Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004862.1 Hibiscus syriacus cultivar Beakdansim tig00010968_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2846896
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 13
Found at i:1640010 original size:38 final size:38
Alignment explanation
Indices: 1639959--1640764 Score: 1116
Period size: 38 Copynumber: 21.2 Consensus size: 38
1639949 CAATACTGAG
*
1639959 AGATTGACTTCTCTTCACGAGAAAGTCAAGAATAACAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
* *
1639997 AGATTGAATTCTCTTCACAAGGAAGTCAAGAATAACAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
*
1640035 AGATTGACTTCTCTTCATGAGGAAGTCAAGAATAACAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
1640073 AGATTGACTTCTCTTCACGA-GAAGTCAAGAATAACAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
1640110 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
* *
1640148 AGATTGACTTCTCTTCACGAGGAAGTCAATAATAAAAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
* *
1640186 AGATTGACTTATCTTCATGAGGAAGTCAAGAATAACAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
* **
1640224 AGATTGACTTATCTTCATAAGGAAGTCAAGAATAACAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
* * *
1640262 AGATTGACTTTTCTTCACGA-GATAGTCAAAAATAACGA
1 AGATTGACTTCTCTTCACGAGGA-AGTCAAGAATAACAA
* * *
1640300 AGATTGAATTATCTTCATGAGGAAGTCAAGAATAACAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
* * *
1640338 AGATTGTA-TTCTCTTCATGAGGAAGTCAATAATAAAAA
1 AGATTG-ACTTCTCTTCACGAGGAAGTCAAGAATAACAA
* *
1640376 AGATTGACTTATCTTCATGAGGAAGTCAAGAATAACAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
1640414 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
* * *
1640452 AGGTTGACTTCTCTTCACGAGGAAGTCAATAATAAAAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
* *
1640490 AGATTGACTTATCTTCATGAGGAAGTCAAGAATAACAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
* ** *
1640528 AGATTGACTTATCTTCATAAGGAAGTCAAGAATAAAAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
* * * * *
1640566 AGATTGAATTTTCTTCAAGA-GATAGTCAAAAAATAACGA
1 AGATTGACTTCTCTTCACGAGGA-AGTC-AAGAATAACAA
*
1640605 AGATTGAATTCTCTTCACGAGGAAGTCAAGAATAACAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
* *
1640643 AGATTTACTTCTCTTCATGAGGAAGTCAAGAATAACAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
* * * * *
1640681 AGATTGAGTTCTCTTTCACGAGGGATTTAGGAATAACAA
1 AGATTGACTTCTC-TTCACGAGGAAGTCAAGAATAACAA
* * *
1640720 AGATTGACTTTTCTTCACGAGGAGGTCAGGAATAACAA
1 AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
1640758 AGATTGA
1 AGATTGA
1640765 AAATTGGCAC
Statistics
Matches: 690, Mismatches: 69, Indels: 18
0.89 0.09 0.02
Matches are distributed among these distances:
37 42 0.06
38 582 0.84
39 64 0.09
40 2 0.00
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26
Consensus pattern (38 bp):
AGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAA
Found at i:1643802 original size:12 final size:12
Alignment explanation
Indices: 1643785--1643810 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1643775 TCGAGCTCTT
1643785 TCGATTTCTAGG
1 TCGATTTCTAGG
1643797 TCGATTTCTAGG
1 TCGATTTCTAGG
1643809 TC
1 TC
1643811 AAAATCTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.19, G:0.23, T:0.42
Consensus pattern (12 bp):
TCGATTTCTAGG
Found at i:1647329 original size:19 final size:20
Alignment explanation
Indices: 1647299--1647340 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
1647289 ATGTATTTTG
1647299 TAATACAAATGGACTTATAT
1 TAATACAAATGGACTTATAT
*
1647319 TAATA-AAATGGACTTGTAT
1 TAATACAAATGGACTTATAT
1647338 TAA
1 TAA
1647341 GTATATACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.36
Consensus pattern (20 bp):
TAATACAAATGGACTTATAT
Found at i:1647673 original size:39 final size:37
Alignment explanation
Indices: 1647553--1647694 Score: 182
Period size: 37 Copynumber: 3.8 Consensus size: 37
1647543 TATAATATTC
** *
1647553 ATATATATAATATATA-TTTTT-AATTTTTTTTTGAAA
1 ATATATATAATATATAGTTTTTGAA-AATATTTTGAAA
1647589 ATATATATAATATATAGTTTTTGAAAATATTTTGAAA
1 ATATATATAATATATAGTTTTTGAAAATATTTTGAAA
*
1647626 ATATATATAATATATAGTTTTT-CAAATCATTTTGAAA
1 ATATATATAATATATAGTTTTTGAAAAT-ATTTTGAAA
*
1647663 ATATAAATATAATATATAATTTTTGAAAATAT
1 ATAT--ATATAATATATAGTTTTTGAAAATAT
1647695 ATATTATATT
Statistics
Matches: 94, Mismatches: 6, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
36 20 0.21
37 49 0.52
38 2 0.02
39 19 0.20
40 4 0.04
ACGTcount: A:0.45, C:0.01, G:0.05, T:0.49
Consensus pattern (37 bp):
ATATATATAATATATAGTTTTTGAAAATATTTTGAAA
Found at i:1649020 original size:90 final size:88
Alignment explanation
Indices: 1648906--1649079 Score: 312
Period size: 89 Copynumber: 2.0 Consensus size: 88
1648896 TCCCAAATAT
*
1648906 TTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGATTAG
1 TTAAATTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAA-CCCTAATATGATTAG
1648971 GGTAACTTGGATATAAAAGGATTA
65 GGTAACTTGGATATAAAAGGATTA
1648995 TTAAATTCTAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAG
1 TTAAATTC-AATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAG
*
1649060 GGTAACTTGGCTATAAAAGG
65 GGTAACTTGGATATAAAAGG
1649080 GTGTGTAAGG
Statistics
Matches: 82, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
89 41 0.50
90 41 0.50
ACGTcount: A:0.45, C:0.06, G:0.11, T:0.37
Consensus pattern (88 bp):
TTAAATTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAGG
GTAACTTGGATATAAAAGGATTA
Found at i:1657863 original size:13 final size:13
Alignment explanation
Indices: 1657845--1657869 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1657835 TTTATTTAAT
1657845 ATATATAATATAC
1 ATATATAATATAC
1657858 ATATATAATATA
1 ATATATAATATA
1657870 TAGTTTTTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (13 bp):
ATATATAATATAC
Found at i:1657896 original size:28 final size:28
Alignment explanation
Indices: 1657858--1657976 Score: 134
Period size: 28 Copynumber: 4.0 Consensus size: 28
1657848 TATAATATAC
1657858 ATATATAATATATAGTTTTTGAAAATAT
1 ATATATAATATATAGTTTTTGAAAATAT
1657886 ATATATAATATATAGTTTTTGAAAATATTTTGAAAAT
1 ATATATAATATATAGTTTTTG-AAA-A---T----AT
1657923 ATATATAATATATAGTTTTTG-AAA-AT
1 ATATATAATATATAGTTTTTGAAAATAT
*
1657949 ATATATAATATATAGTTTTTTAAAATAT
1 ATATATAATATATAGTTTTTGAAAATAT
1657977 TTTGAAAAAA
Statistics
Matches: 79, Mismatches: 1, Indels: 22
0.77 0.01 0.22
Matches are distributed among these distances:
26 22 0.28
27 3 0.04
28 23 0.29
29 3 0.04
30 1 0.01
33 1 0.01
34 1 0.01
35 2 0.03
37 23 0.29
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.47
Consensus pattern (28 bp):
ATATATAATATATAGTTTTTGAAAATAT
Found at i:1657899 original size:37 final size:35
Alignment explanation
Indices: 1657858--1657962 Score: 109
Period size: 37 Copynumber: 3.1 Consensus size: 35
1657848 TATAATATAC
1657858 ATATATAATATATAGTTTTTG-AAA--AT----AT
1 ATATATAATATATAGTTTTTGAAAATTATGAAAAT
*
1657886 ATATATAATATATAGTTTTTGAAAATATTTTGAAAAT
1 ATATATAATATATAGTTTTTG-AAA-ATTATGAAAAT
*
1657923 ATATATAATATATAGTTTTTGAAAATATAT-ATAAT
1 ATATATAATATATAGTTTTTGAAAAT-TATGAAAAT
1657958 ATATA
1 ATATA
1657963 GTTTTTTAAA
Statistics
Matches: 64, Mismatches: 3, Indels: 13
0.80 0.04 0.16
Matches are distributed among these distances:
28 21 0.33
30 2 0.03
31 1 0.02
33 1 0.02
35 11 0.17
36 5 0.08
37 23 0.36
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.46
Consensus pattern (35 bp):
ATATATAATATATAGTTTTTGAAAATTATGAAAAT
Found at i:1657917 original size:39 final size:37
Alignment explanation
Indices: 1657874--1658028 Score: 170
Period size: 39 Copynumber: 4.4 Consensus size: 37
1657864 AATATATAGT
1657874 TTTTGAAAATATATATATAATATATAGTTTTTGAAAATA
1 TTTTG-AAA-ATATATATAATATATAGTTTTTGAAAATA
1657913 TTTTGAAAATATATATAATATATA------G----T-
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAATA
*
1657939 TTTTGAAAATATATATAATATATAGTTTTTTAAAATA
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAATA
* *
1657976 TTTTGAAAAAATAAATATAATATATAATTTTTGAAAATA
1 TTTTG--AAAATATATATAATATATAGTTTTTGAAAATA
1658015 TTTTGAAAATATAT
1 TTTTGAAAATATAT
1658029 TATATTTATG
Statistics
Matches: 98, Mismatches: 5, Indels: 28
0.75 0.04 0.21
Matches are distributed among these distances:
26 24 0.24
27 1 0.01
31 1 0.01
36 1 0.01
37 29 0.30
38 3 0.03
39 39 0.40
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (37 bp):
TTTTGAAAATATATATAATATATAGTTTTTGAAAATA
Found at i:1657942 original size:65 final size:66
Alignment explanation
Indices: 1657858--1658015 Score: 259
Period size: 65 Copynumber: 2.4 Consensus size: 66
1657848 TATAATATAC
1657858 ATATATAATATATAGTTTTTGAAAATATATATATAATATATAGTTTTTGAAAATATTTTG-AAAA
1 ATATATAATATATAGTTTTTGAAAATATATATATAATATATAGTTTTTGAAAATATTTTGAAAAA
1657922 T
66 T
*
1657923 ATATATAATATATAGTTTTTG-AAA-ATATATATAATATATAGTTTTTTAAAATATTTTGAAAAA
1 ATATATAATATATAGTTTTTGAAAATATATATATAATATATAGTTTTTGAAAATATTTTG-AAAA
1657986 AT
65 AT
* *
1657988 AAATATAATATATAATTTTTGAAAATAT
1 ATATATAATATATAGTTTTTGAAAATAT
1658016 TTTGAAAATA
Statistics
Matches: 86, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
63 33 0.38
64 3 0.03
65 45 0.52
66 3 0.03
67 2 0.02
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (66 bp):
ATATATAATATATAGTTTTTGAAAATATATATATAATATATAGTTTTTGAAAATATTTTGAAAAA
T
Found at i:1657959 original size:24 final size:26
Alignment explanation
Indices: 1657913--1657976 Score: 119
Period size: 26 Copynumber: 2.5 Consensus size: 26
1657903 TTTGAAAATA
1657913 TTTTGAAAATATATATAATATATAGT
1 TTTTGAAAATATATATAATATATAGT
1657939 TTTTGAAAATATATATAATATATAGT
1 TTTTGAAAATATATATAATATATAGT
*
1657965 TTTTTAAAATAT
1 TTTTGAAAATAT
1657977 TTTGAAAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (26 bp):
TTTTGAAAATATATATAATATATAGT
Found at i:1658070 original size:4 final size:4
Alignment explanation
Indices: 1658026--1658112 Score: 78
Period size: 4 Copynumber: 22.2 Consensus size: 4
1658016 TTTGAAAATA
*
1658026 TATT ATATT TATG TATT ATATT T-TAT TATT TA-T TATAT TATT TATT
1 TATT -TATT TATT TATT -TATT TAT-T TATT TATT TAT-T TATT TATT
*
1658072 TATT TA-T TATT TATT T-TT TATT TATT T-TT TATA T-TT TATT T
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT T
1658113 TGGTCTAAAT
Statistics
Matches: 69, Mismatches: 4, Indels: 19
0.75 0.04 0.21
Matches are distributed among these distances:
