Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr11
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: 61124829
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1263459 characters in sequence are not A, C, G, or T
File 6 of 205
Found at i:1631971 original size:14 final size:13
Alignment explanation
Indices: 1631952--1631996 Score: 63
Period size: 15 Copynumber: 3.2 Consensus size: 13
1631942 AATGATGATG
1631952 AATGAAAATGAAAA
1 AATGAAAATG-AAA
1631966 AATGAAAATGAAA
1 AATGAAAATGAAA
1631979 AATGAAAAAATGAAA
1 AATG--AAAATGAAA
1631994 AAT
1 AAT
1631997 AGAGAGGCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
13 7 0.24
14 10 0.34
15 12 0.41
ACGTcount: A:0.71, C:0.00, G:0.13, T:0.16
Consensus pattern (13 bp):
AATGAAAATGAAA
Found at i:1631980 original size:21 final size:20
Alignment explanation
Indices: 1631952--1631994 Score: 77
Period size: 21 Copynumber: 2.1 Consensus size: 20
1631942 AATGATGATG
1631952 AATGAAAATGAAAAAATGAA
1 AATGAAAATGAAAAAATGAA
1631972 AATGAAAAATGAAAAAATGAA
1 AATG-AAAATGAAAAAATGAA
1631993 AA
1 AA
1631995 ATAGAGAGGC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.72, C:0.00, G:0.14, T:0.14
Consensus pattern (20 bp):
AATGAAAATGAAAAAATGAA
Found at i:1633322 original size:44 final size:42
Alignment explanation
Indices: 1633250--1633699 Score: 248
Period size: 44 Copynumber: 10.8 Consensus size: 42
1633240 AGAATTGCAG
*
1633250 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGTTAGTA
1 ATCTTATCTCCCTGAGATTACAGCGGAGCGGATTGAA-TTAG-A
* * * *
1633294 ATCCTATCTCGCTGAGATTACAGTGGAGCGGATT-AA--AGG
1 ATCTTATCTCCCTGAGATTACAGCGGAGCGGATTGAATTAGA
* * * * * *
1633333 ATCTTATCTCTCTGA-AGTTACAGTGGAGTAGG-TCGTATCAG-
1 ATCTTATCTCCCTGAGA-TTACAGCGGAG-CGGATTGAATTAGA
* * *
1633374 GTCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTA
1 ATCTTATCTCCCTGAGATTACAGCGGAGCGGATTGAA-TTAG-A
* ** * * *
1633418 ATCCTATCTCATTGAGATTACAGTGGAGTGGATT-AA--AGG
1 ATCTTATCTCCCTGAGATTACAGCGGAGCGGATTGAATTAGA
** * * * * *
1633457 ATCTTATCTCTTTGACG-TTACAGCAGAGTGGATCGCATCA-A
1 ATCTTATCTCCCTGA-GATTACAGCGGAGCGGATTGAATTAGA
* * *
1633498 GTCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTA
1 ATCTTATCTCCCTGAGATTACAGCGGAGCGGATTGAA-TTAG-A
* ** * * *
1633542 ATCCTATCTCATTGAGATTACAGTGGAGTGGATT-AA--AGG
1 ATCTTATCTCCCTGAGATTACAGCGGAGCGGATTGAATTAGA
** * * * * *
1633581 ATCTTATCTCTTTGA-AGTTACAGCAGAGTGGATCGCATCA-A
1 ATCTTATCTCCCTGAGA-TTACAGCGGAGCGGATTGAATTAGA
* * *
1633622 GTCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTA
1 ATCTTATCTCCCTGAGATTACAGCGGAGCGGATTGAA-TTAG-A
* *
1633666 ATCCTATCTCCCTGAGATTACAGTGGAGCGGATT
1 ATCTTATCTCCCTGAGATTACAGCGGAGCGGATT
1633700 AAGGGATTTT
Statistics
Matches: 307, Mismatches: 73, Indels: 52
0.71 0.17 0.12
Matches are distributed among these distances:
38 2 0.01
39 79 0.26
40 14 0.05
41 80 0.26
42 10 0.03
43 6 0.02
44 116 0.38
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (42 bp):
ATCTTATCTCCCTGAGATTACAGCGGAGCGGATTGAATTAGA
Found at i:1633477 original size:124 final size:124
Alignment explanation
Indices: 1633251--1633889 Score: 922
Period size: 124 Copynumber: 5.1 Consensus size: 124
1633241 GAATTGCAGA
* **
1633251 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGTTAGTAATCCTATCTCGCTGAGATTACA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCATTGAGATTACA
* *
1633316 GTGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTGGAGTAGGTCGTATCAGG
66 GTGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGGTCGTATCAAG
1633375 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCATTGAGATTACA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCATTGAGATTACA
* * * * *
1633440 GTGGAGTGGATTAAAGGATCTTATCTCTTTGACGTTACAGCAGAGT-GGATCGCATCAAG
66 GTGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGG-TCGTATCAAG
1633499 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCATTGAGATTACA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCATTGAGATTACA
* * * *
1633564 GTGGAGTGGATTAAAGGATCTTATCTCTTTGAAGTTACAGCAGAGT-GGATCGCATCAAG
66 GTGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGG-TCGTATCAAG
* **
1633623 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCATTGAGATTACA
* * *
1633688 GTGGAGCGGATTAAGGGATTTTATCTCTCTGAAGTTACAGTAGAGTAGATCGTATCAAG
66 GTGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGGTCGTATCAAG
* * * * * *
1633747 TCTTATCTCCTTGAGATTACAACGAAGCAGATTGAAGCTAGTAATCCTATCTCCTTGAGATTACG
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCATTGAGATTACA
* * * *
1633812 GTAGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATTGTATCAGG
66 GTGGAGCGGA-T----TAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGGTCGTATCAAG
*
1633876 TCTTATATCCCTGA
1 TCTTATCTCCCTGA
1633890 TGTTGCAGTG
Statistics
Matches: 475, Mismatches: 33, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
123 2 0.00
124 415 0.87
125 2 0.00
129 56 0.12
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (124 bp):
TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGATAGTAATCCTATCTCATTGAGATTACA
GTGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGGTCGTATCAAG
Found at i:1633519 original size:41 final size:41
Alignment explanation
Indices: 1633474--1633645 Score: 113
Period size: 41 Copynumber: 4.2 Consensus size: 41
1633464 CTCTTTGACG
1633474 TTACAGCAGAGTGGATCGCATCAAGTCTTATCTCCCTGAGA
1 TTACAGCAGAGTGGATCGCATCAAGTCTTATCTCCCTGAGA
* ** * * * * **
1633515 TTACAGCGGAGCAGATTGAAGAT-AGTAATCCTATCTCATTGAGA
1 TTACAGCAGAGTGGATCG--CATCA--AGTCTTATCTCCCTGAGA
** * **
1633559 TTACAGTGGAGTGGAT----TAAAGGATCTTATCTCTTTGA-A
1 TTACAGCAGAGTGGATCGCATCAA-G-TCTTATCTCCCTGAGA
1633597 GTTACAGCAGAGTGGATCGCATCAAGTCTTATCTCCCTGAGA
1 -TTACAGCAGAGTGGATCGCATCAAGTCTTATCTCCCTGAGA
1633639 TTACAGC
1 TTACAGC
1633646 GGAGCAGATT
Statistics
Matches: 98, Mismatches: 20, Indels: 26
0.68 0.14 0.18
Matches are distributed among these distances:
37 1 0.01
38 2 0.02
39 27 0.28
41 33 0.34
42 3 0.03
43 5 0.05
44 27 0.28
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (41 bp):
TTACAGCAGAGTGGATCGCATCAAGTCTTATCTCCCTGAGA
Found at i:1635468 original size:3 final size:3
Alignment explanation
Indices: 1635460--1635496 Score: 56
Period size: 3 Copynumber: 12.0 Consensus size: 3
1635450 TATTTTAGTG
*
1635460 TTA TTA TTA TTA TTA TTA TTA CTA TTA TTTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
1635497 GTTTTATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1636301 original size:109 final size:109
Alignment explanation
Indices: 1636005--1636396 Score: 545
Period size: 109 Copynumber: 3.6 Consensus size: 109
1635995 TCAAAAAAGG
* * * * *
1636005 AAAATATTTCCAATTAAGGTAATATTTAGCGTTTGGAAATTCGAGAAAACGTGCCCTAAAGTGCT
1 AAAA-ATTTCAAAATAAGGTAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAAGTGCT
* *
1636070 GGGTGTCGATTTTTCTCGTTCAACTAAATGGCTAAATATCCTTTT
65 GGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTT
* * * *
1636115 AAAAAATTTTAAAATAAGGTAATGTTTTGCGTTTGGAAATTTGAGAAAACGTGCCCTAAGGTGCT
1 -AAAAATTTCAAAATAAGGTAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAAGTGCT
*
1636180 GGGTGTTGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTT
65 GGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTT
** * * *
1636225 AAAAATTTCAAAATAAGACAATGTTTTGCATTTGGGAAATTCGAG-GAACATGCTCTAAAGTGCT
1 AAAAATTTCAAAATAAGGTAATGTTTTGCGTTT-GGAAATTCGAGAAAACATGCCCTAAAGTGCT
1636289 GGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTT
65 GGGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTT
* * * * *
1636334 AAAATTTTCAAAATAAGGTAAAGTTTTGCGTTTGGAAATTCGAG-GAACAAGCCCTAATGTGCT
1 AAAAATTTCAAAATAAGGTAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAAGTGCT
1636397 AGGTTTTGAT
Statistics
Matches: 252, Mismatches: 28, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
108 27 0.11
109 116 0.46
110 105 0.42
111 4 0.02
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.34
Consensus pattern (109 bp):
AAAAATTTCAAAATAAGGTAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAAGTGCTG
GGTGTCGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTT
Found at i:1646416 original size:10 final size:10
Alignment explanation
Indices: 1646386--1646421 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
1646376 AATAAAGTAG
1646386 ATTATATATT
1 ATTATATATT
*
1646396 ATTTTTATATT
1 A-TTATATATT
1646407 ATTATATATT
1 ATTATATATT
1646417 ATTAT
1 ATTAT
1646422 TTTAGTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
10 14 0.61
11 9 0.39
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
ATTATATATT
Found at i:1646522 original size:56 final size:57
Alignment explanation
Indices: 1646411--1646543 Score: 155
Period size: 56 Copynumber: 2.3 Consensus size: 57
1646401 TATATTATTA
* * *
1646411 TATATTATTATTTTAGTAAATTCATATAAGAATAATTATATTAAGAATTTTATTAAAT
1 TATA-TATTATTTTATTAAATTCATATAAGAATAATTATATTAAGAATATGATTAAAT
* *
1646469 TATATATT-TTTTATTAAATT-ATATTTAATAATAATTATGTTAA-AATATGATTAAAT
1 TATATATTATTTTATTAAATTCATA--TAAGAATAATTATATTAAGAATATGATTAAAT
*
1646525 TATTTATTATTTATATTAA
1 TATATATTATTT-TATTAA
1646544 TAATCTTATT
Statistics
Matches: 65, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
55 3 0.05
56 29 0.45
57 23 0.35
58 10 0.15
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.52
Consensus pattern (57 bp):
TATATATTATTTTATTAAATTCATATAAGAATAATTATATTAAGAATATGATTAAAT
Found at i:1646741 original size:45 final size:44
Alignment explanation
Indices: 1646653--1646745 Score: 134
Period size: 45 Copynumber: 2.1 Consensus size: 44
1646643 AGTACAACAT
*
1646653 CATTCCATTCAACCAAACACAAGAATACTATTACAGTTCTATTC
1 CATTCCATTCAACCAAACACAAGAATACTATTACAGCTCTATTC
* *
1646697 CATTCCATTCAATCAAACA-ATTGAATTACTATTACAGCTCTATTC
1 CATTCCATTCAACCAAACACA-AGAA-TACTATTACAGCTCTATTC
1646742 CATT
1 CATT
1646746 ACAGCGAACC
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
43 1 0.02
44 21 0.48
45 22 0.50
ACGTcount: A:0.37, C:0.26, G:0.04, T:0.33
Consensus pattern (44 bp):
CATTCCATTCAACCAAACACAAGAATACTATTACAGCTCTATTC
Found at i:1655783 original size:22 final size:22
Alignment explanation
Indices: 1655758--1655803 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
1655748 AAGTTTATAC
1655758 ATAAAGATCTAAATAGCTAAAT
1 ATAAAGATCTAAATAGCTAAAT
1655780 ATAAAGATCTAAATAGCTAAAT
1 ATAAAGATCTAAATAGCTAAAT
1655802 AT
1 AT
1655804 GTCAGACCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.54, C:0.09, G:0.09, T:0.28
Consensus pattern (22 bp):
ATAAAGATCTAAATAGCTAAAT
Found at i:1656186 original size:6 final size:6
Alignment explanation
Indices: 1656154--1656204 Score: 54
Period size: 6 Copynumber: 8.5 Consensus size: 6
1656144 GTCTACCTGC
1656154 AAAAT- AAAAT- AAAATA GAAGGAATA AAAATA AAAATA AAAAT- AAAATA
1 AAAATA AAAATA AAAATA -AA--AATA AAAATA AAAATA AAAATA AAAATA
1656202 AAA
1 AAA
1656205 TGTGTAATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
5 15 0.37
6 18 0.44
7 2 0.05
8 2 0.05
9 4 0.10
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:1666459 original size:20 final size:20
Alignment explanation
Indices: 1666403--1666467 Score: 71
Period size: 22 Copynumber: 3.1 Consensus size: 20
1666393 TAAACATTTT
*
1666403 TAAATTTTAATT-AATTCAG
1 TAAATTTTAATTCAATTGAG
1666422 TAAATTTTATATTTCAATTGA-
1 TAAATTTTA-A-TTCAATTGAG
1666443 TAAACTTTTAATTCAATTGTAG
1 TAAA-TTTTAATTCAATTG-AG
1666465 TAA
1 TAA
1666468 TCATATTTTG
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
19 9 0.23
20 9 0.23
21 8 0.21
22 13 0.33
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.48
Consensus pattern (20 bp):
TAAATTTTAATTCAATTGAG
Found at i:1671379 original size:10 final size:10
Alignment explanation
Indices: 1671364--1671388 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1671354 ACAAAAAATT
1671364 GAAAATCATA
1 GAAAATCATA
1671374 GAAAATCATA
1 GAAAATCATA
1671384 GAAAA
1 GAAAA
1671389 AAAACTCGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.64, C:0.08, G:0.12, T:0.16
Consensus pattern (10 bp):
GAAAATCATA
Found at i:1673328 original size:31 final size:31
Alignment explanation
Indices: 1673288--1673350 Score: 74
Period size: 30 Copynumber: 2.0 Consensus size: 31
1673278 ATTTTAGGCA
*
1673288 CTGTCGTTAACAACAATTTTTATTTTGGTCAC
1 CTGTCGTTAA-AACAATTTTCATTTTGGTCAC
** *
1673320 CTGT-GTTAATTCAATTTTCATTTTTGTCAC
1 CTGTCGTTAAAACAATTTTCATTTTGGTCAC
1673350 C
1 C
1673351 CAACCTTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 18 0.67
31 5 0.19
32 4 0.15
ACGTcount: A:0.22, C:0.19, G:0.11, T:0.48
Consensus pattern (31 bp):
CTGTCGTTAAAACAATTTTCATTTTGGTCAC
