACGTGACTGACTTGAGAC
32104351 ATT
1 ATT
32104354 GCATGACTAG
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
20 5 0.14
21 18 0.50
22 13 0.36
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (21 bp):
ATTACGTGACTGACTTGAGAC
Found at i:32104360 original size:21 final size:21
Alignment explanation
Indices: 32104319--32104361 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
32104309 ATTATGTGAT
*
32104319 TGACTTTGAGCATTACGTGAC
1 TGACTTTGAGCATTACATGAC
*
32104340 TGAC-TTGAGACATTGCATGAC
1 TGACTTTGAG-CATTACATGAC
32104361 T
1 T
32104362 AGTTTTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.33
Consensus pattern (21 bp):
TGACTTTGAGCATTACATGAC
Found at i:32104421 original size:22 final size:23
Alignment explanation
Indices: 32104371--32104425 Score: 103
Period size: 23 Copynumber: 2.4 Consensus size: 23
32104361 TAGTTTTTTA
32104371 TAAGGCATTGCGTGACTTGTTAG
1 TAAGGCATTGCGTGACTTGTTAG
32104394 TAAGGCATTGCGTGACTTGTT-G
1 TAAGGCATTGCGTGACTTGTTAG
32104416 TAAGGCATTG
1 TAAGGCATTG
32104426 TGTGTTTTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 11 0.34
23 21 0.66
ACGTcount: A:0.22, C:0.13, G:0.31, T:0.35
Consensus pattern (23 bp):
TAAGGCATTGCGTGACTTGTTAG
Found at i:32104477 original size:22 final size:22
Alignment explanation
Indices: 32104444--32104525 Score: 103
Period size: 22 Copynumber: 3.8 Consensus size: 22
32104434 AGGCATTACT
* *
32104444 TAAAAATCAGTCACGCAATGCC
1 TAAAAACCAATCACGCAATGCC
* *
32104466 TAAAAACTAGTCACGCAATGCC
1 TAAAAACCAATCACGCAATGCC
*
32104488 T-AAAACCAATCACGTAATGCC
1 TAAAAACCAATCACGCAATGCC
*
32104509 TTAAAACCAATCACGCA
1 TAAAAACCAATCACGCA
32104526 GTGATTAAGT
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
21 18 0.34
22 35 0.66
ACGTcount: A:0.43, C:0.28, G:0.11, T:0.18
Consensus pattern (22 bp):
TAAAAACCAATCACGCAATGCC
Found at i:32106751 original size:15 final size:17
Alignment explanation
Indices: 32106721--32106753 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
32106711 TATTTTATGT
32106721 TAACATTACAAAAATTA
1 TAACATTACAAAAATTA
32106738 TAAC-TTAC-AAAATTA
1 TAACATTACAAAAATTA
32106753 T
1 T
32106754 TAATTATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 4 0.25
17 4 0.25
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (17 bp):
TAACATTACAAAAATTA
Found at i:32107252 original size:325 final size:333
Alignment explanation
Indices: 32106686--32107337 Score: 923
Period size: 325 Copynumber: 2.0 Consensus size: 333
32106676 ATATATATAC
32106686 TTTTAATATAAATATATTTACTACCTATTTTATGTTAACATTACAAAAATTATAACTTACAAAAT
1 TTTTAATATAAATATATTTACTACCTATTTTATGTTAACATTACAAAAATTATAACTTACAAAAT
* *
32106751 TATTAATTATAATATTTATACCATTATTTGTATAAACTTAGAATATATATATATATACACTTAAA
66 TATTAATTATAATATATATACCATTATTTATATAAACTT--AATATATATATATATACACTTAAA
* *
32106816 GAGAACTTTTGAGATTAGAATAATTTTGGAACCTAACTATATTTTTAATTTCATGAAATTAAGGA
129 GAGAACTTGTGAGATTAGAATAATTTTGAAACCTAACTATATTTTTAATTTCATGAAATTAAGGA
*
32106881 CAAATCCATATAGTTAATTAAATTAATTCATGAAACTATAATTATTAATTAACTTGTAATGTCTT
194 CAAACCCATATAGTTAATTAAATTAATTCATGAAACTATAATTATTAATTAACTTGTAATGTCTT
**
32106946 TTAATATATATAG-TTTATATAT-TA-T-GTTAATTTATAAGAAATATAATTTCTATTATATATA
259 TTAATATATAT-GCTTTATATATATATTAGTTAATTTATAAGAAATATAATTAATATTATATATA
32107007 TACTTAAATAT
323 TACTTAAATAT
* ** * * * *
32107018 TTTTAGTATAAATATATTTACTTTCTATTTT-TTTTAATATTACAAAAATTATAAGTTATAAAAT
1 TTTTAATATAAATATATTTACTACCTATTTTATGTTAACATTACAAAAATTATAACTTACAAAAT
* *
32107082 TATTAATTATAATATATGTACCTTTATTTATATAAACTT-ATA-ATATATA-A-AC-C-TAAAGA
66 TATTAATTATAATATATATACCATTATTTATATAAACTTAATATATATATATATACACTTAAAGA
* * * ** *
32107141 GAAGTTGTGAGATTATAATAGTTTTGAAACCTAGTTAT-TTTTTAAAATTTTCATGTAATTAAGG
131 GAACTTGTGAGATTAGAATAATTTTGAAACCTAACTATATTTTT--AA-TTTCATGAAATTAAGG
* * *
32107205 GCAAACCCATATAGTTAATTAAATTAATTTATGAAACTATTATTATTAATTAACTTGTAATGTCT
193 ACAAACCCATATAGTTAATTAAATTAATTCATGAAACTATAATTATTAATTAACTTGTAATGTCT
*
32107270 TTTAATATATATGCTTTATATATATATTAGGTTCATTTATAAGAAATATAATTAATATTATATAT
258 TTTAATATATATGCTTTATATATATATTA-GTTAATTTATAAGAAATATAATTAATATTATATAT
32107335 ATA
322 ATA
32107338 TATTAAAACA
Statistics
Matches: 286, Mismatches: 26, Indels: 19
0.86 0.08 0.06
Matches are distributed among these distances:
322 5 0.02
323 37 0.13
324 4 0.01
325 99 0.35
326 3 0.01
327 8 0.03
328 3 0.01
329 35 0.12
331 64 0.22
332 28 0.10
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.45
Consensus pattern (333 bp):
TTTTAATATAAATATATTTACTACCTATTTTATGTTAACATTACAAAAATTATAACTTACAAAAT
TATTAATTATAATATATATACCATTATTTATATAAACTTAATATATATATATATACACTTAAAGA
GAACTTGTGAGATTAGAATAATTTTGAAACCTAACTATATTTTTAATTTCATGAAATTAAGGACA
AACCCATATAGTTAATTAAATTAATTCATGAAACTATAATTATTAATTAACTTGTAATGTCTTTT
AATATATATGCTTTATATATATATTAGTTAATTTATAAGAAATATAATTAATATTATATATATAC
TTAAATAT
Found at i:32139361 original size:2 final size:2
Alignment explanation
Indices: 32139356--32139399 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
32139346 ACACACACAC
32139356 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
32139397 AT A
1 AT A
32139400 CTTTCAACCA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32139456 original size:2 final size:2
Alignment explanation
Indices: 32139451--32139490 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
32139441 ACACACACAC
32139451 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
32139491 TTTATAATAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32145837 original size:20 final size:20
Alignment explanation
Indices: 32145812--32145857 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
32145802 TTTTGGCCCC
*
32145812 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGAAGTATA
*
32145832 ATTTGACTTATTGAAGTATG
1 ATTTGACTTATTGAAGTATA
32145852 ATTTGA
1 ATTTGA
32145858 GGTTTAGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.30, C:0.04, G:0.20, T:0.46
Consensus pattern (20 bp):
ATTTGACTTATTGAAGTATA
Found at i:32145960 original size:28 final size:28
Alignment explanation
Indices: 32145902--32145960 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
32145892 TTTGGAGTAT
* * *
32145902 AGGGGTAAAATGGTAATTTTGCCATCTC
1 AGGGGCAAAATGGTAATTTTGCCACCCC
*
32145930 AGGGGCAAAATTGTAATTTT-CCACCACC
1 AGGGGCAAAATGGTAATTTTGCCACC-CC
32145958 AGG
1 AGG
32145961 ATTTTTTTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 4 0.15
28 22 0.85
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.27
Consensus pattern (28 bp):
AGGGGCAAAATGGTAATTTTGCCACCCC
Found at i:32152441 original size:27 final size:27
Alignment explanation
Indices: 32152411--32152464 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
32152401 TGAGCAACAG
32152411 TATCCATCCACTT-CTAATGGGTAAAAT
1 TATCCATCCA-TTCCTAATGGGTAAAAT
*
32152438 TATCCATCCATTCCTAGTGGGTAAAAT
1 TATCCATCCATTCCTAATGGGTAAAAT
32152465 AATTATCCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 2 0.08
27 23 0.92
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.33
Consensus pattern (27 bp):
TATCCATCCATTCCTAATGGGTAAAAT
Found at i:32170490 original size:42 final size:42
Alignment explanation
Indices: 32170438--32170705 Score: 231
Period size: 42 Copynumber: 6.5 Consensus size: 42
32170428 TTTTTAATTA
*
32170438 AATATTTTATTTATAATTTAATCATTAGCATTTTAAAATATT
1 AATATTTTATTTATAATTTAATCATTAACATTTTAAAATATT
*
32170480 AATATGTTATTTATAATTTAATCATTAACATTTTAAAATATT
1 AATATTTTATTTATAATTTAATCATTAACATTTTAAAATATT
* ** *
32170522 AATATTTTATTTATAATTTAAAT-GTTATTATGATTAAAATATT
1 AATATTTTATTTATAATTT-AATCATTAACAT-TTTAAAATATT
* *
32170565 GATATTTTCAATT-T-A-TT--T--TTAA-ATTTT-AAATATT
1 AATATTTT-ATTTATAATTTAATCATTAACATTTTAAAATATT
* * **
32170599 -ATTTTTTACAATATATAA-TTAAAAATTANA-ATAATTT-AAATATT
1 AATATTTT---ATTTATAATTTAATCATTA-ACAT--TTTAAAATATT
* *
32170643 AATATTTTATTTATAATTTTATCATTAATATTTTAAAATATT
1 AATATTTTATTTATAATTTAATCATTAACATTTTAAAATATT
32170685 AATATTTTATTTATAATTTAA
1 AATATTTTATTTATAATTTAA
32170706 ATGTTATTAT
Statistics
Matches: 186, Mismatches: 22, Indels: 36
0.76 0.09 0.15
Matches are distributed among these distances:
33 6 0.03
34 7 0.04
35 4 0.02
36 3 0.02
37 6 0.03
38 1 0.01
41 8 0.04
42 102 0.55
43 30 0.16
44 13 0.07
45 6 0.03
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (42 bp):
AATATTTTATTTATAATTTAATCATTAACATTTTAAAATATT
Found at i:32170659 original size:14 final size:15
Alignment explanation
Indices: 32170639--32170698 Score: 56
Period size: 16 Copynumber: 4.2 Consensus size: 15
32170629 ATAATTTAAA
32170639 TATTAATATTTTATT
1 TATTAATATTTTATT
32170654 TA-T-A-ATTTTA-T
1 TATTAATATTTTATT
* **
32170665 CATTAATATTTTAAAA
1 TATTAATATTTT-ATT
32170681 TATTAATATTTTATT
1 TATTAATATTTTATT
32170696 TAT
1 TAT
32170699 AATTTAAATG
Statistics
Matches: 35, Mismatches: 5, Indels: 10
0.70 0.10 0.20
Matches are distributed among these distances:
11 2 0.06
12 7 0.20
13 2 0.06
14 6 0.17
15 7 0.20
16 11 0.31
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (15 bp):
TATTAATATTTTATT
Found at i:32170796 original size:23 final size:23
Alignment explanation
Indices: 32170743--32170812 Score: 72
Period size: 24 Copynumber: 3.1 Consensus size: 23
32170733 TTTTGATTAA
* *
32170743 TTTTTAA-ATTTAAAATATTATT
1 TTTTTAATATATAAAATATAATT
*
32170765 TTTTATAATATATAATATATAATT
1 TTTT-TAATATATAAAATATAATT
* *
32170789 TTTTTAATTTATAAAAGAT-ATT
1 TTTTTAATATATAAAATATAATT
32170811 TT
1 TT
32170813 GATCTTTATC
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
22 9 0.22
23 15 0.38
24 16 0.40
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (23 bp):
TTTTTAATATATAAAATATAATT
Found at i:32170799 original size:163 final size:163
Alignment explanation
Indices: 32170473--32170780 Score: 501
Period size: 163 Copynumber: 1.9 Consensus size: 163
32170463 TAGCATTTTA
32170473 AAATATTAATATGTTATTTATAATTTAATCATTAACATTTTAAAATATTAATATTTTATTTATAA
1 AAATATTAATATGTTATTTATAATTTAATCATTAACATTTTAAAATATTAATATTTTATTTATAA
* * *
32170538 TTTAAATGTTATTATGATTAAAATATTGATATTTTCAATTTATTTTTAAATTTTAAATATTATTT
66 TTTAAATGTTATTATGATTAAAATATTAATATTTTCAATTAATTTTTAAATTTAAAATATTATTT
*
32170603 TTTACAATATATAATTAAAAATTANAATAATTT
131 TTTACAATATATAATTAAAAATTATAATAATTT
* * *
32170636 AAATATTAATATTTTATTTATAATTTTATCATTAATATTTTAAAATATTAATATTTTATTTATAA
1 AAATATTAATATGTTATTTATAATTTAATCATTAACATTTTAAAATATTAATATTTTATTTATAA
* * *
32170701 TTTAAATGTTATTATGATTCAAGTATTAATAATTTT-GATTAATTTTTAAATTTAAAATATTATT
66 TTTAAATGTTATTATGATTAAAATATTAAT-ATTTTCAATTAATTTTTAAATTTAAAATATTATT
*
32170765 TTTTATAATATATAAT
130 TTTTACAATATATAAT
32170781 ATATAATTTT
Statistics
Matches: 134, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
163 129 0.96
164 5 0.04
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (163 bp):
AAATATTAATATGTTATTTATAATTTAATCATTAACATTTTAAAATATTAATATTTTATTTATAA
TTTAAATGTTATTATGATTAAAATATTAATATTTTCAATTAATTTTTAAATTTAAAATATTATTT
TTTACAATATATAATTAAAAATTATAATAATTT
Found at i:32176458 original size:3 final size:3
Alignment explanation
Indices: 32176450--32176477 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
32176440 ACACAAAAAT
32176450 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
32176478 GGAGTTTTTA
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:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:32176876 original size:44 final size:44
Alignment explanation
Indices: 32176819--32176920 Score: 186