3 15 0.22
4 41 0.59
5 13 0.19
ACGTcount: A:0.26, C:0.00, G:0.01, T:0.72
Consensus pattern (4 bp):
TATT
Found at i:1658108 original size:18 final size:18
Alignment explanation
Indices: 1658024--1658112 Score: 72
Period size: 18 Copynumber: 4.7 Consensus size: 18
1658014 ATTTTGAAAA
* * *
1658024 TATATTATATTTATGTAT
1 TATATTTTATTTATTTTT
1658042 TATATTTTA-TTATTTATT
1 TATATTTTATTTATTT-TT
*
1658060 ATATTATTTATTTATTTATTATT
1 -TA-TA--T-TTTATTTATTTTT
*
1658083 TATTTTTTATTTATTTTT
1 TATATTTTATTTATTTTT
1658101 TATATTTTATTT
1 TATATTTTATTT
1658113 TGGTCTAAAT
Statistics
Matches: 57, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
17 5 0.09
18 32 0.56
19 3 0.05
20 2 0.04
21 1 0.02
22 3 0.05
23 6 0.11
24 5 0.09
ACGTcount: A:0.27, C:0.00, G:0.01, T:0.72
Consensus pattern (18 bp):
TATATTTTATTTATTTTT
Found at i:1685284 original size:17 final size:17
Alignment explanation
Indices: 1685264--1685307 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
1685254 TTTTATAAAA
* *
1685264 AAAATAATATGGTGACT
1 AAAATAAGAAGGTGACT
1685281 AAAATAAGAAGGTGACT
1 AAAATAAGAAGGTGACT
1685298 AAAATAAGAA
1 AAAATAAGAA
1685308 AGAGACAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.57, C:0.05, G:0.18, T:0.20
Consensus pattern (17 bp):
AAAATAAGAAGGTGACT
Found at i:1685727 original size:2 final size:2
Alignment explanation
Indices: 1685722--1685756 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
1685712 TGGGCGTGTG
1685722 TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1685757 CATAAAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1688988 original size:221 final size:221
Alignment explanation
Indices: 1688605--1689044 Score: 837
Period size: 221 Copynumber: 2.0 Consensus size: 221
1688595 ATGACACCAT
1688605 CTGAAACGTTGTTTAAGAAGAAACCAGAGTATGATTCGTTAAAAGTATTCGGGTGTCAATGCTTC
1 CTGAAACGTTGTTTAAGAAGAAACCAGAGTATGATTCGTTAAAAGTATTCGGGTGTCAATGCTTC
1688670 CTACATTGAGACTATTTCAGAATCACGAATTAGATTTTCGATTACAACCGTGCACTTACCTTGGC
66 CTACATTGAGACTATTTCAGAATCACGAATTAGATTTTCGATTACAACCGTGCACTTACCTTGGC
1688735 TTCAAACCCCCAGTACAAAGGATATAGTGCCTTGCGAGTGATGGTAGGGTGTATATATCACGTCA
131 TTCAAACCCCCAGTACAAAGGATATAGTGCCTTGCGAGTGATGGTAGGGTGTATATATCACGTCA
1688800 TGTCATGTTTAACGAGATGATCTTTC
196 TGTCATGTTTAACGAGATGATCTTTC
1688826 CTGAAACGTTGTTTAAGAAGAAACCAGAGTATGATTCGTTAAAAGTATTCGGGTGTCAATGCTTC
1 CTGAAACGTTGTTTAAGAAGAAACCAGAGTATGATTCGTTAAAAGTATTCGGGTGTCAATGCTTC
*
1688891 CTACATTTGAGACTATTTCAGAATCACGAATTAGATTTTCGATTACAACCGTGTACTTACCTTGG
66 CTACA-TTGAGACTATTTCAGAATCACGAATTAGATTTTCGATTACAACCGTGCACTTACCTTGG
*
1688956 CTTC-AACCCCCAGTACAAAGGATATAGTGCCTTGCGAGTGATGGTAGGGTGTATATATCATGTC
130 CTTCAAACCCCCAGTACAAAGGATATAGTGCCTTGCGAGTGATGGTAGGGTGTATATATCACGTC
*
1689020 ATGTCTTGTTTAACGAGATGATCTT
195 ATGTCATGTTTAACGAGATGATCTT
1689045 CCCTTTGCAG
Statistics
Matches: 215, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
221 153 0.71
222 62 0.29
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (221 bp):
CTGAAACGTTGTTTAAGAAGAAACCAGAGTATGATTCGTTAAAAGTATTCGGGTGTCAATGCTTC
CTACATTGAGACTATTTCAGAATCACGAATTAGATTTTCGATTACAACCGTGCACTTACCTTGGC
TTCAAACCCCCAGTACAAAGGATATAGTGCCTTGCGAGTGATGGTAGGGTGTATATATCACGTCA
TGTCATGTTTAACGAGATGATCTTTC
Found at i:1689083 original size:18 final size:18
Alignment explanation
Indices: 1689057--1689095 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
1689047 CTTTGCAGTT
*
1689057 AAAGCAGTGCCTTGTTCG
1 AAAGCAGTGCCTTATTCG
*
1689075 AAAGTAGTGCCTTATTCG
1 AAAGCAGTGCCTTATTCG
1689093 AAA
1 AAA
1689096 AGTCATTGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (18 bp):
AAAGCAGTGCCTTATTCG
Found at i:1696634 original size:119 final size:119
Alignment explanation
Indices: 1696423--1696662 Score: 480
Period size: 119 Copynumber: 2.0 Consensus size: 119
1696413 ATGACCTACT
1696423 TCACGTGCAAGCAAGCCTTAATTATTCTAACAGCCACCAGCCGCCTTTCCTATTTTAAGTCTGGG
1 TCACGTGCAAGCAAGCCTTAATTATTCTAACAGCCACCAGCCGCCTTTCCTATTTTAAGTCTGGG
1696488 CATTTAATAACAGCTACTTAAGGAAACTCCAAAAGCATGCAAAGCCCTAGGAGA
66 CATTTAATAACAGCTACTTAAGGAAACTCCAAAAGCATGCAAAGCCCTAGGAGA
1696542 TCACGTGCAAGCAAGCCTTAATTATTCTAACAGCCACCAGCCGCCTTTCCTATTTTAAGTCTGGG
1 TCACGTGCAAGCAAGCCTTAATTATTCTAACAGCCACCAGCCGCCTTTCCTATTTTAAGTCTGGG
1696607 CATTTAATAACAGCTACTTAAGGAAACTCCAAAAGCATGCAAAGCCCTAGGAGA
66 CATTTAATAACAGCTACTTAAGGAAACTCCAAAAGCATGCAAAGCCCTAGGAGA
1696661 TC
1 TC
1696663 TTTCCTTATA
Statistics
Matches: 121, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
119 121 1.00
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.25
Consensus pattern (119 bp):
TCACGTGCAAGCAAGCCTTAATTATTCTAACAGCCACCAGCCGCCTTTCCTATTTTAAGTCTGGG
CATTTAATAACAGCTACTTAAGGAAACTCCAAAAGCATGCAAAGCCCTAGGAGA
Found at i:1699945 original size:47 final size:47
Alignment explanation
Indices: 1699876--1699970 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
1699866 GTAGTTGCAT
1699876 GAGTTTTAGTGGCGGAGAAACCTACTGGGTGTATTGGAAGCTTATCG
1 GAGTTTTAGTGGCGGAGAAACCTACTGGGTGTATTGGAAGCTTATCG
1699923 GAGTTTTAGTGGCGGAGAAACCTACTGGGTGTATTGGAAGCTTATCG
1 GAGTTTTAGTGGCGGAGAAACCTACTGGGTGTATTGGAAGCTTATCG
1699970 G
1 G
1699971 GTGAAATGAG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.23, C:0.13, G:0.35, T:0.29
Consensus pattern (47 bp):
GAGTTTTAGTGGCGGAGAAACCTACTGGGTGTATTGGAAGCTTATCG
Found at i:1702938 original size:58 final size:58
Alignment explanation
Indices: 1702843--1702965 Score: 237
Period size: 58 Copynumber: 2.1 Consensus size: 58
1702833 TGTTTGAGTT
*
1702843 GACTAGTAAGGCTAAGGTGAGTGTATACTATTAGATATATAGTGTTTTATGGAAATAA
1 GACTTGTAAGGCTAAGGTGAGTGTATACTATTAGATATATAGTGTTTTATGGAAATAA
1702901 GACTTGTAAGGCTAAGGTGAGTGTATACTATTAGATATATAGTGTTTTATGGAAATAA
1 GACTTGTAAGGCTAAGGTGAGTGTATACTATTAGATATATAGTGTTTTATGGAAATAA
1702959 GACTTGT
1 GACTTGT
1702966 GATAAGTCTA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 64 1.00
ACGTcount: A:0.34, C:0.06, G:0.24, T:0.36
Consensus pattern (58 bp):
GACTTGTAAGGCTAAGGTGAGTGTATACTATTAGATATATAGTGTTTTATGGAAATAA
Found at i:1703331 original size:21 final size:22
Alignment explanation
Indices: 1703305--1703399 Score: 99
Period size: 21 Copynumber: 4.4 Consensus size: 22
1703295 TTCTACGCGA
1703305 TCCTTCGGGACA-TATATGTGG
1 TCCTTCGGGACATTATATGTGG
**
1703326 TCCTTCGGGA-ATTTTATACATGG
1 TCCTTCGGGACA--TTATATGTGG
*
1703349 TCCTTCAGGACA-TATATGTGG
1 TCCTTCGGGACATTATATGTGG
*
1703370 TCCTTCGGGACATTTTATGTGG
1 TCCTTCGGGACATTATATGTGG
1703392 -CACTTCGG
1 TC-CTTCGG
1703400 TGCATTTTTA
Statistics
Matches: 61, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
20 1 0.02
21 29 0.48
22 14 0.23
23 16 0.26
24 1 0.02
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.36
Consensus pattern (22 bp):
TCCTTCGGGACATTATATGTGG
Found at i:1703434 original size:22 final size:23
Alignment explanation
Indices: 1703392--1703436 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1703382 TTTTATGTGG
*
1703392 CACTTCGGTGCATTTTTATACGA
1 CACTTCGGTGCATATTTATACGA
*
1703415 CACTTTGGTGCA-ATTTATACGA
1 CACTTCGGTGCATATTTATACGA
1703437 GCTGTGGTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.38
Consensus pattern (23 bp):
CACTTCGGTGCATATTTATACGA
Found at i:1703876 original size:41 final size:41
Alignment explanation
Indices: 1703799--1703881 Score: 157
Period size: 42 Copynumber: 2.0 Consensus size: 41
1703789 TAATCGATTT
1703799 AAGAGTACCCCTAAAGTTCAGAAAAGATGTTAAAAAATGAA
1 AAGAGTACCCCTAAAGTTCAGAAAAGATGTTAAAAAATGAA
1703840 AAGAGTACCCCTAAAAGTTCAGAAAAGATGTTAAAAAATGAA
1 AAGAGTACCCCT-AAAGTTCAGAAAAGATGTTAAAAAATGAA
1703882 GTACTGAATT
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 12 0.29
42 29 0.71
ACGTcount: A:0.52, C:0.12, G:0.17, T:0.19
Consensus pattern (41 bp):
AAGAGTACCCCTAAAGTTCAGAAAAGATGTTAAAAAATGAA
Found at i:1705456 original size:73 final size:74
Alignment explanation
Indices: 1705356--1705528 Score: 178
Period size: 73 Copynumber: 2.4 Consensus size: 74
1705346 AAATAAAGAA
* * **
1705356 TAAAAATAATATATAATAT-TATATATATAAATATAT-TTTTTAAAAAC-TATATGACATA-TTT
1 TAAAAA-ACTATATTATATATATATATATAAATA-ATGTTTAGAAAAACATATATGACATATTTT
*
1705417 TCCAAATGTTTT
64 TCAAAATG-TTT
* * *
1705429 TAAAAAACTATATTATATATATATATATATATAATGTTTAGAAAAACTATATATTATATATTTTT
1 TAAAAAACTATATTATATATATATATATAAATAATGTTTAGAAAAAC-ATATATGACATA-TTTT
1705494 TCAAAATGTTT
64 TCAAAATGTTT
*
1705505 TGAAAAACTATA-TAT-TATATATAT
1 TAAAAAACTATATTATATATATATAT
1705529 GTTTTCAAAA
Statistics
Matches: 85, Mismatches: 9, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
72 12 0.14
73 28 0.33
74 9 0.11
75 12 0.14
76 14 0.16
77 10 0.12
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (74 bp):
TAAAAAACTATATTATATATATATATATAAATAATGTTTAGAAAAACATATATGACATATTTTTC
AAAATGTTT
Found at i:1705502 original size:37 final size:38
Alignment explanation
Indices: 1705427--1705562 Score: 172
Period size: 37 Copynumber: 3.6 Consensus size: 38
1705417 TCCAAATGTT
* * *
1705427 TTTA-AAAAACTATATTATATATATATATATAT-ATAATG
1 TTTAGAAAAACTATA-TAT-TATATATATTTTTCAAAATG
1705465 TTTAGAAAAACTATATATTATATAT-TTTTTCAAAATG
1 TTTAGAAAAACTATATATTATATATATTTTTCAAAATG
*
1705502 TTTTGAAAAACTATATATTATATATATGTTTTCAAAATG
1 TTTAGAAAAACTATATATTATATATAT-TTTTCAAAATG
*
1705541 -TTATAAAAACTATATATTATAT
1 TTTAGAAAAACTATATATTATAT
1705563 CTTATATATG
Statistics
Matches: 88, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
36 3 0.03
37 36 0.41
38 28 0.32
39 21 0.24
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (38 bp):
TTTAGAAAAACTATATATTATATATATTTTTCAAAATG
Found at i:1710735 original size:35 final size:35
Alignment explanation
Indices: 1710696--1710767 Score: 101
Period size: 35 Copynumber: 2.1 Consensus size: 35
1710686 AGGATAAAAC
* *
1710696 AAAGTAATGAGTGAAATAAAATTGAA-TTCAAAAGA
1 AAAGTAATGAATGAAAGAAAATT-AAGTTCAAAAGA
*
1710731 AAAGTATTGAATGAAAGAAAATTAAGTTCAAAAGA
1 AAAGTAATGAATGAAAGAAAATTAAGTTCAAAAGA
1710766 AA
1 AA
1710768 TAAGAAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
34 2 0.06
35 31 0.94
ACGTcount: A:0.58, C:0.03, G:0.17, T:0.22
Consensus pattern (35 bp):
AAAGTAATGAATGAAAGAAAATTAAGTTCAAAAGA
Found at i:1714332 original size:18 final size:20
Alignment explanation
Indices: 1714309--1714346 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1714299 AAAAAAATGA
1714309 AATGCAAG-T-TATGAAAAT
1 AATGCAAGATGTATGAAAAT
*
1714327 AATGCATGATGTATGAAAAT