Found at i:1678103 original size:41 final size:41
Alignment explanation
Indices: 1678041--1678233 Score: 314
Period size: 41 Copynumber: 4.7 Consensus size: 41
1678031 TTAATTTAAA
1678041 CAGATTCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
1 CAGA-TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
*
1678083 CAAATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
* *
1678124 CAGATCACCGGCACTTAGCCTACTAGGCTTATAGCCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
***
1678165 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAGTTTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
*
1678206 TAGATCACCGGCACTTAGCCTGCTAGGC
1 CAGATCACCGGCACTTAGCCTGCTAGGC
1678234 GCTAAGCCTG
Statistics
Matches: 143, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
41 140 0.98
42 3 0.02
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.27
Consensus pattern (41 bp):
CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
Found at i:1683685 original size:11 final size:11
Alignment explanation
Indices: 1683669--1683693 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1683659 ATAAAATGAA
1683669 AAAAGTTGTTT
1 AAAAGTTGTTT
1683680 AAAAGTTGTTT
1 AAAAGTTGTTT
1683691 AAA
1 AAA
1683694 CTGCCCCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (11 bp):
AAAAGTTGTTT
Found at i:1685379 original size:113 final size:114
Alignment explanation
Indices: 1685194--1685746 Score: 380
Period size: 114 Copynumber: 4.8 Consensus size: 114
1685184 AAATCTCAAG
* * *
1685194 ACCAACACGCAGCGTTCTGGTCTTGATGTAT-TTGGC-ATTAGTGGCGCTTACGAA-CAAACGCC
1 ACCAAAACGCAGCGTT-TGGTCTTGATGTATATT-GCAATTAGTGGCGCTTA-TAAGAAAACGCC
* * *
1685256 GGTAATGTATAGTATTAGCGGCGCTTAGAGG-AAGCGCCGCAAAAGAT-GTA
63 GCTAAAGTATAGTATTAGCGGCGCTTAGAGGTAAGCGCCGCAAAAGATCTTA
*
1685306 ACCAAAACGCAGAGTTTGGTCTTGATGTATATTGCAATTAGTGGCGCTTATAAAGAAAACGCCGC
1 ACCAAAACGCAGCGTTTGGTCTTGATGTATATTGCAATTAGTGGCGCTTAT-AAGAAAACGCCGC
* ** * * *
1685371 TAATGTATAGTATTAGCGGCGCTCGGCGGCGCCGAGCGTTAAACGCCGCAAGACATCTTA
65 TAAAGTATAGTATTAGCGGCGCT--------TAGAG-G-TAAGCGCCGCAAAAGATCTTA
* * **
1685431 ATCAAAACGCAGCGTGTTGGTCTTGATGTATAATATAATTAGTGGCG-TT-TAAGGAAAACGCCA
1 ACCAAAACGCAGCGT-TTGGTCTTGATGTATATTGCAATTAGTGGCGCTTATAA-GAAAACGCC-
* * * * * * *
1685494 G-TAAAGGATAGT-TATAGCAGCGTTTGGTGGTAAGCGCCTCAAAATATCTTA
63 GCTAAAGTATAGTAT-TAGCGGCGCTTAGAGGTAAGCGCCGCAAAAGATCTTA
* * * * *
1685545 ACCAAAACGCAGAGTTTGCTCTTGAGGTGTATTAG-AATTAGTGGCGCTTGATGA-AAAACGCCG
1 ACCAAAACGCAGCGTTTGGTCTTGATGTATATT-GCAATTAGTGGCGCTT-ATAAGAAAACGCCG
* * *
1685608 CTAAAGTATA-TCATTAGCGGCG-TTTGTGG-AACGCGCCG-TAAAGTATCTTA
64 CTAAAGTATAGT-ATTAGCGGCGCTTAGAGGTAA-GCGCCGCAAAAG-ATCTTA
* * * ** * ** **
1685658 ACCAAAACACAGCTTTTAGTTCTTGATGTATACCGGAATTAGTGGCGCACATGGGAAAACGCCGC
1 ACCAAAACGCAGCGTTT-GGTCTTGATGTATATTGCAATTAGTGGCGCTTATAAGAAAACGCCGC
* * *
1685723 TGAAGCATAGTATTAGTGGCGCTT
65 TAAAGTATAGTATTAGCGGCGCTT
1685747 TTACCGAAAC
Statistics
Matches: 352, Mismatches: 55, Indels: 65
0.75 0.12 0.14
Matches are distributed among these distances:
111 16 0.05
112 37 0.11
113 93 0.26
114 104 0.30
115 5 0.01
116 4 0.01
121 3 0.01
122 1 0.00
123 3 0.01
124 40 0.11
125 18 0.05
126 28 0.08
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (114 bp):
ACCAAAACGCAGCGTTTGGTCTTGATGTATATTGCAATTAGTGGCGCTTATAAGAAAACGCCGCT
AAAGTATAGTATTAGCGGCGCTTAGAGGTAAGCGCCGCAAAAGATCTTA
Found at i:1686860 original size:7 final size:7
Alignment explanation
Indices: 1686844--1686890 Score: 85
Period size: 7 Copynumber: 6.7 Consensus size: 7
1686834 TGTTCGAGGT
1686844 TTTGGGG
1 TTTGGGG
*
1686851 TTTAGGG
1 TTTGGGG
1686858 TTTGGGG
1 TTTGGGG
1686865 TTTGGGG
1 TTTGGGG
1686872 TTTGGGG
1 TTTGGGG
1686879 TTTGGGG
1 TTTGGGG
1686886 TTTGG
1 TTTGG
1686891 TTTTTGAGGT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.02, C:0.00, G:0.53, T:0.45
Consensus pattern (7 bp):
TTTGGGG
Found at i:1686901 original size:21 final size:21
Alignment explanation
Indices: 1686844--1686902 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
1686834 TGTTCGAGGT
1686844 TTTGGGGTTT-AGGGTTTGGGG
1 TTTGGGGTTTGA-GGTTTGGGG
*
1686865 TTTGGGGTTTGGGGTTTGGGG
1 TTTGGGGTTTGAGGTTTGGGG
**
1686886 TTTGGTTTTTGAGGTTT
1 TTTGGGGTTTGAGGTTT
1686903 AAGGTTTACA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.03, C:0.00, G:0.47, T:0.49
Consensus pattern (21 bp):
TTTGGGGTTTGAGGTTTGGGG
Found at i:1689120 original size:16 final size:16
Alignment explanation
Indices: 1689099--1689134 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
1689089 GTATTTATAA
*
1689099 TTATCGATTTGCAATT
1 TTATCGATTTACAATT
1689115 TTATCGATTTACAATT
1 TTATCGATTTACAATT
1689131 TTAT
1 TTAT
1689135 TTCAATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.28, C:0.11, G:0.08, T:0.53
Consensus pattern (16 bp):
TTATCGATTTACAATT
Found at i:1689271 original size:67 final size:67
Alignment explanation
Indices: 1689194--1689399 Score: 369
Period size: 67 Copynumber: 3.1 Consensus size: 67
1689184 ATTAATTGAT
*
1689194 TGAATGTCAATGAATTATCAATTTTGGTTA-TGTAATTGATTGAATGTTTTATAAATTCATTATA
1 TGAATGTCAATGAATTATCAATTTTGGTTAGT-TAATTGATTGAATGTTTAATAAATTCATTATA
*
1689258 TAC
65 TAA
*
1689261 TGAATGTCAATGAATTTTCAATTTTGGTTAGTTAATTGATTGAATGTTTAATAAATTCATTATAT
1 TGAATGTCAATGAATTATCAATTTTGGTTAGTTAATTGATTGAATGTTTAATAAATTCATTATAT
1689326 AA
66 AA
1689328 TGAATGTCAATGAATTATCAATTTTGGTTAGTTAATTGATTGAATGTTTAATAAATTCATTATAT
1 TGAATGTCAATGAATTATCAATTTTGGTTAGTTAATTGATTGAATGTTTAATAAATTCATTATAT
1689393 AA
66 AA
1689395 TGAAT
1 TGAAT
1689400 TCTCAACAAA
Statistics
Matches: 134, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
67 133 0.99
68 1 0.01
ACGTcount: A:0.36, C:0.05, G:0.14, T:0.46
Consensus pattern (67 bp):
TGAATGTCAATGAATTATCAATTTTGGTTAGTTAATTGATTGAATGTTTAATAAATTCATTATAT
AA
Found at i:1689597 original size:34 final size:34
Alignment explanation
Indices: 1689535--1689756 Score: 165
Period size: 34 Copynumber: 6.0 Consensus size: 34
1689525 CTTATTAATG
* * *
1689535 AATATATATTTTAAAATTGATATCTTACATTACTTA
1 AATATATATTTT-TAAGT-ATATCTTACATGACTTA
* * *
1689571 AATATATATTATTAAGTATATTTTACACGACTTA
1 AATATATATTTTTAAGTATATCTTACATGACTTA
* *
1689605 TTAATGAATATATATTTTAAAATTGATATCTTACATTACTTA
1 --AAT--ATATAT-TTTT--AAGT-ATATCTTACATGACTTA
* *
1689647 AATATATATTATTAAGTATATTTTACATGACTTA
1 AATATATATTTTTAAGTATATCTTACATGACTTA
* *
1689681 TTAATAAATATATATTTTAAAATTGATATCTTACATTACTTA
1 --AAT--ATATAT-TTTT--AAGT-ATATCTTACATGACTTA
*
1689723 AATATATATTTTTAAGTATATTTTACATGACTTA
1 AATATATATTTTTAAGTATATCTTACATGACTTA
1689757 CATTACTTAC
Statistics
Matches: 148, Mismatches: 22, Indels: 34
0.73 0.11 0.17
Matches are distributed among these distances:
34 44 0.30
35 9 0.06
36 17 0.11
37 7 0.05
38 24 0.16
39 6 0.04
40 6 0.04
41 6 0.04
42 29 0.20
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.47
Consensus pattern (34 bp):
AATATATATTTTTAAGTATATCTTACATGACTTA
Found at i:1689618 original size:76 final size:76
Alignment explanation
Indices: 1689524--1689756 Score: 439
Period size: 76 Copynumber: 3.1 Consensus size: 76
1689514 ATTTCATTTA
1689524 ACTTATTAATGAATATATATTTTAAAATTGATATCTTACATTACTTAAATATATATTATTAAGTA
1 ACTTATTAATGAATATATATTTTAAAATTGATATCTTACATTACTTAAATATATATTATTAAGTA
*
1689589 TATTTTACACG
66 TATTTTACATG
1689600 ACTTATTAATGAATATATATTTTAAAATTGATATCTTACATTACTTAAATATATATTATTAAGTA
1 ACTTATTAATGAATATATATTTTAAAATTGATATCTTACATTACTTAAATATATATTATTAAGTA
1689665 TATTTTACATG
66 TATTTTACATG
* *
1689676 ACTTATTAATAAATATATATTTTAAAATTGATATCTTACATTACTTAAATATATATTTTTAAGTA
1 ACTTATTAATGAATATATATTTTAAAATTGATATCTTACATTACTTAAATATATATTATTAAGTA
1689741 TATTTTACATG
66 TATTTTACATG
1689752 ACTTA
1 ACTTA
1689757 CATTACTTAC
Statistics
Matches: 154, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
76 154 1.00
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.47
Consensus pattern (76 bp):
ACTTATTAATGAATATATATTTTAAAATTGATATCTTACATTACTTAAATATATATTATTAAGTA
TATTTTACATG
Found at i:1689813 original size:13 final size:12
Alignment explanation
Indices: 1689787--1689835 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 12
1689777 TTTTTACTAA
*
1689787 AATTAACTTGAAT
1 AATT-ACTTAAAT
1689800 ATATTACTTAAAT
1 A-ATTACTTAAAT
1689813 AATTTACTTAAAT
1 AA-TTACTTAAAT
1689826 ACATTACTTA
1 A-ATTACTTA
1689836 CTAAAATTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
12 1 0.03
13 27 0.84
14 4 0.12
ACGTcount: A:0.45, C:0.10, G:0.02, T:0.43
Consensus pattern (12 bp):
AATTACTTAAAT
Found at i:1690188 original size:9 final size:9
Alignment explanation
Indices: 1690176--1690406 Score: 162
Period size: 9 Copynumber: 26.4 Consensus size: 9
1690166 TAGTTACATA
*
1690176 ATAACTTAT
1 ATAACTTAC
1690185 ATAAACTTAC
1 AT-AACTTAC
*
1690195 ATAA-TACAC
1 ATAACT-TAC
*
1690204 ATTACTTAC
1 ATAACTTAC
* *
1690213 ATAGCATAC
1 ATAACTTAC
1690222 ATAACTTAC
1 ATAACTTAC
* *
1690231 ACAACTTAA
1 ATAACTTAC
1690240 ATAA--TAC
1 ATAACTTAC
*
1690247 AAAACTTAC
1 ATAACTTAC
1690256 ATAACTTAC
1 ATAACTTAC
*
1690265 ATAACCTAC
1 ATAACTTAC
*
1690274 ATAATACATA-
1 AT-A-ACTTAC
1690284 ATAACTTAC
1 ATAACTTAC
1690293 --AACTTAC
1 ATAACTTAC
*
1690300 ATAACATAC
1 ATAACTTAC
* **
1690309 ATTACTTTG
1 ATAACTTAC
1690318 ATAACTTAC
1 ATAACTTAC
1690327 ATAACTTAC
1 ATAACTTAC
1690336 AT-AC-TAC
1 ATAACTTAC
* *
1690343 ACAACTTAA
1 ATAACTTAC
*
1690352 ATAGCTTAC
1 ATAACTTAC
*
1690361 TTAA--TAC
1 ATAACTTAC
1690368 ATAACTTAC
1 ATAACTTAC
1690377 ATAACTT--
1 ATAACTTAC
*
1690384 ATACACGTAC
1 ATA-ACTTAC
1690394 ATAACTTAC
1 ATAACTTAC
1690403 ATAA
1 ATAA
1690407 TTGACTTAAT
Statistics
Matches: 169, Mismatches: 36, Indels: 34
0.71 0.15 0.14
Matches are distributed among these distances:
7 25 0.15
8 12 0.07
9 113 0.67
10 15 0.09
11 4 0.02
ACGTcount: A:0.46, C:0.21, G:0.02, T:0.31
Consensus pattern (9 bp):
ATAACTTAC
Found at i:1690252 original size:25 final size:25
Alignment explanation
Indices: 1690218--1690268 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
1690208 CTTACATAGC
*
1690218 ATACATAACTTACACAACTTAAATA
1 ATACAAAACTTACACAACTTAAATA
* *
1690243 ATACAAAACTTACATAACTTACATA
1 ATACAAAACTTACACAACTTAAATA
1690268 A
1 A
1690269 CCTACATAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.53, C:0.20, G:0.00, T:0.27
Consensus pattern (25 bp):
ATACAAAACTTACACAACTTAAATA
Found at i:1690266 original size:43 final size:45
Alignment explanation
Indices: 1690188--1690310 Score: 121
Period size: 43 Copynumber: 2.8 Consensus size: 45
1690178 AACTTATATA
* * * *
1690188 AACTTACATAATACACATTACTTACATAGCATACATAACTTACAC
1 AACTTAAATAATACACATAACTTACATAACATACATAACCTACAC
* *
1690233 AACTTAAATAATACA-A-AACTTACATAACTTACATAACCTACAT
1 AACTTAAATAATACACATAACTTACATAACATACATAACCTACAC
* *
1690276 AA--TACATAATA-ACTTACAACTTACATAACATACAT
1 AACTTAAATAATACAC--ATAACTTACATAACATACAT
1690311 TACTTTGATA
Statistics
Matches: 66, Mismatches: 8, Indels: 9
0.80 0.10 0.11
Matches are distributed among these distances:
40 1 0.02
41 8 0.12
43 25 0.38
44 18 0.27
45 14 0.21
ACGTcount: A:0.49, C:0.22, G:0.01, T:0.28
Consensus pattern (45 bp):
AACTTAAATAATACACATAACTTACATAACATACATAACCTACAC
Found at i:1690359 original size:25 final size:25
Alignment explanation
Indices: 1690340--1690419 Score: 54
Period size: 25 Copynumber: 3.2 Consensus size: 25
1690330 ACTTACATAC
* * *
1690340 TACACAACTTAAATAGCTTACTTAA
1 TACACAACTTACATAACTTACATAA
* * * *
1690365 TACATAACTTACATAACTTATACACG
1 TACACAACTTACATAACTTACATA-A
* *
1690391 TACATAACTTACATAA-TTGACTTAA
1 TACACAACTTACATAACTT-ACATAA
1690416 TACA
1 TACA
1690420 TAAATATATA
Statistics
Matches: 42, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
25 24 0.57
26 18 0.43
ACGTcount: A:0.44, C:0.20, G:0.04, T:0.33
Consensus pattern (25 bp):
TACACAACTTACATAACTTACATAA
Found at i:1696287 original size:713 final size:713
Alignment explanation
Indices: 1694922--1696347 Score: 2798
Period size: 713 Copynumber: 2.0 Consensus size: 713
1694912 GGCGAGGTTT
1694922 GTTTTAGAGGTCTCGGATGCTTACGTAAAGAAGGCATTGGGAAAAATATGGAGAGACAATAAAAG
1 GTTTTAGAGGTCTCGGATGCTTACGTAAAGAAGGCATTGGGAAAAATATGGAGAGACAATAAAAG
1694987 TACTTTGAAGAAAAATTATTATAAAACAAAAACAACCCTAGATGAGAAATTGCAAAATGTCCCGC
66 TACTTTGAAGAAAAATTATTATAAAACAAAAACAACCCTAGATGAGAAATTGCAAAATGTCCCGC
1695052 CGGGTATGTTGAGGTACCAATGGGAAGATGCGGTTAGATTTTGGCATTCGAAGAAAGGCGAGGTA
131 CGGGTATGTTGAGGTACCAATGGGAAGATGCGGTTAGATTTTGGCATTCGAAGAAAGGCGAGGTA
1695117 TGACGTACTTCCAAACTATTGTAATTATTTTGGTTTATAGTATTTTCTATTTACGTACTAAAAAT
196 TGACGTACTTCCAAACTATTGTAATTATTTTGGTTTATAGTATTTTCTATTTACGTACTAAAAAT