Period size: 44 Copynumber: 2.3 Consensus size: 44
32176809 TCCACCTCTT
*
32176819 TCAAATTCTCTCTCAAATACAACCAGAATTTTTTTAACTTTGCA
1 TCAAATTCCCTCTCAAATACAACCAGAATTTTTTTAACTTTGCA
*
32176863 TCAAATTCCCTCTCAAATAGAACCAGAATTTTTTTAACTTTGCA
1 TCAAATTCCCTCTCAAATACAACCAGAATTTTTTTAACTTTGCA
32176907 TCAAATTCCCTCTC
1 TCAAATTCCCTCTC
32176921 TCGATTCTTC
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
44 56 1.00
ACGTcount: A:0.32, C:0.25, G:0.05, T:0.37
Consensus pattern (44 bp):
TCAAATTCCCTCTCAAATACAACCAGAATTTTTTTAACTTTGCA
Found at i:32179161 original size:17 final size:16
Alignment explanation
Indices: 32179122--32179172 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 16
32179112 CCAAACTAGT
* *
32179122 TGTATATATATATTTTA
1 TGTATTTATATA-TATA
32179139 TGTATTT-TAATATATA
1 TGTATTTAT-ATATATA
32179155 TGATATTTATATATATA
1 TG-TATTTATATATATA
32179172 T
1 T
32179173 TAAGAAGAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
16 6 0.21
17 22 0.76
18 1 0.03
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (16 bp):
TGTATTTATATATATA
Found at i:32181648 original size:110 final size:108
Alignment explanation
Indices: 32181525--32181722 Score: 274
Period size: 110 Copynumber: 1.8 Consensus size: 108
32181515 GAAATAAAAT
**
32181525 TAAATTATAACATAAAATTTCATTAATTATTTAAATATAAATTTTTAGATTCACCAATATAAA-T
1 TAAATTATAACATAAAATTTCATTAACAATTTAAATATAAATTTTTAGATTCACCAATA-AAAGT
*
32181589 AGACATAAAATAGAAA-AAAAATTAATATTAAATTTTCACATTAAC
65 A-A-ACAAAATAGAAATAAAAATTAATATTAAATTTTCACATTAAC
* * * *
32181634 TAAATTTATAACATAAAATTTTATTGACAATTTAAATATAAGTTTTTAGATTCACTAATAAAAGT
1 TAAA-TTATAACATAAAATTTCATTAACAATTTAAATATAAATTTTTAGATTCACCAATAAAAGT
*
32181699 AAACAAAGTAGAAATAAAAATTAA
65 AAACAAAATAGAAATAAAAATTAA
32181723 CATATGATTT
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
108 10 0.13
109 17 0.22
110 51 0.65
ACGTcount: A:0.53, C:0.07, G:0.05, T:0.36
Consensus pattern (108 bp):
TAAATTATAACATAAAATTTCATTAACAATTTAAATATAAATTTTTAGATTCACCAATAAAAGTA
AACAAAATAGAAATAAAAATTAATATTAAATTTTCACATTAAC
Found at i:32181898 original size:158 final size:158
Alignment explanation
Indices: 32181605--32181920 Score: 449
Period size: 158 Copynumber: 2.0 Consensus size: 158
32181595 AAAATAGAAA
* * *
32181605 AAAAATTAATATTAAATTTTCACATTAACTAAATTTATAACATAAAATTTTATTGACAATTTAAA
1 AAAAATTAATATTAAATTATCACATTAACTAAATTTATAACATAAAATTTCATTCACAATTTAAA
* * * * *
32181670 TATAAGTTTTTAGATTCACTAATAAAAGTAAACAAAGTAGAAATAAAAATTAACATATGATTTTT
66 TATAAATTTTTAGATTCACTAATAAAAGTAAACAAAGTAGAAAGAAAAAATAACATATAATTTTC
*
32181735 GCTTTGTTTAGAATACTTATTTAGTTTG
131 ACTTTGTTTAGAATACTTATTTAGTTTG
** *
32181763 AAAAATTAATATTAAATTATCACATTAGGTAAATTTGTAACATAAAATTTCATTCACAATTTAAA
1 AAAAATTAATATTAAATTATCACATTAACTAAATTTATAACATAAAATTTCATTCACAATTTAAA
* *
32181828 TATAAATTTTTAGATTCA-TCAATATAAA-TAGATAAAGTAGAAAGAAAAAATAACATCA-AATT
66 TATAAATTTTTAGATTCACT-AATA-AAAGTAAACAAAGTAGAAAGAAAAAATAACAT-ATAATT
*
32181890 TTCACTTTGTTTAGTATACTTATTTAGTTTG
128 TTCACTTTGTTTAGAATACTTATTTAGTTTG
32181921 GACAAAAAAC
Statistics
Matches: 140, Mismatches: 15, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
157 1 0.01
158 135 0.96
159 4 0.03
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.40
Consensus pattern (158 bp):
AAAAATTAATATTAAATTATCACATTAACTAAATTTATAACATAAAATTTCATTCACAATTTAAA
TATAAATTTTTAGATTCACTAATAAAAGTAAACAAAGTAGAAAGAAAAAATAACATATAATTTTC
ACTTTGTTTAGAATACTTATTTAGTTTG
Found at i:32182000 original size:26 final size:25
Alignment explanation
Indices: 32181945--32182009 Score: 78
Period size: 28 Copynumber: 2.5 Consensus size: 25
32181935 AAAAGAAGAA
*
32181945 GAAAAGAAAAAAAATGGAAAAAATTTG
1 GAAAAGAAAAAAAAGGGAAAAAA--TG
32181972 GAAAAGGAAAAAAAAGGGAAAAACA-G
1 GAAAA-GAAAAAAAAGGGAAAAA-ATG
32181998 GAAAAGAAAAAA
1 GAAAAGAAAAAA
32182010 TTTTGGACCT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
25 7 0.20
26 6 0.17
27 5 0.14
28 16 0.46
29 1 0.03
ACGTcount: A:0.71, C:0.02, G:0.22, T:0.06
Consensus pattern (25 bp):
GAAAAGAAAAAAAAGGGAAAAAATG
Found at i:32184533 original size:30 final size:30
Alignment explanation
Indices: 32184499--32184562 Score: 112
Period size: 30 Copynumber: 2.1 Consensus size: 30
32184489 TCATCCCAGT
32184499 CACCTCCTAGCCCTTC-TAAGCAGCAATCAC
1 CACCTCCTAGCCC-TCATAAGCAGCAATCAC
32184529 CACCTCCTAGCCCTCATAAGCAGCAATCAC
1 CACCTCCTAGCCCTCATAAGCAGCAATCAC
32184559 CACC
1 CACC
32184563 ATCTCTCAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 2 0.06
30 31 0.94
ACGTcount: A:0.28, C:0.45, G:0.09, T:0.17
Consensus pattern (30 bp):
CACCTCCTAGCCCTCATAAGCAGCAATCAC
Found at i:32193167 original size:2 final size:2
Alignment explanation
Indices: 32193160--32193197 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
32193150 ATTATGCCCC
32193160 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
32193198 TATCTTTTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32194202 original size:33 final size:33
Alignment explanation
Indices: 32194047--32194205 Score: 153
Period size: 33 Copynumber: 4.8 Consensus size: 33
32194037 ACCTTTGATG
* *
32194047 TCCCCATGTCCAGGCATTCTGAATCCC-GTGGGA
1 TCCCCATTTCCAGGCATTCTGAA-CCCTCTGGGA
* *
32194080 TCCCCATTTCCAGGCATTCTAAATCCTGC-GGGA
1 TCCCCATTTCCAGGCATTCTGAACCCT-CTGGGA
* * ** *
32194113 TCCCCATTTCCTGGCATTCTTATTCCTCTAGGA
1 TCCCCATTTCCAGGCATTCTGAACCCTCTGGGA
*
32194146 TCCCCATGTT-CAGGAATTCTGAACCCTCTGGGA
1 TCCCCAT-TTCCAGGCATTCTGAACCCTCTGGGA
* * *
32194179 TCTCCATTTCCGGGCATTTTGAACCCT
1 TCCCCATTTCCAGGCATTCTGAACCCT
32194206 TTGCTGGGAT
Statistics
Matches: 103, Mismatches: 18, Indels: 10
0.79 0.14 0.08
Matches are distributed among these distances:
