Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A01
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: 104050246
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4660000 characters in sequence are not A, C, G, or T
File 6 of 316
Found at i:1595409 original size:28 final size:28
Alignment explanation
Indices: 1595369--1595429 Score: 122
Period size: 28 Copynumber: 2.2 Consensus size: 28
1595359 ATGGTCCCCT
1595369 TCTAAATTCCTAGGTGTACCCCAAAGAA
1 TCTAAATTCCTAGGTGTACCCCAAAGAA
1595397 TCTAAATTCCTAGGTGTACCCCAAAGAA
1 TCTAAATTCCTAGGTGTACCCCAAAGAA
1595425 TCTAA
1 TCTAA
1595430 TCTCTCTCCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.36, C:0.25, G:0.13, T:0.26
Consensus pattern (28 bp):
TCTAAATTCCTAGGTGTACCCCAAAGAA
Found at i:1595889 original size:12 final size:11
Alignment explanation
Indices: 1595862--1595887 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1595852 AATTGAACTT
1595862 AAAACAAAAAA
1 AAAACAAAAAA
1595873 AAAACAAAAAA
1 AAAACAAAAAA
1595884 AAAA
1 AAAA
1595888 ACTTAACAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAACAAAAAA
Found at i:1596213 original size:6 final size:6
Alignment explanation
Indices: 1596204--1596234 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
1596194 GCTGAAGCTA
1596204 GCAATG GCAATG GCAATG GCAATG GCAATG G
1 GCAATG GCAATG GCAATG GCAATG GCAATG G
1596235 TTGCTCCAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.16, G:0.35, T:0.16
Consensus pattern (6 bp):
GCAATG
Found at i:1596638 original size:25 final size:25
Alignment explanation
Indices: 1596604--1596655 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
1596594 TTAAAGTGTA
1596604 TTGTAAAGGTACCTCTATCTCTTTT
1 TTGTAAAGGTACCTCTATCTCTTTT
1596629 TTGTAAAGGTACCTCTATCTCTTTT
1 TTGTAAAGGTACCTCTATCTCTTTT
1596654 TT
1 TT
1596656 TTATGTCCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.19, C:0.19, G:0.12, T:0.50
Consensus pattern (25 bp):
TTGTAAAGGTACCTCTATCTCTTTT
Found at i:1608031 original size:18 final size:17
Alignment explanation
Indices: 1607998--1608036 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
1607988 TTGTATAAAT
1607998 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
1608016 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
1608033 TGTG
1 TGTG
1608037 GAAGGAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:1608293 original size:23 final size:23
Alignment explanation
Indices: 1608263--1608336 Score: 114
Period size: 23 Copynumber: 3.3 Consensus size: 23
1608253 GTGTTATTGA
1608263 TCAGTGGTAGCTTCGGCTACATT
1 TCAGTGGTAGCTTCGGCTACATT
*
1608286 TCAGTGGTAGCTTTGGCTACA-T
1 TCAGTGGTAGCTTCGGCTACATT
* *
1608308 CCAGTGGTAGCTTCGGCTACATA
1 TCAGTGGTAGCTTCGGCTACATT
1608331 TCAGTG
1 TCAGTG
1608337 TGGCACTTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
22 20 0.44
23 25 0.56
ACGTcount: A:0.19, C:0.22, G:0.27, T:0.32
Consensus pattern (23 bp):
TCAGTGGTAGCTTCGGCTACATT
Found at i:1608315 original size:22 final size:22
Alignment explanation
Indices: 1608264--1608329 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
1608254 TGTTATTGAT
*
1608264 CAGTGGTAGCTTCGGCTACATTT
1 CAGTGGTAGCTTCGGCTACA-TC
*
1608287 CAGTGGTAGCTTTGGCTACATC
1 CAGTGGTAGCTTCGGCTACATC
1608309 CAGTGGTAGCTTCGGCTACAT
1 CAGTGGTAGCTTCGGCTACAT
1608330 ATCAGTGTGG
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
22 21 0.52
23 19 0.47
ACGTcount: A:0.18, C:0.23, G:0.27, T:0.32
Consensus pattern (22 bp):
CAGTGGTAGCTTCGGCTACATC
Found at i:1613160 original size:31 final size:31
Alignment explanation
Indices: 1613092--1613165 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
1613082 AAAAAATATT
1613092 AGGTACTAAATTAAGAAAAAGAGTCAAGTTC
1 AGGTACTAAATTAAGAAAAAGAGTCAAGTTC
* * * * * *
1613123 AAGTACTAGATTAGGAAAACGTGTCAAGTTT
1 AGGTACTAAATTAAGAAAAAGAGTCAAGTTC
*
1613154 GGGTACTAAATT
1 AGGTACTAAATT
1613166 GGACCCAAAA
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.42, C:0.09, G:0.22, T:0.27
Consensus pattern (31 bp):
AGGTACTAAATTAAGAAAAAGAGTCAAGTTC
Found at i:1615675 original size:30 final size:32
Alignment explanation
Indices: 1615634--1615724 Score: 95
Period size: 31 Copynumber: 3.0 Consensus size: 32
1615624 CTATACGCAT
*
1615634 AATAC-AAGACTAAAATTTTA-AAA-TTAAAA
1 AATACAAAGACTAAAATTTAACAAATTTAAAA
* *
1615663 AGTATAAAGACTAAAA-TTAACAAATTTAAAA
1 AATACAAAGACTAAAATTTAACAAATTTAAAA
*
1615694 AATACAAAAACTAAAA-TTAATCAAA-TTAAAA
1 AATACAAAGACTAAAATTTAA-CAAATTTAAAA
1615725 TATAAAAATC
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
29 6 0.12
30 13 0.25
31 29 0.56
32 4 0.08
ACGTcount: A:0.64, C:0.08, G:0.03, T:0.25
Consensus pattern (32 bp):
AATACAAAGACTAAAATTTAACAAATTTAAAA
Found at i:1615707 original size:31 final size:30
Alignment explanation
Indices: 1615654--1615732 Score: 97
Period size: 31 Copynumber: 2.6 Consensus size: 30
1615644 TAAAATTTTA
* *
1615654 AAATTAAAAAGTATAAAGACTAAAATTAA-C
1 AAATTAAAAAATA-AAAAACTAAAATTAATC
1615684 AAATTTAAAAAATACAAAAACTAAAATTAATC
1 AAA-TTAAAAAATA-AAAAACTAAAATTAATC
*
1615716 AAATTAAAATATAAAAA
1 AAATTAAAAAATAAAAA
1615733 TCAACCCACC
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
30 7 0.16
31 32 0.74
32 4 0.09
ACGTcount: A:0.67, C:0.06, G:0.03, T:0.24
Consensus pattern (30 bp):
AAATTAAAAAATAAAAAACTAAAATTAATC
Found at i:1629791 original size:39 final size:38
Alignment explanation
Indices: 1629748--1629821 Score: 89
Period size: 38 Copynumber: 1.9 Consensus size: 38
1629738 TAGCGGATTT
*
1629748 GGAAT-TAAAT-AAATTAATGAAAATATTTAAAAATTTACG
1 GGAATCTAAATAAAATT-AT-AAAA-AATTAAAAATTTACG
*
1629787 GGAATCTAATTAAAATTATAAAAAATTAAAAATTT
1 GGAATCTAAATAAAATTATAAAAAATTAAAAATTT
1629822 TTTTAAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
38 11 0.35
39 9 0.29
40 6 0.19
41 5 0.16
ACGTcount: A:0.55, C:0.03, G:0.08, T:0.34
Consensus pattern (38 bp):
GGAATCTAAATAAAATTATAAAAAATTAAAAATTTACG
Found at i:1645541 original size:15 final size:15
Alignment explanation
Indices: 1645521--1645553 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
1645511 CCAAAAAGTC
1645521 AAAAAACT-AAACTCT
1 AAAAAACTCAAAC-CT
1645536 AAAAAACTCAAACCT
1 AAAAAACTCAAACCT
1645551 AAA
1 AAA
1645554 CAAGTTCCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.64, C:0.21, G:0.00, T:0.15
Consensus pattern (15 bp):
AAAAAACTCAAACCT
Found at i:1646934 original size:14 final size:14
Alignment explanation
Indices: 1646915--1646945 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
1646905 AATACTTGTC
1646915 TTGTAGGGTCAAAA
1 TTGTAGGGTCAAAA
1646929 TTGTAGGGTCAAAA
1 TTGTAGGGTCAAAA
1646943 TTG
1 TTG
1646946 CAGTGAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.32, C:0.06, G:0.29, T:0.32
Consensus pattern (14 bp):
TTGTAGGGTCAAAA
Found at i:1647331 original size:5 final size:5
Alignment explanation
Indices: 1647321--1647360 Score: 53
Period size: 5 Copynumber: 7.4 Consensus size: 5
1647311 TAGGGTATAG
1647321 TAAAA TAAAA TAAAA TAAAA TAAAA TGAATATA TAAAA TA
1 TAAAA TAAAA TAAAA TAAAA TAAAA T-AA-A-A TAAAA TA
1647361 TGGGACACGT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
5 24 0.75
6 3 0.09
7 3 0.09
8 2 0.06
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (5 bp):
TAAAA
Found at i:1647341 original size:15 final size:18
Alignment explanation
Indices: 1647316--1647360 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 18
1647306 GTATATAGGG
1647316 TATAGTAAAATAAAAT-AA
1 TATA-TAAAATAAAATGAA
1647334 -A-ATAAAATAAAATGAA
1 TATATAAAATAAAATGAA
1647350 TATATAAAATA
1 TATATAAAATA
1647361 TGGGACACGT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
15 11 0.46
16 3 0.12
17 2 0.08
18 8 0.33
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (18 bp):
TATATAAAATAAAATGAA
Found at i:1652499 original size:18 final size:18
Alignment explanation
Indices: 1652451--1652543 Score: 89
Period size: 18 Copynumber: 5.2 Consensus size: 18
1652441 CCCAACTACT
* *
1652451 GTATATGTGAACAGTACC
1 GTATACGTGAATAGTACC
* *
1652469 GTATACATGAATAGTGCC
1 GTATACGTGAATAGTACC
* *
1652487 GTATACGTAAATAGTACT
1 GTATACGTGAATAGTACC
* *
1652505 ATATACGTGAATAGTGA-T
1 GTATACGTGAATAGT-ACC
*
1652523 ATATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
1652541 GTA
1 GTA
1652544 AACGGTCGTA
Statistics
Matches: 61, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
17 1 0.02
18 59 0.97
19 1 0.02
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:1652503 original size:36 final size:36
Alignment explanation
Indices: 1652463--1652543 Score: 99
Period size: 36 Copynumber: 2.2 Consensus size: 36
1652453 ATATGTGAAC
* *
1652463 AGTACCGTATACATGAATAGTGCCGTATACGTAAAT
1 AGTACCGTATACATGAATAGTGACATATACGTAAAT
** * * *
1652499 AGTACTATATACGTGAATAGTGATATATACGTGAAT
1 AGTACCGTATACATGAATAGTGACATATACGTAAAT
1652535 AGTACCGTA
1 AGTACCGTA
1652544 AACGGTCGTA
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.30
Consensus pattern (36 bp):
AGTACCGTATACATGAATAGTGACATATACGTAAAT
Found at i:1656000 original size:6 final size:7
Alignment explanation
Indices: 1655984--1656011 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
1655974 AATTGTATCT
1655984 AAAAACA
1 AAAAACA
1655991 AAAAACA
1 AAAAACA
1655998 AAAAACA
1 AAAAACA
1656005 AAAAACA
1 AAAAACA
1656012 TTTATTTCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAAACA
Found at i:1657002 original size:133 final size:133
Alignment explanation
Indices: 1656762--1657158 Score: 424
Period size: 144 Copynumber: 2.9 Consensus size: 133
1656752 AAACAATAAT
* * * * * *
1656762 CGAAGATTAGCAGAGAAGAGAGAACAACTTCGAAAGCTGGTAACCACTTCAAAGTTATCGAAATT
1 CGAAGATTAGCAGAGAAGAGAGAACAATTTCG-ACGCTCGTAATCACTACAAAGCTATCGAAATT
* *