1695182 TTCATAACGTAGGATCGTGAACAAGTTGGAAAAAGCAGCAGGCAGAAACAAAAATTCACCCACAC
261 TTCATAACGTAGGATCGTGAACAAGTTGGAAAAAGCAGCAGGCAGAAACAAAAATTCACCCACAC
*
1695247 AGCCGGGTCGAGAAGTTTTGCATGTGTAGCTGAGGCGGAGGTATTTTTAATTTTTTTAATATTGT
326 AGCCGGGTCGAGAAGTTTCGCATGTGTAGCTGAGGCGGAGGTATTTTTAATTTTTTTAATATTGT
*
1695312 CGAATATGTATAACTTTCTGTTAAATAATATTTATACTACCATATTGTAGGAACTGTCGTCCGGT
391 CGAATATGTATAACTTTCTATTAAATAATATTTATACTACCATATTGTAGGAACTGTCGTCCGGT
1695377 CAAAAAGTTGGACGCCTTCAACTTTTTGAAATTACACATAGGAAGAAAGATGGATCTCCCATGAC
456 CAAAAAGTTGGACGCCTTCAACTTTTTGAAATTACACATAGGAAGAAAGATGGATCTCCCATGAC
1695442 TCCTGAAGCTGGTGAAATAATGGTACGTTTACTTAATAAGATTTGACTTATTTTAGTTATTTTTA
521 TCCTGAAGCTGGTGAAATAATGGTACGTTTACTTAATAAGATTTGACTTATTTTAGTTATTTTTA
1695507 GTGTTTATTTTCTAATGGTTTAATTCATTGCTTGTAATGCAACTATGGTTATGTTGCATATGTTT
586 GTGTTTATTTTCTAATGGTTTAATTCATTGCTTGTAATGCAACTATGGTTATGTTGCATATGTTT
1695572 TTTAATATATAATATTACGTTCCTAACTATGTGATTTATTTATTAGGAAAAACTAAAGGATAA
651 TTTAATATATAATATTACGTTCCTAACTATGTGATTTATTTATTAGGAAAAACTAAAGGATAA
1695635 GTTTTAGAGGTCTCGGATGCTTACGTAAAGAAGGCATTGGGAAAAATATGGAGAGACAATAAAAG
1 GTTTTAGAGGTCTCGGATGCTTACGTAAAGAAGGCATTGGGAAAAATATGGAGAGACAATAAAAG
1695700 TACTTTGAAGAAAAATTATTATAAAACAAAAACAACCCTAGATGAGAAATTGCAAAATGTCCCGC
66 TACTTTGAAGAAAAATTATTATAAAACAAAAACAACCCTAGATGAGAAATTGCAAAATGTCCCGC
1695765 CGGGTATGTTGAGGTACCAATGGGAAGATGCGGTTAGATTTTGGCATTCGAAGAAAGGCGAGGTA
131 CGGGTATGTTGAGGTACCAATGGGAAGATGCGGTTAGATTTTGGCATTCGAAGAAAGGCGAGGTA
1695830 TGACGTACTTCCAAACTATTGTAATTATTTTGGTTTATAGTATTTTCTATTTACGTACTAAAAAT
196 TGACGTACTTCCAAACTATTGTAATTATTTTGGTTTATAGTATTTTCTATTTACGTACTAAAAAT
1695895 TTCATAACGTAGGATCGTGAACAAGTTGGAAAAAGCAGCAGGCAGAAACAAAAATTCACCCACAC
261 TTCATAACGTAGGATCGTGAACAAGTTGGAAAAAGCAGCAGGCAGAAACAAAAATTCACCCACAC
1695960 AGCCGGGTCGAGAAGTTTCGCATGTGTAGCTGAGGCGGAGGTATTTTTAATTTTTTTAATATTGT
326 AGCCGGGTCGAGAAGTTTCGCATGTGTAGCTGAGGCGGAGGTATTTTTAATTTTTTTAATATTGT
*
1696025 CGAATATGTATAACTTTCTATTAAATAATATTTATACTACTATATTGTAGGAACTGTCGTCCGGT
391 CGAATATGTATAACTTTCTATTAAATAATATTTATACTACCATATTGTAGGAACTGTCGTCCGGT
1696090 CAAAAAGTTGGACGCCTTCAACTTTTTGAAATTACACATAGGAAGAAAGATGGATCTCCCATGAC
456 CAAAAAGTTGGACGCCTTCAACTTTTTGAAATTACACATAGGAAGAAAGATGGATCTCCCATGAC
1696155 TCCTGAAGCTGGTGAAATAATGGTACGTTTACTTAATAAGATTTGACTTATTTTAGTTATTTTTA
521 TCCTGAAGCTGGTGAAATAATGGTACGTTTACTTAATAAGATTTGACTTATTTTAGTTATTTTTA
* *
1696220 GTGTTTATTTTCTAATGGTTTAATTCATTGCTTGTAATGCGACTATTGTTATGTTGCATATGTTT
586 GTGTTTATTTTCTAATGGTTTAATTCATTGCTTGTAATGCAACTATGGTTATGTTGCATATGTTT
*
1696285 TTTAATATATAATATTGCGTTCCTAACTATGTGATTTATTTATTAGGAAAAACTAAAGGATAA
651 TTTAATATATAATATTACGTTCCTAACTATGTGATTTATTTATTAGGAAAAACTAAAGGATAA
1696348 AAAGGCGGAG
Statistics
Matches: 707, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
713 707 1.00
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.34
Consensus pattern (713 bp):
GTTTTAGAGGTCTCGGATGCTTACGTAAAGAAGGCATTGGGAAAAATATGGAGAGACAATAAAAG
TACTTTGAAGAAAAATTATTATAAAACAAAAACAACCCTAGATGAGAAATTGCAAAATGTCCCGC
CGGGTATGTTGAGGTACCAATGGGAAGATGCGGTTAGATTTTGGCATTCGAAGAAAGGCGAGGTA
TGACGTACTTCCAAACTATTGTAATTATTTTGGTTTATAGTATTTTCTATTTACGTACTAAAAAT
TTCATAACGTAGGATCGTGAACAAGTTGGAAAAAGCAGCAGGCAGAAACAAAAATTCACCCACAC
AGCCGGGTCGAGAAGTTTCGCATGTGTAGCTGAGGCGGAGGTATTTTTAATTTTTTTAATATTGT
CGAATATGTATAACTTTCTATTAAATAATATTTATACTACCATATTGTAGGAACTGTCGTCCGGT
CAAAAAGTTGGACGCCTTCAACTTTTTGAAATTACACATAGGAAGAAAGATGGATCTCCCATGAC
TCCTGAAGCTGGTGAAATAATGGTACGTTTACTTAATAAGATTTGACTTATTTTAGTTATTTTTA
GTGTTTATTTTCTAATGGTTTAATTCATTGCTTGTAATGCAACTATGGTTATGTTGCATATGTTT
TTTAATATATAATATTACGTTCCTAACTATGTGATTTATTTATTAGGAAAAACTAAAGGATAA
Found at i:1696661 original size:21 final size:21
Alignment explanation
Indices: 1696635--1696684 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
1696625 CTACAACTTA
*
1696635 AAGCAGAGGCGGCAGCGAGGG
1 AAGCAGAGGCGGCAGCGAGAG
* *
1696656 AAGCAGAAGCTGCAGCGAGAG
1 AAGCAGAGGCGGCAGCGAGAG
1696677 AAGCAGAG
1 AAGCAGAG
1696685 CAGGCCAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.36, C:0.18, G:0.44, T:0.02
Consensus pattern (21 bp):
AAGCAGAGGCGGCAGCGAGAG
Found at i:1697328 original size:42 final size:41
Alignment explanation
Indices: 1697239--1697375 Score: 222
Period size: 42 Copynumber: 3.3 Consensus size: 41
1697229 TAAGAATAAA
*
1697239 CGCCGCTAAAGAACATGATCTTTAGCGGC-TTTTTTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCTTTTTTTCTAAG
*
1697279 CGTCGCTAAAGAACATGGTCTTTAGCGGCATTTTTTTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGC-TTTTTTTCTAAG
*
1697321 CGCCGCTAAAGAACATGGTCTTTAGAGGCGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGC-TTTTTTTCTAAG
1697363 CGCCGCTAAAGAA
1 CGCCGCTAAAGAA
1697376 TTCTTTAGCG
Statistics
Matches: 90, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
40 27 0.30
42 63 0.70
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (41 bp):
CGCCGCTAAAGAACATGGTCTTTAGCGGCTTTTTTTCTAAG
Found at i:1697513 original size:21 final size:21
Alignment explanation
Indices: 1697470--1697513 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1697460 TTAGTGGCGT
* *
1697470 TAAAAAGCGCCGCTAAAGGCC
1 TAAAAAACGCCGCTAAAGACC
*
1697491 TAAAAAACGCCGCTAGAGACC
1 TAAAAAACGCCGCTAAAGACC
1697512 TA
1 TA
1697514 TTTTGGTGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.41, C:0.27, G:0.20, T:0.11
Consensus pattern (21 bp):
TAAAAAACGCCGCTAAAGACC
Found at i:1699121 original size:16 final size:15
Alignment explanation
Indices: 1699073--1699123 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
1699063 AGCATCACCA
*
1699073 ATCCTTATCGCTGCCC
1 ATCC-TATCGCTCCCC
*
1699089 ATCC-ATTGCTCCCCC
1 ATCCTATCGCT-CCCC
1699104 ATCTCTATCGCTCCCC
1 ATC-CTATCGCTCCCC
1699120 ATCC
1 ATCC
1699124 CACTGCCCTC
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
14 5 0.17
15 7 0.24
16 12 0.41
17 5 0.17
ACGTcount: A:0.14, C:0.49, G:0.08, T:0.29
Consensus pattern (15 bp):
ATCCTATCGCTCCCC
Found at i:1699827 original size:19 final size:21
Alignment explanation
Indices: 1699793--1699833 Score: 68
Period size: 19 Copynumber: 2.0 Consensus size: 21
1699783 CTCCAAATCC
1699793 TAATTTAAAGATTATTATGAA
1 TAATTTAAAGATTATTATGAA
1699814 TAATTT-AA-ATTATTATGAA
1 TAATTTAAAGATTATTATGAA
1699833 T
1 T
1699834 TTGACAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 12 0.60
20 2 0.10
21 6 0.30
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.46
Consensus pattern (21 bp):
TAATTTAAAGATTATTATGAA
Found at i:1701764 original size:77 final size:77
Alignment explanation
Indices: 1701637--1701790 Score: 290
Period size: 77 Copynumber: 2.0 Consensus size: 77
1701627 CATTATAAAG
*
1701637 CGCTGGATCAAAATTTTAGGAAACACATATAATTAGACCTAATACATAAGAGGCTCAATTTATCC
1 CGCTGGATCAAAAGTTTAGGAAACACATATAATTAGACCTAATACATAAGAGGCTCAATTTATCC
1701702 ATCATGTAACAT
66 ATCATGTAACAT
1701714 CGCTGGATCAAAAGTTTAGGAAACACATATAATTAGACCTAATACATAAGAGGCTCAATTTATCC
1 CGCTGGATCAAAAGTTTAGGAAACACATATAATTAGACCTAATACATAAGAGGCTCAATTTATCC
*
1701779 CTCATGTAACAT
66 ATCATGTAACAT
1701791 GAGGGGGCGG
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
77 75 1.00
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.28
Consensus pattern (77 bp):
CGCTGGATCAAAAGTTTAGGAAACACATATAATTAGACCTAATACATAAGAGGCTCAATTTATCC
ATCATGTAACAT
Found at i:1709990 original size:78 final size:78
Alignment explanation
Indices: 1709861--1710011 Score: 266
Period size: 78 Copynumber: 1.9 Consensus size: 78
1709851 GTCGTGACTT
* *
1709861 GTAGGATATGATGCAACTCTTCAAGCTTCATGTACAACTCATCGAAGTTGTGCACAAGAGACAAC
1 GTAGGAGATGATGCAACTCTTCAAGCTTCATGTACAACTCATCGAACTTGTGCACAAGAGACAAC
1709926 AACTATGCAACTC
66 AACTATGCAACTC
* *
1709939 GTAGGAGATGATGCAACTCTTCAAGCTTCATGTACAATTCATTGAACTTGTGCACAAGAGACAAC
1 GTAGGAGATGATGCAACTCTTCAAGCTTCATGTACAACTCATCGAACTTGTGCACAAGAGACAAC
1710004 AACTATGC
66 AACTATGC
1710012 CAGGAGTACT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
78 69 1.00
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (78 bp):
GTAGGAGATGATGCAACTCTTCAAGCTTCATGTACAACTCATCGAACTTGTGCACAAGAGACAAC
AACTATGCAACTC
Found at i:1712878 original size:14 final size:14
Alignment explanation
Indices: 1712861--1712888 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1712851 ATCAATAGTC
1712861 AAAGCTTAATACGA
1 AAAGCTTAATACGA
1712875 AAAGCTTAATACGA
1 AAAGCTTAATACGA
1712889 GGATATTATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.14, G:0.14, T:0.21
Consensus pattern (14 bp):
AAAGCTTAATACGA
Found at i:1715487 original size:18 final size:18
Alignment explanation
Indices: 1715466--1715516 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
1715456 ACAATTTATA
*
1715466 TATATACATATATATTTT
1 TATATACATATATATTTC
*
1715484 TATATAC-TTTATAATTTC
1 TATATACATATAT-ATTTC
*
1715502 CATATACATATATAT
1 TATATACATATATAT
1715517 ACATATTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
17 4 0.15
18 19 0.70
19 4 0.15
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.51
Consensus pattern (18 bp):
TATATACATATATATTTC
Found at i:1715500 original size:38 final size:39
Alignment explanation
Indices: 1715427--1715527 Score: 105
Period size: 40 Copynumber: 2.6 Consensus size: 39
1715417 TCATAATTCG
* * *
1715427 TATACACATATATTTTTTATATATATTTTACAATTT-ATA
1 TATATACATATATATTTT-TATATACTTTACAATTTCATA
*
1715466 TATATACATATATATTTTTATATACTTTATAATTTCCATA
1 TATATACATATATATTTTTATATACTTTACAATTT-CATA
* * * *
1715506 TACATATATATACATATTTATA
1 TATATACATATATATTTTTATA
1715528 CTTTTTTATT
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
38 15 0.29
39 16 0.31
40 21 0.40
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (39 bp):
TATATACATATATATTTTTATATACTTTACAATTTCATA
Found at i:1717146 original size:24 final size:23
Alignment explanation
Indices: 1717118--1717197 Score: 80
Period size: 24 Copynumber: 3.6 Consensus size: 23
1717108 TATGTTATAA
1717118 AAATATTATATTAATTATATATTT
1 AAAT-TTATATTAATTATATATTT
1717142 AAA--TA-A-TAATTATATATTT
1 AAATTTATATTAATTATATATTT
*
1717161 ATATTTATATTTATATT-TATATTT
1 AAATTTATA-TTA-ATTATATATTT
*
1717185 ATATTTATATTAA
1 AAATTTATATTAA
1717198 ATCACGAACC
Statistics
Matches: 49, Mismatches: 1, Indels: 14
0.77 0.02 0.22
Matches are distributed among these distances:
19 15 0.31
20 1 0.02
21 4 0.08
22 2 0.04
23 3 0.06
24 21 0.43
25 3 0.06
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
AAATTTATATTAATTATATATTT
Found at i:1717165 original size:6 final size:6
Alignment explanation
Indices: 1717154--1717195 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
1717144 ATAATAATTA
1717154 TATATT TATATT TATATT TATATT TATATT TATATT TATATT
1 TATATT TATATT TATATT TATATT TATATT TATATT TATATT
1717196 AAATCACGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TATATT
Found at i:1718261 original size:50 final size:50
Alignment explanation
Indices: 1718198--1718305 Score: 162
Period size: 50 Copynumber: 2.2 Consensus size: 50
1718188 CCGAAATGAT
* ** * *
1718198 ATTTTTTTTATGGCGCCTATCTGAGAGGCGCCAATGTTTATTTTGTATTA
1 ATTTTTTTAATGGCGCCTATCTGAGAGGCGCCAATGAATATTATATATTA
*
1718248 ATTTTTTTAATGGCGCCTATCTGATAGGCGCCAATGAATATTATATATTA
1 ATTTTTTTAATGGCGCCTATCTGAGAGGCGCCAATGAATATTATATATTA
1718298 ATTTTTTT
1 ATTTTTTT
1718306 TCTTTTAATA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.24, C:0.13, G:0.17, T:0.46
Consensus pattern (50 bp):
ATTTTTTTAATGGCGCCTATCTGAGAGGCGCCAATGAATATTATATATTA
Found at i:1721583 original size:18 final size:18
Alignment explanation
Indices: 1721562--1721617 Score: 80
Period size: 18 Copynumber: 3.2 Consensus size: 18
1721552 AAGGCAACAT
1721562 AAATTAAATTGATAAATA
1 AAATTAAATTGATAAATA
* *
1721580 AAATTAAA-AGA-AAAAA
1 AAATTAAATTGATAAATA
1721596 AAATTAAATTGATAAATA
1 AAATTAAATTGATAAATA
1721614 AAAT
1 AAAT
1721618 GCCAACAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
16 12 0.38
17 4 0.12
18 16 0.50
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (18 bp):
AAATTAAATTGATAAATA
Found at i:1721965 original size:18 final size:18
Alignment explanation
Indices: 1721944--1721978 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1721934 TGCCTCCAGG
1721944 TCCGGCTCTAACTCTGGC
1 TCCGGCTCTAACTCTGGC
*
1721962 TCCGGCTCTAGCTCTGG
1 TCCGGCTCTAACTCTGG
1721979 GTCTGGTGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.09, C:0.37, G:0.26, T:0.29
Consensus pattern (18 bp):
TCCGGCTCTAACTCTGGC
Found at i:1723622 original size:15 final size:15
Alignment explanation
Indices: 1723604--1723643 Score: 71
Period size: 16 Copynumber: 2.6 Consensus size: 15
1723594 TAAAAATCAA
1723604 ATAAAATTACATTAT
1 ATAAAATTACATTAT