32 5 0.05
33 96 0.93
34 2 0.02
ACGTcount: A:0.18, C:0.33, G:0.18, T:0.31
Consensus pattern (33 bp):
TCCCCATTTCCAGGCATTCTGAACCCTCTGGGA
Found at i:32203396 original size:30 final size:30
Alignment explanation
Indices: 32203360--32203416 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
32203350 TGTCATCGTG
* *
32203360 TAATAACAGTGTACATTTACGCATGGCACT
1 TAATAACAATGTACATATACGCATGGCACT
* *
32203390 TAATAACAATGTATATATAGGCATGGC
1 TAATAACAATGTACATATACGCATGGC
32203417 GTGTAACAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.30
Consensus pattern (30 bp):
TAATAACAATGTACATATACGCATGGCACT
Found at i:32203447 original size:28 final size:28
Alignment explanation
Indices: 32203404--32203458 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
32203394 AACAATGTAT
*
32203404 ATATAGGCATGGCGTGTAACAACACAAG
1 ATATAGGCATGACGTGTAACAACACAAG
32203432 ATATAGGCATGACGTGTAACAACACAA
1 ATATAGGCATGACGTGTAACAACACAA
32203459 TACATTTGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.42, C:0.18, G:0.22, T:0.18
Consensus pattern (28 bp):
ATATAGGCATGACGTGTAACAACACAAG
Found at i:32206897 original size:15 final size:16
Alignment explanation
Indices: 32206877--32206908 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
32206867 ATACTTTCAG
32206877 GAAAAAAAAAAG-AAA
1 GAAAAAAAAAAGTAAA
32206892 GAAAAAAAAAAGTAAA
1 GAAAAAAAAAAGTAAA
32206908 G
1 G
32206909 GCTTTATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (16 bp):
GAAAAAAAAAAGTAAA
Found at i:32209288 original size:52 final size:52
Alignment explanation
Indices: 32209226--32209449 Score: 421
Period size: 52 Copynumber: 4.3 Consensus size: 52
32209216 AGCTTTGTAC
* *
32209226 TAACTGATTAAGGCTCTACTGTCTTACTTTTGTATAGTGCCTAGCATTGCCT
1 TAACTGATTAAGGCTTTACTGTCTTGCTTTTGTATAGTGCCTAGCATTGCCT
32209278 TAACTGATTAAGGCTTTACTGTCTTGCTTTTGTATAGTGCCTAGCATTGCCT
1 TAACTGATTAAGGCTTTACTGTCTTGCTTTTGTATAGTGCCTAGCATTGCCT
32209330 TAACTGATTAAGGCTTTACTGTCTTGCTTTTGTATAGTGCCTAGCATTGCCT
1 TAACTGATTAAGGCTTTACTGTCTTGCTTTTGTATAGTGCCTAGCATTGCCT
*
32209382 TAACTGATTAAGGCTTTACTGTCTTGCTTTTGTATAGTGCCTAGCTTTGCCT
1 TAACTGATTAAGGCTTTACTGTCTTGCTTTTGTATAGTGCCTAGCATTGCCT
32209434 TAACTGATTAAGGCTT
1 TAACTGATTAAGGCTT
32209450 CACGTTAAGT
Statistics
Matches: 169, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 169 1.00
ACGTcount: A:0.20, C:0.19, G:0.19, T:0.42
Consensus pattern (52 bp):
TAACTGATTAAGGCTTTACTGTCTTGCTTTTGTATAGTGCCTAGCATTGCCT
Found at i:32211262 original size:28 final size:28
Alignment explanation
Indices: 32211230--32211443 Score: 111
Period size: 28 Copynumber: 7.7 Consensus size: 28
32211220 CAATTGAATC
32211230 TCAACATGACGTGTAACAACTACATTTT
1 TCAACATGACGTGTAACAACTACATTTT
* * *
32211258 TCAACATGACTTGTGACAACTA-AATTT
1 TCAACATGACGTGTAACAACTACATTTT
** * **
32211285 TCAATTTGCCGAATAACAACTACACTTTT
1 TCAACATGACGTGTAACAACTACA-TTTT
*
32211314 T-AACAT--CGTTTGTAACAACTAAAGTTTT
1 TCAACATGACG--TGTAACAACTACA-TTTT
* * * *
32211342 T-TACTTGTCGTGTAACAACTACATTTAA
1 TCAACATGACGTGTAACAACTACATTT-T
** * * **
32211370 AAAACATGACGTGTAACAACCAAAAATT
1 TCAACATGACGTGTAACAACTACATTTT
* * *
32211398 ACAACATTG-TGTGTAAC-ACTATATTTT
1 TCAACA-TGACGTGTAACAACTACATTTT
*
32211425 TCAACATGACAT-TAACAAC
1 TCAACATGACGTGTAACAAC
32211444 ATCACAAAAC
Statistics
Matches: 136, Mismatches: 39, Indels: 23
0.69 0.20 0.12
Matches are distributed among these distances:
26 8 0.06
27 36 0.26
28 66 0.49
29 24 0.18
30 2 0.01
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (28 bp):
TCAACATGACGTGTAACAACTACATTTT
Found at i:32211707 original size:23 final size:23
Alignment explanation
Indices: 32211681--32211725 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
32211671 CCTAGTATAT
32211681 CAACACTTCGAAT-AAATCATTAG
1 CAACACTTC-AATCAAATCATTAG
*
32211704 CAACACTTCATTCAAATCATTA
1 CAACACTTCAATCAAATCATTA
32211726 ATAAGTTGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.42, C:0.24, G:0.04, T:0.29
Consensus pattern (23 bp):
CAACACTTCAATCAAATCATTAG
Found at i:32213866 original size:19 final size:21
Alignment explanation
Indices: 32213827--32213866 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
32213817 TATTTTTTTA
32213827 AATTTTTTAAAAATATAATAAT
1 AATTTTTT-AAAATATAATAAT
32213849 AATTTTTT-AAAT-TAATAA
1 AATTTTTTAAAATATAATAA
32213867 AAAAATATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 4 0.22
22 8 0.44
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
AATTTTTTAAAATATAATAAT
Found at i:32213866 original size:22 final size:21
Alignment explanation
Indices: 32213826--32213879 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
32213816 TTATTTTTTT
32213826 AAATTTTTTAAAAATATAATAA
1 AAATTTTTTAAAAATATAA-AA
* *
32213848 TAATTTTTT-AAATTAATAAAA
1 AAATTTTTTAAAAAT-ATAAAA
*
32213869 AAATATTTTAA
1 AAATTTTTTAA
32213880 TTTTTTCACA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 13 0.50
22 13 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
AAATTTTTTAAAAATATAAAA
Found at i:32224432 original size:9 final size:9
Alignment explanation
Indices: 32224418--32224444 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
32224408 TAAACTGGAG
32224418 CAAGATGCT
1 CAAGATGCT
32224427 CAAGATGCT
1 CAAGATGCT
32224436 CAAGATGCT
1 CAAGATGCT
32224445 AAGCGTATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.22
Consensus pattern (9 bp):
CAAGATGCT
Found at i:32239965 original size:12 final size:12
Alignment explanation
Indices: 32239940--32239980 Score: 57
Period size: 12 Copynumber: 3.3 Consensus size: 12
32239930 CCAAGAACTG
32239940 TTTTCTCTCTCTT
1 TTTTCTCTC-CTT
32239953 TTTTCTCTCCTT
1 TTTTCTCTCCTT
32239965 TTTT-TCTTCCTT
1 TTTTCTC-TCCTT