1656827 CGATCAAACGAAC-TTCATAATTC-AGCTATAAAACAACCATCCATCATCAAAAAAAAA-AAATT
65 CTATCAAACGAACTTTCATAATTCGA-CTATAAAACAACGATCCATCA-CAAAAAAAAAGAAATT
1656889 CAAAAG
128 CAAAAG
* * * *
1656895 CGAAGGTTAGCAGAGAAGAGAGAACGATTTCGACGCTCGTAATCACTCCAAAGCTATCGAAGTTC
1 CGAAGATTAGCAGAGAAGAGAGAACAATTTCGACGCTCGTAATCACTACAAAGCTATCGAAATTC
1656960 TATCAAACGAACTTTCATAATTCGACTATAAAACAACGATCCATCACAAAAAAAAGAAAGAAAGA
66 TATCAAACGAACTTTCATAATTCGACTATAAAACAACGATCCATCAC---------AAA-AAA-A
1657025 AAGAAATTCAAAAG
120 AAGAAATTCAAAAG
* * * * * *
1657039 CAAAGATTAGCAGAGCAGATAGAACAATTTCGACGCTCGTAATCACTACAAATCTTTCTAAATT-
1 CGAAGATTAGCAGAGAAGAGAGAACAATTTCGACGCTCGTAATCACTACAAAGCTATCGAAATTC
* ** * *
1657103 TGATCAAACGAACTTGCATAACCCGACTATTAAACAACGATCCATCACCAAAAAAA
66 T-ATCAAACGAACTTTCATAATTCGACTATAAAACAACGATCCATCACAAAAAAAA
1657159 TTCAAAAAAC
Statistics
Matches: 223, Mismatches: 26, Indels: 30
0.80 0.09 0.11
Matches are distributed among these distances:
132 39 0.17
133 61 0.27
134 4 0.02
135 2 0.01
141 3 0.01
142 3 0.01
143 4 0.02
144 107 0.48
ACGTcount: A:0.45, C:0.20, G:0.14, T:0.20
Consensus pattern (133 bp):
CGAAGATTAGCAGAGAAGAGAGAACAATTTCGACGCTCGTAATCACTACAAAGCTATCGAAATTC
TATCAAACGAACTTTCATAATTCGACTATAAAACAACGATCCATCACAAAAAAAAAGAAATTCAA
AAG
Found at i:1672382 original size:16 final size:17
Alignment explanation
Indices: 1672339--1672387 Score: 57
Period size: 16 Copynumber: 3.0 Consensus size: 17
1672329 TAGACATGAA
*
1672339 ATAAATTATTAATTAAT
1 ATAAATTATTAAATAAT
*
1672356 ATAAATT-TTAAATATT
1 ATAAATTATTAAATAAT
*
1672372 A-AAATTATTAATTAAT
1 ATAAATTATTAAATAAT
1672388 CCAATAACTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
15 5 0.19
16 15 0.56
17 7 0.26
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATAAATTATTAAATAAT
Found at i:1677199 original size:21 final size:21
Alignment explanation
Indices: 1677155--1677215 Score: 77
Period size: 21 Copynumber: 2.7 Consensus size: 21
1677145 TAATTCTTCT
1677155 ATTTTTTTATTTTGAAGTAAATAAA
1 ATTTTTTTA-TTTG--G-AAATAAA
*
1677180 ATTTTTTTATTTGGAAATAAG
1 ATTTTTTTATTTGGAAATAAA
1677201 ATTTTTTTATTTGGA
1 ATTTTTTTATTTGGA
1677216 CTTAAAAACT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
21 21 0.60
22 1 0.03
24 4 0.11
25 9 0.26
ACGTcount: A:0.33, C:0.00, G:0.11, T:0.56
Consensus pattern (21 bp):
ATTTTTTTATTTGGAAATAAA
Found at i:1677928 original size:43 final size:43
Alignment explanation
Indices: 1677867--1677955 Score: 169
Period size: 43 Copynumber: 2.1 Consensus size: 43
1677857 TCAATCAATT
*
1677867 TAGTGAATTTCATTTTTGGCCTTTTTCTGTTATGGGTTGGGCC
1 TAGTGAATTTCATTTTTGGCCTTTTTCTGTTATGGGTTAGGCC
1677910 TAGTGAATTTCATTTTTGGCCTTTTTCTGTTATGGGTTAGGCC
1 TAGTGAATTTCATTTTTGGCCTTTTTCTGTTATGGGTTAGGCC
1677953 TAG
1 TAG
1677956 AGGGTTATTT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.13, C:0.13, G:0.25, T:0.48
Consensus pattern (43 bp):
TAGTGAATTTCATTTTTGGCCTTTTTCTGTTATGGGTTAGGCC
Found at i:1678819 original size:21 final size:21
Alignment explanation
Indices: 1678795--1678850 Score: 61
Period size: 20 Copynumber: 2.9 Consensus size: 21
1678785 ATCGAAATAA
1678795 TAAAATCAAATTATATTAAAT
1 TAAAATCAAATTATATTAAAT
1678816 T-AAA--AAA-TATA-TAAAT
1 TAAAATCAAATTATATTAAAT
1678832 TAAATATCAAATT-TATTAA
1 TAAA-ATCAAATTATATTAA
1678851 TTTCATTTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 12
0.71 0.00 0.29
Matches are distributed among these distances:
16 6 0.21
17 6 0.21
18 4 0.14
20 8 0.28
21 5 0.17
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.38
Consensus pattern (21 bp):
TAAAATCAAATTATATTAAAT
Found at i:1681894 original size:31 final size:31
Alignment explanation
Indices: 1681859--1681918 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
1681849 CTTTTAACCC
*
1681859 CTAAATCTGA-TAATTAGATTCATTTTGGTAT
1 CTAAAT-TGAGTAATTAGATTCAATTTGGTAT
*
1681890 CTAAATTTAGTAATTAGATTCAATTTGGT
1 CTAAATTGAGTAATTAGATTCAATTTGGT
1681919 CATTGATCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 2 0.08
31 24 0.92
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.45
Consensus pattern (31 bp):
CTAAATTGAGTAATTAGATTCAATTTGGTAT
Found at i:1695559 original size:13 final size:13
Alignment explanation
Indices: 1695541--1695569 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1695531 ATAATTCTAC
1695541 AATGAACAAATAA
1 AATGAACAAATAA
1695554 AATGAACAAATAA
1 AATGAACAAATAA
1695567 AAT
1 AAT
1695570 ACTCTCAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.69, C:0.07, G:0.07, T:0.17
Consensus pattern (13 bp):
AATGAACAAATAA
Found at i:1701185 original size:19 final size:17
Alignment explanation
Indices: 1701154--1701241 Score: 95
Period size: 17 Copynumber: 4.9 Consensus size: 17
1701144 CTGTTTAGGT
1701154 ACTATTCACGTATACGC
1 ACTATTCACGTATACGC
*
1701171 ACTATTTCTACGTATACATGT
1 ACTA-TTC-ACGTATAC--GC
*
1701192 ACTATTCACATATACGC
1 ACTATTCACGTATACGC
*
1701209 ACTATTCACGTATACGGT
1 ACTATTCACGTATAC-GC
*
1701227 ACTGTTCACGTATAC
1 ACTATTCACGTATAC
1701242 AGTAGTTGGG
Statistics
Matches: 60, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
17 19 0.32
18 18 0.30
19 15 0.25
20 3 0.05
21 5 0.08
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.34
Consensus pattern (17 bp):
ACTATTCACGTATACGC
Found at i:1701194 original size:38 final size:35
Alignment explanation
Indices: 1701151--1701241 Score: 128
Period size: 38 Copynumber: 2.5 Consensus size: 35
1701141 CGACTGTTTA
1701151 GGTACTATTCACGTATACGCACTATTTCTACGTATAC
1 GGTACTATTCACGTATACGCACTA-TTC-ACGTATAC
* *
1701188 ATGTACTATTCACATATACGCACTATTCACGTATAC
1 -GGTACTATTCACGTATACGCACTATTCACGTATAC
*
1701224 GGTACTGTTCACGTATAC
1 GGTACTATTCACGTATAC
1701242 AGTAGTTGGG
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
35 15 0.31
36 8 0.17
37 3 0.06
38 22 0.46
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34
Consensus pattern (35 bp):
GGTACTATTCACGTATACGCACTATTCACGTATAC
Found at i:1708098 original size:117 final size:113
Alignment explanation
Indices: 1707896--1708105 Score: 303
Period size: 114 Copynumber: 1.8 Consensus size: 113
1707886 ATTCAGTAAC
* * * *
1707896 AGGAATAAATAAGCAAGCAAATGGGAGTTGGTAGGTGTCAGCTATGGTACAAGCCTTAACCGTGA
1 AGGAATAAATAAGCAAGCAAATGGGAGTTGGTAGGTGTCAGCAATGGTACAAACCTAAACAGTGA
* *
1707961 AGCAAATAAGCATTAAAGGTAAGCATTTAATAGGCAAATTTGACTAAG
66 AGCAAAGAAGCATAAAAGGTAAGCATTTAATAGGCAAATTTGACTAAG
* * *
1708009 AGGAATAAATAAGCAAGCAAAATGTGAGTTGGTAGGTGTCATCAATGGTGCAAACCGTAAACATA
1 AGGAATAAATAAGCAAGC-AAATGGGAGTTGGTAGGTGTCAGCAATGGTACAAACC-TAAAC--A
1708074 GTGAAGCAAAGAAGCATAAAAGGTAAGCATTT
62 GTGAAGCAAAGAAGCATAAAAGGTAAGCATTT
1708106 GATGATCCAT
Statistics
Matches: 84, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
113 18 0.21
114 32 0.38
115 4 0.05
117 30 0.36
ACGTcount: A:0.41, C:0.12, G:0.25, T:0.22
Consensus pattern (113 bp):
AGGAATAAATAAGCAAGCAAATGGGAGTTGGTAGGTGTCAGCAATGGTACAAACCTAAACAGTGA
AGCAAAGAAGCATAAAAGGTAAGCATTTAATAGGCAAATTTGACTAAG
Found at i:1709725 original size:20 final size:21
Alignment explanation
Indices: 1709685--1709725 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1709675 AAAATAATAA
*
1709685 AAATATATTATAATATTATTT
1 AAATATATGATAATATTATTT
*
1709706 AAATATATGA-AATGTTATTT
1 AAATATATGATAATATTATTT
1709726 CAGACAAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (21 bp):
AAATATATGATAATATTATTT
Found at i:1710781 original size:18 final size:18
Alignment explanation
Indices: 1710760--1710846 Score: 95
Period size: 18 Copynumber: 4.8 Consensus size: 18
1710750 CTTTTACGGT
1710760 ACTATTCACGTATACGAC
1 ACTATTCACGTATACGAC
* *
1710778 ACTATTCACATATAC-AGT
1 ACTATTCACGTATACGA-C
* *
1710796 ACTATTCACATATACGGC
1 ACTATTCACGTATACGAC
**
1710814 ACTATTCACGTATACGGT
1 ACTATTCACGTATACGAC
*
1710832 ACTGTTCACGTATAC
1 ACTATTCACGTATAC
1710847 AATAGTTGGG
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
17 1 0.02
18 59 0.98
ACGTcount: A:0.32, C:0.25, G:0.11, T:0.31
Consensus pattern (18 bp):
ACTATTCACGTATACGAC
Found at i:1710810 original size:36 final size:36
Alignment explanation
Indices: 1710758--1710846 Score: 133
Period size: 36 Copynumber: 2.5 Consensus size: 36
1710748 ACCTTTTACG
1710758 GTACTATTCACGTATACGACACTATTCACATATACA
1 GTACTATTCACGTATACGACACTATTCACATATACA
* * * *
1710794 GTACTATTCACATATACGGCACTATTCACGTATACG
1 GTACTATTCACGTATACGACACTATTCACATATACA
*
1710830 GTACTGTTCACGTATAC
1 GTACTATTCACGTATAC
1710847 AATAGTTGGG
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 47 1.00
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.31
Consensus pattern (36 bp):
GTACTATTCACGTATACGACACTATTCACATATACA
Found at i:1717773 original size:117 final size:113
Alignment explanation
Indices: 1717571--1717780 Score: 303
Period size: 114 Copynumber: 1.8 Consensus size: 113
1717561 ATTCAGTAAC
* * * *
1717571 AGGAATAAATAAGCAAGCAAATGGGAGTTGGTAGGTGTCAGCTATGGTACAAGCCTTAACCGTGA
1 AGGAATAAATAAGCAAGCAAATGGGAGTTGGTAGGTGTCAGCAATGGTACAAACCTAAACAGTGA
* *
1717636 AGCAAATAAGCATTAAAGGTAAGCATTTAATAGGCAAATTTGACTAAG
66 AGCAAAGAAGCATAAAAGGTAAGCATTTAATAGGCAAATTTGACTAAG
* * *
1717684 AGGAATAAATAAGCAAGCAAAATGTGAGTTGGTAGGTGTCATCAATGGTGCAAACCGTAAACATA
1 AGGAATAAATAAGCAAGC-AAATGGGAGTTGGTAGGTGTCAGCAATGGTACAAACC-TAAAC--A
1717749 GTGAAGCAAAGAAGCATAAAAGGTAAGCATTT
62 GTGAAGCAAAGAAGCATAAAAGGTAAGCATTT
1717781 GATGATCCAT
Statistics
Matches: 84, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
113 18 0.21
114 32 0.38
115 4 0.05
117 30 0.36
ACGTcount: A:0.41, C:0.12, G:0.25, T:0.22
Consensus pattern (113 bp):
AGGAATAAATAAGCAAGCAAATGGGAGTTGGTAGGTGTCAGCAATGGTACAAACCTAAACAGTGA
AGCAAAGAAGCATAAAAGGTAAGCATTTAATAGGCAAATTTGACTAAG
Found at i:1719397 original size:20 final size:21
Alignment explanation
Indices: 1719357--1719397 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1719347 AAAATAATAA