1 AATGCAAGATGTATGAAAAT
1714347 TTATAGGCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.41
19 1 0.06
20 9 0.53
ACGTcount: A:0.47, C:0.05, G:0.18, T:0.29
Consensus pattern (20 bp):
AATGCAAGATGTATGAAAAT
Found at i:1715051 original size:77 final size:77
Alignment explanation
Indices: 1714959--1715112 Score: 308
Period size: 77 Copynumber: 2.0 Consensus size: 77
1714949 TGGGTATCAG
1714959 CATCCAACTTCCACTGGAATCTTTCAGCCTTGAGTTCCTTTAGACTTTGTTTCATCTCCTACTTT
1 CATCCAACTTCCACTGGAATCTTTCAGCCTTGAGTTCCTTTAGACTTTGTTTCATCTCCTACTTT
1715024 TCAGCTTCAAAA
66 TCAGCTTCAAAA
1715036 CATCCAACTTCCACTGGAATCTTTCAGCCTTGAGTTCCTTTAGACTTTGTTTCATCTCCTACTTT
1 CATCCAACTTCCACTGGAATCTTTCAGCCTTGAGTTCCTTTAGACTTTGTTTCATCTCCTACTTT
1715101 TCAGCTTCAAAA
66 TCAGCTTCAAAA
1715113 TCTTTCCTTA
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 77 1.00
ACGTcount: A:0.22, C:0.29, G:0.10, T:0.39
Consensus pattern (77 bp):
CATCCAACTTCCACTGGAATCTTTCAGCCTTGAGTTCCTTTAGACTTTGTTTCATCTCCTACTTT
TCAGCTTCAAAA
Found at i:1715748 original size:153 final size:152
Alignment explanation
Indices: 1715437--1715749 Score: 592
Period size: 153 Copynumber: 2.0 Consensus size: 152
1715427 TGGGTGTAAT
1715437 TCAATCACTTTTTGGCTTACAACAAATCCCAAAAGTTTACCAGAGGTCACCCCAAATGTACACTT
1 TCAATCACTTTTTGGCTTACAACAAATCCCAAAAGTTTACCAGAGGTCACCCCAAATGTACACTT
1715502 ATTTAGATTGAGCTTTAATTGACATTCCCTTAATCTTGGAAAGCTTCCTAGAATTCTCAACATGC
66 ATTTAGATTGAGCTTTAATTGACATTCCCTTAATCTTGGAAAGCTTCCTAGAATTCTCAACATGC
1715567 TCTTCTTCGGACTTGGCTTTAA
131 TCTTCTTCGGACTTGGCTTTAA
1715589 TTCAATCACTTTTTGGCTTACAACAAATCCCAAAAGTTTACCAGAGGTCACCCCAAATGTACACT
1 -TCAATCACTTTTTGGCTTACAACAAATCCCAAAAGTTTACCAGAGGTCACCCCAAATGTACACT
1715654 TATTTAGATTGAGCTTTAATTGACATTCCCTTAATCTTTGGAAAAGCTTCCTAGAATTCTCAACA
65 TATTTAGATTGAGCTTTAATTGACATTCCCTTAATC-TTGG-AAAGCTTCCTAGAATTCTCAACA
1715719 TGCTCTTCTTCGGACTTGGCTTTAA
128 TGCTCTTCTTCGGACTTGGCTTTAA
1715744 -CAATCA
1 TCAATCA
1715750 TATCATCGAC
Statistics
Matches: 158, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
153 106 0.67
154 4 0.03
155 48 0.30
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34
Consensus pattern (152 bp):
TCAATCACTTTTTGGCTTACAACAAATCCCAAAAGTTTACCAGAGGTCACCCCAAATGTACACTT
ATTTAGATTGAGCTTTAATTGACATTCCCTTAATCTTGGAAAGCTTCCTAGAATTCTCAACATGC
TCTTCTTCGGACTTGGCTTTAA
Found at i:1716485 original size:145 final size:145
Alignment explanation
Indices: 1716222--1716513 Score: 584
Period size: 145 Copynumber: 2.0 Consensus size: 145
1716212 CTGGCTTACA
1716222 TTATGATTTTATTGGTAACTTGTGTACTACCAATTCTATATCCAATCCTGGCATGTCCTCGTATG
1 TTATGATTTTATTGGTAACTTGTGTACTACCAATTCTATATCCAATCCTGGCATGTCCTCGTATG
1716287 ACCAAGCAAATACATCCTTGTATTCTTGCAGCAACTCAATCAAATCATGTCACCCTTTATCAGAT
66 ACCAAGCAAATACATCCTTGTATTCTTGCAGCAACTCAATCAAATCATGTCACCCTTTATCAGAT
1716352 AAAGTGGTACCAATT
131 AAAGTGGTACCAATT
1716367 TTATGATTTTATTGGTAACTTGTGTACTACCAATTCTATATCCAATCCTGGCATGTCCTCGTATG
1 TTATGATTTTATTGGTAACTTGTGTACTACCAATTCTATATCCAATCCTGGCATGTCCTCGTATG
1716432 ACCAAGCAAATACATCCTTGTATTCTTGCAGCAACTCAATCAAATCATGTCACCCTTTATCAGAT
66 ACCAAGCAAATACATCCTTGTATTCTTGCAGCAACTCAATCAAATCATGTCACCCTTTATCAGAT
1716497 AAAGTGGTACCAATT
131 AAAGTGGTACCAATT
1716512 TT
1 TT
1716514 CATCTCCTTC
Statistics
Matches: 147, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
145 147 1.00
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.35
Consensus pattern (145 bp):
TTATGATTTTATTGGTAACTTGTGTACTACCAATTCTATATCCAATCCTGGCATGTCCTCGTATG
ACCAAGCAAATACATCCTTGTATTCTTGCAGCAACTCAATCAAATCATGTCACCCTTTATCAGAT
AAAGTGGTACCAATT
Found at i:1725078 original size:8 final size:8
Alignment explanation
Indices: 1725049--1725121 Score: 52
Period size: 8 Copynumber: 9.9 Consensus size: 8
1725039 AAATTATATT
1725049 TATTGATAA
1 TATT-ATAA
1725058 T-TT-TAA
1 TATTATAA
*
1725064 TAATATAA
1 TATTATAA
1725072 TATTAT-A
1 TATTATAA
* *
1725079 T-TTTTAT
1 TATTATAA
*
1725086 TGTTAT-A
1 TATTATAA
1725093 -ATTATAA
1 TATTATAA
1725100 TATTATAA
1 TATTATAA
1725108 TA-TATAA
1 TATTATAA
1725115 TATTATA
1 TATTATA
1725122 CTTTATATTT
Statistics
Matches: 50, Mismatches: 7, Indels: 15
0.69 0.10 0.21
Matches are distributed among these distances:
6 11 0.22
7 12 0.24
8 26 0.52
9 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (8 bp):
TATTATAA
Found at i:1725128 original size:36 final size:36
Alignment explanation
Indices: 1725054--1725141 Score: 101
Period size: 36 Copynumber: 2.5 Consensus size: 36
1725044 ATATTTATTG
* *
1725054 ATAATTTTAATAATATAATATTATATTTTTATTGTT
1 ATAATTTTAATAATATAATATTATATTTATACTGTT
* *
1725090 ATAATTATAATATTATAATA-TATAATATTATACT-TT
1 ATAATTTTAATAATATAATATTAT-AT-TTATACTGTT
1725126 AT-ATTTTAATAATATA
1 ATAATTTTAATAATATA
1725142 TAAAAATTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
35 15 0.34
36 24 0.55
37 5 0.11
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (36 bp):
ATAATTTTAATAATATAATATTATATTTATACTGTT
Found at i:1725320 original size:35 final size:36
Alignment explanation
Indices: 1725274--1725381 Score: 112
Period size: 35 Copynumber: 2.9 Consensus size: 36
1725264 GTTTTAATAA
*
1725274 TATTATTATTTTAATAAGTAATTAATATAA-TT-AAT
1 TATT-TTATTTTAATAAATAATTAATATAATTTAAAT
*
1725309 TATTCTTATTTTAATAAATAATTTATATAATTTACAAT
1 TATT-TTATTTTAATAAATAATTAATATAATTTA-AAT
* *
1725347 TACTTTATTTTAATAAAATATAATAATACTAATTT
1 TATTTTATTTTAAT-AAATA-ATTAATA-TAATTT
1725382 TTTTATTTAT
Statistics
Matches: 61, Mismatches: 6, Indels: 7
0.82 0.08 0.09
Matches are distributed among these distances:
35 27 0.44
36 2 0.03
37 10 0.16
38 11 0.18
39 5 0.08
40 6 0.10
ACGTcount: A:0.44, C:0.04, G:0.01, T:0.51
Consensus pattern (36 bp):
TATTTTATTTTAATAAATAATTAATATAATTTAAAT
Found at i:1737981 original size:22 final size:22
Alignment explanation
Indices: 1737939--1737981 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1737929 ATAAATTTTA
*
1737939 TTTTAATTCAAATTATTATAGT
1 TTTTAATTCAAATTATCATAGT
*
1737961 TTTTAAATTTAAATT-TCATAG
1 TTTT-AATTCAAATTATCATAG
1737982 GCTGTATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.53
Consensus pattern (22 bp):
TTTTAATTCAAATTATCATAGT
Found at i:1739101 original size:18 final size:18
Alignment explanation
Indices: 1739078--1739120 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
1739068 CTTTAGATTA
*
1739078 TTTATTTAATTATTTTCT
1 TTTATTTAATTATTATCT
*
1739096 TTTATTTAATTCTTATCT
1 TTTATTTAATTATTATCT
1739114 TTTATTT
1 TTTATTT
1739121 TAAAAATAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:1739191 original size:16 final size:14
Alignment explanation
Indices: 1739169--1739220 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 14
1739159 GCTATTATTA
1739169 TTTATTTTGTTATAT
1 TTTATTTTGTT-TAT
1739184 TTTCA-TTT-TTTAT
1 TTT-ATTTTGTTTAT
1739197 TTTATTTTGTTTTAT
1 TTTATTTTG-TTTAT
1739212 CTTTATTTT
1 -TTTATTTT
1739221 CCCACTTCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
12 1 0.03
13 9 0.28
14 2 0.06
15 11 0.34
16 9 0.28
ACGTcount: A:0.15, C:0.04, G:0.04, T:0.77
Consensus pattern (14 bp):
TTTATTTTGTTTAT
Found at i:1739267 original size:10 final size:10
Alignment explanation
Indices: 1739229--1739279 Score: 54
Period size: 10 Copynumber: 5.3 Consensus size: 10
1739219 TTCCCACTTC
1739229 TTTTTTAT-T
1 TTTTTTATAT
1739238 TTTATTT-TAT
1 TTT-TTTATAT
* *
1739248 CTTTTAATAT
1 TTTTTTATAT
1739258 TTTTTTATAT
1 TTTTTTATAT
1739268 TTTTTTAT-T
1 TTTTTTATAT
1739277 TTT
1 TTT
1739280 ATTTTCTGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
9 10 0.29
10 25 0.71
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTTTTATAT
Found at i:1739276 original size:18 final size:20
Alignment explanation
Indices: 1739227--1739282 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
1739217 TTTTCCCACT
*
1739227 TCTTTTTTATTTTTATTTTA
1 TCTTTTTTATTTTTATTATA
*
1739247 TCTTTTAATATTTTT-TTATA
1 TCTTTT-TTATTTTTATTATA
1739267 T-TTTTTTATTTTTATT
1 TCTTTTTTATTTTTATT
1739283 TTCTGAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 7 0.23
19 6 0.19
20 11 0.35
21 7 0.23
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.79
Consensus pattern (20 bp):
TCTTTTTTATTTTTATTATA
Found at i:1747540 original size:271 final size:269
Alignment explanation
Indices: 1747054--1747656 Score: 831
Period size: 271 Copynumber: 2.2 Consensus size: 269
1747044 GGATATCTAA
* * * * *
1747054 TTCATAGCTCAACTTCACAAAAAAGGAGCCACCTATGATTTTGACTTCACAACAAAGGATATCGT
1 TTCAAAGCTCAACTTCACAAAGAATGAGCCACCTACGATTTTGACTTCACAACGAAGGATATCGT
* * ** *
1747119 ACCCAAAGATTGACCTTACTTCACGATGAATGAGTCATCTGTAACACAACAATGAAAAACCAGTT
66 ACCAAAAAATTGACCCAACTTCACGATGAATGAGTCATATGTAACACAACAATGAAAAACCAGTT
*
1747184 TCATACCAAAGTCTTCAGGTCAAATTTCAGCTTCACAACGAAGTATATTGGGCTAGAAGACGATA
131 TCATACCAAAGTCTTCAGGTCAAATTTCAGCTTCACAACGAAGTATATTAGGCTAGAAGACGATA
* * * *
1747249 TAGGAGCGACTTTCCAATGCTTTGAGCCCAGTTTTAACTTCAC-AACTAAGGATATCGTGCTCAT
196 CAGGAGAGACTTTCCAATGCTTTGAGCCCAGTTTCAACTTCACGAA-GAAGGATATCGTGCTCA-
*
1747313 GAATTTTT-AT
259 GAATTTTTCAG
* * * *
1747323 TTCAAAGCTCAACTACACAATGAATGAGTCACCTACGATTTTGACTTCATAACGAAGGATATCGT
1 TTCAAAGCTCAACTTCACAAAGAATGAGCCACCTACGATTTTGACTTCACAACGAAGGATATCGT
1747388 ACCAAAACAATTGACCCAACTTCACGATGAA-GAAGTCATATGTAACACAACAAT-AAAAACACT
66 ACCAAAA-AATTGACCCAACTTCACGATGAATG-AGTCATATGTAACACAACAATGAAAAAC-C-
*
1747451 AGTTTCATACCAAAGTCTTCAGGTCAAATTTCAGCTTCACGACGAAGTATATTAGGCTAGAAGAC
127 AGTTTCATACCAAAGTCTTCAGGTCAAATTTCAGCTTCACAACGAAGTATATTAGGCTAGAAGAC
* *
1747516 GATACAGGAGAGACTTTTCAATGCTTTGAGCCCGGTTTCAACTTCACGAAGAAGGATATCGTGCT
192 GATACAGGAGAGACTTTCCAATGCTTTGAGCCCAGTTTCAACTTCACGAAGAAGGATATCGTGCT
*
1747581 CAGGATTTTTCAG
257 CAGAATTTTTCAG
** * **
1747594 TTCAAAATTCAACTTCACAACGAATGAGCCA-CTCACGATTTCAACTTCACGAA-GAAGGATATC
1 TTCAAAGCTCAACTTCACAAAGAATGAGCCACCT-ACGATTTTGACTTCAC-AACGAAGGATATC
1747657 ATGCTCAATG
Statistics
Matches: 294, Mismatches: 32, Indels: 14
0.86 0.09 0.04
Matches are distributed among these distances:
269 69 0.23
270 50 0.17
271 171 0.58
272 4 0.01
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (269 bp):
TTCAAAGCTCAACTTCACAAAGAATGAGCCACCTACGATTTTGACTTCACAACGAAGGATATCGT
ACCAAAAAATTGACCCAACTTCACGATGAATGAGTCATATGTAACACAACAATGAAAAACCAGTT
TCATACCAAAGTCTTCAGGTCAAATTTCAGCTTCACAACGAAGTATATTAGGCTAGAAGACGATA
CAGGAGAGACTTTCCAATGCTTTGAGCCCAGTTTCAACTTCACGAAGAAGGATATCGTGCTCAGA
ATTTTTCAG
Found at i:1748513 original size:18 final size:18