32239977 TTTT
1 TTTT
32239981 TTGACACTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
11 2 0.07
12 16 0.59
13 9 0.33
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTTCTCTCCTT
Found at i:32239982 original size:13 final size:13
Alignment explanation
Indices: 32239940--32239981 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
32239930 CCAAGAACTG
32239940 TTTTCTCT-CTCTT
1 TTTTCTCTCCT-TT
32239953 TTTTCTCTCCTTT
1 TTTTCTCTCCTTT
32239966 TTTTCT-TCCTTT
1 TTTTCTCTCCTTT
32239978 TTTT
1 TTTT
32239982 TGACACTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
12 10 0.36
13 16 0.57
14 2 0.07
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTTCTCTCCTTT
Found at i:32242762 original size:20 final size:21
Alignment explanation
Indices: 32242739--32242778 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
32242729 AAGTGAGTTA
*
32242739 TTTTAATTTTA-TGTTATTTC
1 TTTTAATTTGATTGTTATTTC
32242759 TTTTAATTTGATTGTTATTT
1 TTTTAATTTGATTGTTATTT
32242779 ATTAGTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.20, C:0.03, G:0.07, T:0.70
Consensus pattern (21 bp):
TTTTAATTTGATTGTTATTTC
Found at i:32243833 original size:19 final size:19
Alignment explanation
Indices: 32243809--32243848 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
32243799 ATTGTAATCC
32243809 TTCTGAAGTTATTATTATT
1 TTCTGAAGTTATTATTATT
32243828 TTCTGAAGTTATTATTATT
1 TTCTGAAGTTATTATTATT
32243847 TT
1 TT
32243849 GATTTTTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.25, C:0.05, G:0.10, T:0.60
Consensus pattern (19 bp):
TTCTGAAGTTATTATTATT
Found at i:32252556 original size:31 final size:25
Alignment explanation
Indices: 32252489--32252540 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
32252479 ACTTCAATTG
32252489 CCTGTTAACCTTAAATTATGTTTAA
1 CCTGTTAACCTTAAATTATGTTTAA
32252514 CCTGTTAACCTTAAATTATGTTTAA
1 CCTGTTAACCTTAAATTATGTTTAA
32252539 CC
1 CC
32252541 AAAATGATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.31, C:0.19, G:0.08, T:0.42
Consensus pattern (25 bp):
CCTGTTAACCTTAAATTATGTTTAA
Found at i:32273659 original size:64 final size:64
Alignment explanation
Indices: 32273579--32273734 Score: 231
Period size: 64 Copynumber: 2.4 Consensus size: 64
32273569 GAACAAAGAC
* * * * *
32273579 AAAATATGCATGCAAAATGCGTTGAAAATGCACAATGCTGTTTTTTCCTTGGAAAAATAAATTA
1 AAAACATGCATGCAAAATGCATTGAAAATGCAAAATGCTGTTTTTCCCTTGGAAAAAGAAATTA
* *
32273643 AAAACATGCATGCAAAATGCTTTGAAAATGCAAAATGCTGTTTTTCCCTTGGACAAAGAAATTA
1 AAAACATGCATGCAAAATGCATTGAAAATGCAAAATGCTGTTTTTCCCTTGGAAAAAGAAATTA
* *
32273707 AGAACATGCATGCAACATGCATTGAAAA
1 AAAACATGCATGCAAAATGCATTGAAAA
32273735 AAATACAATG
Statistics
Matches: 83, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
64 83 1.00
ACGTcount: A:0.42, C:0.15, G:0.16, T:0.28
Consensus pattern (64 bp):
AAAACATGCATGCAAAATGCATTGAAAATGCAAAATGCTGTTTTTCCCTTGGAAAAAGAAATTA
Found at i:32275957 original size:21 final size:22
Alignment explanation
Indices: 32275912--32275966 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
32275902 TGGTCCATAA
*
32275912 GTTGATTACTGCTGTAGATGTT
1 GTTGATTACTGCTGTAGAGGTT
32275934 GTTGATTACTGCTGTAG-GGTT
1 GTTGATTACTGCTGTAGAGGTT
*
32275955 GTTG-TTTCTGCT
1 GTTGATTACTGCT
32275967 TCAAGTTTAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 7 0.23
21 7 0.23
22 17 0.55
ACGTcount: A:0.13, C:0.11, G:0.29, T:0.47
Consensus pattern (22 bp):
GTTGATTACTGCTGTAGAGGTT
Found at i:32282867 original size:2 final size:2
Alignment explanation
Indices: 32282860--32282946 Score: 144
Period size: 2 Copynumber: 45.0 Consensus size: 2
32282850 AATTAGAAAC
32282860 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
32282901 AT -T AT -T AN AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
32282941 AT AT AT
1 AT AT AT
32282947 TTATGATTTA
Statistics
Matches: 80, Mismatches: 2, Indels: 6
0.91 0.02 0.07
Matches are distributed among these distances:
1 3 0.04
2 77 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:32288317 original size:35 final size:35
Alignment explanation
Indices: 32288278--32288347 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 35
32288268 ACTACAAAAA
* *
32288278 AAGTACTACTTCACATAAAACAATTAAAATAAGTG
1 AAGTACTACTTCACACAAAACAACTAAAATAAGTG
* * *
32288313 AAGTATTACTTCACACGAAACAACTAGAATAAGTG
1 AAGTACTACTTCACACAAAACAACTAAAATAAGTG
32288348 GAGCACTATT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.49, C:0.16, G:0.11, T:0.24
Consensus pattern (35 bp):
AAGTACTACTTCACACAAAACAACTAAAATAAGTG
Found at i:32291915 original size:15 final size:16
Alignment explanation
Indices: 32291876--32291915 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 16
32291866 CGTGACAAAT
*
32291876 ATATATAATAAATAAA
1 ATATATAATTAATAAA
32291892 AT-TAT-ATTAA-AAA
1 ATATATAATTAATAAA
32291905 ATATATAATTA
1 ATATATAATTA
32291916 TTTCATTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
13 5 0.24
14 7 0.33
15 7 0.33
16 2 0.10
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
ATATATAATTAATAAA
Found at i:32292100 original size:16 final size:16
Alignment explanation
Indices: 32292076--32292113 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
32292066 ATAATTTATT
*
32292076 ATTT-TAAAAATTAAA
1 ATTTATAAAAAATAAA
32292091 A-TTATAAAAAATAAA
1 ATTTATAAAAAATAAA
32292106 ATTTATAA
1 ATTTATAA
32292114 GATAAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 2 0.10
15 12 0.60
16 6 0.30
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
ATTTATAAAAAATAAA
Found at i:32292344 original size:38 final size:37
Alignment explanation
Indices: 32292301--32292375 Score: 132
Period size: 38 Copynumber: 2.0 Consensus size: 37