*
1719357 AAATATATTATAATATTATTT
1 AAATATATGATAATATTATTT
*
1719378 AAATATATGA-AATGTTATTT
1 AAATATATGATAATATTATTT
1719398 CAGACAAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (21 bp):
AAATATATGATAATATTATTT
Found at i:1720454 original size:18 final size:18
Alignment explanation
Indices: 1720433--1720519 Score: 95
Period size: 18 Copynumber: 4.8 Consensus size: 18
1720423 CTTTTACGGT
1720433 ACTATTCACGTATACGAC
1 ACTATTCACGTATACGAC
* *
1720451 ACTATTCACATATAC-AGT
1 ACTATTCACGTATACGA-C
* *
1720469 ACTATTCACATATACGGC
1 ACTATTCACGTATACGAC
**
1720487 ACTATTCACGTATACGGT
1 ACTATTCACGTATACGAC
*
1720505 ACTGTTCACGTATAC
1 ACTATTCACGTATAC
1720520 AATAGTTGGG
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
17 1 0.02
18 59 0.98
ACGTcount: A:0.32, C:0.25, G:0.11, T:0.31
Consensus pattern (18 bp):
ACTATTCACGTATACGAC
Found at i:1720483 original size:36 final size:36
Alignment explanation
Indices: 1720431--1720519 Score: 133
Period size: 36 Copynumber: 2.5 Consensus size: 36
1720421 ACCTTTTACG
1720431 GTACTATTCACGTATACGACACTATTCACATATACA
1 GTACTATTCACGTATACGACACTATTCACATATACA
* * * *
1720467 GTACTATTCACATATACGGCACTATTCACGTATACG
1 GTACTATTCACGTATACGACACTATTCACATATACA
*
1720503 GTACTGTTCACGTATAC
1 GTACTATTCACGTATAC
1720520 AATAGTTGGG
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 47 1.00
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.31
Consensus pattern (36 bp):
GTACTATTCACGTATACGACACTATTCACATATACA
Found at i:1739439 original size:43 final size:43
Alignment explanation
Indices: 1739378--1739633 Score: 244
Period size: 43 Copynumber: 6.0 Consensus size: 43
1739368 TTAGTGGCGC
* * * *
1739378 CTATAGATCACGACCTTTAGCTACACTTTTATTACAAACGCCG
1 CTATAGATCACGACCTTTAGCGACGCTTTTCTCACAAACGCCG
* *
1739421 CTATAGATCACGACCTTTAACGACGCTTTTCTCACAAACGCTG
1 CTATAGATCACGACCTTTAGCGACGCTTTTCTCACAAACGCCG
* * * *
1739464 TTATAGATCATGACTTTTAGCGACGCTTCTCTCACAAACGCCG
1 CTATAGATCACGACCTTTAGCGACGCTTTTCTCACAAACGCCG
* * * *** * *
1739507 CTATAGATCATGA-CTTTAGTGGCGCTTCAATCACAAATGCTG
1 CTATAGATCACGACCTTTAGCGACGCTTTTCTCACAAACGCCG
* * ** *
1739549 CTATAGATCATGACTTTTAATGACGCTTTTCTCACAAACGCTG
1 CTATAGATCACGACCTTTAGCGACGCTTTTCTCACAAACGCCG
* * * * * *
1739592 CTATAGATCATGACTTTTAACGGCGCTTTTATCATAAACGCC
1 CTATAGATCACGACCTTTAGCGACGCTTTTCTCACAAACGCC
1739634 ACAAATTTTG
Statistics
Matches: 180, Mismatches: 32, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
42 35 0.19
43 145 0.81
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.31
Consensus pattern (43 bp):
CTATAGATCACGACCTTTAGCGACGCTTTTCTCACAAACGCCG
Found at i:1739559 original size:85 final size:85
Alignment explanation
Indices: 1739378--1739619 Score: 286
Period size: 85 Copynumber: 2.8 Consensus size: 85
1739368 TTAGTGGCGC
* * * * * * *
1739378 CTATAGATCACGACCTTTAGCTACACTTTTATTACAAACGCCGCTATAGATCACGACCTTTAACG
1 CTATAGATCATGACTTTTAGCGACGCTTTTCTCACAAACGCCGCTATAGATCATGA-CTTTAACG
***
1739443 ACGCTTTTCTCACAAACGCTG
65 ACGCTTCAATCACAAACGCTG
* * ** *
1739464 TTATAGATCATGACTTTTAGCGACGCTTCTCTCACAAACGCCGCTATAGATCATGACTTTAGTGG
1 CTATAGATCATGACTTTTAGCGACGCTTTTCTCACAAACGCCGCTATAGATCATGACTTTAACGA
*
1739529 CGCTTCAATCACAAATGCTG
66 CGCTTCAATCACAAACGCTG
** *
1739549 CTATAGATCATGACTTTTAATGACGCTTTTCTCACAAACGCTGCTATAGATCATGACTTTTAACG
1 CTATAGATCATGACTTTTAGCGACGCTTTTCTCACAAACGCCGCTATAGATCATGAC-TTTAACG
*
1739614 GCGCTT
65 ACGCTT
1739620 TTATCATAAA
Statistics
Matches: 132, Mismatches: 23, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
85 74 0.56
86 58 0.44
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.31
Consensus pattern (85 bp):
CTATAGATCATGACTTTTAGCGACGCTTTTCTCACAAACGCCGCTATAGATCATGACTTTAACGA
CGCTTCAATCACAAACGCTG
Found at i:1739916 original size:21 final size:21
Alignment explanation
Indices: 1739890--1739935 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
1739880 TTTTGCTCTG
1739890 CTCTGCTTCCCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
* *
1739911 CTCTGCTTCCCTCGTTGCTGC
1 CTCTGCTTCCCTCGCTGCAGC
1739932 CTCT
1 CTCT
1739936 TGTTTCCTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.02, C:0.46, G:0.17, T:0.35
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:1745455 original size:9 final size:9
Alignment explanation
Indices: 1745443--1745502 Score: 61
Period size: 9 Copynumber: 6.3 Consensus size: 9
1745433 TTGATAAATT
1745443 TAAGTTATG
1 TAAGTTATG
1745452 TAAGTTATG
1 TAAGTTATG
1745461 T-A-TTATG
1 TAAGTTATG
1745468 TAAGTTTATG
1 TAAG-TTATG
1745478 TATTTAGGTTATG
1 TA---A-GTTATG
1745491 TAAGTTATG
1 TAAGTTATG
1745500 TAA
1 TAA
1745503 TGTATCAATT
Statistics
Matches: 44, Mismatches: 0, Indels: 14
0.76 0.00 0.24
Matches are distributed among these distances:
7 6 0.14
8 2 0.05
9 19 0.43
10 8 0.18
13 8 0.18
14 1 0.02
ACGTcount: A:0.32, C:0.00, G:0.20, T:0.48
Consensus pattern (9 bp):
TAAGTTATG
Found at i:1745468 original size:16 final size:17
Alignment explanation
Indices: 1745447--1745481 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
1745437 TAAATTTAAG
1745447 TTATGTAAG-TTATGTA
1 TTATGTAAGTTTATGTA
1745463 TTATGTAAGTTTATGTA
1 TTATGTAAGTTTATGTA
1745480 TT
1 TT
1745482 TAGGTTATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.29, C:0.00, G:0.17, T:0.54
Consensus pattern (17 bp):
TTATGTAAGTTTATGTA
Found at i:1745533 original size:19 final size:19
Alignment explanation
Indices: 1745509--1745546 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1745499 GTAATGTATC
1745509 AATTTTAAAAAAATATATA
1 AATTTTAAAAAAATATATA
*
1745528 AATTTTAAAAATATATATA
1 AATTTTAAAAAAATATATA
1745547 TTAAAACTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AATTTTAAAAAAATATATA
Found at i:1745558 original size:17 final size:16
Alignment explanation
Indices: 1745518--1745561 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
1745508 CAATTTTAAA
* *
1745518 AAAATATATAAATTTT
1 AAAATATATATATATT
1745534 AAAA-ATATATATATT
1 AAAATATATATATATT
1745549 AAAACTATATATA
1 AAAA-TATATATA
1745562 AATATTAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 13 0.54
16 4 0.17
17 7 0.29
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (16 bp):
AAAATATATATATATT
Found at i:1754724 original size:21 final size:21
Alignment explanation
Indices: 1754700--1754744 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1754690 GATAAATTTA
1754700 ATTATCACAAAGATAAATAAC
1 ATTATCACAAAGATAAATAAC
* * *
1754721 ATTATCATAAATATAAATATC
1 ATTATCACAAAGATAAATAAC
1754742 ATT
1 ATT
1754745 TCAATATCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.53, C:0.11, G:0.02, T:0.33
Consensus pattern (21 bp):
ATTATCACAAAGATAAATAAC
Found at i:1761995 original size:6 final size:6
Alignment explanation
Indices: 1761984--1762009 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1761974 ATTCAAATAA
1761984 ATATAC ATATAC ATATAC ATATAC AT
1 ATATAC ATATAC ATATAC ATATAC AT
1762010 GTATATGCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (6 bp):
ATATAC
Found at i:1766860 original size:20 final size:19
Alignment explanation
Indices: 1766816--1766863 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 19
1766806 GAATGGTTTC
1766816 AATTTTATAATTATTTTTAT
1 AATTTTATAA-TATTTTTAT
*
1766836 GATTTTATAA-ATTTTTACT
1 AATTTTATAATATTTTTA-T
1766855 AAATTTTAT
1 -AATTTTAT
1766864 TCTATATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 7 0.29
19 1 0.04
20 16 0.67
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (19 bp):
AATTTTATAATATTTTTAT
Found at i:1769897 original size:168 final size:168
Alignment explanation
Indices: 1769619--1769947 Score: 480
Period size: 168 Copynumber: 2.0 Consensus size: 168
1769609 AGGGTAGAAC
* * * * *
1769619 GTTAATTTAATCTATACTAATATTTAGGATTGACAGAGTTGATGTCGCTCATCAATTGAGATAAC
1 GTTAATTTAATCTATACTAATATTTAGGATTGACAGACTAGATATCACTCATCAATTGAGACAAC
* * * * *
1769684 CGAGTTCTAACTTAGTTGAAAAATTACGGAAAATCTATTTTTTATAAAATAAGGAATATTATTAT
66 CGAGTTCTAACTTAATTGAAAAATTACAGAAAACCCATTTTTTATAAAATAAGGAACATTATTAT
*
1769749 GACGATATTTTTGTCATTTTATATTTTAGGACAAAAAA
131 GACGATATTTTTGTCATTTTATATTCTAGGACAAAAAA
* * *
1769787 GTTAATTTAATCTATACTAATATTTAGGATTGGCTGAACTAG-TATCACTCATCAATTGAGGCAA
1 GTTAATTTAATCTATACTAATATTTAGGATTGACAG-ACTAGATATCACTCATCAATTGAGACAA
* ** *
1769851 TCGAGTTCTAACTTAATTGGGAAATTACAGAAAACCCGTTTTTTATAAAATAAGGAACATTATTA
65 CCGAGTTCTAACTTAATTGAAAAATTACAGAAAACCCATTTTTTATAAAATAAGGAACATTATTA
1769916 TGACGATATTTTTGTCATTTTATATTCTAGGA
130 TGACGATATTTTTGTCATTTTATATTCTAGGA
1769948 TAGTAATTTA
Statistics
Matches: 142, Mismatches: 18, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
168 139 0.98
169 3 0.02
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (168 bp):
GTTAATTTAATCTATACTAATATTTAGGATTGACAGACTAGATATCACTCATCAATTGAGACAAC
CGAGTTCTAACTTAATTGAAAAATTACAGAAAACCCATTTTTTATAAAATAAGGAACATTATTAT
GACGATATTTTTGTCATTTTATATTCTAGGACAAAAAA
Found at i:1776445 original size:6 final size:6
Alignment explanation
Indices: 1776434--1776477 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
1776424 GGCAACCCAA
* *
1776434 TTTTAT TTTTAT TTTTAT ATATA- TTTTAT TTTTAT TTTTAT TTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTT
1776478 CTTCATGTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
5 3 0.09
6 30 0.91
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTAT
Found at i:1779554 original size:22 final size:21
Alignment explanation
Indices: 1779503--1779556 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 21
1779493 TTTAATTAAA
* *
1779503 ATTAAAATTAAAATTATTTTT
1 ATTAAAATTAAAATAATTGTT
*
1779524 AATAAAATTAAAACTAATTGTT
1 ATTAAAATTAAAA-TAATTGTT
1779546 ATTAAAATTAA
1 ATTAAAATTAA