Alignment explanation
Indices: 1748490--1748532 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
1748480 CTTTAGATTA
*
1748490 TTTATTTAATTATTTTCT
1 TTTATTTAATTATTATCT
*
1748508 TTTATTTAATTCTTATCT
1 TTTATTTAATTATTATCT
1748526 TTTATTT
1 TTTATTT
1748533 TTAAAACAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:1748683 original size:17 final size:17
Alignment explanation
Indices: 1748633--1748685 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
1748623 TCCCACTTCG
1748633 TTTT-TATTTTATT-TT
1 TTTTATATTTTATTATT
* **
1748648 ATTTTATCTTTTAACATT
1 -TTTTATATTTTATTATT
1748666 TTTTATATTTTATTATT
1 TTTTATATTTTATTATT
1748683 TTT
1 TTT
1748686 CTTTTCTGAA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
16 4 0.14
17 23 0.79
18 2 0.07
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTATATTTTATTATT
Found at i:1750410 original size:21 final size:22
Alignment explanation
Indices: 1750374--1750424 Score: 79
Period size: 21 Copynumber: 2.4 Consensus size: 22
1750364 AAATTAATGA
1750374 ATCAATTTTCAAATTCGAATTTT
1 ATCAA-TTTCAAATTCGAATTTT
1750397 ATCAATTT-AAATTCGAATTTT
1 ATCAATTTCAAATTCGAATTTT
1750418 AT-AATTT
1 ATCAATTT
1750425 GTTTGTTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.18
21 15 0.54
22 3 0.11
23 5 0.18
ACGTcount: A:0.37, C:0.10, G:0.04, T:0.49
Consensus pattern (22 bp):
ATCAATTTCAAATTCGAATTTT
Found at i:1751052 original size:2 final size:2
Alignment explanation
Indices: 1751045--1751077 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1751035 AAATGAATAC
1751045 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1751078 GTCTTGCATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1752390 original size:15 final size:15
Alignment explanation
Indices: 1752366--1752422 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
1752356 AACCGGGTAT
1752366 CGGGTACCCGATTAC
1 CGGGTACCCGATTAC
* ** *
1752381 CGGATACCCGCAAAATT
1 CGGGTACCCG-ATTA-C
1752398 CGGGTACCCGATTAC
1 CGGGTACCCGATTAC
1752413 CGGGTACCCG
1 CGGGTACCCG
1752423 TAACATTCGG
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
15 19 0.59
16 4 0.12
17 9 0.28
ACGTcount: A:0.23, C:0.33, G:0.26, T:0.18
Consensus pattern (15 bp):
CGGGTACCCGATTAC
Found at i:1752406 original size:32 final size:32
Alignment explanation
Indices: 1752365--1752434 Score: 113
Period size: 32 Copynumber: 2.2 Consensus size: 32
1752355 AAACCGGGTA
1752365 TCGGGTACCCGATTACCGGATACCCGCAAAAT
1 TCGGGTACCCGATTACCGGATACCCGCAAAAT
* * *
1752397 TCGGGTACCCGATTACCGGGTACCCGTAACAT
1 TCGGGTACCCGATTACCGGATACCCGCAAAAT
1752429 TCGGGT
1 TCGGGT
1752435 CGGGACACGG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.23, C:0.30, G:0.26, T:0.21
Consensus pattern (32 bp):
TCGGGTACCCGATTACCGGATACCCGCAAAAT
Found at i:1753045 original size:7 final size:7
Alignment explanation
Indices: 1753033--1753057 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1753023 TGTTAGGAAA
1753033 AAAAAAT
1 AAAAAAT
1753040 AAAAAAT
1 AAAAAAT
1753047 AAAAAAT
1 AAAAAAT
1753054 AAAA
1 AAAA
1753058 TAGATAAAAT
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:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:1755514 original size:104 final size:103
Alignment explanation
Indices: 1755334--1755670 Score: 409
Period size: 104 Copynumber: 3.3 Consensus size: 103
1755324 ATCCTCCGTC
* * * * *
1755334 GTGAAGTTGAAATTGGCTCTGGAACTGGAAAATTATTTGTTGACAGTCAGCCGCCCCTTCGCCGT
1 GTGAAGTTGAAATTGGATCTGAAATTGG-GAATTATTTGTTGACAATCAGCCGCCCCTTCGCCGT
1755399 GAAGTTGAGCTTGTGTTGTCTTGGGTCCAATATCTTCAT
65 GAAGTTGAGCTTGTGTTGTCTTGGGTCCAATATCTTCAT
* * *
1755438 GTGAAGGTGAAATTGGATCTGAAATTGGGGAATTATTTGTTGACAATCAGCCACCCCTTCGCCCT
1 GTGAAGTTGAAATTGGATCTGAAATT-GGGAATTATTTGTTGACAATCAGCCGCCCCTTCGCCGT
* *
1755503 GAAGTTGAGCTTGTGCTGTCTTGAGTCCAATATCCTTCATT
65 GAAGTTGAGCTTGTGTTGTCTTGGGTCCAATAT-CTTCA-T
* * * *
1755544 GTGAAGTTGAAATT-GACTCTGAAA----G--TTGTTTGTTGACAATCAACTGCCCCTTCGTCGT
1 GTGAAGTTGAAATTGGA-TCTGAAATTGGGAATTATTTGTTGACAATCAGCCGCCCCTTCGCCGT
*
1755602 GAAGTTGAGCTTGTGTTGTCTTGGGTCCAATATCATTCGCT
65 GAAGTTGAGCTTGTGTTGTCTTGGGTCCAATATC-TTC-AT
* *
1755643 GTGAAGTTGAAATTGGTTATGAAATTGG
1 GTGAAGTTGAAATTGGATCTGAAATTGG
1755671 AAAGCCCCTT
Statistics
Matches: 200, Mismatches: 22, Indels: 23
0.82 0.09 0.09
Matches are distributed among these distances:
98 1 0.00
99 82 0.41
100 1 0.00
101 1 0.00
104 85 0.43
105 9 0.05
106 21 0.10
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (103 bp):
GTGAAGTTGAAATTGGATCTGAAATTGGGAATTATTTGTTGACAATCAGCCGCCCCTTCGCCGTG
AAGTTGAGCTTGTGTTGTCTTGGGTCCAATATCTTCAT
Found at i:1755666 original size:99 final size:99
Alignment explanation
Indices: 1755365--1755658 Score: 378
Period size: 99 Copynumber: 2.9 Consensus size: 99
1755355 GAACTGGAAA
*
1755365 ATTATTTGTTGACAGTCAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGTTGTCTTGGGTCCAAT
1 ATTATTTGTTGACAATCAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGTTGTCTTGGGTCCAAT
*
1755430 ATCTTCATGTGAAGGTGAAATTGGATCTGAAATTGGGG
66 ATCTTCATGTGAAGTTGAAATTGGATCTGAAA----GG
* * * *
1755468 AATTATTTGTTGACAATCAGCCACCCCTTCGCCCTGAAGTTGAGCTTGTGCTGTCTTGAGTCCAA
1 -ATTATTTGTTGACAATCAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGTTGTCTTGGGTCCAA
1755533 TATCCTTCATTGTGAAGTTGAAATT-GACTCTGAAA-G
65 TAT-CTTCA-TGTGAAGTTGAAATTGGA-TCTGAAAGG
* * * *
1755569 -TTGTTTGTTGACAATCAACTGCCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTGGGTCCAAT
1 ATTATTTGTTGACAATCAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGTTGTCTTGGGTCCAAT
*
1755633 ATCATTCGCTGTGAAGTTGAAATTGG
66 ATC-TTC-ATGTGAAGTTGAAATTGG
1755659 TTATGAAATT
Statistics
Matches: 169, Mismatches: 15, Indels: 16
0.85 0.08 0.08
Matches are distributed among these distances:
98 1 0.01
99 76 0.45
100 1 0.01
101 1 0.01
104 62 0.37
105 7 0.04
106 21 0.12
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.35
Consensus pattern (99 bp):
ATTATTTGTTGACAATCAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGTTGTCTTGGGTCCAAT
ATCTTCATGTGAAGTTGAAATTGGATCTGAAAGG
Found at i:1767453 original size:2 final size:2
Alignment explanation
Indices: 1767441--1767478 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
1767431 CTATTAAAAG
* *
1767441 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1767479 AACGTAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:1768310 original size:21 final size:23
Alignment explanation
Indices: 1768268--1768310 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 23
1768258 ATATATATAT
* *
1768268 ATATATTTAAATATTATTTAAAA
1 ATATATTTAAATAATATCTAAAA
1768291 ATAT-TTTAAA-AATATCTAAA
1 ATATATTTAAATAATATCTAAA
1768311 CATGACATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 8 0.44
22 6 0.33
23 4 0.22
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
ATATATTTAAATAATATCTAAAA
Found at i:1773388 original size:24 final size:24
Alignment explanation
Indices: 1773361--1773417 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
1773351 GCTTCTTTTG
1773361 CAGCTTCAGCCGCTGCCATGTATT
1 CAGCTTCAGCCGCTGCCATGTATT
1773385 CAGCTTCAGCCGCTGCCATGTATT
1 CAGCTTCAGCCGCTGCCATGTATT
*
1773409 CAACTTCAG
1 CAGCTTCAG
1773418 TTGTAGATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.19, C:0.33, G:0.19, T:0.28
Consensus pattern (24 bp):
CAGCTTCAGCCGCTGCCATGTATT
Found at i:1778999 original size:27 final size:26
Alignment explanation
Indices: 1778968--1779053 Score: 87
Period size: 27 Copynumber: 3.5 Consensus size: 26
1778958 GCATTAAGGC
1778968 ATGAAAGGATGCCATAATTGAAAATG
1 ATGAAAGGATGCCATAATTGAAAATG
*
1778994 TATGAAAGGATG-CATTAA--G-GAATG
1 -ATGAAAGGATGCCA-TAATTGAAAATG
1779018 A-G--AGGATGCCATAATTGAAAATG
1 ATGAAAGGATGCCATAATTGAAAATG
1779041 CATGAAAGGATGC
1 -ATGAAAGGATGC
1779054 ATTAAGGCAT
Statistics
Matches: 48, Mismatches: 2, Indels: 18
0.71 0.03 0.26
Matches are distributed among these distances:
20 9 0.19
21 2 0.04
22 2 0.04
23 5 0.10
24 5 0.10
25 2 0.04
26 2 0.04
27 21 0.44
ACGTcount: A:0.43, C:0.08, G:0.27, T:0.22
Consensus pattern (26 bp):
ATGAAAGGATGCCATAATTGAAAATG
Found at i:1779007 original size:47 final size:47
Alignment explanation
Indices: 1778932--1779292 Score: 526
Period size: 47 Copynumber: 7.6 Consensus size: 47
1778922 TAAATCGAAT
* **
1778932 CCATAATTGAAAATACATGAAATTATGCATTAAGGCATGAAAGGATG
1 CCATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* * *
1778979 CCATAATTGAAAATGTATGAAAGGATGCATTAAGGAATGAGAGGATG
1 CCATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
1779026 CCATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
1 CCATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
1779073 CCATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
1 CCATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* * *
1779120 TCATAATTGAAAATTCATGAAAGGATGCCTTAAGGCATGAAAGGATG
1 CCATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* *
1779167 CCATAATTGAAAATGCATGAAAGGATGTGCATTAAGGCATAAAAGGATT
1 CCATAATTGAAAATGCATGAAAGGA--TGCATTAAGGCATGAAAGGATG
* * *
1779216 CCATATTTGAAAAATGCATGAAATGATGCATTAAGGCATGAAATGATG
1 CCATAATTG-AAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
*
1779264 CCATATATATTAAAATGCAT-AAATGGATG
1 CCATA-AT-TGAAAATGCATGAAA-GGATG
1779293 TGTTAATACG
Statistics
Matches: 283, Mismatches: 25, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
47 199 0.70
48 27 0.10
49 41 0.14
50 16 0.06
ACGTcount: A:0.43, C:0.10, G:0.23, T:0.25
Consensus pattern (47 bp):
CCATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
Found at i:1779168 original size:20 final size:20
Alignment explanation
Indices: 1779040--1779167 Score: 94
Period size: 20 Copynumber: 5.7 Consensus size: 20
1779030 AATTGAAAAT
1779040 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
1779060 GCATGAAAGGATGCCATAATTGAAAAT
1 GCATGAAAGGATG-C---ATT---AAG
1779087 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
1779107 GCATGAAAGGATGTCATAATTGAAAAT
1 GCATGAAAGGATG-C---ATT---AAG
* *
1779134 TCATGAAAGGATGCCTTAAG
1 GCATGAAAGGATGCATTAAG
1779154 GCATGAAAGGATGC
1 GCATGAAAGGATGC
1779168 CATAATTGAA
Statistics
Matches: 87, Mismatches: 7, Indels: 28
0.71 0.06 0.23
Matches are distributed among these distances:
20 43 0.49
21 2 0.02
23 5 0.06
24 6 0.07
26 2 0.02
27 29 0.33
ACGTcount: A:0.41, C:0.11, G:0.27, T:0.22
Consensus pattern (20 bp):