1723619 ATAAAAATTACATTAT
1 AT-AAAATTACATTAT
1723635 ATAAAATTA
1 ATAAAATTA
1723644 AATGAGTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 9 0.38
16 15 0.62
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (15 bp):
ATAAAATTACATTAT
Found at i:1723963 original size:57 final size:57
Alignment explanation
Indices: 1723882--1724000 Score: 170
Period size: 56 Copynumber: 2.1 Consensus size: 57
1723872 TAATATTTAT
*
1723882 TTAAACAAAAAATATTTTTAATATAAAAAATTAATTCGCGCCTGTTAGATAGGCGCGA
1 TTAAACAAAAAATATTTTTAATAT-AAAAATTAATTCGCGCCTGTCAGATAGGCGCGA
* * *
1723940 TTAAA-AAAACAAT-TTTTTAATATAAAACTTTATTCGCGTCTGTCAGATAGGCGCGA
1 TTAAACAAAA-AATATTTTTAATATAAAAATTAATTCGCGCCTGTCAGATAGGCGCGA
1723996 TTAAA
1 TTAAA
1724001 TTTTTTTTTA
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
56 34 0.61
57 14 0.25
58 8 0.14
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (57 bp):
TTAAACAAAAAATATTTTTAATATAAAAATTAATTCGCGCCTGTCAGATAGGCGCGA
Found at i:1724399 original size:60 final size:60
Alignment explanation
Indices: 1724306--1724424 Score: 193
Period size: 60 Copynumber: 2.0 Consensus size: 60
1724296 ATACTAAACT
* * * *
1724306 AAACACAACAATTTATAACTTAATCCTAAATTACTAATAAAATAATTTTAAAATAATTAC
1 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAAATAATTATAAAATAATTAC
*
1724366 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTAATTATAAAATAATTA
1 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAAATAATTATAAAATAATTA
1724425 TTAAAAGCAA
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 54 1.00
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (60 bp):
AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAAATAATTATAAAATAATTAC
Found at i:1724622 original size:17 final size:16
Alignment explanation
Indices: 1724592--1724625 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1724582 ACATTACCTT
1724592 TTTTTATTCTTTCTTC
1 TTTTTATTCTTTCTTC
*
1724608 TTTTTCTTCTCTTCTTC
1 TTTTTATTCT-TTCTTC
1724625 T
1 T
1724626 CCTTTCTCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTTATTCTTTCTTC
Found at i:1727971 original size:42 final size:43
Alignment explanation
Indices: 1727864--1728022 Score: 130
Period size: 43 Copynumber: 3.7 Consensus size: 43
1727854 TCTCGTACAT
* * * * *
1727864 TGCCAACGTCCCAGACGTGGTCTTACATG-TAT-TCAAATAACGA
1 TGCCAATGTCCCAAACATGGTCTTACACGAAATCTCAAAT--CGA
* * * *
1727907 TGCCACTGTCCCAGACAGGGTCTTACACGAAAT-T-ATATACGA
1 TGCCAATGTCCCAAACATGGTCTTACACGAAATCTCAAAT-CGA
* *
1727949 TGTCGATGTCCCAAACATGGTCTTACACGTAAATCTCAAATCGA
1 TGCCAATGTCCCAAACATGGTCTTACACG-AAATCTCAAATCGA
*
1727993 TGCCAACGTCCCAAA-AGTGGTCTTACACGA
1 TGCCAATGTCCCAAACA-TGGTCTTACACGA
1728023 TATCACATAT
Statistics
Matches: 95, Mismatches: 16, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
42 28 0.29
43 33 0.35
44 31 0.33
45 3 0.03
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (43 bp):
TGCCAATGTCCCAAACATGGTCTTACACGAAATCTCAAATCGA
Found at i:1729246 original size:16 final size:16
Alignment explanation
Indices: 1729209--1729248 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
1729199 TTAATAAAAT
* *
1729209 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
1729225 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
1729241 TAAAATTA
1 TAAAATTA
1729249 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:1729248 original size:22 final size:22
Alignment explanation
Indices: 1729177--1729233 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
1729167 AGGCCCGTTT
* * * *
1729177 TTAATTAAATTAAAATTATTTT
1 TTAATAAAATTAAAACTAATTG
1729199 TTAATAAAATTAAAACTAATTG
1 TTAATAAAATTAAAACTAATTG
*
1729221 TTATTAAAATTAA
1 TTAATAAAATTAA
1729234 TTGTTAGTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (22 bp):
TTAATAAAATTAAAACTAATTG
Found at i:1729280 original size:59 final size:67
Alignment explanation
Indices: 1729241--1729398 Score: 217
Period size: 59 Copynumber: 2.5 Consensus size: 67
1729231 TAATTGTTAG
1729241 TAAAATTATCAAATTATTAATTG-TTAATTGTACTAATTGTTGTAATAAAATCTAACATTTGATT
1 TAAAATTATCAAATTATTAATTGATTAATTGTACTAATTGTTGTAATAAAATCTAACATTTGATT
1729305 AA
66 AA
*
1729307 TAAATTTATCAAATTATTAATTG--T-A---T--TAATTGTTGTAATAAAATCTAACATTTGATT
1 TAAAATTATCAAATTATTAATTGATTAATTGTACTAATTGTTGTAATAAAATCTAACATTTGATT
*
1729364 AG
66 AA
*
1729366 TAAATTTATCAAATTATTAATTGTATTAATTGT
1 TAAAATTATCAAATTATTAATTG-ATTAATTGT
1729399 TGTAACAAAA
Statistics
Matches: 83, Mismatches: 2, Indels: 14
0.84 0.02 0.14
Matches are distributed among these distances:
59 55 0.66
61 1 0.01
62 1 0.01
63 1 0.01
64 1 0.01
65 1 0.01
66 23 0.28
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.46
Consensus pattern (67 bp):
TAAAATTATCAAATTATTAATTGATTAATTGTACTAATTGTTGTAATAAAATCTAACATTTGATT
AA
Found at i:1729399 original size:59 final size:59
Alignment explanation
Indices: 1729259--1729428 Score: 304
Period size: 59 Copynumber: 2.9 Consensus size: 59
1729249 TCAAATTATT
* * *
1729259 AATTGTTAATTGTACTAATTGTTGTAATAAAATCTAACATTTGATTAATAAATTTATCA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
1729318 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
*
1729377 AATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTAAA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAA
1729429 ACAAACTTGA
Statistics
Matches: 107, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
59 107 1.00
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (59 bp):
AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
Found at i:1730511 original size:43 final size:43
Alignment explanation
Indices: 1730450--1730650 Score: 278
Period size: 43 Copynumber: 4.7 Consensus size: 43
1730440 ATGTTCCAAT
1730450 ATCGATTTGAGATTTCGTGTAAGACCATAGCTGGGCTATTGGC
1 ATCGATTTGAGATTTCGTGTAAGACCATAGCTGGGCTATTGGC
* *
1730493 ATCGATTTGAGATTTCGTGTAAGACCATAGTTGGGTTATTGG-
1 ATCGATTTGAGATTTCGTGTAAGACCATAGCTGGGCTATTGGC
* *
1730535 AGTCAATCTGAGATTTCGTGTAAGACCATAGCTGGGCTATTGGC
1 A-TCGATTTGAGATTTCGTGTAAGACCATAGCTGGGCTATTGGC
* ***
1730579 ATCGATTTGAGATTTCGTGTAAAACCATAGCTAAACTATTGGC
1 ATCGATTTGAGATTTCGTGTAAGACCATAGCTGGGCTATTGGC
** *
1730622 ATCGATACGAGATTTCCATGTAAGACCAT
1 ATCGATTTGAGATTT-CGTGTAAGACCAT
1730651 GTTTGGGACA
Statistics
Matches: 139, Mismatches: 16, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
42 1 0.01
43 126 0.91
44 12 0.09
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.32
Consensus pattern (43 bp):
ATCGATTTGAGATTTCGTGTAAGACCATAGCTGGGCTATTGGC
Found at i:1743185 original size:15 final size:17
Alignment explanation
Indices: 1743160--1743191 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1743150 AATTATTAAA
1743160 AAAACTTAT-AAATTTT
1 AAAACTTATAAAATTTT
1743176 AAAA-TTATAAAATTTT
1 AAAACTTATAAAATTTT
1743192 TATTAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
AAAACTTATAAAATTTT
Found at i:1743335 original size:44 final size:46
Alignment explanation
Indices: 1743287--1743376 Score: 114
Period size: 44 Copynumber: 2.0 Consensus size: 46
1743277 ATATTGTTAT
* *
1743287 TTTTAATAAAAATT-TTTGTAATTT-TGTAATTTTTAA-AACTTTTA
1 TTTT-ATAAAAATTGTTTATAATTTCTATAATTTTTAATAACTTTTA
* *
1743331 TTTTATAAAATTTGTTTATAATTTCTATGATTTTTAATAACTTTTA
1 TTTTATAAAAATTGTTTATAATTTCTATAATTTTTAATAACTTTTA
1743377 AAATTTAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
43 8 0.21
44 13 0.33
45 10 0.26
46 8 0.21
ACGTcount: A:0.34, C:0.03, G:0.04, T:0.58
Consensus pattern (46 bp):
TTTTATAAAAATTGTTTATAATTTCTATAATTTTTAATAACTTTTA
Found at i:1752919 original size:16 final size:16
Alignment explanation
Indices: 1752890--1752940 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 16
1752880 TTTTGGCATC
*
1752890 TAAAAATTTAAAACTTA
1 TAAAAATAT-AAACTTA
1752907 TAAAAATATAAAC-TA
1 TAAAAATATAAACTTA
* *
1752922 TTAAAATAATAAAATTA
1 TAAAAAT-ATAAACTTA
1752939 TA
1 TA
1752941 TTTTTACTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 8 0.29
16 9 0.32
17 11 0.39
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (16 bp):
TAAAAATATAAACTTA
Found at i:1759392 original size:21 final size:21
Alignment explanation
Indices: 1759367--1759407 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1759357 ACAGAAAAAT
1759367 GTCATATCGTCAAAGAGGGAG
1 GTCATATCGTCAAAGAGGGAG
*
1759388 GTCATATTGTCAAAGAGGGA
1 GTCATATCGTCAAAGAGGGA
1759408 ATAATCGTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.34, C:0.12, G:0.32, T:0.22
Consensus pattern (21 bp):
GTCATATCGTCAAAGAGGGAG
Found at i:1760066 original size:31 final size:30
Alignment explanation
Indices: 1760032--1760092 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
1760022 AAAAGTCTTT
1760032 TTTTTTTAA--ATTTACCGAAATGGGCCAC
1 TTTTTTTAATTATTTACCGAAATGGGCCAC
*
1760060 TTTTTTTAATTATTTACCGGAATGGGCCA-
1 TTTTTTTAATTATTTACCGAAATGGGCCAC
1760089 TTTT
1 TTTT
1760093 CCGTGAAATC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 9 0.30
29 4 0.13
30 17 0.57
ACGTcount: A:0.25, C:0.15, G:0.15, T:0.46
Consensus pattern (30 bp):
TTTTTTTAATTATTTACCGAAATGGGCCAC
Found at i:1760859 original size:29 final size:29
Alignment explanation
Indices: 1760796--1760852 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
1760786 TTGAAAATAT
*
1760796 TAAAATTA-TTAAAATTATTTTTAAAAAA
1 TAAAAATATTTAAAATTATTTTTAAAAAA
1760824 TAAAAATATTTAAAATT-TTCTTTAAAAAA
1 TAAAAATATTTAAAATTATT-TTTAAAAAA
1760853 ATGAAATTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 9 0.35
29 17 0.65
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (29 bp):
TAAAAATATTTAAAATTATTTTTAAAAAA
Found at i:1760913 original size:22 final size:22
Alignment explanation
Indices: 1760888--1760990 Score: 91
Period size: 22 Copynumber: 4.4 Consensus size: 22
1760878 TAATATGGAT
*
1760888 TTGAGAGATTTTTTGAAGGAAA
1 TTGAGAGATTTTTGGAAGGAAA
1760910 TTGAGAGGA-TTTTGGAAGGAATTTGAGA
1 TTGAGA-GATTTTTGGAAGG-A----A-A
* *
1760938 GTTAAGAGAATTTTGGAAGGAAA
1 -TTGAGAGATTTTTGGAAGGAAA
*
1760961 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGATTTTTGGAAGGAAA
1760983 TTGAGAGA
1 TTGAGAGA
1760991 ATATTTGTTT
Statistics
Matches: 69, Mismatches: 3, Indels: 18
0.77 0.03 0.20
Matches are distributed among these distances:
22 44 0.64
23 4 0.06
24 1 0.01
27 1 0.01
28 4 0.06
29 15 0.22
ACGTcount: A:0.38, C:0.00, G:0.32, T:0.30
Consensus pattern (22 bp):
TTGAGAGATTTTTGGAAGGAAA
Found at i:1760946 original size:51 final size:51
Alignment explanation
Indices: 1760891--1760989 Score: 162
Period size: 51 Copynumber: 1.9 Consensus size: 51
1760881 TATGGATTTG
* * * *
1760891 AGAGATTTTTTGAAGGAAATTGAGAGGATTTTGGAAGGAATTTGAGAGTTA
1 AGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAAGGAAATTGAGAGTTA
1760942 AGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAAGGAAATTGAGAG
1 AGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAAGGAAATTGAGAG
1760990 AATATTTGTT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.38, C:0.00, G:0.32, T:0.29
Consensus pattern (51 bp):
AGAGAATTTTGGAAGGAAATTGAGAGAATTTTGGAAGGAAATTGAGAGTTA
Found at i:1761006 original size:24 final size:22
Alignment explanation
Indices: 1760942--1760997 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
1760932 TTGAGAGTTA
1760942 AGAGAATTTTGGAAGGAAATTG
1 AGAGAATTTTGGAAGGAAATTG
1760964 AGAGAATTTTGGAAGGAAATTG
1 AGAGAATTTTGGAAGGAAATTG
1760986 AGAGAATATTTG
1 AGAGAAT-TTTG
1760998 TTTGTGAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 29 0.88
23 4 0.12
ACGTcount: A:0.41, C:0.00, G:0.30, T:0.29
Consensus pattern (22 bp):
AGAGAATTTTGGAAGGAAATTG
Found at i:1761771 original size:26 final size:26
Alignment explanation
Indices: 1761742--1761794 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
1761732 GATGACATGG
1761742 TACTTTTATAATTTATGTTTATTTAA
1 TACTTTTATAATTTATGTTTATTTAA
1761768 TACTTTTATAATTTATGTTTATTTAA
1 TACTTTTATAATTTATGTTTATTTAA
1761794 T
1 T
1761795 TAAATATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.62
Consensus pattern (26 bp):
TACTTTTATAATTTATGTTTATTTAA
Found at i:1765716 original size:25 final size:26
Alignment explanation
Indices: 1765688--1765741 Score: 65
Period size: 27 Copynumber: 2.1 Consensus size: 26
1765678 AGAGCTTGCA
*
1765688 TAATTATACATT-ATCAAAATTCATG
1 TAATTACACATTAATCAAAATTCATG
* *
1765713 TAATTACATATTAAATCAAAATTTATG
1 TAATTACACATT-AATCAAAATTCATG
1765740 TA
1 TA
1765742 CCCAAAAGAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 10 0.42
27 14 0.58
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (26 bp):
TAATTACACATTAATCAAAATTCATG
Found at i:1768250 original size:7 final size:7
Alignment explanation