1779557 TTGTTAGTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 12 0.43
22 16 0.57
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (21 bp):
ATTAAAATTAAAATAATTGTT
Found at i:1779569 original size:16 final size:16
Alignment explanation
Indices: 1779532--1779571 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
1779522 TTAATAAAAT
* *
1779532 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
1779548 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
1779564 TAAAATTA
1 TAAAATTA
1779572 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:1779601 original size:59 final size:67
Alignment explanation
Indices: 1779560--1779760 Score: 312
Period size: 68 Copynumber: 3.1 Consensus size: 67
1779550 AAATTAATTG
*
1779560 TTAGTAAAATTATCAAATTATTAATTG-TTAATTGTATTAATTGTTGTAATAAAATCTAACATTT
1 TTAGTAAATTTATCAAATTATTAATTGATTAATTGTATTAATTGTTGTAATAAAATCTAACATTT
1779624 GA
66 GA
1779626 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTG-ATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1779691 TGA
65 TGA
*
1779694 TTAGTAAATTTATC-----A--AATT-ATTAATTGTATTAATTGTTGTAACAAAATCTAACATTT
1 TTAGTAAATTTATCAAATTATTAATTGATTAATTGTATTAATTGTTGTAATAAAATCTAACATTT
1779751 GA
66 GA
1779753 TTAGTAAA
1 TTAGTAAA
1779761 ACAAACTTGA
Statistics
Matches: 131, Mismatches: 2, Indels: 11
0.91 0.01 0.08
Matches are distributed among these distances:
59 47 0.36
61 4 0.03
63 1 0.01
66 26 0.20
68 53 0.40
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45
Consensus pattern (67 bp):
TTAGTAAATTTATCAAATTATTAATTGATTAATTGTATTAATTGTTGTAATAAAATCTAACATTT
GA
Found at i:1779677 original size:9 final size:9
Alignment explanation
Indices: 1779644--1779671 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
1779634 TTTATCAAAT
1779644 TATTAATTG
1 TATTAATTG
1779653 TATTAATTG
1 TATTAATTG
1779662 TATTAATTG
1 TATTAATTG
1779671 T
1 T
1779672 TGTAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:1779681 original size:68 final size:68
Alignment explanation
Indices: 1779560--1779730 Score: 319
Period size: 68 Copynumber: 2.5 Consensus size: 68
1779550 AAATTAATTG
*
1779560 TTAGTAAAATTATCAAATTATTAATTG--TTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1779623 TGA
66 TGA
1779626 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1779691 TGA
66 TGA
1779694 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGT
1779731 TGTAACAAAA
Statistics
Matches: 102, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
66 26 0.25
68 76 0.75
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.47
Consensus pattern (68 bp):
TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
TGA
Found at i:1779867 original size:22 final size:24
Alignment explanation
Indices: 1779827--1779870 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1779817 AAATAAACTT
1779827 AAAATAAAAAACTATTATATTTTA
1 AAAATAAAAAACTATTATATTTTA
1779851 AAAATAAAAAA-TA-TATATTT
1 AAAATAAAAAACTATTATATTT
1779871 AATATTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 2 0.10
24 11 0.55
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
AAAATAAAAAACTATTATATTTTA
Found at i:1785073 original size:42 final size:42
Alignment explanation
Indices: 1785010--1785110 Score: 148
Period size: 42 Copynumber: 2.4 Consensus size: 42
1785000 ACAATCAAGC
** * *
1785010 TACTCGAATTCAAGCTCAATTAAGCTCGCTTACTAATTTTTG
1 TACTCGAGCTCAAGCTTAATTAAGCTCACTTACTAATTTTTG
*
1785052 TACTCGAGCTCAAGCTTAATTAAGCTCATTTACTAATTTTTG
1 TACTCGAGCTCAAGCTTAATTAAGCTCACTTACTAATTTTTG
*
1785094 TACTCAAGCTCAAGCTT
1 TACTCGAGCTCAAGCTT
1785111 GAGCTCGAGC
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.38
Consensus pattern (42 bp):
TACTCGAGCTCAAGCTTAATTAAGCTCACTTACTAATTTTTG
Found at i:1787195 original size:55 final size:55
Alignment explanation
Indices: 1787116--1787227 Score: 224
Period size: 55 Copynumber: 2.0 Consensus size: 55
1787106 ATTAGGCGTA
1787116 TCCAAAATGTTAGGTATTTAGAAACATTAAATGTATGAATCCCTAAATTAATTAG
1 TCCAAAATGTTAGGTATTTAGAAACATTAAATGTATGAATCCCTAAATTAATTAG
1787171 TCCAAAATGTTAGGTATTTAGAAACATTAAATGTATGAATCCCTAAATTAATTAG
1 TCCAAAATGTTAGGTATTTAGAAACATTAAATGTATGAATCCCTAAATTAATTAG
1787226 TC
1 TC
1787228 GTGAGTATTT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 57 1.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (55 bp):
TCCAAAATGTTAGGTATTTAGAAACATTAAATGTATGAATCCCTAAATTAATTAG
Found at i:1787394 original size:6 final size:6
Alignment explanation
Indices: 1787383--1787407 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1787373 TAATATTTTA
1787383 TAATTT TAATTT TAATTT TAATTT T
1 TAATTT TAATTT TAATTT TAATTT T
1787408 TTTATCTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TAATTT
Found at i:1793888 original size:36 final size:36
Alignment explanation
Indices: 1793845--1793927 Score: 121
Period size: 36 Copynumber: 2.3 Consensus size: 36
1793835 TATTTTTAAG
*
1793845 CTCGAGCTTGATTAAGCTCGTTGACTAATTTTTGTA
1 CTCGAGCTTGATTAAGCTCATTGACTAATTTTTGTA
* * *
1793881 CTTGAGCTCGATTAAGCTCATTTACTAATTTTTGTA
1 CTCGAGCTTGATTAAGCTCATTGACTAATTTTTGTA
*
1793917 CTCAAGCTTGA
1 CTCGAGCTTGA
1793928 ACTCGAGCTC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.24, C:0.18, G:0.17, T:0.41
Consensus pattern (36 bp):
CTCGAGCTTGATTAAGCTCATTGACTAATTTTTGTA
Found at i:1796170 original size:55 final size:55
Alignment explanation
Indices: 1796086--1796189 Score: 147
Period size: 55 Copynumber: 1.9 Consensus size: 55
1796076 ATGTAATAAC
* * *
1796086 CGATTTAAACATATAAACAATCGATTCAAAAGAAGAAGTATTCCAACAAGACACT
1 CGATTTAAAAATATAAACAATAGATTCAAAAGAACAAGTATTCCAACAAGACACT
* *
1796141 CGATTTAAAAATAT-AACAAATATATTCAAAAGAACCAGTATTCCAACAA
1 CGATTTAAAAATATAAAC-AATAGATTCAAAAGAACAAGTATTCCAACAA
1796190 TTAAGACGAA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
54 3 0.07
55 40 0.93
ACGTcount: A:0.51, C:0.17, G:0.09, T:0.23
Consensus pattern (55 bp):
CGATTTAAAAATATAAACAATAGATTCAAAAGAACAAGTATTCCAACAAGACACT
Found at i:1797195 original size:108 final size:108
Alignment explanation
Indices: 1796952--1797276 Score: 580
Period size: 108 Copynumber: 3.0 Consensus size: 108
1796942 CCATACTTTG
* *
1796952 AAGTTTTAAGAGGATATTTGGCTATTTAGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCAC
1 AAGTTTAAAAAGGATATTTGGCTATTTAGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCAC
* * * *
1797017 GTTTCCTCG-ATTTTCCAAACGCGAAGTATTGCCTTATTTTAA
66 ATTTTCTCGAATTTTCCAAACGCGAAATATTGCCTTAATTTAA
1797059 AAGTTTAAAAAGGATATTTGGCTATTTAGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCAC
1 AAGTTTAAAAAGGATATTTGGCTATTTAGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCAC
1797124 ATTTTCTCGAATTTTCCAAACGCGAAATATTGCCTTAATTTAA
66 ATTTTCTCGAATTTTCCAAACGCGAAATATTGCCTTAATTTAA
1797167 AAGTTTAAAAAGGATATTTGGCTATTTAGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCAC
1 AAGTTTAAAAAGGATATTTGGCTATTTAGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCAC
*
1797232 ATTTTCTCGAATTTTCCAAACGTGAAATATTGCCTTAATTTAA
66 ATTTTCTCGAATTTTCCAAACGCGAAATATTGCCTTAATTTAA
1797275 AA
1 AA
1797277 CTTTTCCCTT
Statistics
Matches: 210, Mismatches: 7, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
107 70 0.33
108 140 0.67
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (108 bp):
AAGTTTAAAAAGGATATTTGGCTATTTAGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCAC
ATTTTCTCGAATTTTCCAAACGCGAAATATTGCCTTAATTTAA
Found at i:1797589 original size:2 final size:2
Alignment explanation
Indices: 1797577--1797628 Score: 65
Period size: 2 Copynumber: 27.5 Consensus size: 2
1797567 ATAAAACAAA
* *
1797577 AT AT A- AT AT AT AT AT AT A- AT -T AT AT AT AT AT AT AT GT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1797616 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
1797629 CAACAATCTA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
1 3 0.07
2 42 0.93
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1804510 original size:16 final size:16
Alignment explanation
Indices: 1804473--1804512 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
1804463 TTAATAAAAT
* *
1804473 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
1804489 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
1804505 TAAAATTA
1 TAAAATTA
1804513 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:1804618 original size:9 final size:9
Alignment explanation
Indices: 1804585--1804612 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
1804575 CTTATCAAAT
1804585 TATTAATTG
1 TATTAATTG
1804594 TATTAATTG
1 TATTAATTG
1804603 TATTAATTG
1 TATTAATTG
1804612 T
1 T
1804613 TGTAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:1804622 original size:68 final size:68
Alignment explanation
Indices: 1804501--1804711 Score: 381
Period size: 68 Copynumber: 3.1 Consensus size: 68
1804491 AAATTAATTG
1804501 TTAGTAAAATTATCAAATTATTAATTG--TTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAAATTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1804564 TGA
66 TGA
*
1804567 TTAGTAAACTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAAATTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1804632 TGA
66 TGA
* *
1804635 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAACAAAATCTAACATT
1 TTAGTAAAATTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1804700 TGA
66 TGA
1804703 TTAGTAAAA
1 TTAGTAAAA
1804712 CAAATTTGAT
Statistics
Matches: 139, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
66 26 0.19
68 113 0.81
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45
Consensus pattern (68 bp):
TTAGTAAAATTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
TGA
Found at i:1804665 original size:9 final size:9
Alignment explanation