32292291 AACTGAATCA
32292301 AGCATATAAAATTATTTTATTATTTTTTATTGGTATT
1 AGCATATAAAATTATTTTATTATTTTTTATTGGTATT
*
32292338 NAGCATATGAAATTATTTTATTATTTTTTATTGGTATT
1 -AGCATATAAAATTATTTTATTATTTTTTATTGGTATT
32292376 TATTATTAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.31, C:0.03, G:0.09, T:0.56
Consensus pattern (37 bp):
AGCATATAAAATTATTTTATTATTTTTTATTGGTATT
Found at i:32295540 original size:32 final size:32
Alignment explanation
Indices: 32295503--32295567 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
32295493 ATTCATCACA
32295503 AAAATCTTCAGATCAGAAAGGCAACCAACAAG
1 AAAATCTTCAGATCAGAAAGGCAACCAACAAG
32295535 AAAATCTTCAGATCAGAAAGGCAACCAACAAG
1 AAAATCTTCAGATCAGAAAGGCAACCAACAAG
32295567 A
1 A
32295568 TTTCTCAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.51, C:0.22, G:0.15, T:0.12
Consensus pattern (32 bp):
AAAATCTTCAGATCAGAAAGGCAACCAACAAG
Found at i:32302650 original size:17 final size:17
Alignment explanation
Indices: 32302606--32302655 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
32302596 TACCTCTTAC
32302606 TCAAAGAAA-AATT-GA
1 TCAAAGAAACAATTAGA
* *
32302621 TCAATGAACACAATTATA
1 TCAAAGAA-ACAATTAGA
32302639 TCAAAGAAACAATTAGA
1 TCAAAGAAACAATTAGA
32302656 AGACTGCACA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 7 0.25
16 1 0.04
17 12 0.43
18 8 0.29
ACGTcount: A:0.56, C:0.12, G:0.10, T:0.22
Consensus pattern (17 bp):
TCAAAGAAACAATTAGA
Found at i:32308029 original size:23 final size:22
Alignment explanation
Indices: 32307986--32308029 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
32307976 AAATACAAAT
* **
32307986 ATATTTTTATTATAATTTAATA
1 ATATTTTTATTAGAAGATAATA
32308008 ATATTTTGTATTAGAAGATAAT
1 ATATTTT-TATTAGAAGATAAT
32308030 TAAACCTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (22 bp):
ATATTTTTATTAGAAGATAATA
Found at i:32308958 original size:17 final size:16
Alignment explanation
Indices: 32308935--32308982 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 16
32308925 TTCTTCGTTT
*
32308935 AAATTCAAAGTAAAGC
1 AAATTCAAAGAAAAGC
*
32308951 ATAATTCAAAGAAAAAC
1 A-AATTCAAAGAAAAGC
*
32308968 AAATTCAAAGCAAAG
1 AAATTCAAAGAAAAG
32308983 TTGGTCCTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
16 13 0.48
17 14 0.52
ACGTcount: A:0.60, C:0.12, G:0.10, T:0.17
Consensus pattern (16 bp):
AAATTCAAAGAAAAGC
Found at i:32324167 original size:22 final size:22
Alignment explanation
Indices: 32324140--32324184 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
32324130 TCAGTAGGAG
32324140 TAGTTCCTACTTATCTACTATT
1 TAGTTCCTACTTATCTACTATT
* * *
32324162 TAGTTCCTATTTATTTGCTATT
1 TAGTTCCTACTTATCTACTATT
32324184 T
1 T
32324185 TGTTAGATGT
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:0.20, C:0.18, G:0.07, T:0.56
Consensus pattern (22 bp):
TAGTTCCTACTTATCTACTATT
Found at i:32326081 original size:15 final size:15
Alignment explanation
Indices: 32326056--32326090 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
32326046 TTTTCGGCAG
32326056 ATTTT-CAACGAAAA
1 ATTTTCCAACGAAAA
*
32326070 TTTTTCCAACGAAAA
1 ATTTTCCAACGAAAA
32326085 ATTTTC
1 ATTTTC
32326091 ATTAGAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.40, C:0.17, G:0.06, T:0.37
Consensus pattern (15 bp):
ATTTTCCAACGAAAA
Found at i:32330613 original size:54 final size:54
Alignment explanation
Indices: 32330523--32330691 Score: 155
Period size: 54 Copynumber: 3.1 Consensus size: 54
32330513 TTACTAACGG
* * *
32330523 AATTTTT-AATGAAATTTTTCGTTGGAAAAGTATTTCCAACGAAAATTCTGTGGGA
1 AATTTTTCAATGAAA--TTTCGTTGGAAATGTTTTTCCAACGAAAATTCTATGGGA
* ** * *
32330578 AATTTTTCAATGAAATTTCGTGGGAAATGTTTTTCCAATTAAAAGTTCCATTGGA
1 AATTTTTCAATGAAATTTCGTTGGAAATGTTTTTCCAACGAAAA-TTCTATGGGA
* * * * *
32330633 AA-TTTTCAATGGAATTCCATTGGAAATGCTTTTT-CAACGAAAAATTCTATTGAA
1 AATTTTTCAATGAAATTTCGTTGGAAATG-TTTTTCCAACG-AAAATTCTATGGGA
32330687 AATTT
1 AATTT
32330692 CCAACAGAAT
Statistics
Matches: 93, Mismatches: 16, Indels: 10
0.78 0.13 0.08
Matches are distributed among these distances:
54 59 0.63
55 27 0.29
56 7 0.08
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.39
Consensus pattern (54 bp):
AATTTTTCAATGAAATTTCGTTGGAAATGTTTTTCCAACGAAAATTCTATGGGA
Found at i:32330702 original size:54 final size:53
Alignment explanation
Indices: 32330600--32330755 Score: 143
Period size: 54 Copynumber: 2.9 Consensus size: 53
32330590 AAATTTCGTG
** * * * **
32330600 GGAAATG-TTTTTCCAATTAAAAGTTCCATTGGAAATTTTCAATGGAATTCCATT
1 GGAAATGCTTTTT-CAACGAAAAATT-CATTGAAAATTTCCAACAGAATTCCATT
*
32330654 GGAAATGCTTTTTCAACGAAAAATTCTATTGAAAATTTCCAACAGAATTCCGTT
1 GGAAATGCTTTTTCAACGAAAAATTC-ATTGAAAATTTCCAACAGAATTCCATT
** * * * * *
32330708 GGAAAAACATTTCCAACGAAAATTTCATTAAAAATTTCTAACAGAATT
1 GGAAATGCTTTTTCAACGAAAAATTCATTGAAAATTTCCAACAGAATT
32330756 GATACAGATT
Statistics
Matches: 85, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
53 21 0.25
54 59 0.69
55 5 0.06
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.34
Consensus pattern (53 bp):
GGAAATGCTTTTTCAACGAAAAATTCATTGAAAATTTCCAACAGAATTCCATT
Found at i:32330753 original size:53 final size:54
Alignment explanation
Indices: 32330644--32330755 Score: 145
Period size: 54 Copynumber: 2.1 Consensus size: 54
32330634 ATTTTCAATG
** * * *
32330644 GAATTCCATTGGAAATGCTTTTTCAACGAAAAATTCTATTGAAAATTTCCAACA
1 GAATTCCATTGGAAAAACATTTCCAACGAAAAATTCTATTAAAAATTTCCAACA
* * *
32330698 GAATTCCGTTGGAAAAACATTTCCAACGAAAATTTC-ATTAAAAATTTCTAACA
1 GAATTCCATTGGAAAAACATTTCCAACGAAAAATTCTATTAAAAATTTCCAACA
32330751 GAATT
1 GAATT
32330756 GATACAGATT
Statistics
Matches: 50, Mismatches: 8, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