Indices: 1768238--1768262 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1768228 AAATAAATTA
1768238 ACTTTTC
1 ACTTTTC
1768245 ACTTTTC
1 ACTTTTC
1768252 ACTTTTC
1 ACTTTTC
1768259 ACTT
1 ACTT
1768263 GATGAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.28, G:0.00, T:0.56
Consensus pattern (7 bp):
ACTTTTC
Found at i:1769826 original size:23 final size:23
Alignment explanation
Indices: 1769780--1769823 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1769770 CCAACTAAAC
*
1769780 TAAACCATAATATATATTTATTA
1 TAAACCATAATATAAATTTATTA
*
1769803 TAAATCATAATA-AAATTTATT
1 TAAACCATAATATAAATTTATT
1769824 TATTTATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (23 bp):
TAAACCATAATATAAATTTATTA
Found at i:1774596 original size:12 final size:14
Alignment explanation
Indices: 1774569--1774600 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
1774559 GTTTTGGAAG
1774569 AATAAAAGTCAAAA
1 AATAAAAGTCAAAA
1774583 AATAAAA-T-AAAA
1 AATAAAAGTCAAAA
1774595 AATAAA
1 AATAAA
1774601 GTAATGAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 10 0.56
13 1 0.06
14 7 0.39
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.16
Consensus pattern (14 bp):
AATAAAAGTCAAAA
Found at i:1777301 original size:36 final size:36
Alignment explanation
Indices: 1777236--1777834 Score: 550
Period size: 37 Copynumber: 16.4 Consensus size: 36
1777226 AAAAATGGAA
*
1777236 TACTGATTCTATTG-AAGTGCTCAACAAGCAATATC
1 TACTGATTCTACTGAAAGTGCTCAACAAGCAATATC
* * *
1777271 TACTGATACTATTGAAAGTGCTCAATAAGCAATATC
1 TACTGATTCTACTGAAAGTGCTCAACAAGCAATATC
* * * **
1777307 TACTGATCCTACTGAATGAGCTCAA-ATGAGCAATGCC
1 TACTGATTCTACTGAAAGTGCTCAACA--AGCAATATC
* * *
1777344 TATTGGTTCTACTGAAAGTGCTCAAACAAGCAATACC
1 TACTGATTCTACTGAAAGTGCTC-AACAAGCAATATC
* *
1777381 TACTGATACTACTGAAAGTGCTCAAATAAGCAATATC
1 TACTGATTCTACTGAAAGTGCTC-AACAAGCAATATC
* * * * *
1777418 TATTGATCCTACTGAATGTGCTCAAACGAGCAATGTC
1 TACTGATTCTACTGAAAGTGCTC-AACAAGCAATATC
* * *
1777455 TACTTATTTTACTGAAAGTGCTCAAACGAGC---ATC
1 TACTGATTCTACTGAAAGTGCTC-AACAAGCAATATC
* * * *
1777489 TACTGATCCTACTAAAAGTGCTCAACGAGCAATGTC
1 TACTGATTCTACTGAAAGTGCTCAACAAGCAATATC
* *
1777525 TACTGATTCTACTGAAAGTGCTAAAACGAGCAATATC
1 TACTGATTCTACTGAAAGTGCT-CAACAAGCAATATC
* * *
1777562 TACT-AGTTCTATTGGAAGTGCTCAACGAGCAATATC
1 TACTGA-TTCTACTGAAAGTGCTCAACAAGCAATATC
* * *
1777598 TATTGGTCCTACTGAAAGTGCTCAACAAGCAATATC
1 TACTGATTCTACTGAAAGTGCTCAACAAGCAATATC
* * * *
1777634 TACTAATCCTACT-AAATGTGCTCAAACGAGCAATGTC
1 TACTGATTCTACTGAAA-GTGCTC-AACAAGCAATATC
* *
1777671 TACTAATTCTACTG-AAGTGCTCAAACGAGCAATATC
1 TACTGATTCTACTGAAAGTGCTC-AACAAGCAATATC
* * *
1777707 TACTAATTCTACTGAAAGTGGTCAACGAGCAATATC
1 TACTGATTCTACTGAAAGTGCTCAACAAGCAATATC
* * * *
1777743 TACT-AGTCCTACTGAATGTGCTCAAACAAGTAATGTC
1 TACTGA-TTCTACTGAAAGTGCTC-AACAAGCAATATC
*
1777780 TACTGATTCTACTAAATAGTTGCTCAAACAAGCAATATC
1 TACTGATTCTACTGAA-AG-TGCTC-AACAAGCAATATC
*
1777819 TACTGATTTTACTGAA
1 TACTGATTCTACTGAA
1777835 TAGTTACTCA
Statistics
Matches: 474, Mismatches: 70, Indels: 36
0.82 0.12 0.06
Matches are distributed among these distances:
33 7 0.01
34 21 0.04
35 18 0.04
36 186 0.39
37 206 0.43
38 4 0.01
39 32 0.07
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.29
Consensus pattern (36 bp):
TACTGATTCTACTGAAAGTGCTCAACAAGCAATATC
Found at i:1777646 original size:109 final size:110
Alignment explanation
Indices: 1777249--1777834 Score: 686
Period size: 109 Copynumber: 5.4 Consensus size: 110
1777239 TGATTCTATT
* * *
1777249 GAAGTGCTC-AACAAGCAATATCTACTGATACTATTGAAAGTGCTCAATAAGCAATATCTACTGA
1 GAAGTGCTCAAACGAGCAATATCTACTGATACTACTGAAAGTGCTCAACAAGCAATATCTACTGA
* * * * *
1777313 TCCTACTGAATGAGCTCAAATGAGCAATGCCTATTGGTTCTACTG
66 TCCTACTGAATGTGCTCAAACGAGCAATGTCTACTAGTTCTACTG
* * * * *
1777358 AAAGTGCTCAAACAAGCAATACCTACTGATACTACTGAAAGTGCTCAAATAAGCAATATCTATTG
1 GAAGTGCTCAAACGAGCAATATCTACTGATACTACTGAAAGTGCTC-AACAAGCAATATCTACTG
*
1777423 ATCCTACTGAATGTGCTCAAACGAGCAATGTCTACTTA-TTTTACTG
65 ATCCTACTGAATGTGCTCAAACGAGCAATGTCTAC-TAGTTCTACTG
* * * * *
1777469 AAAGTGCTCAAACGAGC---ATCTACTGATCCTACTAAAAGTGCTCAACGAGCAATGTCTACTGA
1 GAAGTGCTCAAACGAGCAATATCTACTGATACTACTGAAAGTGCTCAACAAGCAATATCTACTGA
* * * * *
1777531 TTCTACTGAAAGTGCTAAAACGAGCAATATCTACTAGTTCTATTG
66 TCCTACTGAATGTGCTCAAACGAGCAATGTCTACTAGTTCTACTG
* * * *
1777576 GAAGTGCTC-AACGAGCAATATCTATTGGTCCTACTGAAAGTGCTCAACAAGCAATATCTACTAA
1 GAAGTGCTCAAACGAGCAATATCTACTGATACTACTGAAAGTGCTCAACAAGCAATATCTACTGA
* *
1777640 TCCTACTAAATGTGCTCAAACGAGCAATGTCTACTAATTCTACT-
66 TCCTACTGAATGTGCTCAAACGAGCAATGTCTACTAGTTCTACTG
* * * *
1777684 GAAGTGCTCAAACGAGCAATATCTACTAATTCTACTGAAAGTGGTCAACGAGCAATATCTACT-A
1 GAAGTGCTCAAACGAGCAATATCTACTGATACTACTGAAAGTGCTCAACAAGCAATATCTACTGA
* * *
1777748 GTCCTACTGAATGTGCTCAAACAAGTAATGTCTACT-GATTCTACTA
66 -TCCTACTGAATGTGCTCAAACGAGCAATGTCTACTAG-TTCTACTG
* * **
1777794 AATAGTTGCTCAAACAAGCAATATCTACTGATTTTACTGAA
1 GA-AG-TGCTCAAACGAGCAATATCTACTGATACTACTGAA
1777835 TAGTTACTCA
Statistics
Matches: 412, Mismatches: 52, Indels: 23
0.85 0.11 0.05
Matches are distributed among these distances:
106 9 0.02
107 59 0.14
108 33 0.08
109 170 0.41
110 35 0.08
111 73 0.18
112 33 0.08
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (110 bp):
GAAGTGCTCAAACGAGCAATATCTACTGATACTACTGAAAGTGCTCAACAAGCAATATCTACTGA
TCCTACTGAATGTGCTCAAACGAGCAATGTCTACTAGTTCTACTG
Found at i:1777865 original size:39 final size:39
Alignment explanation
Indices: 1777253--1777914 Score: 273
Period size: 37 Copynumber: 17.9 Consensus size: 39
1777243 TCTATTGAAG
* * *
1777253 TGCTC-AACAAGCAATATCTACTGA-TACTATTGAA-AG-
1 TGCTCAAACGAGCAATATCCACTGATTA-TACTGAATAGT
* **
1777289 TGCTCAATA--AGCAATATCTACTGATCCTACTGAAT-G-
1 TGCTCAA-ACGAGCAATATCCACTGATTATACTGAATAGT
* * * * * *
1777325 AGCTCAAATGAGCAAT-GCCTATTGGTTCTACTGAA-AG-
1 TGCTCAAACGAGCAATATCC-ACTGATTATACTGAATAGT
*
1777362 TGCTCAAACAAGCAATA-CCTACTGA-TACTACTGAA-AG-
1 TGCTCAAACGAGCAATATCC-ACTGATTA-TACTGAATAGT
** * * **
1777399 TGCTCAAATAAGCAATATCTATTGATCCTACTGAAT-G-
1 TGCTCAAACGAGCAATATCCACTGATTATACTGAATAGT
* * * *
1777436 TGCTCAAACGAGCAATGTCTACTTATTTTACTGAA-AG-
1 TGCTCAAACGAGCAATATCCACTGATTATACTGAATAGT
* ** *
1777473 TGCTCAAACGAGC---ATCTACTGATCCTACT-AAAAG-
1 TGCTCAAACGAGCAATATCCACTGATTATACTGAATAGT
* * *
1777507 TGCTC-AACGAGCAATGTCTACTGATTCTACTGAA-AG-
1 TGCTCAAACGAGCAATATCCACTGATTATACTGAATAGT
* * * * *
1777543 TGCTAAAACGAGCAATATCTACT-AGTTCTATTGGA-AG-
1 TGCTCAAACGAGCAATATCCACTGA-TTATACTGAATAGT
* * * **
1777580 TGCTC-AACGAGCAATATCTATTGGTCCTACTGAA-AG-
1 TGCTCAAACGAGCAATATCCACTGATTATACTGAATAGT
* * * ** *
1777616 TGCTC-AACAAGCAATATCTACTAATCCTACTAAAT-G-
1 TGCTCAAACGAGCAATATCCACTGATTATACTGAATAGT
* * * *
1777652 TGCTCAAACGAGCAATGTCTACTAATTCTACTG-A-AG-
1 TGCTCAAACGAGCAATATCCACTGATTATACTGAATAGT
* * *
1777688 TGCTCAAACGAGCAATATCTACTAATTCTACTGAA-AG-
1 TGCTCAAACGAGCAATATCCACTGATTATACTGAATAGT
* * **
1777725 TGGTC-AACGAGCAATATCTACT-AGTCCTACTGAAT-G-
1 TGCTCAAACGAGCAATATCCACTGA-TTATACTGAATAGT
* * * * * *
1777761 TGCTCAAACAAGTAATGTCTACTGATTCTACTAAATAGT
1 TGCTCAAACGAGCAATATCCACTGATTATACTGAATAGT
* * *
1777800 TGCTCAAACAAGCAATATCTACTGATTTTACTGAATAGT
1 TGCTCAAACGAGCAATATCCACTGATTATACTGAATAGT
* * * * *
1777839 TACTCAAACGAGAAATATCCATTGATTATAATGAAT-GCG
1 TGCTCAAACGAGCAATATCCACTGATTATACTGAATAG-T
* *
1777878 TGCTCAAACGAGCATTATCCACTGATTATACTCAATA
1 TGCTCAAACGAGCAATATCCACTGATTATACTGAATA
1777915 AGATTTTCTG
Statistics
Matches: 513, Mismatches: 79, Indels: 64
0.78 0.12 0.10
Matches are distributed among these distances:
33 9 0.02
34 19 0.04
35 2 0.00
36 181 0.35
37 203 0.40
38 5 0.01
39 94 0.18
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (39 bp):
TGCTCAAACGAGCAATATCCACTGATTATACTGAATAGT
Found at i:1778846 original size:205 final size:205
Alignment explanation
Indices: 1778494--1778877 Score: 768
Period size: 205 Copynumber: 1.9 Consensus size: 205
1778484 GAAATATTGT
1778494 GCTGTTAATGATGACACATTAGTTAGGCATTTAGATTGATTGTGTTTACAGGAGTTGAAGGTATT
1 GCTGTTAATGATGACACATTAGTTAGGCATTTAGATTGATTGTGTTTACAGGAGTTGAAGGTATT
1778559 TAATGTCATATAGGATTGTATGTTTGAATATATTTAAGTACTTAGTCGTATGGGTGAAGAAAGGA
66 TAATGTCATATAGGATTGTATGTTTGAATATATTTAAGTACTTAGTCGTATGGGTGAAGAAAGGA
1778624 ACATGATTTAGGTAAATTTTGGGTACACACGGTCTGGGACACGAGCTGTATCACAGTCATGTGAG
131 ACATGATTTAGGTAAATTTTGGGTACACACGGTCTGGGACACGAGCTGTATCACAGTCATGTGAG
1778689 GGTATTTTGA
196 GGTATTTTGA
1778699 GCTGTTAATGATGACACATTAGTTAGGCATTTAGATTGATTGTGTTTACAGGAGTTGAAGGTATT
1 GCTGTTAATGATGACACATTAGTTAGGCATTTAGATTGATTGTGTTTACAGGAGTTGAAGGTATT
1778764 TAATGTCATATAGGATTGTATGTTTGAATATATTTAAGTACTTAGTCGTATGGGTGAAGAAAGGA
66 TAATGTCATATAGGATTGTATGTTTGAATATATTTAAGTACTTAGTCGTATGGGTGAAGAAAGGA
1778829 ACATGATTTAGGTAAATTTTGGGTACACACGGTCTGGGACACGAGCTGT
131 ACATGATTTAGGTAAATTTTGGGTACACACGGTCTGGGACACGAGCTGT
1778878 CACTCTATTG
Statistics
Matches: 179, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
205 179 1.00
ACGTcount: A:0.29, C:0.09, G:0.26, T:0.35
Consensus pattern (205 bp):
GCTGTTAATGATGACACATTAGTTAGGCATTTAGATTGATTGTGTTTACAGGAGTTGAAGGTATT
TAATGTCATATAGGATTGTATGTTTGAATATATTTAAGTACTTAGTCGTATGGGTGAAGAAAGGA
ACATGATTTAGGTAAATTTTGGGTACACACGGTCTGGGACACGAGCTGTATCACAGTCATGTGAG
GGTATTTTGA
Found at i:1780132 original size:9 final size:9
Alignment explanation
Indices: 1780118--1780248 Score: 79
Period size: 9 Copynumber: 15.9 Consensus size: 9
1780108 TTCATAATAA
1780118 ATAACTTAC
1 ATAACTTAC
1780127 ATAACTTAC
1 ATAACTTAC
1780136 ATAA--TAC
1 ATAACTTAC
* *
1780143 ATAACGTAT
1 ATAACTTAC
*
1780152 ATGACTTAC
1 ATAACTTAC
1780161 ATAACTTAC
1 ATAACTTAC
*
1780170 AT-A---GC
1 ATAACTTAC
* *
1780175 ATAATTTTC
1 ATAACTTAC
1780184 ATAA--TAC
1 ATAACTTAC
*
1780191 ACAACTTAC
1 ATAACTTAC
* *
1780200 ATAATTTTC
1 ATAACTTAC
*
1780209 ATAA--TAA
1 ATAACTTAC
1780216 ATAACTTAC
1 ATAACTTAC
1780225 ATAA--TAC
1 ATAACTTAC
1780232 ATAACTTAC
1 ATAACTTAC
*
1780241 ATAGCTTA
1 ATAACTTA
1780249 ATTATACTTA
Statistics
Matches: 94, Mismatches: 16, Indels: 24
0.70 0.12 0.18
Matches are distributed among these distances:
5 3 0.03
6 1 0.01
7 24 0.26
8 1 0.01
9 65 0.69
ACGTcount: A:0.45, C:0.18, G:0.03, T:0.34
Consensus pattern (9 bp):
ATAACTTAC
Found at i:1780143 original size:16 final size:16
Alignment explanation
Indices: 1780124--1780243 Score: 87
Period size: 16 Copynumber: 7.9 Consensus size: 16
1780114 ATAAATAACT
1780124 TACATAACTTACATAA
1 TACATAACTTACATAA
* * *
1780140 TACATAACGTATATGACT
1 TACATAACTTACAT-A-A
1780158 TACATAACTTACAT-A
1 TACATAACTTACATAA
* * *
1780173 -GCATAATTTTCATAA
1 TACATAACTTACATAA
*
1780188 TACACAACTTACATAA
1 TACATAACTTACATAA
1780204 T---T---TT-CATAA
1 TACATAACTTACATAA
*
1780213 TAAATAACTTACATAA
1 TACATAACTTACATAA
1780229 TACATAACTTACATA
1 TACATAACTTACATA
1780244 GCTTAATTAT
Statistics
Matches: 78, Mismatches: 15, Indels: 22
0.68 0.13 0.19
Matches are distributed among these distances:
9 6 0.08
10 2 0.03
12 1 0.01
14 10 0.13
15 3 0.04
16 43 0.55
17 1 0.01
18 12 0.15
ACGTcount: A:0.46, C:0.17, G:0.03, T:0.34
Consensus pattern (16 bp):
TACATAACTTACATAA
Found at i:1780146 original size:25 final size:25
Alignment explanation
Indices: 1780110--1780235 Score: 100
Period size: 25 Copynumber: 5.2 Consensus size: 25
1780100 NNNNNNTTTT
*
1780110 CATAATAAATAACTTACATAACTTA
1 CATAATACATAACTTACATAACTTA
* * *
1780135 CATAATACATAACGTATATGACTTA
1 CATAATACATAACTTACATAACTTA
* * * *
1780160 CAT-A-AC-TTACATAGCATAATTTT
1 CATAATACATAACTTA-CATAACTTA
* * *
1780183 CATAATACACAACTTACATAATTTT
1 CATAATACATAACTTACATAACTTA
*
1780208 CATAATAAATAACTTACATAA--TA
1 CATAATACATAACTTACATAACTTA
1780231 CATAA
1 CATAA
1780236 CTTACATAGC
Statistics
Matches: 81, Mismatches: 16, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
22 5 0.06
23 16 0.20
24 2 0.02
25 54 0.67
26 4 0.05
ACGTcount: A:0.48, C:0.17, G:0.02, T:0.33
Consensus pattern (25 bp):
CATAATACATAACTTACATAACTTA
Found at i:1780371 original size:49 final size:49
Alignment explanation
Indices: 1780315--1780418 Score: 199
Period size: 49 Copynumber: 2.1 Consensus size: 49
1780305 AGAAACTAAC
*
1780315 AATGGACCGGTCTTGGATGAATTTGTCAAGGGTAAGCGACGGTTGTCGA
1 AATGGACCGGTCTTGGATGAATTTGTCAAGGGTAAGCGACGGTTGCCGA
1780364 AATGGACCGGTCTTGGATGAATTTGTCAAGGGTAAGCGACGGTTGCCGA
1 AATGGACCGGTCTTGGATGAATTTGTCAAGGGTAAGCGACGGTTGCCGA
1780413 AATGGA
1 AATGGA
1780419 GTACAAACTT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 54 1.00
ACGTcount: A:0.26, C:0.14, G:0.35, T:0.25
Consensus pattern (49 bp):
AATGGACCGGTCTTGGATGAATTTGTCAAGGGTAAGCGACGGTTGCCGA
Found at i:1786180 original size:579 final size:579