Indices: 1804653--1804680 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
1804643 TTTATCAAAT
1804653 TATTAATTG
1 TATTAATTG
1804662 TATTAATTG
1 TATTAATTG
1804671 TATTAATTG
1 TATTAATTG
1804680 T
1 T
1804681 TGTAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:1804816 original size:22 final size:24
Alignment explanation
Indices: 1804776--1804819 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
1804766 AAATAAACTT
*
1804776 AAAATACAAAACTATTATATTTTA
1 AAAATACAAAAATATTATATTTTA
1804800 AAAATA-AAAAATA-TATATTT
1 AAAATACAAAAATATTATATTT
1804820 AATATTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 6 0.32
24 6 0.32
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (24 bp):
AAAATACAAAAATATTATATTTTA
Found at i:1804849 original size:15 final size:16
Alignment explanation
Indices: 1804829--1804859 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1804819 TAATATTTTT
1804829 TGGGCCGGG-CCGGGC
1 TGGGCCGGGCCCGGGC
1804844 TGGGCCGGGCCCGGGC
1 TGGGCCGGGCCCGGGC
1804860 CAAAAAATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.00, C:0.35, G:0.58, T:0.06
Consensus pattern (16 bp):
TGGGCCGGGCCCGGGC
Found at i:1812398 original size:42 final size:42
Alignment explanation
Indices: 1812351--1812432 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 42
1812341 CTCAAGTTCA
* * * *
1812351 AGCTCAATTAAGCTCGCTTACTAATTTTTGTACTCGAGCTAG
1 AGCTCAATGAAGCTCACTTACTAATTTTTGGACTCAAGCTAG
*
1812393 AGCTCAATGAAGCTCATTTACTAATTTTTGGACTCAAGCT
1 AGCTCAATGAAGCTCACTTACTAATTTTTGGACTCAAGCT
1812433 CAAGCTTGAG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (42 bp):
AGCTCAATGAAGCTCACTTACTAATTTTTGGACTCAAGCTAG
Found at i:1812498 original size:19 final size:19
Alignment explanation
Indices: 1812476--1812512 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1812466 AGCTTAAGGT
1812476 TAATAATATAAATTAAAAG
1 TAATAATATAAATTAAAAG
* *
1812495 TAATAATGTAATTTAAAA
1 TAATAATATAAATTAAAA
1812513 ATATAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.35
Consensus pattern (19 bp):
TAATAATATAAATTAAAAG
Found at i:1817852 original size:17 final size:17
Alignment explanation
Indices: 1817832--1817900 Score: 61
Period size: 17 Copynumber: 3.9 Consensus size: 17
1817822 ATAAAAATCT
* *
1817832 TAAAAATTTATAAATAA
1 TAAAAAATTATAAAAAA
1817849 TAAAAACATTA-AAAAAA
1 TAAAAA-ATTATAAAAAA
1817866 TTATAAAAATTAT-AAAAA
1 -TA-AAAAATTATAAAAAA
1817884 TATAAAAATTAATAAAA
1 TA-AAAAATT-ATAAAA
1817901 CATATTTAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
17 21 0.48
18 16 0.36
19 7 0.16
ACGTcount: A:0.70, C:0.01, G:0.00, T:0.29
Consensus pattern (17 bp):
TAAAAAATTATAAAAAA
Found at i:1817854 original size:27 final size:27
Alignment explanation
Indices: 1817822--1817940 Score: 98
Period size: 27 Copynumber: 4.2 Consensus size: 27
1817812 ATATTTTCCC
1817822 ATAAAAATCTTAAAAATTTATAAATAA-T
1 ATAAAAAT-TTAAAAATTTATAAA-AATT
* *
1817850 A-AAAACATTAAAAAAATTATAAAAATT
1 ATAAAA-ATTTAAAAATTTATAAAAATT
* *
1817877 ATAAAAATATAAAAATTAATAAAACATAT
1 ATAAAAATTTAAAAATTTATAAAA-AT-T
* * *
1817906 TTAAAATATTTAAAATTTTATAAAAACAT
1 ATAAAA-ATTTAAAAATTTATAAAAA-TT
1817935 ATAAAA
1 ATAAAA
1817941 TTTCTTTAAA
Statistics
Matches: 72, Mismatches: 12, Indels: 13
0.74 0.12 0.13
Matches are distributed among these distances:
26 2 0.03
27 33 0.46
28 9 0.12
29 13 0.18
30 15 0.21
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (27 bp):
ATAAAAATTTAAAAATTTATAAAAATT
Found at i:1817873 original size:8 final size:9
Alignment explanation
Indices: 1817822--1818076 Score: 96
Period size: 10 Copynumber: 26.9 Consensus size: 9
1817812 ATATTTTCCC
1817822 ATAAAAATCT
1 ATAAAAAT-T
1817832 -TAAAAATTT
1 ATAAAAA-TT
1817841 ATAAATAA-T
1 ATAAA-AATT
1817850 A-AAAACATT
1 ATAAAA-ATT
*
1817859 AAAAAAATT
1 ATAAAAATT
1817868 ATAAAAATT
1 ATAAAAATT
1817877 ATAAAAA-T
1 ATAAAAATT
1817885 ATAAAAATT
1 ATAAAAATT
1817894 AATAAAACATAT
1 -ATAAAA-AT-T
*
1817906 TTAAAATATT
1 ATAAAA-ATT
*
1817916 -TAAAATTTT
1 ATAAAA-ATT
*
1817925 ATAAAAACAT
1 ATAAAAA-TT
*
1817935 ATAAAATTTCT
1 ATAAAA-AT-T
* *
1817946 TTAAAACTT
1 ATAAAAATT
*
1817955 ATAAAAAAATC
1 AT--AAAAATT
1817966 ATAAAAA-T
1 ATAAAAATT
*
1817974 ATAAATATT
1 ATAAAAATT
*
1817983 -TAAGAA-T
1 ATAAAAATT
* *
1817990 ATTAAAATAG
1 ATAAAAAT-T
*
1818000 ATATAAACTT
1 ATA-AAAATT
*
1818010 AAAAAAATTT
1 ATAAAAA-TT
*
1818020 ATAAAAAATC
1 AT-AAAAATT
1818030 ATAAAAACTT
1 ATAAAAA-TT
*
1818040 ATAATAAAAT
1 ATAA-AAATT
*
1818050 ATAATAAAAT
1 ATAA-AAATT
1818060 ATAAAATATT
1 ATAAAA-ATT
1818070 A-AAAAAT
1 ATAAAAAT
1818077 CATTTAAACC
Statistics
Matches: 189, Mismatches: 30, Indels: 54
0.69 0.11 0.20
Matches are distributed among these distances:
7 2 0.01
8 28 0.15
9 60 0.32
10 62 0.33
11 36 0.19
12 1 0.01
ACGTcount: A:0.63, C:0.04, G:0.01, T:0.32
Consensus pattern (9 bp):
ATAAAAATT
Found at i:1818707 original size:11 final size:9
Alignment explanation
Indices: 1818645--1818811 Score: 72
Period size: 9 Copynumber: 17.7 Consensus size: 9
1818635 TTTTATGTTC
1818645 TTTTATAAT
1 TTTTATAAT
1818654 TTTTATAAAT
1 TTTTAT-AAT
*
1818664 TTGTATCAACT
1 TTTTAT-AA-T
* **
1818675 TTAATATTTT
1 TT-TTATAAT
1818685 TTTTATAAT
1 TTTTATAAT
1818694 TTTTATAAGCT
1 TTTTATAA--T
* *
1818705 TTTAAGAAT
1 TTTTATAAT
*
1818714 TTTTATAAAA
1 TTTTAT-AAT
*
1818724 TTTCA-AAT
1 TTTTATAAT
*
1818732 ATTTTAAATAT
1 -TTTTATA-AT
1818743 GTTTTATTAA-
1 -TTTTA-TAAT
1818753 TTTTATAAT
1 TTTTATAAT
*
1818762 TTATTAGAAT
1 TT-TTATAAT
1818772 TTTTAT-AT
1 TTTTATAAT
* *
1818780 TTCTACAAT
1 TTTTATAAT
* *
1818789 ATTTAT-TT
1 TTTTATAAT
1818797 TTTTATAAT
1 TTTTATAAT
1818806 TTTTAT
1 TTTTAT
1818812 GTCGATTTAA
Statistics
Matches: 116, Mismatches: 28, Indels: 28
0.67 0.16 0.16
Matches are distributed among these distances:
8 17 0.15
9 49 0.42
10 28 0.24
11 18 0.16
12 4 0.03
ACGTcount: A:0.34, C:0.04, G:0.03, T:0.59
Consensus pattern (9 bp):
TTTTATAAT
Found at i:1818810 original size:17 final size:17
Alignment explanation
Indices: 1818744--1818811 Score: 55
Period size: 17 Copynumber: 3.9 Consensus size: 17
1818734 TTTAAATATG
*
1818744 TTTTATTAATTTTATAATT
1 TTTTA-TAATTTT-TATTT
* * *
1818763 TATTAGAATTTTTATAT
1 TTTTATAATTTTTATTT
* * *
1818780 TTCTACAATATTTATTT
1 TTTTATAATTTTTATTT
1818797 TTTTATAATTTTTAT
1 TTTTATAATTTTTAT
1818812 GTCGATTTAA
Statistics
Matches: 37, Mismatches: 12, Indels: 2
0.73 0.24 0.04
Matches are distributed among these distances:
17 27 0.73
18 6 0.16
19 4 0.11
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65
Consensus pattern (17 bp):
TTTTATAATTTTTATTT
Found at i:1830058 original size:45 final size:46
Alignment explanation
Indices: 1829985--1830367 Score: 643
Period size: 46 Copynumber: 8.5 Consensus size: 46
1829975 TACGTATGAT
* *
1829985 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
1830028 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
1830073 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCT-AGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
1830118 CACTTATCACTTTGTCACTTGATCAGATAAGAGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
1830164 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
1830209 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1830255 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
1830301 CACTTATCACTTTGTCACTTGATCAGATAAGTGTATCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1830347 CACTTATCACTTTGTCACTTG
1 CACTTATCACTTTGTCACTTG
1830368 TCACTGATCA
Statistics
Matches: 325, Mismatches: 11, Indels: 5
0.95 0.03 0.01
Matches are distributed among these distances:
43 10 0.03
44 5 0.02
45 151 0.46
46 159 0.49
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.33
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:1830209 original size:91 final size:91
Alignment explanation
Indices: 1829985--1830367 Score: 673
Period size: 91 Copynumber: 4.2 Consensus size: 91
1829975 TACGTATGAT
*
1829985 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTGTCACTT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTGTCACTT
*
1830048 GATCAGATAAGTGTAGCT-AGGCTAC
66 GATCAGATAAGTGTAGCTAAAGCTAC
*
1830073 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCTAGGCTACCACTTATCACTTTGTCACTT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTGTCACTT
*
1830138 GATCAGATAAGAGTAGCTAAAGCTAC
66 GATCAGATAAGTGTAGCTAAAGCTAC
1830164 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTGTCACTT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTGTCACTT
*
1830229 GATCAGATAAGTGTAGCTAAAGCTAT
66 GATCAGATAAGTGTAGCTAAAGCTAC
*
1830255 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AGGCTACCACTTATCACTTTGTCACT
*
1830320 TGATCAGATAAGTGTATCTAAAGCTAC
65 TGATCAGATAAGTGTAGCTAAAGCTAC
1830347 CACTTATCACTTTGTCACTTG
1 CACTTATCACTTTGTCACTTG
1830368 TCACTGATCA
Statistics
Matches: 281, Mismatches: 10, Indels: 4
0.95 0.03 0.01
Matches are distributed among these distances:
88 10 0.04
89 5 0.02
90 63 0.22
91 132 0.47
92 71 0.25
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.33
Consensus pattern (91 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTGTCACTT
GATCAGATAAGTGTAGCTAAAGCTAC
Found at i:1832863 original size:25 final size:25
Alignment explanation
Indices: 1832842--1833048 Score: 175
Period size: 25 Copynumber: 8.3 Consensus size: 25
1832832 GATTTTCTAG
*
1832842 AGAATTCGCCACAAAAGCTTTCCAA
1 AGAATTCGCCACAAAGGCTTTCCAA
* * *
1832867 ACAATTCACCACAAAGGCTTTCTAA
1 AGAATTCGCCACAAAGGCTTTCCAA
* *
1832892 AGAATTCGCCATAAAGGATTTCCAA
1 AGAATTCGCCACAAAGGCTTTCCAA
* * *
1832917 AGGATTTGCCACAAAGGCTTTCCAG
1 AGAATTCGCCACAAAGGCTTTCCAA
* * *
1832942 AGAATTCGTCACAAAGGCTTTTCAG
1 AGAATTCGCCACAAAGGCTTTCCAA
* ** * *
1832967 AGGATTC-ATATAAAGGCTTTTCAA