GCATGAAAGGATGCATTAAG
Found at i:1784849 original size:2 final size:2
Alignment explanation
Indices: 1784842--1784868 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1784832 CATGAGTTAG
1784842 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1784869 GGAATTGGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1785743 original size:22 final size:22
Alignment explanation
Indices: 1785715--1785780 Score: 132
Period size: 22 Copynumber: 3.0 Consensus size: 22
1785705 AGAGTCGAGG
1785715 GTATCCAGTGGTCCTTCGGGAC
1 GTATCCAGTGGTCCTTCGGGAC
1785737 GTATCCAGTGGTCCTTCGGGAC
1 GTATCCAGTGGTCCTTCGGGAC
1785759 GTATCCAGTGGTCCTTCGGGAC
1 GTATCCAGTGGTCCTTCGGGAC
1785781 AAATATTTAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.14, C:0.27, G:0.32, T:0.27
Consensus pattern (22 bp):
GTATCCAGTGGTCCTTCGGGAC
Found at i:1793060 original size:136 final size:137
Alignment explanation
Indices: 1792816--1793088 Score: 523
Period size: 136 Copynumber: 2.0 Consensus size: 137
1792806 AAATACACCC
1792816 GATTTCGACCGAGAATCGGCTAAACCTGTAGCTATGGTACCAATAAATGTAACACTCATTTCTCG
1 GATTTCGACCGAGAATCGGCTAAACCTGTAGCTATGGTACCAATAAATGTAACACTCATTTCTCG
1792881 TATATGTTTCTGTACACAAGTCACAAGTGTCACTTGACTTTTAAAAACATTTTCCTTATTC-TAA
66 TATATGTTTCTGTACACAAGTCACAAGTGTCACTTGACTTTT-AAAACATTTTCCTTATTCGTAA
1792945 A-CCATTT
130 ACCCATTT
1792952 GATTTCGACCGAGAATCGGCTAAACCTGTAGCTATGGTACCAATAAATGTAACACTCATTTCTCG
1 GATTTCGACCGAGAATCGGCTAAACCTGTAGCTATGGTACCAATAAATGTAACACTCATTTCTCG
1793017 TATATGTTTCTGTACACAAGTCACAAGTGTCACTTGACTTTTAAAACATTTTCCTTATTCGTAAA
66 TATATGTTTCTGTACACAAGTCACAAGTGTCACTTGACTTTTAAAACATTTTCCTTATTCGTAAA
1793082 CCCATTT
131 CCCATTT
1793089 TAATTTTGTT
Statistics
Matches: 135, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
135 18 0.13
136 111 0.82
137 6 0.04
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.34
Consensus pattern (137 bp):
GATTTCGACCGAGAATCGGCTAAACCTGTAGCTATGGTACCAATAAATGTAACACTCATTTCTCG
TATATGTTTCTGTACACAAGTCACAAGTGTCACTTGACTTTTAAAACATTTTCCTTATTCGTAAA
CCCATTT
Found at i:1798063 original size:29 final size:30
Alignment explanation
Indices: 1797989--1798064 Score: 86
Period size: 30 Copynumber: 2.6 Consensus size: 30
1797979 GTATTTTTTA
1797989 TTAAAATTTTACT-TTTATCTCCTAAAATT
1 TTAAAATTTTACTCTTTATCTCCTAAAATT
* * *
1798018 TTATAAA-TTTATTTCTTT-TTTCTTAAAATT
1 TTA-AAATTTTA-CTCTTTATCTCCTAAAATT
1798048 TTAAAATTTTACTCTTT
1 TTAAAATTTTACTCTTT
1798065 CTTAAATGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
29 15 0.38
30 21 0.54
31 3 0.08
ACGTcount: A:0.32, C:0.11, G:0.00, T:0.58
Consensus pattern (30 bp):
TTAAAATTTTACTCTTTATCTCCTAAAATT
Found at i:1798615 original size:13 final size:13
Alignment explanation
Indices: 1798593--1798623 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1798583 ATTTGAATAA
1798593 GTTT-TTTTTTGT
1 GTTTGTTTTTTGT
1798605 GTTTGTTTTTTGT
1 GTTTGTTTTTTGT
1798618 GTTTGT
1 GTTTGT
1798624 ATCGTTTATG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.22
13 14 0.78
ACGTcount: A:0.00, C:0.00, G:0.23, T:0.77
Consensus pattern (13 bp):
GTTTGTTTTTTGT
Found at i:1798651 original size:23 final size:24
Alignment explanation
Indices: 1798608--1798658 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
1798598 TTTTTGTGTT
*
1798608 TGTTTTTTGTGTTTGTATCGTTTA
1 TGTTTTTTGTATTTGTATCGTTTA
1798632 TGTTTTTT-TATTATGT-TCGTTTA
1 TGTTTTTTGTATT-TGTATCGTTTA
1798655 TGTT
1 TGTT
1798659 CATTCGTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 14 0.56
24 11 0.44
ACGTcount: A:0.10, C:0.04, G:0.18, T:0.69
Consensus pattern (24 bp):
TGTTTTTTGTATTTGTATCGTTTA
Found at i:1798655 original size:10 final size:10
Alignment explanation
Indices: 1798642--1798699 Score: 53
Period size: 10 Copynumber: 5.4 Consensus size: 10
1798632 TGTTTTTTTA
1798642 TTATGTTCGT
1 TTATGTTCGT
1798652 TTATGTTCATTCGT
1 TTATG----TTCGT
* *
1798666 TTGTATTCGT
1 TTATGTTCGT
*
1798676 TTACGTTCGT
1 TTATGTTCGT
1798686 TTATGTTCGT
1 TTATGTTCGT
1798696 TTAT
1 TTAT
1798700 CATTTAATGA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
10 30 0.79
14 8 0.21
ACGTcount: A:0.12, C:0.12, G:0.17, T:0.59
Consensus pattern (10 bp):
TTATGTTCGT
Found at i:1798721 original size:10 final size:10
Alignment explanation
Indices: 1798706--1798731 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1798696 TTATCATTTA
1798706 ATGAACGAAC
1 ATGAACGAAC
1798716 ATGAACGAAC
1 ATGAACGAAC
1798726 ATGAAC
1 ATGAAC
1798732 AAACTATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.50, C:0.19, G:0.19, T:0.12
Consensus pattern (10 bp):
ATGAACGAAC
Found at i:1800585 original size:19 final size:19
Alignment explanation
Indices: 1800563--1800602 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1800553 TCGGGTCGGG
1800563 TCAGACCAATCAAACCGGT
1 TCAGACCAATCAAACCGGT
** *
1800582 TCAGACCGGTCAATCCGGT
1 TCAGACCAATCAAACCGGT
1800601 TC
1 TC
1800603 GAACCGGTCG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.28, C:0.33, G:0.20, T:0.20
Consensus pattern (19 bp):
TCAGACCAATCAAACCGGT
Found at i:1800609 original size:10 final size:9
Alignment explanation
Indices: 1800586--1800669 Score: 89
Period size: 10 Copynumber: 8.7 Consensus size: 9
1800576 ACCGGTTCAG
1800586 ACCGGTC-A
1 ACCGGTCGA
1800594 ATCCGGTTCGA
1 A-CCGG-TCGA
1800605 ACCGGTCGAA
1 ACCGGTCG-A
1800615 ACCGGTCAGA
1 ACCGGTC-GA
1800625 ACCGGTCGAA
1 ACCGGTCG-A
1800635 ACCGGTCAGA
1 ACCGGTC-GA
1800645 ACCGGTCGAA
1 ACCGGTCG-A
*
1800655 ACCGGTCAA
1 ACCGGTCGA
1800664 ACCGGT
1 ACCGGT
1800670 TTCCAGCCCT
Statistics
Matches: 67, Mismatches: 1, Indels: 15
0.81 0.01 0.18
Matches are distributed among these distances:
8 1 0.01
9 16 0.24
10 46 0.69
11 4 0.06
ACGTcount: A:0.27, C:0.31, G:0.29, T:0.13
Consensus pattern (9 bp):
ACCGGTCGA
Found at i:1800626 original size:20 final size:20
Alignment explanation
Indices: 1800574--1800669 Score: 137
Period size: 20 Copynumber: 4.9 Consensus size: 20
1800564 CAGACCAATC
1800574 AAACCGGTTCAG-ACCGGTC-
1 AAACCGG-TCAGAACCGGTCG
*
1800593 AATCCGGTTC-GAACCGGTCG
1 AAACCGG-TCAGAACCGGTCG
1800613 AAACCGGTCAGAACCGGTCG
1 AAACCGGTCAGAACCGGTCG
1800633 AAACCGGTCAGAACCGGTCG
1 AAACCGGTCAGAACCGGTCG
1800653 AAACCGGTCA-AACCGGT
1 AAACCGGTCAGAACCGGT
1800670 TTCCAGCCCT
Statistics
Matches: 72, Mismatches: 2, Indels: 6
0.90 0.03 0.08
Matches are distributed among these distances:
18 1 0.01
19 25 0.35
20 46 0.64
ACGTcount: A:0.28, C:0.30, G:0.28, T:0.14
Consensus pattern (20 bp):
AAACCGGTCAGAACCGGTCG
Found at i:1800638 original size:30 final size:30
Alignment explanation
Indices: 1800574--1800669 Score: 105
Period size: 30 Copynumber: 3.3 Consensus size: 30
1800564 CAGACCAATC
*
1800574 AAACCGGTTCAG-ACCGGTCA-ATCCGGTTCG
1 AAACCGG-TCAGAACCGGTCAGAACCGG-TCG
1800604 -AACCGGTC-GAAACCGGTCAGAACCGGTCG
1 AAACCGGTCAG-AACCGGTCAGAACCGGTCG
1800633 AAACCGGTCAGAACCGGTC-GAAACCGGTC-
1 AAACCGGTCAGAACCGGTCAG-AACCGGTCG
1800662 AAACCGGT
1 AAACCGGT
1800670 TTCCAGCCCT
Statistics
Matches: 59, Mismatches: 1, Indels: 13
0.81 0.01 0.18
Matches are distributed among these distances:
27 1 0.02
28 2 0.03
29 26 0.44
30 29 0.49
31 1 0.02
ACGTcount: A:0.28, C:0.30, G:0.28, T:0.14
Consensus pattern (30 bp):
AAACCGGTCAGAACCGGTCAGAACCGGTCG
Found at i:1807759 original size:7 final size:7
Alignment explanation
Indices: 1807747--1807803 Score: 64
Period size: 7 Copynumber: 8.4 Consensus size: 7
1807737 GTCAAAGGAA
1807747 GTCAACG
1 GTCAACG
1807754 GTCAACG
1 GTCAACG
1807761 GTC-ACG
1 GTCAACG
*
1807767 ATCAACG
1 GTCAACG
1807774 GTC-ACG
1 GTCAACG
*
1807780 GTCAATG
1 GTCAACG
* *
1807787 GTCATCA
1 GTCAACG
1807794 GTCAACG
1 GTCAACG
1807801 GTC
1 GTC
1807804 GGGTCGGGTT
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
6 11 0.28
7 29 0.73
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.19
Consensus pattern (7 bp):
GTCAACG
Found at i:1807773 original size:13 final size:13
Alignment explanation
Indices: 1807755--1807803 Score: 55
Period size: 13 Copynumber: 3.7 Consensus size: 13
1807745 AAGTCAACGG
1807755 TCAACGGTCACGA
1 TCAACGGTCACGA
*
1807768 TCAACGGTCACGG
1 TCAACGGTCACGA
*
1807781 TCAATGGTCATC-A
1 TCAACGGTCA-CGA
1807794 GTCAACGGTC
1 -TCAACGGTC
1807804 GGGTCGGGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
13 21 0.70
14 9 0.30
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (13 bp):
TCAACGGTCACGA
Found at i:1807781 original size:26 final size:27
Alignment explanation
Indices: 1807751--1807803 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
1807741 AAGGAAGTCA
1807751 ACGGTCAACGGTCA-C-GATCAACGGTC
1 ACGGTCAACGGTCATCAG-TCAACGGTC
*
1807777 ACGGTCAATGGTCATCAGTCAACGGTC
1 ACGGTCAACGGTCATCAGTCAACGGTC
1807804 GGGTCGGGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 13 0.54
27 10 0.42
28 1 0.04
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.19
Consensus pattern (27 bp):
ACGGTCAACGGTCATCAGTCAACGGTC
Found at i:1807818 original size:14 final size:14
Alignment explanation
Indices: 1807801--1807843 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
1807791 TCAGTCAACG
*
1807801 GTCGGGTCGGGTTA
1 GTCGGGTCGGGTCA
* * *
1807815 GTCGGTTTGGGTCG
1 GTCGGGTCGGGTCA
1807829 GTCGGGTCGGGTCA
1 GTCGGGTCGGGTCA
1807843 G
1 G
1807844 GTCAGTCGGG
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.05, C:0.16, G:0.51, T:0.28
Consensus pattern (14 bp):
GTCGGGTCGGGTCA
Found at i:1807837 original size:19 final size:19
Alignment explanation
Indices: 1807824--1807862 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1807814 AGTCGGTTTG
*
1807824 GGTCGGTCGGGTCGGGTCA
1 GGTCAGTCGGGTCGGGTCA
1807843 GGTCAGTCGGGTCGGGTCA
1 GGTCAGTCGGGTCGGGTCA
1807862 G
1 G
1807863 ACCGGTCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.08, C:0.21, G:0.51, T:0.21
Consensus pattern (19 bp):
GGTCAGTCGGGTCGGGTCA
Found at i:1807854 original size:28 final size:28
Alignment explanation
Indices: 1807799--1807857 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
1807789 CATCAGTCAA
* * *
1807799 CGGTCGGGTCGGGTTAGTCGGTTTGGGT
1 CGGTCGGGTCGGGTCAGTCAGTTCGGGT
1807827 CGGTCGGGTCGGGTCAGGTCAG-TCGGGT
1 CGGTCGGGTCGGGTCA-GTCAGTTCGGGT
1807855 CGG
1 CGG
1807858 GTCAGACCGG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 23 0.85
29 4 0.15
ACGTcount: A:0.05, C:0.19, G:0.51, T:0.25
Consensus pattern (28 bp):
CGGTCGGGTCGGGTCAGTCAGTTCGGGT