53 20 0.40
54 30 0.60
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.32
Consensus pattern (54 bp):
GAATTCCATTGGAAAAACATTTCCAACGAAAAATTCTATTAAAAATTTCCAACA
Found at i:32337411 original size:214 final size:215
Alignment explanation
Indices: 32337182--32337598 Score: 631
Period size: 214 Copynumber: 1.9 Consensus size: 215
32337172 ATAAATATAT
*
32337182 TATATATACATATATTTAATTTATACATAAA-CATTACAATAACTTATAATAAACTTTATTTATA
1 TATATATACATATATTTAATTTATACA-AAAGCATTACAACAACTTATAATAAACTTTATTTATA
**
32337246 TGATTATGCTTAATAACTTTATTAGTTATCACCTTAGATTTTATAACATATTATTTATAATTAGT
65 TGATTACACTTAATAACTTTATTAGTTATCACCTTAGATTTTATAACATATTATTTATAATTAGT
* * * * * *
32337311 TATTATTTATACAAACTGTGATATAAAATATTTTAACCTACAATTTGTATCATTAATTTTATATA
130 TATTATTTATACAAACTGTGATATAAAATATTATAACATACAAGTTATATCATTAATTTCACATA
32337376 TATA-ATAAAATAATAAATTC
195 TATATATAAAATAATAAATTC
* ** * *
32337396 TATATATATATATATTTAATTTATGTAAAAGCATTACTACAACTTGTAATAAACTTTATTTATAT
1 TATATATACATATATTTAATTTATACAAAAGCATTACAACAACTTATAATAAACTTTATTTATAT
* * *
32337461 GATTACACTTAATAACTTTTTTAGTTATCACTTTAGATTTTATAACATATTGTTTATAATTAGTT
66 GATTACACTTAATAACTTTATTAGTTATCACCTTAGATTTTATAACATATTATTTATAATTAGTT
* * *
32337526 ATTATTTATACAAACTTTGATATAAAATATTATAATATATAAGTTATATCATTAATTTCACATAT
131 ATTATTTATACAAACTGTGATATAAAATATTATAACATACAAGTTATATCATTAATTTCACATAT
32337591 ATATATAA
196 ATATATAA
32337599 TTAAAAATGA
Statistics
Matches: 181, Mismatches: 20, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
213 3 0.02
214 174 0.96
215 4 0.02
ACGTcount: A:0.41, C:0.08, G:0.04, T:0.46
Consensus pattern (215 bp):
TATATATACATATATTTAATTTATACAAAAGCATTACAACAACTTATAATAAACTTTATTTATAT
GATTACACTTAATAACTTTATTAGTTATCACCTTAGATTTTATAACATATTATTTATAATTAGTT
ATTATTTATACAAACTGTGATATAAAATATTATAACATACAAGTTATATCATTAATTTCACATAT
ATATATAAAATAATAAATTC
Found at i:32339463 original size:34 final size:35
Alignment explanation
Indices: 32339394--32339490 Score: 99
Period size: 34 Copynumber: 2.8 Consensus size: 35
32339384 CAAATTAATA
* * * *
32339394 AAACCTACAAGTAATATAATTAATTAT-TTTACAT
1 AAACTTACTAGTAATATAATTAATCATCCTTACAT
32339428 AAACTTACTAGTAATATAATTAATCATCCTT-CAT
1 AAACTTACTAGTAATATAATTAATCATCCTTACAT
* * * *
32339462 AAACTTTATTAGGAATATAGTTAGTCATC
1 AAAC-TTACTAGTAATATAATTAATCATC
32339491 ATACATTATG
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
34 31 0.58
35 22 0.42
ACGTcount: A:0.42, C:0.13, G:0.06, T:0.38
Consensus pattern (35 bp):
AAACTTACTAGTAATATAATTAATCATCCTTACAT
Found at i:32339490 original size:35 final size:34
Alignment explanation
Indices: 32339406--32339490 Score: 91
Period size: 35 Copynumber: 2.5 Consensus size: 34
32339396 ACCTACAAGT
* * *
32339406 AATATAATTAATTAT-TTTACATAAACTTACTAGT
1 AATATAATTAATCATCCTT-CATAAACTTACTAGG
*
32339440 AATATAATTAATCATCCTTCATAAACTTTATTAGG
1 AATATAATTAATCATCCTTCATAAAC-TTACTAGG
* *
32339475 AATATAGTTAGTCATC
1 AATATAATTAATCATC
32339491 ATACATTATG
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
34 21 0.49
35 22 0.51
ACGTcount: A:0.41, C:0.12, G:0.06, T:0.41
Consensus pattern (34 bp):
AATATAATTAATCATCCTTCATAAACTTACTAGG
Found at i:32342100 original size:2 final size:2
Alignment explanation
Indices: 32342093--32342128 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
32342083 ATAATATCAC
32342093 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
32342129 TAATAANTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32347677 original size:64 final size:64
Alignment explanation
Indices: 32347600--32347791 Score: 384
Period size: 64 Copynumber: 3.0 Consensus size: 64
32347590 CCTGATAACA
32347600 TGCCTGTATAATCTCACATAGTGGGAACTGGGAACGAGTGTAATCCCATCAAAGAAGAATGCCT
1 TGCCTGTATAATCTCACATAGTGGGAACTGGGAACGAGTGTAATCCCATCAAAGAAGAATGCCT
32347664 TGCCTGTATAATCTCACATAGTGGGAACTGGGAACGAGTGTAATCCCATCAAAGAAGAATGCCT
1 TGCCTGTATAATCTCACATAGTGGGAACTGGGAACGAGTGTAATCCCATCAAAGAAGAATGCCT
32347728 TGCCTGTATAATCTCACATAGTGGGAACTGGGAACGAGTGTAATCCCATCAAAGAAGAATGCCT
1 TGCCTGTATAATCTCACATAGTGGGAACTGGGAACGAGTGTAATCCCATCAAAGAAGAATGCCT
32347792 ATAAACTAGG
Statistics
Matches: 128, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 128 1.00
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.23
Consensus pattern (64 bp):
TGCCTGTATAATCTCACATAGTGGGAACTGGGAACGAGTGTAATCCCATCAAAGAAGAATGCCT
Found at i:32351820 original size:24 final size:24
Alignment explanation
Indices: 32351788--32351835 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
32351778 GGGACTTCTT
* * *
32351788 CTTTGGGCTTGGGTGATGGAGGAG
1 CTTTCGGCTTAGGAGATGGAGGAG
32351812 CTTTCGGCTTAGGAGATGGAGGAG
1 CTTTCGGCTTAGGAGATGGAGGAG
32351836 TTTTATGAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.17, C:0.10, G:0.46, T:0.27
Consensus pattern (24 bp):
CTTTCGGCTTAGGAGATGGAGGAG
Found at i:32362096 original size:2 final size:2
Alignment explanation
Indices: 32362089--32362128 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
32362079 TTCTGTATAA
32362089 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
32362129 ATGAAAGTGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:32369909 original size:30 final size:30
Alignment explanation
Indices: 32369836--32369933 Score: 108
Period size: 30 Copynumber: 3.3 Consensus size: 30
32369826 CATTAATCAT
*
32369836 AAAAGCTTATTT-GACTCAAAATAAAAGTAA
1 AAAAACTTATTTGGA-TCAAAATAAAAGTAA
*
32369866 AAAAACTTATTTGGATCAAAATAAAAGTAT
1 AAAAACTTATTTGGATCAAAATAAAAGTAA
* * * ** *
32369896 AAGAACTTATTTGGTTTAAAATAAGTGTAC
1 AAAAACTTATTTGGATCAAAATAAAAGTAA
32369926 AAAAACTT
1 AAAAACTT
32369934 GATTGAACAC
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