1 AGAATTCGCCACAAAGGCTTTCCAA
* ** * *
1832991 AAAAGTT-ATCACAAAGGTTTTCCAT
1 AGAA-TTCGCCACAAAGGCTTTCCAA
* *
1833016 AGAATTCGCCACAAAGGCTTTCTAG
1 AGAATTCGCCACAAAGGCTTTCCAA
1833041 AGAATTCG
1 AGAATTCG
1833049 TATTTACTGT
Statistics
Matches: 142, Mismatches: 37, Indels: 6
0.77 0.20 0.03
Matches are distributed among these distances:
24 17 0.12
25 125 0.88
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.26
Consensus pattern (25 bp):
AGAATTCGCCACAAAGGCTTTCCAA
Found at i:1840719 original size:8 final size:9
Alignment explanation
Indices: 1840705--1840765 Score: 52
Period size: 9 Copynumber: 6.8 Consensus size: 9
1840695 CTTATTCTTT
*
1840705 AAAAAAAAC
1 AAAAAAAGC
1840714 AAAAAAAGC
1 AAAAAAAGC
**
1840723 AAAAAGCGC
1 AAAAAAAGC
1840732 AAAAAAAG-
1 AAAAAAAGC
*
1840740 AAGAAGAAGC
1 AA-AAAAAGC
**
1840750 AAAAAGCGC
1 AAAAAAAGC
1840759 AAAAAAA
1 AAAAAAA
1840766 AAAGTTGCCT
Statistics
Matches: 39, Mismatches: 11, Indels: 4
0.72 0.20 0.07
Matches are distributed among these distances:
8 2 0.05
9 35 0.90
10 2 0.05
ACGTcount: A:0.74, C:0.11, G:0.15, T:0.00
Consensus pattern (9 bp):
AAAAAAAGC
Found at i:1840749 original size:27 final size:26
Alignment explanation
Indices: 1840706--1840765 Score: 93
Period size: 27 Copynumber: 2.3 Consensus size: 26
1840696 TTATTCTTTA
1840706 AAAAAAACAAAAAAAGCAAAAAGCGC
1 AAAAAAACAAAAAAAGCAAAAAGCGC
* *
1840732 AAAAAAAGAAGAAGAAGCAAAAAGCGC
1 AAAAAAACAA-AAAAAGCAAAAAGCGC
1840759 AAAAAAA
1 AAAAAAA
1840766 AAAGTTGCCT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
26 9 0.29
27 22 0.71
ACGTcount: A:0.73, C:0.12, G:0.15, T:0.00
Consensus pattern (26 bp):
AAAAAAACAAAAAAAGCAAAAAGCGC
Found at i:1851945 original size:23 final size:21
Alignment explanation
Indices: 1851905--1851952 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 21
1851895 TTTTAAAGTT
1851905 TTGAAAGTTGTCATTGTTGAGAA
1 TTGAAAGTTGTCATTGTT-A-AA
*
1851928 TTGAAAGTT-TTATGTGTTAAA
1 TTGAAAGTTGTCAT-TGTTAAA
1851949 TTGA
1 TTGA
1851953 TAGAAATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 6 0.26
22 4 0.17
23 13 0.57
ACGTcount: A:0.31, C:0.02, G:0.23, T:0.44
Consensus pattern (21 bp):
TTGAAAGTTGTCATTGTTAAA
Found at i:1852192 original size:85 final size:85
Alignment explanation
Indices: 1852067--1852253 Score: 277
Period size: 85 Copynumber: 2.2 Consensus size: 85
1852057 ATGTTGTGCA
** * *
1852067 AACAAGTGGCAATAACTGCAAATATGTGGCTCGTCCACAAAACCCAATGGCAGTTTGTTTAATCT
1 AACAAGTGGCAATAACTAAAAATATGTAGCTCGTCCAC-AAACCCAATGACAGTTTGTTTAATCT
* *
1852132 GCAA-TATGTTGTGCACTTAC
65 GCAACCATGTTGTGCACTCAC
* *
1852152 AACAAGTAGCAATAACTAAAAATATGTAGCTCGTCCACAAACCCAGTGACAGTTTGTTTAATCTG
1 AACAAGTGGCAATAACTAAAAATATGTAGCTCGTCCACAAACCCAATGACAGTTTGTTTAATCTG
1852217 CAACCATGTTGTGCACTCAC
66 CAACCATGTTGTGCACTCAC
*
1852237 AACAAGTGGCAGTAACT
1 AACAAGTGGCAATAACT
1852254 GCAAATGTTT
Statistics
Matches: 91, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
84 28 0.31
85 63 0.69
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (85 bp):
AACAAGTGGCAATAACTAAAAATATGTAGCTCGTCCACAAACCCAATGACAGTTTGTTTAATCTG
CAACCATGTTGTGCACTCAC
Found at i:1854771 original size:50 final size:49
Alignment explanation
Indices: 1854694--1854848 Score: 136
Period size: 50 Copynumber: 3.1 Consensus size: 49
1854684 AACACACCAC
* * *
1854694 AGCTCTCTTGAGCTTTCCGATACTTGGCTCTCATGAGCTTTCCGATTA-AT
1 AGCTCTCTTGAGC-TTCCGATACTTGGCTCGCAAGAGCTTCCCG-TTACAT
* * *
1854744 AGCTCTCTTGAGCTTCCTGGTATTTGGCTCGCAAGAGCTTCCCGTTACTT
1 AGCTCTCTTGAGCTTCC-GATACTTGGCTCGCAAGAGCTTCCCGTTACAT
* * * * *
1854794 AGCTCACATGAGCTTCCCGTTA-TATGGCTCGAAAGAGCTTCTCGTTTACAT
1 AGCTCTCTTGAGCTT-CCGATACT-TGGCTCGCAAGAGCTTCCCG-TTACAT
1854845 -GCTC
1 AGCTC
1854849 GTATGAGCAC
Statistics
Matches: 88, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
49 8 0.09
50 73 0.83
51 7 0.08
ACGTcount: A:0.18, C:0.27, G:0.20, T:0.35
Consensus pattern (49 bp):
AGCTCTCTTGAGCTTCCGATACTTGGCTCGCAAGAGCTTCCCGTTACAT
Found at i:1854809 original size:25 final size:25
Alignment explanation
Indices: 1854694--1854815 Score: 102
Period size: 25 Copynumber: 4.9 Consensus size: 25
1854684 AACACACCAC
* * *
1854694 AGCTCTCTTGAGCTTTCCGATACTT
1 AGCTCTCATGAGCTTCCCGTTACTT
* * *
1854719 GGCTCTCATGAGCTTTCCGATTA-AT
1 AGCTCTCATGAGCTTCCCG-TTACTT
* * * *
1854744 AGCTCTCTTGAGCTTCCTGGTATTT
1 AGCTCTCATGAGCTTCCCGTTACTT
* * *
1854769 GGCTCGCAAGAGCTTCCCGTTACTT
1 AGCTCTCATGAGCTTCCCGTTACTT
*
1854794 AGCTCACATGAGCTTCCCGTTA
1 AGCTCTCATGAGCTTCCCGTTA
1854816 TATGGCTCGA
Statistics
Matches: 75, Mismatches: 20, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
24 2 0.03
25 71 0.95
26 2 0.03
ACGTcount: A:0.17, C:0.28, G:0.20, T:0.35
Consensus pattern (25 bp):
AGCTCTCATGAGCTTCCCGTTACTT
Found at i:1854831 original size:25 final size:24
Alignment explanation
Indices: 1854753--1854839 Score: 77
Period size: 25 Copynumber: 3.5 Consensus size: 24
1854743 TAGCTCTCTT
* * *
1854753 GAGCTTCCTGGTATTTGGCTCGCAA
1 GAGCTTCCCGTTA-TTGGCTCGAAA
* *
1854778 GAGCTTCCCGTTACTTAGCTC-ACAT
1 GAGCTTCCCGTTA-TTGGCTCGA-AA
1854803 GAGCTTCCCGTTATATGGCTCGAAA
1 GAGCTTCCCGTTAT-TGGCTCGAAA
*
1854828 GAGCTTCTCGTT
1 GAGCTTCCCGTT
1854840 TACATGCTCG
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
24 1 0.02
25 48 0.96
26 1 0.02
ACGTcount: A:0.18, C:0.26, G:0.23, T:0.32
Consensus pattern (24 bp):
GAGCTTCCCGTTATTGGCTCGAAA
Found at i:1854856 original size:25 final size:25
Alignment explanation
Indices: 1854768--1854856 Score: 76
Period size: 25 Copynumber: 3.6 Consensus size: 25
1854758 TCCTGGTATT
*
1854768 TGGCTCGCAA-GAGCTTCCCGTTACT
1 TGGCTCG-AATGAGCTTCCCGTTACA
* *
1854793 TAGCTC-ACATGAGCTTCCCGTTATA
1 TGGCTCGA-ATGAGCTTCCCGTTACA
* *
1854818 TGGCTCGAAAGAGCTTCTCGTTTACA
1 TGGCTCGAATGAGCTTCCCG-TTACA
*
1854844 T-GCTCGTATGAGC
1 TGGCTCGAATGAGC
1854857 ACATATGTAT
Statistics
Matches: 51, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
23 1 0.02
24 1 0.02
25 43 0.84
26 6 0.12
ACGTcount: A:0.20, C:0.27, G:0.22, T:0.30
Consensus pattern (25 bp):
TGGCTCGAATGAGCTTCCCGTTACA
Found at i:1869798 original size:22 final size:22
Alignment explanation
Indices: 1869766--1869807 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1869756 GGTCTTTATA
1869766 TTTTTAATTTTAAAATTTAATC
1 TTTTTAATTTTAAAATTTAATC
* **
1869788 TTTTTATTTTTTGAATTTAA
1 TTTTTAATTTTAAAATTTAA
1869808 AGATTTAAGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (22 bp):
TTTTTAATTTTAAAATTTAATC
Found at i:1876492 original size:13 final size:13
Alignment explanation
Indices: 1876474--1876502 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1876464 ATAATTCTAC
1876474 AATGAACAAATAA
1 AATGAACAAATAA
1876487 AATGAACAAATAA
1 AATGAACAAATAA
1876500 AAT
1 AAT
1876503 ACTCTCAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.69, C:0.07, G:0.07, T:0.17
Consensus pattern (13 bp):
AATGAACAAATAA
Found at i:1882147 original size:18 final size:18
Alignment explanation
Indices: 1882124--1882228 Score: 138
Period size: 18 Copynumber: 5.8 Consensus size: 18
1882114 TGTTTATGGT
1882124 ACTATTCACGTATACGGC
1 ACTATTCACGTATACGGC
* *
1882142 ACTATTTACGTATACGGT
1 ACTATTCACGTATACGGC
* * *
1882160 ACTATTCATGTATATGTC
1 ACTATTCACGTATACGGC
*
1882178 ACTATTCACATATACGGC
1 ACTATTCACGTATACGGC
*
1882196 ACTATTCACGTATACGGT
1 ACTATTCACGTATACGGC
*
1882214 ACTGTTCACGTATAC
1 ACTATTCACGTATAC
1882229 AGTAGTTGGG
Statistics
Matches: 73, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 73 1.00
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (18 bp):
ACTATTCACGTATACGGC
Found at i:1882207 original size:54 final size:54
Alignment explanation
Indices: 1882124--1882227 Score: 172
Period size: 54 Copynumber: 1.9 Consensus size: 54
1882114 TGTTTATGGT
* * *
1882124 ACTATTCACGTATACGGCACTATTTACGTATACGGTACTATTCATGTATATGTC
1 ACTATTCACATATACGGCACTATTCACGTATACGGTACTATTCACGTATATGTC
*
1882178 ACTATTCACATATACGGCACTATTCACGTATACGGTACTGTTCACGTATA
1 ACTATTCACATATACGGCACTATTCACGTATACGGTACTATTCACGTATA
1882228 CAGTAGTTGG
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 46 1.00
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (54 bp):
ACTATTCACATATACGGCACTATTCACGTATACGGTACTATTCACGTATATGTC
Found at i:1888061 original size:3 final size:3
Alignment explanation
Indices: 1888053--1888111 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
1888043 ATCACATGTT
1888053 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1888101 TTA TTA TTA TT
1 TTA TTA TTA TT
1888112 TGGATGTAAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1888229 original size:72 final size:72
Alignment explanation
Indices: 1888112--1888371 Score: 504
Period size: 72 Copynumber: 3.6 Consensus size: 72
1888102 TATTATTATT
1888112 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
1 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
1888177 TTTTAAG
66 TTTTAAG
1888184 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
1 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
1888249 TTTTAAG
66 TTTTAAG
1888256 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
1 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
1888321 TTTTAAG
66 TTTTAAG
*
1888328 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAG-TTGTTA
1 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTA
1888372 AGTTGTAAGC
Statistics
Matches: 187, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
71 6 0.03
72 181 0.97
ACGTcount: A:0.27, C:0.06, G:0.24, T:0.42
Consensus pattern (72 bp):
TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
TTTTAAG
Found at i:1892594 original size:3 final size:3
Alignment explanation
Indices: 1892586--1892656 Score: 142
Period size: 3 Copynumber: 23.7 Consensus size: 3