Found at i:1807893 original size:20 final size:19
Alignment explanation
Indices: 1807859--1807918 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 19
1807849 TCGGGTCGGG
1807859 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
* *
1807878 TCAGACCCGATCAAACCAGT
1 TCAGA-CCGGTCAAACCGGT
1807898 TC-GAACCGGTCGAAACCGGT
1 TCAG-ACCGGTC-AAACCGGT
1807918 T
1 T
1807919 TCCAGCCCTC
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
19 11 0.32
20 23 0.68
ACGTcount: A:0.28, C:0.32, G:0.23, T:0.17
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:1810145 original size:20 final size:20
Alignment explanation
Indices: 1810122--1810166 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1810112 AATAAGCGTT
* *
1810122 GCGATAGTCAAATTCGCAAC
1 GCGATAGCCAAATTCGAAAC
*
1810142 GCGAAAGCCAAATTCGAAAC
1 GCGATAGCCAAATTCGAAAC
1810162 GCGAT
1 GCGAT
1810167 TTTCGGTTTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.16
Consensus pattern (20 bp):
GCGATAGCCAAATTCGAAAC
Found at i:1810499 original size:18 final size:18
Alignment explanation
Indices: 1810476--1810511 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1810466 AAGCCAGTTG
*
1810476 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
1810494 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
1810512 CCTTTTTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:1812558 original size:14 final size:14
Alignment explanation
Indices: 1812539--1812566 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1812529 TACATGTAAA
1812539 ACTTACCTTCTTGT
1 ACTTACCTTCTTGT
1812553 ACTTACCTTCTTGT
1 ACTTACCTTCTTGT
1812567 GCCACTTTCA
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:0.14, C:0.29, G:0.07, T:0.50
Consensus pattern (14 bp):
ACTTACCTTCTTGT
Found at i:1812737 original size:38 final size:38
Alignment explanation
Indices: 1812686--1812779 Score: 152
Period size: 38 Copynumber: 2.5 Consensus size: 38
1812676 CGTATAAATA
* *
1812686 TCCCGAATGACCTATCATCCCGAAGGATGTCATATGTG
1 TCCCGAAGGACCTATCATCCCGAAGGATGTAATATGTG
*
1812724 TCCCGAAGGACCTATCATCCCGAAGGATGTAATCTGTG
1 TCCCGAAGGACCTATCATCCCGAAGGATGTAATATGTG
*
1812762 TCCCGTAGGACCTATCAT
1 TCCCGAAGGACCTATCAT
1812780 ATATCTTATA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 52 1.00
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.26
Consensus pattern (38 bp):
TCCCGAAGGACCTATCATCCCGAAGGATGTAATATGTG
Found at i:1812746 original size:17 final size:17
Alignment explanation
Indices: 1812685--1812750 Score: 60
Period size: 17 Copynumber: 3.6 Consensus size: 17
1812675 TCGTATAAAT
*
1812685 ATCCCGAATGACCTATC
1 ATCCCGAAGGACCTATC
* *
1812702 ATCCCGAAGGATGTCATATGT
1 ATCCCGAAGGA---CCTAT-C
*
1812723 GTCCCGAAGGACCTATC
1 ATCCCGAAGGACCTATC
1812740 ATCCCGAAGGA
1 ATCCCGAAGGA
1812751 TGTAATCTGT
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
17 20 0.53
18 4 0.11
20 4 0.11
21 10 0.26
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (17 bp):
ATCCCGAAGGACCTATC
Found at i:1813642 original size:20 final size:20
Alignment explanation
Indices: 1813617--1813682 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
1813607 TTTTTTCATT
1813617 TAGGGGGAATCGATACCCCC
1 TAGGGGGAATCGATACCCCC
*
1813637 TAGGGGGAATCTG-T--TCCC
1 TAGGGGGAATC-GATACCCCC
1813655 ---GGGGAATCGATACCCCC
1 TAGGGGGAATCGATACCCCC
*
1813672 CAGGGGGAATC
1 TAGGGGGAATC
1813683 TGTTCCCCCT
Statistics
Matches: 37, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
14 1 0.03
15 9 0.24
17 3 0.08
18 3 0.08
20 20 0.54
21 1 0.03
ACGTcount: A:0.23, C:0.27, G:0.33, T:0.17
Consensus pattern (20 bp):
TAGGGGGAATCGATACCCCC
Found at i:1813666 original size:35 final size:35
Alignment explanation
Indices: 1813620--1813689 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
1813610 TTTCATTTAG
*
1813620 GGGGAATCGATACCCCCTAGGGGGAATCTGTTCCC
1 GGGGAATCGATACCCCCCAGGGGGAATCTGTTCCC
1813655 GGGGAATCGATACCCCCCAGGGGGAATCTGTTCCC
1 GGGGAATCGATACCCCCCAGGGGGAATCTGTTCCC
1813690 CCTACACATA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.20, C:0.30, G:0.31, T:0.19
Consensus pattern (35 bp):
GGGGAATCGATACCCCCCAGGGGGAATCTGTTCCC
Found at i:1814961 original size:3 final size:3
Alignment explanation
Indices: 1814953--1814977 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1814943 TCTTCGGGGA
1814953 CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT C
1814978 AGGGTTATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:1815190 original size:24 final size:24
Alignment explanation
Indices: 1815152--1815205 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
1815142 TCATCACATC
* *
1815152 ATCAAAATCCGAGTATTCCCCAAG
1 ATCAAAATCCAAGTATTCACCAAG
* *
1815176 ATCAAAGTCCAAGTATTGACCAAG
1 ATCAAAATCCAAGTATTCACCAAG
1815200 ATCAAA
1 ATCAAA
1815206 TTTCGAATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.43, C:0.24, G:0.13, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCAAGTATTCACCAAG
Found at i:1815352 original size:12 final size:12
Alignment explanation
Indices: 1815331--1815364 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1815321 GGTTGTGGGT
*
1815331 TTTGAGATTGTG
1 TTTGATATTGTG
1815343 TTTGATATTGTG
1 TTTGATATTGTG
*
1815355 TTTGGTATTG
1 TTTGATATTG
1815365 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:1816134 original size:19 final size:19
Alignment explanation
Indices: 1816107--1816157 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
1816097 ACTAAAACAT
*
1816107 GTTGAGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
1816126 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
1816145 GTTGCGAATTTGA
1 GTTGCGAATTTGA
1816158 CTATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.31, C:0.08, G:0.24, T:0.37
Consensus pattern (19 bp):
GTTGCGAATTTGAAATTCA
Found at i:1816170 original size:20 final size:21
Alignment explanation
Indices: 1816126--1816236 Score: 110
Period size: 20 Copynumber: 5.6 Consensus size: 21
1816116 TTGAAATTCA
* *
1816126 GTTGCGAATTTGAAAT-TC-A
1 GTTGCGAATTTGACATATCGC
1816145 GTTGCGAATTTGAC-TATCGC
1 GTTGCGAATTTGACATATCGC
1816165 GTTGCGAATTTGAC-TATCGC
1 GTTGCGAATTTGACATATCGC
* * *
1816185 GTTACGAATTTGACTTAT-GT
1 GTTGCGAATTTGACATATCGC
*
1816205 GTTGC-AATTT-ACAAATTCGC
1 GTTGCGAATTTGACATA-TCGC
1816225 GTTGCGAATTTG
1 GTTGCGAATTTG
1816237 GAAAATCGCA
Statistics
Matches: 77, Mismatches: 8, Indels: 11
0.80 0.08 0.11
Matches are distributed among these distances:
18 4 0.05
19 21 0.27
20 44 0.57
21 8 0.10
ACGTcount: A:0.24, C:0.15, G:0.23, T:0.38
Consensus pattern (21 bp):
GTTGCGAATTTGACATATCGC
Found at i:1816330 original size:20 final size:20
Alignment explanation
Indices: 1816287--1816334 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
1816277 ACATATTCGC
*
1816287 GTTGCGAAATTGGAAACTGG
1 GTTGCGAAATTGGAAACTGA
*
1816307 GTTGCGAAATTGGAGA-TCGA
1 GTTGCGAAATTGGAAACT-GA
1816327 GTTGCGAA
1 GTTGCGAA
1816335 TGTGTTGGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 1 0.04
20 24 0.96
ACGTcount: A:0.29, C:0.10, G:0.35, T:0.25
Consensus pattern (20 bp):
GTTGCGAAATTGGAAACTGA
Found at i:1818151 original size:10 final size:9
Alignment explanation
Indices: 1818136--1818160 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1818126 AACTTTTTAA
1818136 TATTTTTTT
1 TATTTTTTT
1818145 TATTTTTTT
1 TATTTTTTT
1818154 TATTTTT
1 TATTTTT
1818161 CCATTTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (9 bp):
TATTTTTTT
Found at i:1820790 original size:23 final size:23
Alignment explanation
Indices: 1820764--1820851 Score: 106
Period size: 23 Copynumber: 3.8 Consensus size: 23
1820754 CAATCTTATA
* *
1820764 TGGCACTACAGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
1820787 TGGCACTTCGGTGCATTTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* *
1820810 ATGTC-CTTCGGGGCAAATTCTACG
1 -TGGCACTTCGGTGC-AATTCTACG
1820834 TGGCACTTCGGTGCAATT
1 TGGCACTTCGGTGCAATT
1820852 TATATGAGCT
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
23 35 0.65
24 19 0.35
ACGTcount: A:0.19, C:0.25, G:0.25, T:0.31
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:1822518 original size:22 final size:22
Alignment explanation
Indices: 1822492--1822534 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1822482 TTCTGGGCTA
* *
1822492 GGGGAATCGGTACCCATTCAAG
1 GGGGAACCGATACCCATTCAAG
*
1822514 GGGGAACCGATACCCCTTCAA
1 GGGGAACCGATACCCATTCAA
1822535 ACGAACAGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.28, T:0.16
Consensus pattern (22 bp):
GGGGAACCGATACCCATTCAAG
Found at i:1829936 original size:131 final size:130
Alignment explanation
Indices: 1829695--1830058 Score: 507
Period size: 131 Copynumber: 2.8 Consensus size: 130
1829685 TCGATATTGA
* *
1829695 AAATAGTA-ATATCTTTACATTTCGATTGGAGAAATAAATGATTGCTTTAAGGCATGAGAGATCA
1 AAATAGTATATATC-TT-CATTTCGATTGGAGTAATAAATGATTGCTTTAAGGCATGAGAGGTCA
* * * *
1829759 TTTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCTCTCGAATCAATATCGATTTTTAAGA
64 TTTATTCTCGATTGAAAATAATTAGATATTATTGTTTTCTCCCGAATCAATATCGAATTTTAAGA
1829824 CG
129 CG
* *
1829826 GAATAGTTATATATCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCAT
1 AAATAG-TATATATCTTCATTTCGATTGGAGTAATAAATGATTGCTTTAAGGCATGAGAGGTCAT
* *
1829891 TTATTCTCGATTGAAAATCATTAGATATTATTGTTTT-TACCCGAATCAATATTGAATTTTAAGA
65 TTATTCTCGATTGAAAATAATTAGATATTATTGTTTTCT-CCCGAATCAATATCGAATTTTAAGA
1829955 CG
129 CG
* * * * * *
1829957 AAATAGGGATATATCTTCATTTCGATTGGAGTCATAAATGGTTGCTTTAATGCATGAGATGTTAT
1 AAATA-GTATATATCTTCATTTCGATTGGAGTAATAAATGATTGCTTTAAGGCATGAGAGGTCAT
* *
1830022 TTATTCTCGATTAAAAATGATTAGATATTATTGTTTT
65 TTATTCTCGATTGAAAATAATTAGATATTATTGTTTT
1830059 ATCTCTTAGA
Statistics
Matches: 209, Mismatches: 20, Indels: 8
0.88 0.08 0.03
Matches are distributed among these distances:
130 1 0.00
131 198 0.95
132 5 0.02
133 5 0.02
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (130 bp):
AAATAGTATATATCTTCATTTCGATTGGAGTAATAAATGATTGCTTTAAGGCATGAGAGGTCATT
TATTCTCGATTGAAAATAATTAGATATTATTGTTTTCTCCCGAATCAATATCGAATTTTAAGACG
Found at i:1832996 original size:9 final size:9
Alignment explanation
Indices: 1832969--1833003 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
1832959 AAATATATAT
1832969 TTTAAAATA
1 TTTAAAATA
*
1832978 TTT-AATTA
1 TTTAAAATA
1832986 TTTAAAATA
1 TTTAAAATA
1832995 TTTAAAATA
1 TTTAAAATA