Alignment explanation
Indices: 1785082--1786202 Score: 2242
Period size: 579 Copynumber: 1.9 Consensus size: 579
1785072 GTCGAAAAGT
1785082 TTTGCGTGTGTAGCTCATGCAGAGGTATTTTGAATTTTTTAATATTGGCAGATATTTATTACTTT
1 TTTGCGTGTGTAGCTCATGCAGAGGTATTTTGAATTTTTTAATATTGGCAGATATTTATTACTTT
1785147 CTATCAATTAATATTTTTACTATTGTATTGTAGGAACTGTCGTCCGGTCAAAAAGTTGGACGCCT
66 CTATCAATTAATATTTTTACTATTGTATTGTAGGAACTGTCGTCCGGTCAAAAAGTTGGACGCCT
1785212 TCAACTTTTTGACATTACACATAGGAAGAAAGATGGAAACCCTATGACTCCTGAAGCTGCAGAAA
131 TCAACTTTTTGACATTACACATAGGAAGAAAGATGGAAACCCTATGACTCCTGAAGCTGCAGAAA
1785277 TTATGGTACGTTTGCTTAATACAATTTCACTTGTTTTAATTATTTATAGTGTTTATTTTCTAATG
196 TTATGGTACGTTTGCTTAATACAATTTCACTTGTTTTAATTATTTATAGTGTTTATTTTCTAATG
1785342 ATTTATTTCATTTATTGTAATGCAAATATTTTTAAGTTATGTTGCATTGGGTTTTTTAATATATA
261 ATTTATTTCATTTATTGTAATGCAAATATTTTTAAGTTATGTTGCATTGGGTTTTTTAATATATA
1785407 TTGCGTTCCTAACTATGTGATTTATTTTTTAGGAAAAATTAAAGGATAAAAAGGCGGAGTACGAA
326 TTGCGTTCCTAACTATGTGATTTATTTTTTAGGAAAAATTAAAGGATAAAAAGGCGGAGTACGAA
1785472 GTGATTGCTTCCAGTGATAGTTCTGTTCATATTGACAACATTGATAACCGGATTATCACTGAAGT
391 GTGATTGCTTCCAGTGATAGTTCTGTTCATATTGACAACATTGATAACCGGATTATCACTGAAGT
1785537 TTTGGGTCCTGAAAGGTATGGTCGGGTTCGATTTCAAGGATCTTTTGTTAACCCATCCCAATATT
456 TTTGGGTCCTGAAAGGTATGGTCGGGTTCGATTTCAAGGATCTTTTGTTAACCCATCCCAATATT
1785602 TTGGATCGAACTCGCAACAATAAATGAAATAAATCATTAGAAAATAAACACTATAAATA
521 TTGGATCGAACTCGCAACAATAAATGAAATAAATCATTAGAAAATAAACACTATAAATA
1785661 TTTGCGTGTGTAGCTCATGCAGAGGTATTTTGAATTTTTTAATATTGGCAGATATTTATTACTTT
1 TTTGCGTGTGTAGCTCATGCAGAGGTATTTTGAATTTTTTAATATTGGCAGATATTTATTACTTT
1785726 CTATCAATTAATATTTTTACTATTGTATTGTAGGAACTGTCGTCCGGTCAAAAAGTTGGACGCCT
66 CTATCAATTAATATTTTTACTATTGTATTGTAGGAACTGTCGTCCGGTCAAAAAGTTGGACGCCT
1785791 TCAACTTTTTGACATTACACATAGGAAGAAAGATGGAAACCCTATGACTCCTGAAGCTGCAGAAA
131 TCAACTTTTTGACATTACACATAGGAAGAAAGATGGAAACCCTATGACTCCTGAAGCTGCAGAAA
1785856 TTATGGTACGTTTGCTTAATACAATTTCACTTGTTTTAATTATTTATAGTGTTTATTTTCTAATG
196 TTATGGTACGTTTGCTTAATACAATTTCACTTGTTTTAATTATTTATAGTGTTTATTTTCTAATG
1785921 ATTTATTTCATTTATTGTAATGCAAATATTTTTAAGTTATGTTGCATTGGGTTTTTTAATATATA
261 ATTTATTTCATTTATTGTAATGCAAATATTTTTAAGTTATGTTGCATTGGGTTTTTTAATATATA
1785986 TTGCGTTCCTAACTATGTGATTTATTTTTTAGGAAAAATTAAAGGATAAAAAGGCGGAGTACGAA
326 TTGCGTTCCTAACTATGTGATTTATTTTTTAGGAAAAATTAAAGGATAAAAAGGCGGAGTACGAA
1786051 GTGATTGCTTCCAGTGATAGTTCTGTTCATATTGACAACATTGATAACCGGATTATCACTGAAGT
391 GTGATTGCTTCCAGTGATAGTTCTGTTCATATTGACAACATTGATAACCGGATTATCACTGAAGT
1786116 TTTGGGTCCTGAAAGGTATGGTCGGGTTCGATTTCAAGGATCTTTTGTTAACCCATCCCAATATT
456 TTTGGGTCCTGAAAGGTATGGTCGGGTTCGATTTCAAGGATCTTTTGTTAACCCATCCCAATATT
1786181 TTGGATCGAACTCGCAACAATA
521 TTGGATCGAACTCGCAACAATA
1786203 TATGCCTTCG
Statistics
Matches: 542, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
579 542 1.00
ACGTcount: A:0.30, C:0.13, G:0.18, T:0.39
Consensus pattern (579 bp):
TTTGCGTGTGTAGCTCATGCAGAGGTATTTTGAATTTTTTAATATTGGCAGATATTTATTACTTT
CTATCAATTAATATTTTTACTATTGTATTGTAGGAACTGTCGTCCGGTCAAAAAGTTGGACGCCT
TCAACTTTTTGACATTACACATAGGAAGAAAGATGGAAACCCTATGACTCCTGAAGCTGCAGAAA
TTATGGTACGTTTGCTTAATACAATTTCACTTGTTTTAATTATTTATAGTGTTTATTTTCTAATG
ATTTATTTCATTTATTGTAATGCAAATATTTTTAAGTTATGTTGCATTGGGTTTTTTAATATATA
TTGCGTTCCTAACTATGTGATTTATTTTTTAGGAAAAATTAAAGGATAAAAAGGCGGAGTACGAA
GTGATTGCTTCCAGTGATAGTTCTGTTCATATTGACAACATTGATAACCGGATTATCACTGAAGT
TTTGGGTCCTGAAAGGTATGGTCGGGTTCGATTTCAAGGATCTTTTGTTAACCCATCCCAATATT
TTGGATCGAACTCGCAACAATAAATGAAATAAATCATTAGAAAATAAACACTATAAATA
Found at i:1786394 original size:66 final size:66
Alignment explanation
Indices: 1786301--1786436 Score: 186
Period size: 66 Copynumber: 2.1 Consensus size: 66
1786291 ACACAACTTA
*
1786301 AAGCGGAGGTTCAAAAAAGATATGAAGAACTCCAGCTA-CAACTGAAAGCAGATGCAGCAGCGAG
1 AAGCGGAGGTTCAAAAAAGATATGAAGAACTCCAGC-AGCAACTGAAAGCAGATGCAGCAGCAAG
1786365 AG
65 AG
* * * * *
1786367 AAGCTGAGGTTCAACGAAAG-TATGAAGAACTCCAGCAGCAGCTTAAAGCAGATGCGGCAGCAAG
1 AAGCGGAGGTTCAA-AAAAGATATGAAGAACTCCAGCAGCAACTGAAAGCAGATGCAGCAGCAAG
1786431 AG
65 AG
1786433 AAGC
1 AAGC
1786437 ACAATGAACC
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
65 1 0.02
66 57 0.92
67 4 0.06
ACGTcount: A:0.40, C:0.19, G:0.28, T:0.12
Consensus pattern (66 bp):
AAGCGGAGGTTCAAAAAAGATATGAAGAACTCCAGCAGCAACTGAAAGCAGATGCAGCAGCAAGA
G
Found at i:1789145 original size:22 final size:22
Alignment explanation
Indices: 1789120--1789165 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
1789110 GTAAACTTGT
1789120 TTTTGAGGAATGGAAAACGTGC
1 TTTTGAGGAATGGAAAACGTGC
* **
1789142 TTTTGAGGAGTGGAGCACGTGC
1 TTTTGAGGAATGGAAAACGTGC
1789164 TT
1 TT
1789166 GTAAAGAGCC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.24, C:0.11, G:0.35, T:0.30
Consensus pattern (22 bp):
TTTTGAGGAATGGAAAACGTGC
Found at i:1791518 original size:8 final size:8
Alignment explanation
Indices: 1791507--1791556 Score: 50
Period size: 8 Copynumber: 6.1 Consensus size: 8
1791497 TCAAATAAAC
1791507 AAAATATA
1 AAAATATA
1791515 AAAA-ACTA
1 AAAATA-TA
*
1791523 AAAATAATTT
1 AAAAT-A-TA
1791533 AAAATATA
1 AAAATATA
1791541 AAAATATA
1 AAAATATA
1791549 AAAA-ATA
1 AAAATATA
1791556 A
1 A
1791557 CATATTAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
7 5 0.14
8 23 0.64
9 1 0.03
10 7 0.19
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (8 bp):
AAAATATA
Found at i:1791697 original size:26 final size:26
Alignment explanation
Indices: 1791600--1791699 Score: 96
Period size: 26 Copynumber: 3.8 Consensus size: 26
1791590 AATTTGAAAG
* * **
1791600 ATATATATAATAGTTTACGATAAATA
1 ATATATATAAAAATTTAAAATAAATA
*
1791626 ATATATAAAAGAAATTT-AAATAAATA
1 ATATATATAA-AAATTTAAAATAAATA
* **
1791652 ATATGTA-AAACAGCTTAAAATAAATA
1 ATATATATAAA-AATTTAAAATAAATA
1791678 ATATATATAAAAATTTAAAATA
1 ATATATATAAAAATTTAAAATA
1791700 GAGAATGATA
Statistics
Matches: 59, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
24 1 0.02
25 5 0.08
26 46 0.78
27 7 0.12
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.33
Consensus pattern (26 bp):
ATATATATAAAAATTTAAAATAAATA
Found at i:1793394 original size:44 final size:45
Alignment explanation
Indices: 1793051--1793958 Score: 499
Period size: 44 Copynumber: 20.3 Consensus size: 45
1793041 GCAGCTCCGA
* * * * *
1793051 GGAGATAAGACTCGCTATCTTTAATCTACTCCACTGCAACTTCAG
1 GGAGATAAGATTTGATATCTTCAATCTGCTCCACTGCAACTTCAG
* *
1793096 GGA-ATAAGACTT-A-A-CTTCAACCTGCTCCACTGC-ACTTCA-
1 GGAGATAAGATTTGATATCTTCAATCTGCTCCACTGCAACTTCAG
* ** * * *
1793135 GGAGGATAAGGTTTG-TGGCTTGAATTTGCTCCACTGCAACTTTAG
1 GGA-GATAAGATTTGATATCTTCAATCTGCTCCACTGCAACTTCAG
* * * * * **
1793180 GGAGATAGGGTTTG-T-T-AT-GATCTACTCTGCTGCAACTTCAG
1 GGAGATAAGATTTGATATCTTCAATCTGCTCCACTGCAACTTCAG
* *
1793221 AGAGATAAGATTTGTAATTTATAGCTTCAATCTGTTCCACTGCAACTTCAG
1 GGAGATAAGATTTG--A--TAT--CTTCAATCTGCTCCACTGCAACTTCAG
* * * * *
1793272 GGAAATGAGATTTGATATCTTCAGTCTACTCCACTGCAACTTCAA
1 GGAGATAAGATTTGATATCTTCAATCTGCTCCACTGCAACTTCAG
* * * * *
1793317 GGAGACAAGACTTGCAGT-T-TT-AATTTGCCCCACTGCAACTTTAG
1 GGAGATAAGATTTG-A-TATCTTCAATCTGCTCCACTGCAACTTCAG
* *
1793361 GGGGATAAGATTTG-TATCTTCAACCTGCTCCACTGCAACTTCAG
1 GGAGATAAGATTTGATATCTTCAATCTGCTCCACTGCAACTTCAG
* * * *
1793405 GGAGATAAGGTTTGATATCTTCAGTCTGCTCAACTGCAACTTCAA
1 GGAGATAAGATTTGATATCTTCAATCTGCTCCACTGCAACTTCAG
* * * ** * * *
1793450 TGAGATAATACTTGTAATGGTAGATTTAAT-TCGAC-CTACTGCAACTTCAA
1 GGAGATAAGA--T-T--TGATATCTTCAATCT-G-CTCCACTGCAACTTCAG
* ** * * * * * *
1793500 AGTTATAGGA-TTCATCGT-TTTAATCTGCTCCACTACAACTTTAG
1 GGAGATAAGATTTGAT-ATCTTCAATCTGCTCCACTGCAACTTCAG
** * * * * *
1793544 GGAGATAAGATCCG---CCAT-GATTTGCTCTACTGCAACTTCAG
1 GGAGATAAGATTTGATATCTTCAATCTGCTCCACTGCAACTTCAG
* * * *
1793585 AGAGATAAGATCTGTGATTTATAGCTTTAATCTGTTCCACTACAACTTCAG
1 GGAGATAAGAT-T-TGA--TAT--CTTCAATCTGCTCCACTGCAACTTCAG
* * * *
1793636 GGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTGCAACTTCAG
1 GGAGATAAGATTTGATATCTTCAATCTGCTCCACTGCAACTTCAG
* * *
1793681 GGAGATAAGACTTG-TAACTTCAATCCGCTCCACTGCAACTTCAG
1 GGAGATAAGATTTGATATCTTCAATCTGCTCCACTGCAACTTCAG
* * ** *
1793725 GGAGATAGGA-TTGTTGGCTTGAATCTGCTCCACTGCAACTTCAG
1 GGAGATAAGATTTGATATCTTCAATCTGCTCCACTGCAACTTCAG
** * *
1793769 GGAGATAAGATTTGCCATCTTCAGTCTGCCCCACTGCAACTTCAG
1 GGAGATAAGATTTGATATCTTCAATCTGCTCCACTGCAACTTCAG
* * * * * *
1793814 AGG-GATAAGACTTGTTTTCTTCAGTCTGCTCCACCGCAACTTCAA
1 -GGAGATAAGATTTGATATCTTCAATCTGCTCCACTGCAACTTCAG
* * * * * *
1793859 GGAGATAAAACTTG-TAACTTTAATCCGCTCCATTGCAACTTCAG
1 GGAGATAAGATTTGATATCTTCAATCTGCTCCACTGCAACTTCAG
* * *
1793903 GGAGATAGGA-TT-AT-TGGCTTTAATCTGCTCCATTGCAACTTCAG
1 GGAGATAAGATTTGATAT--CTTCAATCTGCTCCACTGCAACTTCAG
1793947 GGAGATAAGATT
1 GGAGATAAGATT
1793959 CACCATATTC
Statistics
Matches: 656, Mismatches: 154, Indels: 106
0.72 0.17 0.12
Matches are distributed among these distances:
39 3 0.00
40 6 0.01
41 80 0.12
42 4 0.01
43 26 0.04
44 247 0.38
45 182 0.28
46 6 0.01
47 9 0.01
48 1 0.00
49 3 0.00
50 32 0.05
51 57 0.09
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (45 bp):
GGAGATAAGATTTGATATCTTCAATCTGCTCCACTGCAACTTCAG
Found at i:1793777 original size:133 final size:133
Alignment explanation
Indices: 1793245--1793956 Score: 417
Period size: 133 Copynumber: 5.3 Consensus size: 133
1793235 TAATTTATAG
* * * * * * * * ** *
1793245 CTTCAATCTGTTCCACTGCAACTTCAGGGAAATGAGATTTGATATCTTCAGTCTACTCCACTGCA
1 CTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTTAACTTCAATCCGCTCCACCGCA
* * * * * * * *
1793310 ACTTCAAGGAGACAAGACTTGCAGTTTTAATTTGCCCCACTGCAACTTTAGGGGGATAAGATTTG
66 ACTTCAAGGAGATAAAACTTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTG
1793375 -TAT
130 CTAT
** ** * * * * * *
1793378 CTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGATATCTTCAGTCTGCTCAACTGCA
1 CTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTTAACTTCAATCCGCTCCACCGCA
* * * * ** **
1793443 ACTTCAATGAGATAATACTTGTAATGGTAGATTTAAT-TCGAC-CTACTGCAACTTCAAAGTTAT
66 ACTTCAAGGAGATAAAAC---T--T-GTAGCTTTAATCT-G-CTCCACTGCAACTTCAGGGAGAT
*
1793506 AGGATT-C-AT
123 AAGATTGCTAT
* * * * * * * * ** * *
1793515 CGTTTTAATCTGCTCCACTACAACTTTAGGGAGATAAGA-TCCG---CCAT-GATTTGCTCTACT
1 C--TTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACT-TGTTAACTTCAATCCGCTCCACC
* * *
1793575 GCAACTTC-AGAGAGATAAGATCTGTGATTTATAGCTTTAATCTGTTCCACTACAACTTCAGGGA
63 GCAACTTCAAG-GAGATAA-AACT-TG-----TAGCTTTAATCTGCTCCACTGCAACTTCAGGGA
*
1793639 AATAAGATTCGCTAT
120 GATAAGATT-GCTAT
*
1793654 CTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTG-TAACTTCAATCCGCTCCACTGCA
1 CTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTTAACTTCAATCCGCTCCACCGCA
* ** * *
1793718 ACTTCAGGGAGATAGGA-TTGTTGGCTTGAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTT
66 ACTTCAAGGAGATAAAACTTG-TAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TT
*
1793782 GCCAT
129 GCTAT
* ** * *
1793787 CTTCAGTCTGCCCCACTGCAACTTCAGAGG-GATAAGACTTGTTTTCTTCAGTCTGCTCCACCGC
1 CTTCAGTCTGCTCCACTGCAACTTCAG-GGAGATAAGACTTGTTAACTTCAATCCGCTCCACCGC
* * * * *
1793851 AACTTCAAGGAGATAAAACTTGTAACTTTAATCCGCTCCATTGCAACTTCAGGGAGATAGGATTA
65 AACTTCAAGGAGATAAAACTTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTG
* **
1793916 TTGG
130 CTAT
* * *
1793920 CTTTAATCTGCTCCATTGCAACTTCAGGGAGATAAGA
1 CTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGA
1793957 TTCACCATAT
Statistics
Matches: 455, Mismatches: 90, Indels: 68
0.74 0.15 0.11
Matches are distributed among these distances:
131 1 0.00
132 3 0.01
133 182 0.40
134 71 0.16
135 27 0.06
136 34 0.07
137 39 0.09
138 8 0.02
139 65 0.14
140 24 0.05
141 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.31
Consensus pattern (133 bp):
CTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTTAACTTCAATCCGCTCCACCGCA
ACTTCAAGGAGATAAAACTTGTAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGC
TAT
Found at i:1794318 original size:24 final size:24
Alignment explanation
Indices: 1794286--1794341 Score: 87
Period size: 24 Copynumber: 2.3 Consensus size: 24
1794276 CAGATTTCCC
*
1794286 CCACTGTAATCTTCAAGGT-TCAAT
1 CCACTGTAATCTTCAAAGTGT-AAT
1794310 CCACTGTAATCTTCAAAGTGTAAT
1 CCACTGTAATCTTCAAAGTGTAAT
1794334 CCACTGTA
1 CCACTGTA
1794342 CTTTTAGGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 29 0.97
25 1 0.03
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.32
Consensus pattern (24 bp):
CCACTGTAATCTTCAAAGTGTAAT
Found at i:1795229 original size:7 final size:7
Alignment explanation
Indices: 1795204--1795259 Score: 62
Period size: 7 Copynumber: 8.1 Consensus size: 7
1795194 ACCTTGGCTC
1795204 TCTTTTT