1892576 ATCACATGTT
1892586 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1892634 TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TT
1892657 TGGATGTAAT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1892774 original size:72 final size:72
Alignment explanation
Indices: 1892657--1892916 Score: 504
Period size: 72 Copynumber: 3.6 Consensus size: 72
1892647 TATTATTATT
1892657 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
1 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
1892722 TTTTAAG
66 TTTTAAG
1892729 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
1 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
1892794 TTTTAAG
66 TTTTAAG
1892801 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
1 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
1892866 TTTTAAG
66 TTTTAAG
*
1892873 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAG-TTGTTA
1 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTA
1892917 AGTTGTAAGC
Statistics
Matches: 187, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
71 6 0.03
72 181 0.97
ACGTcount: A:0.27, C:0.06, G:0.24, T:0.42
Consensus pattern (72 bp):
TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGTAGTAGGTGGTGATTTA
TTTTAAG
Found at i:1912391 original size:15 final size:15
Alignment explanation
Indices: 1912371--1912400 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1912361 TTTAATTCTT
*
1912371 TATAAATTATAAAAA
1 TATAAACTATAAAAA
1912386 TATAAACTATAAAAA
1 TATAAACTATAAAAA
1912401 ATTAAAATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (15 bp):
TATAAACTATAAAAA
Found at i:1920147 original size:18 final size:18
Alignment explanation
Indices: 1920124--1920166 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
1920114 TCCAATAGTA
**
1920124 AAAAAAATTTTGAAAAAG
1 AAAAAAATACTGAAAAAG
*
1920142 AAAAAAATACTGAAAATG
1 AAAAAAATACTGAAAAAG
1920160 AAAAAAA
1 AAAAAAA
1920167 AAATTAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.72, C:0.02, G:0.09, T:0.16
Consensus pattern (18 bp):
AAAAAAATACTGAAAAAG
Found at i:1920460 original size:151 final size:146
Alignment explanation
Indices: 1920254--1920540 Score: 389
Period size: 146 Copynumber: 1.9 Consensus size: 146
1920244 TTTATATTAA
* * *
1920254 TTTAATAAATAACCTTGATTTTGACACTTTCTTCGTATTTTTTTATTTTCGTATTTTATTTTTTA
1 TTTAATAAATAACCTTGATTTTGACACTTTATTCATATTTTTTTA-----GTATATTATTTTTTA
* * *
1920319 AAATATATTATATTCGTATTTTATTTCTTCATATTATTTTAGTACATAATGTTTCAAATGTATTA
61 AAATATATTATATTCGTATTTTATTTCTTCATATTATTTTAGCAAAAAATGTTTCAAATGTATTA
*
1920384 TTTAAGTGTTTTTTATGTTTT
126 TGTAAGTGTTTTTTATGTTTT
*
1920405 TTTAATAAATAACCCTT-ATTTT-AGCACTTTATTCATATTTTTTTCGTATATTATTTTTTAAAA
1 TTTAATAAATAA-CCTTGATTTTGA-CACTTTATTCATATTTTTTTAGTATATTATTTTTTAAAA
* * * *
1920468 TATATTATTTTCGTATTTTATTTTTTTATATTGTTTTAGCAAAAAATGTTTCAAATGTATTATGT
64 TATATTATATTCGTATTTTATTTCTTCATATTATTTTAGCAAAAAATGTTTCAAATGTATTATGT
1920533 AAGTGTTT
129 AAGTGTTT
1920541 CTTTTACATT
Statistics
Matches: 122, Mismatches: 12, Indels: 9
0.85 0.08 0.06
Matches are distributed among these distances:
146 82 0.67
150 1 0.01
151 35 0.29
152 4 0.03
ACGTcount: A:0.28, C:0.08, G:0.07, T:0.57
Consensus pattern (146 bp):
TTTAATAAATAACCTTGATTTTGACACTTTATTCATATTTTTTTAGTATATTATTTTTTAAAATA
TATTATATTCGTATTTTATTTCTTCATATTATTTTAGCAAAAAATGTTTCAAATGTATTATGTAA
GTGTTTTTTATGTTTT
Found at i:1920572 original size:146 final size:144
Alignment explanation
Indices: 1920242--1920562 Score: 383
Period size: 146 Copynumber: 2.2 Consensus size: 144
1920232 CTAGTGTATA
* * *
1920242 TTTTTATATTAATTTAATAAATAACCTTGATTTT-GACACTTTCTTCGTATTTTTTTATTTTCGT
1 TTTTTACATTAATTTAATAAATAA-CTT-ATTTTAG-CACTTTATTC--A--TATTT-TTTTCGT
* * * *
1920306 ATTTTATTTTTTAAAATATATTATATTCGTATTTTATTTCTTCATATTATTTTAGTACATAATGT
58 ATATTATTTTTTAAAATATATTATATTCGTATTTTATTTCTTCATATTATTTTAGCAAAAAATGT
*
1920371 TTCAAATGTATTATTTAAGTGT
123 TTCAAATGTATTATGTAAGTGT
** **
1920393 TTTTTATGTTTTTTTAATAAATAACCCTTATTTTAGCACTTTATTCATATTTTTTTCGTATATTA
1 TTTTTACATTAATTTAATAAATAA--CTTATTTTAGCACTTTATTCATATTTTTTTCGTATATTA
* * * *
1920458 TTTTTTAAAATATATTATTTTCGTATTTTATTTTTTTATATTGTTTTAGCAAAAAATGTTTCAAA
64 TTTTTTAAAATATATTATATTCGTATTTTATTTCTTCATATTATTTTAGCAAAAAATGTTTCAAA
1920523 TGTATTATGTAAGTGTT
129 TGTATTATGTAAGTG-T
1920540 TCTTTTACATTAATTTAATAAAT
1 T-TTTTACATTAATTTAATAAAT
1920563 GTATTATTTT
Statistics
Matches: 148, Mismatches: 18, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
146 84 0.57
147 6 0.04
148 17 0.11
149 1 0.01
151 35 0.24
152 5 0.03
ACGTcount: A:0.29, C:0.07, G:0.07, T:0.57
Consensus pattern (144 bp):
TTTTTACATTAATTTAATAAATAACTTATTTTAGCACTTTATTCATATTTTTTTCGTATATTATT
TTTTAAAATATATTATATTCGTATTTTATTTCTTCATATTATTTTAGCAAAAAATGTTTCAAATG
TATTATGTAAGTGT
Found at i:1920877 original size:148 final size:149
Alignment explanation
Indices: 1920622--1920976 Score: 473
Period size: 148 Copynumber: 2.4 Consensus size: 149
1920612 GTATTTTATT
* *
1920622 TACGAAGAAAGTGCCAAAATCAGGGTTATTTATTAAATTAATATAAAAGAAACACTTAAATAATA
1 TACGAATAAAGTGCCAAAATCAGGGTTATTTATTAAATTAATATAAAA-AAAAACTTAAATAATA
* *
1920687 CATTTGAAACATTTTTCGCTAAAACTATATAAAAAAATAAAATAAGAAAATAATATATTTTAAAA
65 CATTTGAAACATTTGTCACTAAAACTATATAAAAAAATAAAATAAGAAAATAATATATTTTAAAA
*
1920752 AATAATATACG-AAAAAAAA
130 AATAAGATACGAAAAAAAAA
* * ** *
1920771 TATGAATAAAGTGCTAAAATCAGGGTTATTTATTAAAAAAATATAAAAAAAAACTTAAATAATAT
1 TACGAATAAAGTGCCAAAATCAGGGTTATTTATTAAATTAATATAAAAAAAAACTTAAATAATAC
* * ** *
1920836 ATTTGAAACATTATGT-ACTAAAA-TAATATGAAGAAATAAAATACTAATATAATATATTTTAAA
66 ATTTGAAACATT-TGTCACTAAAACT-ATATAAAAAAATAAAATAAGAAAATAATATATTTTAAA
1920899 AAATAAGATACGAAAATAAAAAAAA
129 AAATAAGATACG---A-AAAAAAAA
* *
1920924 TACGAATAAAGTGCCAAAATCAAGATTATTTATTAAATTAATATAAAAAAAAA
1 TACGAATAAAGTGCCAAAATCAGGGTTATTTATTAAATTAATATAAAAAAAAA
1920977 ATACACTAGT
Statistics
Matches: 178, Mismatches: 21, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
147 1 0.01
148 77 0.43
149 45 0.25
153 55 0.31
ACGTcount: A:0.57, C:0.06, G:0.08, T:0.29
Consensus pattern (149 bp):
TACGAATAAAGTGCCAAAATCAGGGTTATTTATTAAATTAATATAAAAAAAAACTTAAATAATAC
ATTTGAAACATTTGTCACTAAAACTATATAAAAAAATAAAATAAGAAAATAATATATTTTAAAAA
ATAAGATACGAAAAAAAAA
Found at i:1921035 original size:19 final size:20
Alignment explanation
Indices: 1921011--1921066 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 20
1921001 CAACATGACC
*
1921011 CATTTTTTA-TTTTTTTTTT
1 CATTTTTCAGTTTTTTTTTT
*
1921030 CA-TTTTCAGTATTTTTTTT
1 CATTTTTCAGTTTTTTTTTT
1921049 C-TTTTTCAGTTTTTTTTT
1 CATTTTTCAGTTTTTTTTT
1921067 ATTGTTGGAG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
18 5 0.16
19 27 0.84
ACGTcount: A:0.11, C:0.09, G:0.04, T:0.77
Consensus pattern (20 bp):
CATTTTTCAGTTTTTTTTTT
Found at i:1921044 original size:18 final size:18
Alignment explanation
Indices: 1921021--1921066 Score: 74
Period size: 19 Copynumber: 2.5 Consensus size: 18
1921011 CATTTTTTAT
1921021 TTTTTTTTTCATTTTCAG
1 TTTTTTTTTCATTTTCAG
*
1921039 TATTTTTTTTCTTTTTCAG
1 T-TTTTTTTTCATTTTCAG
1921058 TTTTTTTTT
1 TTTTTTTTT
1921067 ATTGTTGGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 9 0.35
19 17 0.65
ACGTcount: A:0.09, C:0.09, G:0.04, T:0.78
Consensus pattern (18 bp):
TTTTTTTTTCATTTTCAG
Found at i:1926017 original size:17 final size:17
Alignment explanation
Indices: 1925979--1926017 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
1925969 TGAATTCCTG
1925979 ATCATTCTATTAAAATA
1 ATCATTCTATTAAAATA
*
1925996 TTCATTCTATTAATAA-A
1 ATCATTCTATTAA-AATA
1926013 ATCAT
1 ATCAT
1926018 AAAAACTTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
17 17 0.89
18 2 0.11
ACGTcount: A:0.44, C:0.13, G:0.00, T:0.44
Consensus pattern (17 bp):
ATCATTCTATTAAAATA
Found at i:1929721 original size:66 final size:66
Alignment explanation
Indices: 1929615--1929747 Score: 266
Period size: 66 Copynumber: 2.0 Consensus size: 66
1929605 AGCAGCTTAA
1929615 GCGGCTAAACCAAGTTGAGGGTTGGCTTTCGAGGGCTGAAACTCTGATAAACGATGCTGATCAAT
1 GCGGCTAAACCAAGTTGAGGGTTGGCTTTCGAGGGCTGAAACTCTGATAAACGATGCTGATCAAT
1929680 T
66 T
1929681 GCGGCTAAACCAAGTTGAGGGTTGGCTTTCGAGGGCTGAAACTCTGATAAACGATGCTGATCAAT
1 GCGGCTAAACCAAGTTGAGGGTTGGCTTTCGAGGGCTGAAACTCTGATAAACGATGCTGATCAAT
1929746 T
66 T
1929747 G
1 G
1929748 ATTGTCCAAA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26
Consensus pattern (66 bp):
GCGGCTAAACCAAGTTGAGGGTTGGCTTTCGAGGGCTGAAACTCTGATAAACGATGCTGATCAAT
T
Found at i:1932156 original size:75 final size:75
Alignment explanation
Indices: 1932033--1932175 Score: 259
Period size: 75 Copynumber: 1.9 Consensus size: 75
1932023 GAGAGGAGGG
*
1932033 ATGGTGGAAAGATGTAGAATGGGAGGATGAATCCACTCGAGTTGCTTTTCTCCCTTCTTTCAAAC
1 ATGGTGGAAAGATGTAGAATGGGAGGATGAATCCACTCGAATTGCTTTTCTCCCTTCTTTCAAAC
1932098 CTGAGGTGGA
66 CTGAGGTGGA
* *
1932108 ATGGTGGAAAGATGTAGAATGGGAGGATGAATCCAGTCGAATTGCTTTTCTCTCTTCTTTCAAAC
1 ATGGTGGAAAGATGTAGAATGGGAGGATGAATCCACTCGAATTGCTTTTCTCCCTTCTTTCAAAC
1932173 CTG
66 CTG
1932176 GTCTATTCTA
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
75 65 1.00
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.31
Consensus pattern (75 bp):
ATGGTGGAAAGATGTAGAATGGGAGGATGAATCCACTCGAATTGCTTTTCTCCCTTCTTTCAAAC
CTGAGGTGGA
Found at i:1932939 original size:15 final size:14
Alignment explanation
Indices: 1932916--1932956 Score: 64
Period size: 15 Copynumber: 2.9 Consensus size: 14
1932906 TTTAATAATA
1932916 AAAAAATTATTATT
1 AAAAAATTATTATT
*
1932930 ATACAAATTATTATT
1 A-AAAAATTATTATT
1932945 AAAAAATTATTA
1 AAAAAATTATTA
1932957 AAAACCAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (14 bp):
AAAAAATTATTATT
Found at i:1942722 original size:130 final size:130