1833004 ATCATGATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 7 0.30
9 16 0.70
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (9 bp):
TTTAAAATA
Found at i:1833606 original size:23 final size:23
Alignment explanation
Indices: 1833575--1833648 Score: 67
Period size: 23 Copynumber: 3.1 Consensus size: 23
1833565 AATAATATAA
* *
1833575 AATTAATATTATTTCAACTAAAT
1 AATTAATATTATTTAAAATAAAT
* *
1833598 AATTTATATTTTTTAAAATAAAT
1 AATTAATATTATTTAAAATAAAT
* *
1833621 AAATAATATGATTTTGAAAATTAAAT
1 AATTAATATTA-TTT-AAAA-TAAAT
1833647 AA
1 AA
1833649 ATATTTTTAT
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
23 26 0.65
24 3 0.08
25 4 0.10
26 7 0.17
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (23 bp):
AATTAATATTATTTAAAATAAAT
Found at i:1834792 original size:27 final size:27
Alignment explanation
Indices: 1834734--1834787 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
1834724 AGGTCGAATT
* *
1834734 CGGGTCGGGTTGAAGGTGTACATTTTC
1 CGGGTCGGGTGGAAGGTGTAAATTTTC
*
1834761 CGGGTCGGGTGGAGGGTGTAAAATTTT
1 CGGGTCGGGTGGAAGGTGT-AAATTTT
1834788 TGGGTTGGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 17 0.74
28 6 0.26
ACGTcount: A:0.17, C:0.11, G:0.41, T:0.31
Consensus pattern (27 bp):
CGGGTCGGGTGGAAGGTGTAAATTTTC
Found at i:1836835 original size:20 final size:20
Alignment explanation
Indices: 1836806--1836863 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
1836796 TTTGGGTTCG
*
1836806 AATATCGATATTGGATGAAC
1 AATATTGATATTGGATGAAC
* * *
1836826 AATATTGATACTAGATGAAT
1 AATATTGATATTGGATGAAC
*
1836846 AGTATTGAT-TTGGATGAA
1 AATATTGATATTGGATGAA
1836864 TTGGGACACA
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 7 0.23
20 24 0.77
ACGTcount: A:0.40, C:0.05, G:0.21, T:0.34
Consensus pattern (20 bp):
AATATTGATATTGGATGAAC
Found at i:1837973 original size:45 final size:45
Alignment explanation
Indices: 1837918--1838022 Score: 138
Period size: 45 Copynumber: 2.3 Consensus size: 45
1837908 TGATAAGGGT
* * *
1837918 TGATGTTATGTGACCTAGACCTAGCCTAAGATACCTGTGAGGTGC
1 TGATGCTATGTGACCTAGACCTAGCCTAAGATACCTGTGAGATGA
* * * * *
1837963 TGATGCTATGTGACTTGGACCTCGCCTAAGGTACTTGTGAGATGA
1 TGATGCTATGTGACCTAGACCTAGCCTAAGATACCTGTGAGATGA
1838008 TGATGCTATGTGACC
1 TGATGCTATGTGACC
1838023 CAGATCTTAC
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 51 1.00
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (45 bp):
TGATGCTATGTGACCTAGACCTAGCCTAAGATACCTGTGAGATGA
Found at i:1838036 original size:45 final size:44
Alignment explanation
Indices: 1837918--1838043 Score: 126
Period size: 45 Copynumber: 2.8 Consensus size: 44
1837908 TGATAAGGGT
* * * * *
1837918 TGATGTTATGTGACCTAGACCTAGCCTAAGATACCTGTGAGGTGC
1 TGATGCTATGTGACCTAGACTTA-CCTAAGGTACCTGTGAGATGA
* * ** *
1837963 TGATGCTATGTGACTTGGACCTCGCCTAAGGTACTTGTGAGATGA
1 TGATGCTATGTGACCTAGA-CTTACCTAAGGTACCTGTGAGATGA
*
1838008 TGATGCTATGTGACCCAGATCTTACCTAAGGTACCT
1 TGATGCTATGTGACCTAGA-CTTACCTAAGGTACCT
1838044 CTAGTAAGAA
Statistics
Matches: 63, Mismatches: 17, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
45 62 0.98
46 1 0.02
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (44 bp):
TGATGCTATGTGACCTAGACTTACCTAAGGTACCTGTGAGATGA
Found at i:1838129 original size:13 final size:13
Alignment explanation
Indices: 1838111--1838138 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1838101 TGATGCTTAC
1838111 TTATGTTGTGTGA
1 TTATGTTGTGTGA
1838124 TTATGTTGTGTGA
1 TTATGTTGTGTGA
1838137 TT
1 TT
1838139 GTACCTGAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.00, G:0.29, T:0.57
Consensus pattern (13 bp):
TTATGTTGTGTGA
Found at i:1844542 original size:4 final size:4
Alignment explanation
Indices: 1844533--1844559 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1844523 ACTGTTCAAC
1844533 TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TAT
1844560 ACAGGCATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:1844588 original size:6 final size:6
Alignment explanation
Indices: 1844573--1844621 Score: 59
Period size: 6 Copynumber: 8.7 Consensus size: 6
1844563 GGCATTGTAT
* *
1844573 TTTATC TTTATA TTTATC TTTA-- -TTATC TTTATC TTTATC TTTATT
1 TTTATC TTTATC TTTATC TTTATC TTTATC TTTATC TTTATC TTTATC
1844618 TTTA
1 TTTA
1844622 ATTTCCTTGA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
3 3 0.08
6 34 0.92
ACGTcount: A:0.20, C:0.10, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTATC
Found at i:1844600 original size:21 final size:21
Alignment explanation
Indices: 1844574--1844617 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
1844564 GCATTGTATT
1844574 TTATCTTTATATTTATCTTTA
1 TTATCTTTATATTTATCTTTA
*
1844595 TTATCTTTATCTTTATCTTTA
1 TTATCTTTATATTTATCTTTA
1844616 TT
1 TT
1844618 TTTAATTTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.20, C:0.11, G:0.00, T:0.68
Consensus pattern (21 bp):
TTATCTTTATATTTATCTTTA
Found at i:1844603 original size:15 final size:13
Alignment explanation
Indices: 1844573--1844610 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
1844563 GGCATTGTAT
1844573 TTTATCTTTA-TA
1 TTTATCTTTATTA
1844585 TTTATCTTTATTA
1 TTTATCTTTATTA
1844598 TCTTTATCTTTAT
1 --TTTATCTTTAT
1844611 CTTTATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 10 0.43
13 2 0.09
15 11 0.48
ACGTcount: A:0.21, C:0.11, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTATCTTTATTA
Found at i:1845732 original size:14 final size:15
Alignment explanation
Indices: 1845707--1845735 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1845697 TTCAGGTAAA
1845707 TTATGTCCTCTGTCT
1 TTATGTCCTCTGTCT
1845722 TTATG-CCTCTGTCT
1 TTATGTCCTCTGTCT
1845736 GTCAATTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.07, C:0.28, G:0.14, T:0.52
Consensus pattern (15 bp):
TTATGTCCTCTGTCT
Found at i:1847659 original size:23 final size:23
Alignment explanation
Indices: 1847622--1847685 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
1847612 CAGCTCGTAT
1847622 AAATGCACCGAAGTGCCACATAG
1 AAATGCACCGAAGTGCCACATAG
* * * * *
1847645 AATTGCACCGTAGTGTCGCGTAG
1 AAATGCACCGAAGTGCCACATAG
1847668 AAATGCACCGAAGTGCCA
1 AAATGCACCGAAGTGCCA
1847686 TATAATATGT
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.33, C:0.25, G:0.25, T:0.17
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCACATAG
Found at i:1852596 original size:23 final size:23
Alignment explanation
Indices: 1852562--1852621 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
1852552 CACCACAGCT
*
1852562 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
1852585 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
1852608 CGTAGAAATGCACC
1 CGTAGAAATGCACC
1852622 AAAAAGTGCC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.30, C:0.27, G:0.25, T:0.18
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:1853050 original size:2 final size:2
Alignment explanation
Indices: 1853043--1853070 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1853033 AATCATATGA
1853043 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1853071 GCAATAACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1860725 original size:18 final size:19
Alignment explanation
Indices: 1860702--1860737 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1860692 TTCTCTAGCA
*
1860702 AGAATAGA-AACGAAAAAT
1 AGAATAGACAAAGAAAAAT
1860720 AGAATAGACAAAGAAAAA
1 AGAATAGACAAAGAAAAA
1860738 GAAATGGGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.69, C:0.06, G:0.17, T:0.08
Consensus pattern (19 bp):
AGAATAGACAAAGAAAAAT
Found at i:1876698 original size:19 final size:21
Alignment explanation
Indices: 1876674--1876744 Score: 85
Period size: 19 Copynumber: 3.5 Consensus size: 21
1876664 TGCAAAAATG
1876674 GTATCGATACCATA-ATAG-A
1 GTATCGATACCATAGATAGTA
1876693 GTATCGATACCATAGTATAGTA
1 GTATCGATACCATAG-ATAGTA
* **
1876715 GTATCGATACCAT-GGTAGGG
1 GTATCGATACCATAGATAGTA
1876735 GTATCGATAC
1 GTATCGATAC
1876745 TATGGAGCCA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
19 14 0.30
20 13 0.28
21 5 0.11
22 14 0.30
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (21 bp):
GTATCGATACCATAGATAGTA
Found at i:1877160 original size:55 final size:55
Alignment explanation
Indices: 1877073--1877518 Score: 555
Period size: 55 Copynumber: 8.1 Consensus size: 55
1877063 TGTACTATAG
* *
1877073 GCACTATGAGTGCATAATCAC-ATAATTCATCATGAGTTGATGAATAGCCGTACAT
1 GCACTATGTGTGCATAACCACGA-AATTCATCATGAGTTGATGAATAGCCGTACAT
* * *
1877128 GCACTATGTGTGCATAACCATGAAATTGATCATGAGTTGATGAATAGCCATAC-T
1 GCACTATGTGTGCATAACCACGAAATTCATCATGAGTTGATGAATAGCCGTACAT
* * *
1877182 CGCACTATGTGTTCATAACCAC-AGAATTCATCATGAGTTTATGAATAGTCGTACAT
1 -GCACTATGTGTGCATAACCACGA-AATTCATCATGAGTTGATGAATAGCCGTACAT
* * *
1877238 GCACTATATGTGCATAACAAC-AGAATTCATCATGAGTTGATGAATAGCCGTACAA
1 GCACTATGTGTGCATAACCACGA-AATTCATCATGAGTTGATGAATAGCCGTACAT
*
1877293 GCACTATGTGTGCATAACCACGAAATTCATTATGAGTTGATGAATAGCCGTACA-
1 GCACTATGTGTGCATAACCACGAAATTCATCATGAGTTGATGAATAGCCGTACAT
* * * * *
1877347 GACACTATATGTCCATAACCACAAAATTCATCATGAGTTGATGAATAGTCGTACAA
1 G-CACTATGTGTGCATAACCACGAAATTCATCATGAGTTGATGAATAGCCGTACAT
* * * *
1877403 GCACTATGTGTGCATAACCACGAAATTCATCATGAGTTGATGAATAGTCTTATAG
1 GCACTATGTGTGCATAACCACGAAATTCATCATGAGTTGATGAATAGCCGTACAT
* * * *
1877458 GCACTACGTGTGCAAAACCACTG-AATTCATCATGAATTGATGAATTA-CCGTATAT
1 GCACTATGTGTGCATAACCAC-GAAATTCATCATGAGTTGATGAA-TAGCCGTACAT
1877513 GCACTA
1 GCACTA
1877519 CTTATGCATT
Statistics
Matches: 345, Mismatches: 37, Indels: 18
0.86 0.09 0.05
Matches are distributed among these distances:
54 3 0.01
55 335 0.97
56 7 0.02
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.29
Consensus pattern (55 bp):
GCACTATGTGTGCATAACCACGAAATTCATCATGAGTTGATGAATAGCCGTACAT
Found at i:1879815 original size:20 final size:21
Alignment explanation
Indices: 1879749--1879822 Score: 73
Period size: 20 Copynumber: 3.6 Consensus size: 21
1879739 AATCTAATTT
*
1879749 GGGTATCGATACC-TAGA-GG
1 GGGTATCGATACCATAGATGA
* * *
1879768 GGGTATCGGTACCATAGCTTA
1 GGGTATCGATACCATAGATGA
1879789 GGGGTATCGATACCAT-GATGA
1 -GGGTATCGATACCATAGATGA
*
1879810 GGGTATTGATACC
1 GGGTATCGATACC
1879823 TAATAAGGTA
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
19 12 0.27
20 15 0.34
21 3 0.07
22 14 0.32
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (21 bp):
GGGTATCGATACCATAGATGA