30 56 0.97
31 2 0.03
ACGTcount: A:0.50, C:0.08, G:0.11, T:0.31
Consensus pattern (30 bp):
AAAAACTTATTTGGATCAAAATAAAAGTAA
Found at i:32374431 original size:2 final size:2
Alignment explanation
Indices: 32374424--32374459 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
32374414 ACATCAAAAT
32374424 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
32374460 AATTACCCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:32374900 original size:28 final size:28
Alignment explanation
Indices: 32374869--32374925 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
32374859 AATTAAAGTA
*
32374869 TAAATTAATAAATT-ATTAATTTATAAAT
1 TAAA-TAATAAATTAATTAATTAATAAAT
**
32374897 TAAATAATATCTTAATTAATTAATAAAT
1 TAAATAATAAATTAATTAATTAATAAAT
32374925 T
1 T
32374926 TTCATGATCC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 7 0.28
28 18 0.72
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (28 bp):
TAAATAATAAATTAATTAATTAATAAAT
Found at i:32375896 original size:16 final size:16
Alignment explanation
Indices: 32375877--32375962 Score: 54
Period size: 16 Copynumber: 5.4 Consensus size: 16
32375867 TTACTTATTT
32375877 TTAGTTATTTTTATAA
1 TTAGTTATTTTTATAA
*
32375893 TTAGTTTATTTTTA-AG
1 TTAG-TTATTTTTATAA
* * *
32375909 TAAGTTATTTTAAT-T
1 TTAGTTATTTTTATAA
*
32375924 TTATGTTATTTCTTTTAA
1 TTA-GTTATTT-TTATAA
*
32375942 TTTGGTTATTTTT-T-A
1 -TTAGTTATTTTTATAA
32375957 TTAGTT
1 TTAGTT
32375963 TTTATATTTT
Statistics
Matches: 54, Mismatches: 10, Indels: 14
0.69 0.13 0.18
Matches are distributed among these distances:
14 5 0.09
15 11 0.20
16 16 0.30
17 13 0.24
18 7 0.13
19 2 0.04
ACGTcount: A:0.24, C:0.01, G:0.09, T:0.65
Consensus pattern (16 bp):
TTAGTTATTTTTATAA
Found at i:32378781 original size:44 final size:45
Alignment explanation
Indices: 32378726--32378811 Score: 156
Period size: 45 Copynumber: 1.9 Consensus size: 45
32378716 TTTGAATAAG
*
32378726 AAAATTAGAATAT-AATAACTAAAATTAACCAATGAACACAAAGA
1 AAAACTAGAATATAAATAACTAAAATTAACCAATGAACACAAAGA
32378770 AAAACTAGAATATAAATAACTAAAATTAACCAATGAACACAA
1 AAAACTAGAATATAAATAACTAAAATTAACCAATGAACACAA
32378812 GTTAGGGTAG
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
44 12 0.30
45 28 0.70
ACGTcount: A:0.62, C:0.13, G:0.06, T:0.20
Consensus pattern (45 bp):
AAAACTAGAATATAAATAACTAAAATTAACCAATGAACACAAAGA
Found at i:32381738 original size:33 final size:33
Alignment explanation
Indices: 32381652--32381738 Score: 102
Period size: 33 Copynumber: 2.6 Consensus size: 33
32381642 GAAAAAAATT
* * *
32381652 AAAATAAAATATATAATATAGAAAATTATATTAA
1 AAAATAAAA-ATAAAATATATAAAATTATAATAA
* * * *
32381686 GAGATGAAAATAAAATATATAAGATTATAATAA
1 AAAATAAAAATAAAATATATAAAATTATAATAA
32381719 AAAATAAAAATAAAATATAT
1 AAAATAAAAATAAAATATAT
32381739 GATATTAAAA
Statistics
Matches: 43, Mismatches: 10, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
33 37 0.86
34 6 0.14
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.29
Consensus pattern (33 bp):
AAAATAAAAATAAAATATATAAAATTATAATAA
Found at i:32381779 original size:16 final size:15
Alignment explanation
Indices: 32381730--32381779 Score: 59
Period size: 16 Copynumber: 3.3 Consensus size: 15
32381720 AAATAAAAAT
*
32381730 AAAATATATGATATTA
1 AAAATATATTATA-TA
32381746 AAAATATATT-TA-A
1 AAAATATATTATATA
32381759 AAAATAATATTATATA
1 AAAAT-ATATTATATA
32381775 AAAAT
1 AAAAT
32381780 TAACAAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
13 6 0.20
14 5 0.17
15 4 0.13
16 15 0.50
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (15 bp):
AAAATATATTATATA
Found at i:32381788 original size:28 final size:27
Alignment explanation
Indices: 32381704--32381792 Score: 72
Period size: 28 Copynumber: 3.1 Consensus size: 27
32381694 AATAAAATAT
* *
32381704 ATAAGATTATAATAAAAAATAAAAATAAA
1 ATAATATTAT-ATAAAAATTAAAAA-AAA
* **
32381733 AT-ATATGATATTAAAAATATATTTAAAAA
1 ATAATATTATA-TAAAAAT-TA-AAAAAAA
32381762 ATAATATTATATAAAAATTAACAAAAAA
1 ATAATATTATATAAAAATTAA-AAAAAA
32381790 ATA
1 ATA
32381793 CAAGTTTATA
Statistics
Matches: 47, Mismatches: 8, Indels: 11
0.71 0.12 0.17
Matches are distributed among these distances:
27 1 0.02
28 21 0.45
29 16 0.34
30 9 0.19
ACGTcount: A:0.66, C:0.01, G:0.02, T:0.30
Consensus pattern (27 bp):
ATAATATTATATAAAAATTAAAAAAAA
Found at i:32390617 original size:24 final size:23
Alignment explanation
Indices: 32390588--32390648 Score: 70
Period size: 24 Copynumber: 2.7 Consensus size: 23
32390578 ATATAAATAT
* *
32390588 TTTAAATTATAATAATTAATTAA
1 TTTAAATTATAAAAAGTAATTAA
*
32390611 TTATAAATTATAAAAAGTATTTAA
1 TT-TAAATTATAAAAAGTAATTAA
*
32390635 TTTAAAATA-AAAAA
1 TTTAAATTATAAAAA
32390649 TTTTAAATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
22 5 0.15
23 8 0.24
24 20 0.61
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (23 bp):
TTTAAATTATAAAAAGTAATTAA
Found at i:32395590 original size:2 final size:2
Alignment explanation
Indices: 32395583--32395611 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
32395573 CTGTTTTGAG
32395583 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
32395612 TCCTCATGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:32397661 original size:19 final size:18
Alignment explanation
Indices: 32397637--32397682 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
32397627 TCCCTGAAGC
32397637 TTTTTCTAAATCTCTT-TTT
1 TTTTTCTAAAT-T-TTATTT
*
32397656 TTTTTCAAAATTTTATTT
1 TTTTTCTAAATTTTATTT
32397674 TTTTT-TAAA
1 TTTTTCTAAA
32397683 AAAAAGCTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 5 0.21
18 9 0.38
19 10 0.42
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTTCTAAATTTTATTT
Done.