Alignment explanation
Indices: 1942487--1942859 Score: 399
Period size: 130 Copynumber: 2.9 Consensus size: 130
1942477 AAAATTCTTC
* * * * *
1942487 AAAATGAAGGCGAAATTTGATGTTCGGCGATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAA
1 AAAACGAAGACGAGATTTGATGTTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAA
* * * * * * *
1942552 TTTCGTATTTGCTCAGAATAATCGAATTTCCCTTCGAAATTTCATTCATACT-TTTTAAAATCCC
66 TTTCGCATTTGTTCAAAATAATCGAATATCCCTTCAAAATTTCACTCAT-CTCTCTTAAAATCCC
1942616 T
130 T
* * * * *
1942617 TAAATGAATATGAGATTTGATGTTTGGCAATTCGCGGAATTGTGCCCTAACGTGTTGGGTTGCAA
1 AAAACGAAGACGAGATTTGATGTTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAA
** * ** * * *
1942682 TTTCGCATTTGTTCAAAATAATCGAATATCATTTTAAAATTTTGCTCGTGTCTCTTAAAATCTCT
66 TTTCGCATTTGTTCAAAATAATCGAATATCCCTTCAAAATTTCACTCATCTCTCTTAAAATCCCT
* * * * *
1942747 AAAACGAAGGCGATATGTGATATTTGGCAATTCGC-GAGATCGTGCCCTAACGTGTTGGGTAGCA
1 AAAACGAAGACGAGATTTGATGTTTGGCAATTCGCGGA-ATCGTGCCCTAACGTGTTGGGTTGCA
* * * *
1942811 ATTTCCCGATTTTTTTAAAATAATCAAATATCCCTTCAAAATTTCACTC
65 ATTTCGC-ATTTGTTCAAAATAATCGAATATCCCTTCAAAATTTCACTC
1942860 GGCTTTTCTA
Statistics
Matches: 198, Mismatches: 42, Indels: 5
0.81 0.17 0.02
Matches are distributed among these distances:
129 3 0.02
130 162 0.82
131 33 0.17
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.35
Consensus pattern (130 bp):
AAAACGAAGACGAGATTTGATGTTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAA
TTTCGCATTTGTTCAAAATAATCGAATATCCCTTCAAAATTTCACTCATCTCTCTTAAAATCCCT
Found at i:1945027 original size:16 final size:16
Alignment explanation
Indices: 1945003--1945034 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1944993 ATCCGGACAA
*
1945003 CTTATGTGCATGAATT
1 CTTACGTGCATGAATT
1945019 CTTACGTGCATGAATT
1 CTTACGTGCATGAATT
1945035 TGCATGAGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.41
Consensus pattern (16 bp):
CTTACGTGCATGAATT
Found at i:1964207 original size:18 final size:16
Alignment explanation
Indices: 1964160--1964196 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
1964150 AAAATTTTAA
*
1964160 AAAAATGAAATATATT
1 AAAAATTAAATATATT
1964176 AAAAATTAAATATATT
1 AAAAATTAAATATATT
1964192 AAAAA
1 AAAAA
1964197 GGTTAAGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (16 bp):
AAAAATTAAATATATT
Found at i:1964246 original size:61 final size:62
Alignment explanation
Indices: 1964176--1964291 Score: 216
Period size: 62 Copynumber: 1.9 Consensus size: 62
1964166 GAAATATATT
1964176 AAAAATTAAATATATT-AAAAAGGTTAAGTATAACCAATTTTAAAATTTTAATATATTTTTA
1 AAAAATTAAATATATTAAAAAAGGTTAAGTATAACCAATTTTAAAATTTTAATATATTTTTA
*
1964237 AAAAATTAAATATATTAAAAAATGTTAAGTATAACCAATTTTAAAATTTTAATAT
1 AAAAATTAAATATATTAAAAAAGGTTAAGTATAACCAATTTTAAAATTTTAATAT
1964292 GTTCAATATA
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
61 16 0.30
62 37 0.70
ACGTcount: A:0.53, C:0.03, G:0.04, T:0.40
Consensus pattern (62 bp):
AAAAATTAAATATATTAAAAAAGGTTAAGTATAACCAATTTTAAAATTTTAATATATTTTTA
Found at i:1964349 original size:11 final size:10
Alignment explanation
Indices: 1964274--1964350 Score: 58
Period size: 9 Copynumber: 7.9 Consensus size: 10
1964264 AGTATAACCA
1964274 ATTTTAA-A-
1 ATTTTAATAT
1964282 ATTTTAATAT
1 ATTTTAATAT
* *
1964292 -GTTCAATAT
1 ATTTTAATAT
1964301 ATTTTTAAAATAT
1 A-TTTT--AATAT
1964314 ATTTTAA-A-
1 ATTTTAATAT
1964322 ATTTTAATAT
1 ATTTTAATAT
1964332 A-TTTAATATT
1 ATTTTAATA-T
1964342 ATTTTAATA
1 ATTTTAATA
1964351 GGTAAAGAGA
Statistics
Matches: 55, Mismatches: 4, Indels: 17
0.72 0.05 0.22
Matches are distributed among these distances:
8 14 0.25
9 17 0.31
10 5 0.09
11 9 0.16
12 4 0.07
13 6 0.11
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (10 bp):
ATTTTAATAT
Found at i:1964422 original size:17 final size:18
Alignment explanation
Indices: 1964364--1964430 Score: 68
Period size: 17 Copynumber: 3.8 Consensus size: 18
1964354 AAAGAGAAAA
*
1964364 AAAATTTT-AATATATTT
1 AAAATTTTAAATATACTT
* *
1964381 AAATTTTTAAA-AAACTT
1 AAAATTTTAAATATACTT
1964398 AAAAAATTTTAAATATA-TT
1 --AAAATTTTAAATATACTT
1964417 AAAATTTTAAATAT
1 AAAATTTTAAATAT
1964431 GTTAAAGAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
17 25 0.61
18 2 0.05
19 12 0.29
20 2 0.05
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (18 bp):
AAAATTTTAAATATACTT
Found at i:1964514 original size:17 final size:16
Alignment explanation
Indices: 1964492--1964538 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 16
1964482 ATGTCAAAAT
1964492 ATATTAAAATTTTGAA
1 ATATTAAAATTTTGAA
1964508 CATATTAAAAAATTTTGAA
1 -ATATT--AAAATTTTGAA
*
1964527 GTATTAAAATTT
1 ATATTAAAATTT
1964539 CAAAATATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 7 0.26
17 5 0.19
18 4 0.15
19 11 0.41
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (16 bp):
ATATTAAAATTTTGAA
Found at i:1964531 original size:18 final size:19
Alignment explanation
Indices: 1964497--1964535 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1964487 AAAATATATT
1964497 AAAATTTTGAACATATTAA
1 AAAATTTTGAACATATTAA
*
1964516 AAAATTTTGAA-GTATTAA
1 AAAATTTTGAACATATTAA
1964534 AA
1 AA
1964536 TTTCAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.54, C:0.03, G:0.08, T:0.36
Consensus pattern (19 bp):
AAAATTTTGAACATATTAA
Found at i:1965818 original size:21 final size:21
Alignment explanation
Indices: 1965794--1965838 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
1965784 AATTTTTTAA
1965794 TTAAATAAAATATAAAACCAC
1 TTAAATAAAATATAAAACCAC
1965815 TTAAATAAAATATAAAACCAC
1 TTAAATAAAATATAAAACCAC
1965836 TTA
1 TTA
1965839 CAATTTGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.60, C:0.13, G:0.00, T:0.27
Consensus pattern (21 bp):
TTAAATAAAATATAAAACCAC
Found at i:1965954 original size:17 final size:17
Alignment explanation
Indices: 1965903--1965959 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
1965893 CTTAATATAT
1965903 TTAAAATTTTTAAAAAT-
1 TTAAAA-TTTTAAAAATA
*** * *
1965920 TTAAAAAAATGAATATA
1 TTAAAATTTTAAAAATA
1965937 TTAAAATTTTAAAAATA
1 TTAAAATTTTAAAAATA
1965954 TTAAAA
1 TTAAAA
1965960 AATGTTAAGT
Statistics
Matches: 29, Mismatches: 10, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
16 5 0.17
17 24 0.83
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (17 bp):
TTAAAATTTTAAAAATA
Found at i:1965963 original size:33 final size:35
Alignment explanation
Indices: 1965896--1965961 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
1965886 AGATTTTCTT
1965896 AATATATTTAAAATTTTTAAAAATTTAAAAAAATG
1 AATATATTTAAAATTTTTAAAAATTTAAAAAAATG
1965931 AATATA-TTAAAA-TTTTAAAAATATTAAAAAA
1 AATATATTTAAAATTTTTAAAAAT-TTAAAAAA
1965962 TGTTAAGTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
33 10 0.33
34 14 0.47
35 6 0.20
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (35 bp):
AATATATTTAAAATTTTTAAAAATTTAAAAAAATG
Found at i:1966131 original size:18 final size:18
Alignment explanation
Indices: 1966071--1966133 Score: 60
Period size: 17 Copynumber: 3.6 Consensus size: 18
1966061 GAAAAAGATT
*
1966071 TTTTAATATAT-TTAAAA
1 TTTTAAAATATATTAAAA
*
1966088 TTTTAAAA-AAATTTAAAA
1 TTTTAAAATATA-TTAAAA
**
1966106 AATT-AAATATATTAAAA
1 TTTTAAAATATATTAAAA
1966123 TTTTAAAATAT
1 TTTTAAAATAT
1966134 TTTTTAATAG
Statistics
Matches: 35, Mismatches: 7, Indels: 7
0.71 0.14 0.14
Matches are distributed among these distances:
16 1 0.03
17 18 0.51
18 16 0.46
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TTTTAAAATATATTAAAA
Found at i:1979824 original size:19 final size:19
Alignment explanation
Indices: 1979759--1979831 Score: 87
Period size: 18 Copynumber: 3.9 Consensus size: 19
1979749 AATTGATTGG
* *
1979759 TTATCCAGTAACAGTC-AA
1 TTATTCAGTAACAATCAAA
*
1979777 TTATTCAGTAAAAATCAAA
1 TTATTCAGTAACAATCAAA
* *
1979796 -TATACAGTAACAATTAAA
1 TTATTCAGTAACAATCAAA
1979814 TTATTCAGTAACAATCAA
1 TTATTCAGTAACAATCAA
1979832 TCTTTCCAGT
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
18 28 0.62
19 17 0.38
ACGTcount: A:0.48, C:0.15, G:0.07, T:0.30
Consensus pattern (19 bp):
TTATTCAGTAACAATCAAA
Found at i:1980065 original size:12 final size:12
Alignment explanation
Indices: 1980048--1980072 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1980038 AGTGCCGAAT
1980048 CGGTAACAGTAA
1 CGGTAACAGTAA
1980060 CGGTAACAGTAA
1 CGGTAACAGTAA
1980072 C
1 C
1980073 AGTAGTCGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.20, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTAACAGTAA
Found at i:1980866 original size:17 final size:17
Alignment explanation
Indices: 1980844--1980884 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
1980834 AACCTTGAAT
* *
1980844 TTTCCTTTTTTTCTTTC
1 TTTCCTTTCTTTCTTCC
1980861 TTTCCTTTCTTTCTTCC
1 TTTCCTTTCTTTCTTCC
1980878 TTTCCTT
1 TTTCCTT
1980885 CCCCTGCTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTCCTTTCTTTCTTCC
Found at i:1983341 original size:13 final size:13
Alignment explanation
Indices: 1983323--1983347 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1983313 TGTATATATA
1983323 AAAAAGGAAAAAT
1 AAAAAGGAAAAAT
1983336 AAAAAGGAAAAA
1 AAAAAGGAAAAA
1983348 AGAAATAAAG
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:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (13 bp):
AAAAAGGAAAAAT
Found at i:1983451 original size:21 final size:21
Alignment explanation
Indices: 1983401--1983444 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
1983391 AAAGCAGGGG
1983401 AAAGAAAGAAAGAAAAAGAGA
1 AAAGAAAGAAAGAAAAAGAGA
*
1983422 AAAGAAAGAAA-AAAAAGGGA
1 AAAGAAAGAAAGAAAAAGAGA
1983442 AAA
1 AAA
1983445 TCGAAGATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (21 bp):
AAAGAAAGAAAGAAAAAGAGA
Done.