1 TCTTTTT
*
1795211 TC-TTTG
1 TCTTTTT
1795217 TC-TTTT
1 TCTTTTT
1795223 TCTTTTT
1 TCTTTTT
1795230 TCTTTTT
1 TCTTTTT
*
1795237 TCCTTTT
1 TCTTTTT
*
1795244 TATTTTT
1 TCTTTTT
1795251 TCATTTTT
1 TC-TTTTT
1795259 T
1 T
1795260 TAGGACTCAA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
6 10 0.24
7 25 0.61
8 6 0.15
ACGTcount: A:0.04, C:0.14, G:0.02, T:0.80
Consensus pattern (7 bp):
TCTTTTT
Found at i:1799648 original size:22 final size:23
Alignment explanation
Indices: 1799612--1799655 Score: 72
Period size: 22 Copynumber: 1.9 Consensus size: 23
1799602 AAGTAGCGAC
1799612 TAAAAAAATCCAATAATTAAATGA
1 TAAAAAAAT-CAATAATTAAATGA
1799636 TAAAAAAAT-AATAATTAAAT
1 TAAAAAAATCAATAATTAAAT
1799656 AATTACCAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 11 0.55
24 9 0.45
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27
Consensus pattern (23 bp):
TAAAAAAATCAATAATTAAATGA
Found at i:1802631 original size:39 final size:40
Alignment explanation
Indices: 1802580--1802659 Score: 110
Period size: 39 Copynumber: 2.0 Consensus size: 40
1802570 TAAAAAGTAT
* *
1802580 TTATATTAAAAAAATTAC-CACAAACATATTAAATGTTTTA
1 TTATATTAAAAAAA-TACAAACAAACATAATAAATGTTTTA
*
1802620 TTATATT-AAAAAATACAAATAAACATAATAAATGTTTTA
1 TTATATTAAAAAAATACAAACAAACATAATAAATGTTTTA
1802659 T
1 T
1802660 CGTATTAAGC
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
38 3 0.08
39 26 0.72
40 7 0.19
ACGTcount: A:0.53, C:0.07, G:0.03, T:0.38
Consensus pattern (40 bp):
TTATATTAAAAAAATACAAACAAACATAATAAATGTTTTA
Found at i:1806454 original size:21 final size:20
Alignment explanation
Indices: 1806428--1806471 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
1806418 GTTAATCACG
*
1806428 TTTATTCTATTTTCATTTTTA
1 TTTATTCTATTTTC-TTTTCA
*
1806449 TTTATTCTTTTTTCTTTTCA
1 TTTATTCTATTTTCTTTTCA
1806469 TTT
1 TTT
1806472 GTTTTGTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.75
Consensus pattern (20 bp):
TTTATTCTATTTTCTTTTCA
Found at i:1807040 original size:5 final size:5
Alignment explanation
Indices: 1807030--1807054 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1807020 TTTTTTTAAC
1807030 TATTT TATTT TATTT TATTT TATTT
1 TATTT TATTT TATTT TATTT TATTT
1807055 ACGCTATTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TATTT
Found at i:1808852 original size:16 final size:16
Alignment explanation
Indices: 1808831--1808864 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1808821 TGTGTTTCAC
1808831 TTTGACTGCATGGCAT
1 TTTGACTGCATGGCAT
*
1808847 TTTGACTGTATGGCAT
1 TTTGACTGCATGGCAT
1808863 TT
1 TT
1808865 CATTATAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.15, G:0.24, T:0.44
Consensus pattern (16 bp):
TTTGACTGCATGGCAT
Found at i:1809352 original size:24 final size:24
Alignment explanation
Indices: 1809308--1809353 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
1809298 TCTCTTTTCG
* *
1809308 CATTCATTTCATGCATTTGCATTA
1 CATTCATTACATGCATATGCATTA
1809332 CATTACATTACAT-CATATGCAT
1 CATT-CATTACATGCATATGCAT
1809354 CAAACACCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 12 0.63
25 7 0.37
ACGTcount: A:0.30, C:0.22, G:0.07, T:0.41
Consensus pattern (24 bp):
CATTCATTACATGCATATGCATTA
Found at i:1811266 original size:19 final size:19
Alignment explanation
Indices: 1811242--1811282 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
1811232 GCAAATGTTC
1811242 TTTCATTCTTTACGATTTT
1 TTTCATTCTTTACGATTTT
**
1811261 TTTCATTCTTTTGGATTTT
1 TTTCATTCTTTACGATTTT
1811280 TTT
1 TTT
1811283 TTTGCCAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.12, C:0.12, G:0.07, T:0.68
Consensus pattern (19 bp):
TTTCATTCTTTACGATTTT
Found at i:1812229 original size:7 final size:7
Alignment explanation
Indices: 1812204--1812243 Score: 64
Period size: 7 Copynumber: 5.7 Consensus size: 7
1812194 AGTGATGTGA
1812204 AAAAATG
1 AAAAATG
1812211 AAAAGATG
1 AAAA-ATG
1812219 -AAAATG
1 AAAAATG
1812225 AAAAATG
1 AAAAATG
1812232 AAAAATG
1 AAAAATG
1812239 AAAAA
1 AAAAA
1812244 GTAAAAAGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 3 0.10
7 25 0.81
8 3 0.10
ACGTcount: A:0.72, C:0.00, G:0.15, T:0.12
Consensus pattern (7 bp):
AAAAATG
Found at i:1812243 original size:21 final size:20
Alignment explanation
Indices: 1812204--1812259 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 20
1812194 AGTGATGTGA
1812204 AAAAATGAAAAGATGAAAA-T
1 AAAAATGAAAA-ATGAAAAGT
1812224 GAAAAATGAAAAATGAAAAAGT
1 -AAAAATGAAAAATG-AAAAGT
1812246 AAAAA-GTAAAAATG
1 AAAAATG-AAAAATG
1812260 GAGAGGCTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
20 4 0.12
21 27 0.84
22 1 0.03
ACGTcount: A:0.70, C:0.00, G:0.16, T:0.14
Consensus pattern (20 bp):
AAAAATGAAAAATGAAAAGT
Found at i:1812249 original size:14 final size:14
Alignment explanation
Indices: 1812204--1812250 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
1812194 AGTGATGTGA
1812204 AAAAATG-AAAAGAT
1 AAAAATGAAAAAG-T
*
1812218 GAAAATGAAAAA-T
1 AAAAATGAAAAAGT
1812231 GAAAAATGAAAAAGT
1 -AAAAATGAAAAAGT
1812246 AAAAA
1 AAAAA
1812251 GTAAAAATGG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
13 1 0.04
14 22 0.79
15 5 0.18
ACGTcount: A:0.72, C:0.00, G:0.15, T:0.13
Consensus pattern (14 bp):
AAAAATGAAAAAGT
Found at i:1813596 original size:44 final size:45
Alignment explanation
Indices: 1813546--1814222 Score: 399
Period size: 44 Copynumber: 15.2 Consensus size: 45
1813536 GTTGAAAAGC
* * *
1813546 AGCAGATCTTATCTTTATGTATTGACATGAAGTAGATC-AAATAA
1 AGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCGAAATAA
* * **
1813590 AGCAGATCTTATCTTCCCATACTGGTGGCA--AAGTAGATCGAAA-AA
1 AGCAGATCTTGTCTT--CAT-GTATTGGCATGAAGTAGATCGAAATAA
* * * * *
1813635 AGTAGATATTGTCTTCATGTATTGGCGTAAAGTAGATC-AAAGAA
1 AGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCGAAATAA
*
1813679 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGAT-A
1 AGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCGAA-ATAA
* **
1813724 A-CAGATCTTGTCTTCCCATACTGGTGGC--GAAGTAGATCGAAA-AA
1 AGCAGATCTTGTCTT--CAT-GTATTGGCATGAAGTAGATCGAAATAA
* * * * *
1813768 AACAGGTCTTGTCTTCATGTACTGGCGTGAAGTAGATC-AAAGATA
1 AGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCGAAATA-A
* *
1813813 A-CAGATCTTGTCTTC-TCATACTGGTGGC--GAAGTAGATCG-AAGAA
1 AGCAGATCTTGTCTTCAT-GTA-T--TGGCATGAAGTAGATCGAAATAA
* * * *
1813857 AGCAGATCTTGTCTTCATGTACTAGCGTGAAGTAGATC-AAAGATA
1 AGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCGAAATA-A
* ** *
1813902 A-CAGATCTTGTCTTCCCATACTGGTGGC--GAAGTAGATCG-AAGAA
1 AGCAGATCTTGTCTT--CAT-GTATTGGCATGAAGTAGATCGAAATAA
* * * * *
1813946 AGCAGATATTGTCTTCATGTACTGGCGTGAAGTAGATC-AAAGAT
1 AGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCGAAATAA
* * ** *
1813990 ATCAGATCTTGTCTTCCCATACTGGTGGC--GAAGTAGATCGAAAAAA
1 AGCAGATCTTGTCTT--CAT-GTATTGGCATGAAGTAGATCGAAATAA
* * * * *
1814036 AGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGGTC-AAAGAT
1 AGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCGAAATAA
* * * ** *
1814080 ACCAGATCTTATCTTCCCATACTGGTGGC--GAAGTAGATCG-AAGAA
1 AGCAGATCTTGTCTT--CAT-GTATTGGCATGAAGTAGATCGAAATAA
* * * *
1814125 AGCAAATCTTGTCTTCATATATTGGCATGAGGTAGATC-AAAGATA
1 AGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCGAAATA-A
* * *
1814170 A-CAGATCTTGTCTTCATGTATTGGCTTAAAGTAGATC-AAATAC
1 AGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCGAAATAA
1814213 AGCAGATCTT
1 AGCAGATCTT
1814223 ATCTCTCTGA
Statistics
Matches: 508, Mismatches: 73, Indels: 104
0.74 0.11 0.15
Matches are distributed among these distances:
42 23 0.05
43 25 0.05
44 237 0.47
45 158 0.31
46 37 0.07
47 28 0.06
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.29
Consensus pattern (45 bp):
AGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCGAAATAA
Found at i:1813757 original size:89 final size:89
Alignment explanation
Indices: 1813664--1814184 Score: 837
Period size: 89 Copynumber: 5.8 Consensus size: 89
1813654 TATTGGCGTA
* *
1813664 AAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAACAGA
1 AAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGA
1813729 TCTTGTCTTCCCATACTGGTGGCG
66 TCTTGTCTTCCCATACTGGTGGCG
* *
1813753 AAGTAGATCGAAA-AAAACAGGTCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAG
1 AAGTAGATC-AAAGAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAG
*
1813817 ATCTTGTCTTCTCATACTGGTGGCG
65 ATCTTGTCTTCCCATACTGGTGGCG
* *
1813842 AAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTACTAGCGTGAAGTAGATCAAAGATAACAGA
1 AAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGA
1813907 TCTTGTCTTCCCATACTGGTGGCG
66 TCTTGTCTTCCCATACTGGTGGCG
* * *
1813931 AAGTAGATCGAAGAAAGCAGATATTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATATCAGA
1 AAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGA
1813996 TCTTGTCTTCCCATACTGGTGGCG
66 TCTTGTCTTCCCATACTGGTGGCG
* * *
1814020 AAGTAGATCGAAAAAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGGTCAAAGATACCAG
1 AAGTAGATC-AAAGAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAG
*
1814085 ATCTTATCTTCCCATACTGGTGGCG
65 ATCTTGTCTTCCCATACTGGTGGCG
* * * * * *
1814110 AAGTAGATCGAAGAAAGCAAATCTTGTCTTCATATATTGGCATGAGGTAGATCAAAGATAACAGA
1 AAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGA
1814175 TCTTGTCTTC
66 TCTTGTCTTC
1814185 ATGTATTGGC
Statistics
Matches: 400, Mismatches: 29, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
88 2 0.00
89 312 0.78
90 86 0.22
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (89 bp):
AAGTAGATCAAAGAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAACAGA
TCTTGTCTTCCCATACTGGTGGCG
Found at i:1813784 original size:133 final size:134
Alignment explanation
Indices: 1813546--1814222 Score: 680
Period size: 133 Copynumber: 5.1 Consensus size: 134
1813536 GTTGAAAAGC
* * * * * *
1813546 AGCAGATCTTATCTTTATGTATTGACATGAAGTAGATC-AA-ATAAAGCAGATCTTATCTTCCCA
1 AGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCGAAGAT-AAGCAGATCTTGTCTTCCCA
* ** * *
1813609 TACTGGTGGCAAAGTAGATCGAAAAAAGTAGATATTGTCTTCATGTATTGGCGTAAAGTAGATCA
65 TACTGGTGGCGAAGTAGATCGAAAAAAACAGATCTTGTCTTCATGTACTGGCGTAAAGTAGATCA
1813674 AAGAA
130 AAGAA
*
1813679 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAA-CAGATCTTGTCTTCCCAT
1 AGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCGAAGATAAGCAGATCTTGTCTTCCCAT
* *
1813743 ACTGGTGGCGAAGTAGATCGAAAAAAACAGGTCTTGTCTTCATGTACTGGCGTGAAGTAGATCAA
66 ACTGGTGGCGAAGTAGATCGAAAAAAACAGATCTTGTCTTCATGTACTGGCGTAAAGTAGATCAA
1813808 AGATA
131 AGA-A
* * * **
1813813 A-CAGATCTTGTCTTC-TCATACTGGTGGCGAAGTAGATCGAAGA-AAGCAGATCTTGTCTTCAT
1 AGCAGATCTTGTCTTCAT-GTACTGG-CGTGAAGTAGATCGAAGATAAGCAGATCTTGTCTTCCC
* * * * * *** * **
1813875 GTACTAG-CGTGAAGTAGATC-AAAGATAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGA
64 ATACTGGTGGCGAAGTAGATCGAAA-AAAACAGATCTTGTCTTCATGTACTGG-CGTAAAGTAGA
*
1813938 TCGAAGAA
127 TCAAAGAA
* * *
1813946 AGCAGATATTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAT-ATCAGATCTTGTCTTCCCAT
1 AGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCGAAGATAAGCAGATCTTGTCTTCCCAT
* *
1814010 ACTGGTGGCGAAGTAGATCGAAAAAAAGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGGTCA
66 ACTGGTGGCGAAGTAGATCGAAAAAAA-CAGATCTTGTCTTCATGTACTGGCGTAAAGTAGATCA
*
1814075 AAGAT
130 AAGAA
* * *** * * *
1814080 ACCAGATCTTATCTTCCCATACTGGTGGCGAAGTAGATCGAAGA-AAGCAAATCTTGTCTT--CA
1 AGCAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATCGAAGATAAGCAGATCTTGTCTTCCCA
** * * * *
1814142 TA-TATTGGCATGAGGTAGATC-AAAGATAACAGATCTTGTCTTCATGTATTGGCTTAAAGTAGA
65 TACTGGTGGC--GAAGTAGATCGAAA-AAAACAGATCTTGTCTTCATGTACTGGCGTAAAGTAGA
* *
1814205 TCAAATAC
127 TCAAAGAA
1814213 AGCAGATCTT
1 AGCAGATCTT
1814223 ATCTCTCTGA
Statistics
Matches: 452, Mismatches: 73, Indels: 38
0.80 0.13 0.07
Matches are distributed among these distances:
132 9 0.02
133 255 0.56
134 134 0.30
135 54 0.12
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.29
Consensus pattern (134 bp):
AGCAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCGAAGATAAGCAGATCTTGTCTTCCCAT
ACTGGTGGCGAAGTAGATCGAAAAAAACAGATCTTGTCTTCATGTACTGGCGTAAAGTAGATCAA
AGAA
Found at i:1815150 original size:21 final size:20
Alignment explanation
Indices: 1815124--1815167 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
1815114 GTTAATCGCG
*
1815124 TTTATTCTATTTTCATTTTTA
1 TTTATTCTATTTTC-TTTTCA
*
1815145 TTTATTCTTTTTTCTTTTCA
1 TTTATTCTATTTTCTTTTCA
1815165 TTT
1 TTT
1815168 GTTTTGTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.75
Consensus pattern (20 bp):