Found at i:1879862 original size:21 final size:21
Alignment explanation
Indices: 1879812--1879868 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
1879802 CATGATGAGG
*
1879812 GTATTGATACCTAATAAGGTA
1 GTATTGATACCTAAGAAGGTA
* * *
1879833 TTATCGATACCATAAGCAGGT-
1 GTATTGATACC-TAAGAAGGTA
1879854 GTATTGATACCTAAG
1 GTATTGATACCTAAG
1879869 GTCCAAAATA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
20 4 0.14
21 18 0.62
22 7 0.24
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Consensus pattern (21 bp):
GTATTGATACCTAAGAAGGTA
Found at i:1880368 original size:58 final size:59
Alignment explanation
Indices: 1880180--1880442 Score: 419
Period size: 59 Copynumber: 4.5 Consensus size: 59
1880170 AAATTACCAA
*
1880180 AGGGTACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
* * *
1880239 AGGGCACTTTTTGTGCTAAACTGGTAAGGAAATC--A-T-AGTGTATGAATTTCCAAAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
* *
1880294 AGGGCACTTTGTGTGCTAAAATAGTAAGGAAATCATACTAAGTGTATAAATTT-CAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
*
1880352 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTATATGAATTTCCAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
*
1880411 AGGGCACTTTATGTGCTAAAATGGTAAGGAAA
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAA
1880443 GCATGTAACA
Statistics
Matches: 186, Mismatches: 13, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
55 49 0.26
56 1 0.01
57 2 0.01
58 55 0.30
59 79 0.42
ACGTcount: A:0.35, C:0.11, G:0.23, T:0.31
Consensus pattern (59 bp):
AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
Found at i:1890143 original size:147 final size:147
Alignment explanation
Indices: 1889979--1890273 Score: 590
Period size: 147 Copynumber: 2.0 Consensus size: 147
1889969 CACTAAATTT
1889979 CACAGTTTCGGTTAAATCTGAAAATTTGCACATTTCCAGACCAAATTTCTCTGATATAAAATATT
1 CACAGTTTCGGTTAAATCTGAAAATTTGCACATTTCCAGACCAAATTTCTCTGATATAAAATATT
1890044 AAAATAATATTTCCATCCATTTTATAACATCCTTCAAATTTTTGTAAAATTCCAATTCGATCGGA
66 AAAATAATATTTCCATCCATTTTATAACATCCTTCAAATTTTTGTAAAATTCCAATTCGATCGGA
1890109 ATTTACCGATTTCTTAC
131 ATTTACCGATTTCTTAC
1890126 CACAGTTTCGGTTAAATCTGAAAATTTGCACATTTCCAGACCAAATTTCTCTGATATAAAATATT
1 CACAGTTTCGGTTAAATCTGAAAATTTGCACATTTCCAGACCAAATTTCTCTGATATAAAATATT
1890191 AAAATAATATTTCCATCCATTTTATAACATCCTTCAAATTTTTGTAAAATTCCAATTCGATCGGA
66 AAAATAATATTTCCATCCATTTTATAACATCCTTCAAATTTTTGTAAAATTCCAATTCGATCGGA
1890256 ATTTACCGATTTCTTAC
131 ATTTACCGATTTCTTAC
1890273 C
1 C
1890274 GGCTTTAACT
Statistics
Matches: 148, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
147 148 1.00
ACGTcount: A:0.35, C:0.19, G:0.08, T:0.38
Consensus pattern (147 bp):
CACAGTTTCGGTTAAATCTGAAAATTTGCACATTTCCAGACCAAATTTCTCTGATATAAAATATT
AAAATAATATTTCCATCCATTTTATAACATCCTTCAAATTTTTGTAAAATTCCAATTCGATCGGA
ATTTACCGATTTCTTAC
Found at i:1902620 original size:187 final size:187
Alignment explanation
Indices: 1902305--1902682 Score: 747
Period size: 187 Copynumber: 2.0 Consensus size: 187
1902295 ATACCAGGAG
*
1902305 GGAGATAAAGTATTTTTAAAAGTATCGCCTTGGAAGAAGGTATTACGATTTGGGCGAAAAGGAAG
1 GGAGATAAAGTATTTTTAAAAGTATCGCCTTGGAAGAAGGTATTACGATTTGGGCGAAAAGGAAA
1902370 GCTAAGTCCGAGGTTTATTGGACTGTATGAGATATTGAAAATGATTGGACCCGTGGCTTATCAAT
66 GCTAAGTCCGAGGTTTATTGGACTGTATGAGATATTGAAAATGATTGGACCCGTGGCTTATCAAT
1902435 TATCTCTGCCTTCGGATATGGACAAGATCCACAATGTTTTCCATGTATCGATGCTTA
131 TATCTCTGCCTTCGGATATGGACAAGATCCACAATGTTTTCCATGTATCGATGCTTA
1902492 GGAGATAAAGTATTTTTAAAAGTATCGCCTTGGAAGAAGGTATTACGATTTGGGCGAAAAGGAAA
1 GGAGATAAAGTATTTTTAAAAGTATCGCCTTGGAAGAAGGTATTACGATTTGGGCGAAAAGGAAA
1902557 GCTAAGTCCGAGGTTTATTGGACTGTATGAGATATTGAAAATGATTGGACCCGTGGCTTATCAAT
66 GCTAAGTCCGAGGTTTATTGGACTGTATGAGATATTGAAAATGATTGGACCCGTGGCTTATCAAT
1902622 TATCTCTGCCTTCGGATATGGACAAGATCCACAATGTTTTCCATGTATCGATGCTTA
131 TATCTCTGCCTTCGGATATGGACAAGATCCACAATGTTTTCCATGTATCGATGCTTA
1902679 GGAG
1 GGAG
1902683 GTACATATCA
Statistics
Matches: 190, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
187 190 1.00
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.31
Consensus pattern (187 bp):
GGAGATAAAGTATTTTTAAAAGTATCGCCTTGGAAGAAGGTATTACGATTTGGGCGAAAAGGAAA
GCTAAGTCCGAGGTTTATTGGACTGTATGAGATATTGAAAATGATTGGACCCGTGGCTTATCAAT
TATCTCTGCCTTCGGATATGGACAAGATCCACAATGTTTTCCATGTATCGATGCTTA
Found at i:1904531 original size:115 final size:116
Alignment explanation
Indices: 1904313--1904637 Score: 523
Period size: 115 Copynumber: 2.8 Consensus size: 116
1904303 AAATTACCAA
* *
1904313 AGGGTACTTTGTGTGCTAAAATGGTAAGGAATTCATACTAAGTGTATGAATTTCCAGATAGGGCA
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCA
*
1904378 TTTTGTG-CTAAAAT-GTAAGGAAATCATACTAAGTGTATGAATTTCTAGAT
66 CTTTGTGTCTAAAATGGTAAGGAAATCATACTAAG-GTATGAATTTCTAGAT
* * *
1904428 AGGGCACTTTGTTTGCTAAAATTGTAAGGAAATCATACTAAGTGTATTAATTTCCAGATA-GGCA
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCA
1904492 CTTTGTGTACTAAAATGGTAAGGAAATCATACTAA-GTATGAATTTCTAGAT
66 CTTTGTGT-CTAAAATGGTAAGGAAATCATACTAAGGTATGAATTTCTAGAT
* *
1904543 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACAAAGTGTATGAATTTCCAGATAGGGTA
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCA
*
1904608 CTTTGTGTGTAAAATGGTAAGGAAATCATA
66 CTTTGTGTCTAAAATGGTAAGGAAATCATA
1904638 TTGATTGTAT
Statistics
Matches: 194, Mismatches: 12, Indels: 8
0.91 0.06 0.04
Matches are distributed among these distances:
114 10 0.05
115 148 0.76
116 18 0.09
117 18 0.09
ACGTcount: A:0.35, C:0.10, G:0.22, T:0.33
Consensus pattern (116 bp):
AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCA
CTTTGTGTCTAAAATGGTAAGGAAATCATACTAAGGTATGAATTTCTAGAT
Found at i:1904630 original size:173 final size:172
Alignment explanation
Indices: 1904318--1904637 Score: 518
Period size: 173 Copynumber: 1.8 Consensus size: 172
1904308 ACCAAAGGGT
* *
1904318 ACTTTGTGTGCTAAAATGGTAAGGAATTCATACTAAGTGTATGAATTTCCAGATAGGGCATTTTG
1 ACTTTGTGTACTAAAATGGTAAGGAAATCATACTAAG-GTATGAATTTCCAGATAGGGCATTTTG
* * *
1904383 TGCTAAAATGTAAGGAAATCATACTAAGTGTATGAATTTCTAGATAGGGCACTTTGTTTGCTAAA
65 TGCTAAAATGTAAGGAAATCATACAAAGTGTATGAATTTCCAGATAGGGCACTTTGTGTGCTAAA
*
1904448 ATTGTAAGGAAATCATACTAAGTGTATTAATTTCCAGATAGGC
130 ATGGTAAGGAAATCATACTAAGTGTATTAATTTCCAGATAGGC
*
1904491 ACTTTGTGTACTAAAATGGTAAGGAAATCATACTAA-GTATGAATTTCTAGATAGGGCACTTTGT
1 ACTTTGTGTACTAAAATGGTAAGGAAATCATACTAAGGTATGAATTTCCAGATAGGGCA-TTT-T
*
1904555 GTGCTAAAATGGTAAGGAAATCATACAAAGTGTATGAATTTCCAGATAGGGTACTTTGTGTG-TA
64 GTGCTAAAAT-GTAAGGAAATCATACAAAGTGTATGAATTTCCAGATAGGGCACTTTGTGTGCTA
1904619 AAATGGTAAGGAAATCATA
128 AAATGGTAAGGAAATCATA
1904638 TTGATTGTAT
Statistics
Matches: 136, Mismatches: 8, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
171 21 0.15
172 3 0.02
173 65 0.48
174 47 0.35
ACGTcount: A:0.35, C:0.10, G:0.22, T:0.33
Consensus pattern (172 bp):
ACTTTGTGTACTAAAATGGTAAGGAAATCATACTAAGGTATGAATTTCCAGATAGGGCATTTTGT
GCTAAAATGTAAGGAAATCATACAAAGTGTATGAATTTCCAGATAGGGCACTTTGTGTGCTAAAA
TGGTAAGGAAATCATACTAAGTGTATTAATTTCCAGATAGGC
Found at i:1904649 original size:58 final size:59
Alignment explanation
Indices: 1904313--1904656 Score: 513
Period size: 58 Copynumber: 5.9 Consensus size: 59
1904303 AAATTACCAA
* *
1904313 AGGGTACTTTGTGTGCTAAAATGGTAAGGAATTCATACTAAGTGTATGAATTTCCAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
*
1904372 AGGGCA-TTT-TGTGCTAAAAT-GTAAGGAAATCATACTAAGTGTATGAATTTCTAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
* * *
1904428 AGGGCACTTTGTTTGCTAAAATTGTAAGGAAATCATACTAAGTGTATTAATTTCCAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
* *
1904487 A-GGCACTTTGTGTACTAAAATGGTAAGGAAATCATACTAA--GTATGAATTTCTAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
*
1904543 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACAAAGTGTATGAATTTCCAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
* * * * *
1904602 AGGGTACTTTGTGTG-TAAAATGGTAAGGAAATCATATTGATTGTATGAAATTCCA
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCA
1904657 ATTAAATTTA
Statistics
Matches: 259, Mismatches: 20, Indels: 13
0.89 0.07 0.04
Matches are distributed among these distances:
56 55 0.21
57 51 0.20
58 84 0.32
59 69 0.27
ACGTcount: A:0.35, C:0.10, G:0.22, T:0.33
Consensus pattern (59 bp):
AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
Found at i:1905069 original size:21 final size:21
Alignment explanation
Indices: 1905044--1905093 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 21
1905034 TCTTTTGTTG
*
1905044 TTTATTTAAGTTAAG-ATATGT
1 TTTATTTAAG-TAAGTAAATGT
1905065 TTTATTTTAAGTAAGTTAAATGT
1 TTTA-TTTAAGTAAG-TAAATGT
1905088 TTTATT
1 TTTATT
1905094 AAAAATGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 8 0.32
22 8 0.32
23 9 0.36
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (21 bp):
TTTATTTAAGTAAGTAAATGT
Found at i:1905705 original size:14 final size:15
Alignment explanation
Indices: 1905686--1905714 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1905676 TTAAAGACCA
1905686 AAAATTTA-ATATTT
1 AAAATTTATATATTT
1905700 AAAATTTATATATTT
1 AAAATTTATATATTT
1905715 TGGCCTGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
AAAATTTATATATTT
Found at i:1908213 original size:19 final size:19
Alignment explanation
Indices: 1908185--1908252 Score: 73
Period size: 19 Copynumber: 3.6 Consensus size: 19
1908175 TATTGGGTTG
* *
1908185 TGAATATGAAATTAATTTA
1 TGAATTTGAAATTAATTTC
* *
1908204 TGAATTTGAAAATAAGTTC
1 TGAATTTGAAATTAATTTC
* * *
1908223 TGAATCTAAAATTGATTTC
1 TGAATTTGAAATTAATTTC
1908242 TGAATTTGAAA
1 TGAATTTGAAA
1908253 ATGTGTTCTG
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
19 38 1.00
ACGTcount: A:0.43, C:0.04, G:0.13, T:0.40
Consensus pattern (19 bp):
TGAATTTGAAATTAATTTC
Found at i:1908246 original size:38 final size:39
Alignment explanation
Indices: 1908193--1908272 Score: 117
Period size: 38 Copynumber: 2.1 Consensus size: 39
1908183 TGTGAATATG
1908193 AAATTAATTTATGAATTTGAAAATAAGTTCTGAATCT-A
1 AAATTAATTTATGAATTTGAAAATAAGTTCTGAATCTCA
* * **
1908231 AAATTGATTTCTGAATTTGAAAATGTGTTCTGAATCTCA
1 AAATTAATTTATGAATTTGAAAATAAGTTCTGAATCTCA
1908270 AAA
1 AAA
1908273 GAGTTATGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
38 33 0.89
39 4 0.11
ACGTcount: A:0.41, C:0.07, G:0.12, T:0.39
Consensus pattern (39 bp):
AAATTAATTTATGAATTTGAAAATAAGTTCTGAATCTCA
Done.