TTTATTCTATTTTCTTTTCA
Found at i:1815736 original size:5 final size:5
Alignment explanation
Indices: 1815726--1815750 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1815716 TTTTTTTAAC
1815726 TATTT TATTT TATTT TATTT TATTT
1 TATTT TATTT TATTT TATTT TATTT
1815751 ACGCTATTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TATTT
Found at i:1820260 original size:9 final size:9
Alignment explanation
Indices: 1820248--1820374 Score: 53
Period size: 9 Copynumber: 14.0 Consensus size: 9
1820238 CCTTTTTACC
1820248 ATTTTTATT
1 ATTTTTATT
1820257 ATTTTCTTCATT
1 A-TTT-TT-ATT
*
1820269 ATTTTAATGT
1 ATTTTTAT-T
* *
1820279 ATTATCA-T
1 ATTTTTATT
*
1820287 CTTTT-ATT
1 ATTTTTATT
*
1820295 ATTATTATT
1 ATTTTTATT
*
1820304 GTTTTTATT
1 ATTTTTATT
* *
1820313 ATCTTTACT
1 ATTTTTATT
*
1820322 ATTATTATT
1 ATTTTTATT
* *
1820331 AGTATTATT
1 ATTTTTATT
**
1820340 ATTGATATT
1 ATTTTTATT
*
1820349 ATTGTTATT
1 ATTTTTATT
*
1820358 ATTGTTA-T
1 ATTTTTATT
*
1820366 GTTTTTATT
1 ATTTTTATT
1820375 TATATTTACT
Statistics
Matches: 89, Mismatches: 22, Indels: 14
0.71 0.18 0.11
Matches are distributed among these distances:
7 1 0.01
8 14 0.16
9 55 0.62
10 10 0.11
11 5 0.06
12 4 0.04
ACGTcount: A:0.24, C:0.05, G:0.06, T:0.65
Consensus pattern (9 bp):
ATTTTTATT
Found at i:1820298 original size:3 final size:3
Alignment explanation
Indices: 1820290--1820365 Score: 66
Period size: 3 Copynumber: 25.3 Consensus size: 3
1820280 TTATCATCTT
* * * *
1820290 TTA TTA TTA TTA TTG TTT TTA TTA TCT- TTA CTA TTA TTA TTA GTA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA
* *
1820335 TTA TTA TTGA -TA TTA TTG TTA TTA TTG TTA T
1 TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA T
1820366 GTTTTTATTT
Statistics
Matches: 58, Mismatches: 11, Indels: 8
0.75 0.14 0.10
Matches are distributed among these distances:
2 2 0.03
3 54 0.93
4 2 0.03
ACGTcount: A:0.26, C:0.03, G:0.07, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:1820625 original size:17 final size:17
Alignment explanation
Indices: 1820600--1820634 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1820590 TATATATATA
*
1820600 TTATTTTATTTCATTTT
1 TTATCTTATTTCATTTT
*
1820617 TTATCTTATTTTATTTT
1 TTATCTTATTTCATTTT
1820634 T
1 T
1820635 ATAATTCACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (17 bp):
TTATCTTATTTCATTTT
Found at i:1820668 original size:18 final size:18
Alignment explanation
Indices: 1820645--1820679 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1820635 ATAATTCACA
* *
1820645 TACGTATATATTTTCTTC
1 TACGTACATATATTCTTC
1820663 TACGTACATATATTCTT
1 TACGTACATATATTCTT
1820680 ATGTTTTGTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.17, G:0.06, T:0.51
Consensus pattern (18 bp):
TACGTACATATATTCTTC
Found at i:1821837 original size:16 final size:15
Alignment explanation
Indices: 1821811--1821841 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
1821801 AACTGGACAG
1821811 GAAAGAAAAAGGAAA
1 GAAAGAAAAAGGAAA
1821826 GAAAGAAGAAAGGAAA
1 GAAAGAA-AAAGGAAA
1821842 AATTAGGGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (15 bp):
GAAAGAAAAAGGAAA
Found at i:1824936 original size:41 final size:41
Alignment explanation
Indices: 1824875--1825024 Score: 230
Period size: 41 Copynumber: 3.7 Consensus size: 41
1824865 TTTAACATAT
*
1824875 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCCA-A
1 TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT-CAGA
* *
1824916 TCACCGGCACTTAGCTTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
*
1824957 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
* *
1824998 TCATCGGCACTTAGCCTGCTAGACTTA
1 TCACCGGCACTTAGCCTGCTAGGCTTA
1825025 AAGTCCGAAT
Statistics
Matches: 101, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
40 2 0.02
41 99 0.98
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.29
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
Found at i:1825043 original size:82 final size:82
Alignment explanation
Indices: 1824874--1825073 Score: 232
Period size: 82 Copynumber: 2.4 Consensus size: 82
1824864 ATTTAACATA
* * * *
1824874 TTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCCAATCACCGGCACTTAGCTTGCTAGG
1 TTCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCCAATCACCGGCACTTAGCCTGCTAGA
*
1824939 TTTATAACCTGATTCAG
66 CTTATAACCTGATTCAG
* *
1824956 ATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT-CAGATCATCGGCACTTAGCCTGCTAG
1 TTCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCCA-ATCACCGGCACTTAGCCTGCTAG
*
1825020 ACTTA-AAGTCC-GAATT-AT
65 ACTTATAA--CCTG-ATTCAG
1825038 TTCACCGGC-CTTAAGCCTGCTAGGTTT-TAAACCTGA
1 TTCACCGGCACTT-AGCCTGCTAGGTTTAT-AACCTGA
1825074 AAATTTCAAT
Statistics
Matches: 103, Mismatches: 9, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
81 8 0.08
82 90 0.87
83 5 0.05
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.30
Consensus pattern (82 bp):
TTCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCCAATCACCGGCACTTAGCCTGCTAGA
CTTATAACCTGATTCAG
Found at i:1825328 original size:34 final size:34
Alignment explanation
Indices: 1825290--1825355 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 34
1825280 TATATTCACC
* *
1825290 TATTCGAA-ACTAACTATACATATATATTTGTATG
1 TATTC-AATACTAACCATACATATATATATGTATG
* *
1825324 TATTCAATACTACCCATATATATATATATGTA
1 TATTCAATACTAACCATACATATATATATGTA
1825356 AACTTAACAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 2 0.07
34 25 0.93
ACGTcount: A:0.39, C:0.14, G:0.06, T:0.41
Consensus pattern (34 bp):
TATTCAATACTAACCATACATATATATATGTATG
Found at i:1829112 original size:16 final size:17
Alignment explanation
Indices: 1829076--1829112 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
1829066 TTTTTAATTT
*
1829076 TAATAATGAATTTTAAA
1 TAATAATGAAATTTAAA
1829093 -AATAAT-AAATTTAAA
1 TAATAATGAAATTTAAA
1829108 TAATA
1 TAATA
1829113 TTATTCACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
TAATAATGAAATTTAAA
Found at i:1829946 original size:20 final size:21
Alignment explanation
Indices: 1829912--1829955 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
1829902 CACAAACAAC
1829912 TTTAAAAAATTAATATGTATTT
1 TTTAAAAAA-TAATATGTATTT
*
1829934 TTTAAAAAA-AATATTTATTT
1 TTTAAAAAATAATATGTATTT
1829954 TT
1 TT
1829956 AATATTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 12 0.57
22 9 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (21 bp):
TTTAAAAAATAATATGTATTT
Found at i:1839474 original size:2 final size:2
Alignment explanation
Indices: 1839467--1839517 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
1839457 TAAAAGACAA
1839467 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1839509 AG AG AG AG A
1 AG AG AG AG A
1839518 AAAGATTTGT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1847875 original size:20 final size:20
Alignment explanation
Indices: 1847850--1847888 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1847840 ATATGTTTAT
1847850 TTAGAAATAGTTGTTACTAG
1 TTAGAAATAGTTGTTACTAG
1847870 TTAGAAATAGTTGTTACTA
1 TTAGAAATAGTTGTTACTA
1847889 ACACTTAGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.05, G:0.18, T:0.41
Consensus pattern (20 bp):
TTAGAAATAGTTGTTACTAG
Found at i:1849270 original size:16 final size:16
Alignment explanation
Indices: 1849251--1849281 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1849241 TTTGATGATT
1849251 TTAGATAATAATTTTG
1 TTAGATAATAATTTTG
*
1849267 TTAGATATTAATTTT
1 TTAGATAATAATTTT
1849282 AGGACCAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (16 bp):
TTAGATAATAATTTTG
Found at i:1849961 original size:42 final size:42
Alignment explanation
Indices: 1849888--1850082 Score: 153
Period size: 42 Copynumber: 4.6 Consensus size: 42
1849878 GTTTACTTTC
* * * * *
1849888 CGTTTAGCTCTCACGAGCTTCAGTTTAACTCATATGAGTTTT
1 CGTTCAGCTCTTATGAGCTTCTGTTCAACTCATATGAGTTTT
* * *
1849930 CGTTCAGCACTTTTGAGCTTCTGTTCAACTCATATGAGTTTC
1 CGTTCAGCTCTTATGAGCTTCTGTTCAACTCATATGAGTTTT
* * * * * *
1849972 CTTTAAGCTC-TATTGAGCTTCTGTTTAACCCTTATGGGTTTT
1 CGTTCAGCTCTTA-TGAGCTTCTGTTCAACTCATATGAGTTTT
* * ** *
1850014 TGTTCAGCTCTTACGAGCTTCCAATT-AACTCTTATGAG-TTT
1 CGTTCAGCTCTTATGAGCTT-CTGTTCAACTCATATGAGTTTT
* *
1850055 CTGTTTAGCTCTCATGAGCTTCTGTTCA
1 C-GTTCAGCTCTTATGAGCTTCTGTTCA
1850083 GCCTTCGGGC
Statistics
Matches: 117, Mismatches: 31, Indels: 10
0.74 0.20 0.06
Matches are distributed among these distances:
41 7 0.06
42 105 0.90
43 5 0.04
ACGTcount: A:0.19, C:0.22, G:0.16, T:0.43
Consensus pattern (42 bp):
CGTTCAGCTCTTATGAGCTTCTGTTCAACTCATATGAGTTTT
Found at i:1849967 original size:21 final size:21
Alignment explanation
Indices: 1849902--1850082 Score: 84
Period size: 21 Copynumber: 8.6 Consensus size: 21
1849892 TAGCTCTCAC
* * *
1849902 GAGCTTCAGTTTAACTCATAT
1 GAGCTTCTGTTCAACTCTTAT
* * * *
1849923 GAG-TTTTCGTTCAGCACTTTT
1 GAGCTTCT-GTTCAACTCTTAT
*
1849944 GAGCTTCTGTTCAACTCATAT
1 GAGCTTCTGTTCAACTCTTAT
*
1849965 GAGTTTCCT-TT-AAGCTC-TATT
1 GAGCTT-CTGTTCAA-CTCTTA-T
* *
1849986 GAGCTTCTGTTTAACCCTTAT
1 GAGCTTCTGTTCAACTCTTAT
* * * * *
1850007 GGGTTTTTGTTCAGCTCTTAC
1 GAGCTTCTGTTCAACTCTTAT
**
1850028 GAGCTTCCAATT-AACTCTTAT
1 GAGCTT-CTGTTCAACTCTTAT
* * * *
1850049 GAGTTTCTGTTTAGCTCTCAT
1 GAGCTTCTGTTCAACTCTTAT
1850070 GAGCTTCTGTTCA
1 GAGCTTCTGTTCA
1850083 GCCTTCGGGC
Statistics
Matches: 114, Mismatches: 36, Indels: 20
0.67 0.21 0.12
Matches are distributed among these distances:
20 11 0.10
21 92 0.81
22 11 0.10
ACGTcount: A:0.19, C:0.21, G:0.17, T:0.43
Consensus pattern (21 bp):
GAGCTTCTGTTCAACTCTTAT
Found at i:1850032 original size:84 final size:84
Alignment explanation
Indices: 1849884--1850080 Score: 211
Period size: 84 Copynumber: 2.3 Consensus size: 84
1849874 TCATGTTTAC
* * * * * **
1849884 TTTCCGTTTAGCTCTCACGAGCTTCAGTTTAACTCATATGAGTTTTCGTTCAGCACTTTTGAGCT
1 TTTCTGTTAAGCTCTCATGAGCTTCTGTTTAACCCATATGAGTTTTCGTTCAGCACTTACGAGCT
**
1849949 T-CTGTTCAACTCATATGAG
66 TCCAATT-AACTCATATGAG
* * * *
1849968 TTTCCT-TTAAGCTCT-ATTGAGCTTCTGTTTAACCCTTATGGGTTTTTGTTCAGCTCTTACGAG
1 TTT-CTGTTAAGCTCTCA-TGAGCTTCTGTTTAACCCATATGAGTTTTCGTTCAGCACTTACGAG
*
1850031 CTTCCAATTAACTCTTATGAG
64 CTTCCAATTAACTCATATGAG
*
1850052 TTTCTGTTTAGCTCTCATGAGCTTCTGTT
1 TTTCTGTTAAGCTCTCATGAGCTTCTGTT
1850081 CAGCCTTCGG
Statistics
Matches: 93, Mismatches: 15, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
83 3 0.03
84 85 0.91
85 5 0.05
ACGTcount: A:0.18, C:0.22, G:0.16, T:0.44
Consensus pattern (84 bp):
TTTCTGTTAAGCTCTCATGAGCTTCTGTTTAACCCATATGAGTTTTCGTTCAGCACTTACGAGCT
TCCAATTAACTCATATGAG
Found at i:1850628 original size:23 final size:24
Alignment explanation
Indices: 1850602--1850648 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
1850592 TGGTTAAGTG
1850602 ATGAAT-AGTT-TATAGGTATGTTA
1 ATGAATGAGTTATATA-GTATGTTA
1850625 ATGAATGAGTTGATATAGTATGTT
1 ATGAATGAGTT-ATATAGTATGTT
1850649 TGATATAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 6 0.29
24 4 0.19
25 7 0.33
26 4 0.19
ACGTcount: A:0.34, C:0.00, G:0.23, T:0.43
Consensus pattern (24 bp):
ATGAATGAGTTATATAGTATGTTA
Found at i:1855660 original size:13 final size:13
Alignment explanation
Indices: 1855642--1855688 Score: 58
Period size: 13 Copynumber: 3.6 Consensus size: 13
1855632 AGATGCAAGG
*
1855642 GACACACGGCCAA
1 GACACACGACCAA
* *
1855655 GACACACTACCAT
1 GACACACGACCAA
*
1855668 GACACACGACCGA
1 GACACACGACCAA
1855681 GACACACG
1 GACACACG
1855689 CCCGTGTCTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.38, C:0.38, G:0.19, T:0.04
Consensus pattern (13 bp):
GACACACGACCAA
Found at i:1856665 original size:24 final size:24
Alignment explanation
Indices: 1856633--1856819 Score: 69
Period size: 24 Copynumber: 7.6 Consensus size: 24
1856623 TGTAATACGA
*
1856633 GAAGTTCATAAGAGCCATAATCGG
1 GAAGCTCATAAGAGCCATAATCGG
**
1856657 GAAGCTCATGCGAGCCTATAA-CGG
1 GAAGCTCATAAGAGCC-ATAATCGG
* ** **
1856681 GTAGCTCCGAAGAGCCATTAA-CAA
1 GAAGCTCATAAGAGCCA-TAATCGG
*** *
1856705 GAAGCTCCGGATAGCCATATATCGG
1 GAAGCTCATAAGAGCCATA-ATCGG
* *
1856730 GAAG-T-TTAGGCAAGCCAT-ATCGG
1 GAAGCTCATAAG--AGCCATAATCGG
* * *
1856753 GAAGCTCACAAAGAGCCTTTAATCAG
1 GAAGCTCA-TAAGAGCC-ATAATCGG
* * *
1856779 GAAGCTCACGAAGAGCCATATAACGA
1 GAAGCTCA-TAAGAGCCATA-ATCGG
*
1856805 GACGCTCATAAGAGC
1 GAAGCTCATAAGAGC
1856820 TGCGGTGTGT
Statistics
Matches: 119, Mismatches: 32, Indels: 23
0.68 0.18 0.13
Matches are distributed among these distances:
23 12 0.10
24 52 0.44
25 24 0.20
26 31 0.26
ACGTcount: A:0.35, C:0.22, G:0.25, T:0.18
Consensus pattern (24 bp):
GAAGCTCATAAGAGCCATAATCGG
Done.