Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 5 of 182
Found at i:1651359 original size:122 final size:124
Alignment explanation
Indices: 1650968--1651366 Score: 388
Period size: 122 Copynumber: 3.3 Consensus size: 124
1650958 AAAAATTGCA
* * * * * **
1650968 TTTTTGGGTGTTGGCTATCAAATAGTCGACACCCCCTATTTCTCGAGAAAAAAATTTCAATTTTT
1 TTTTTTGGTGTTGACCATCAAATGGCCGACACCCCCTATTTCTCGAGAAAAAAATTTCAA-AATT
* ** ** ** * **
1651033 TTTTTGTGTTGTACATTGAATGGCCGACACCCCCTA-TT-TC-A-AAAAATAA-ATTGCA-
65 TTTTGGTGTTGGCCATCAAATACCCGACACCCCCTATTTCTCGAGAAAAA-AATTTTAAAT
* * * *
1651088 TTTTTGGGTGTCGGCCATCAAATGGCCGACACCCCCTATTTTTCGAGAAAAAAATTTCAAAATTT
1 TTTTTTGGTGTTGACCATCAAATGGCCGACACCCCCTATTTCTCGAGAAAAAAATTTCAAAATTT
** *
1651153 TTTGGTGTTGGCCATCAAATGGCCGACACCCCCTATTTCTCGAGAAAAAATTTTTAAAT
66 TTTGGTGTTGGCCATCAAATACCCGACACCCCCTATTTCTCGAGAAAAAAATTTTAAAT
* * ** *
1651212 TTTTTTGGTGTTGGCCACTGC--ATGGCCGACACCCCCT-TTTCTCGAG-AAAAATTTTTTAATT
1 TTTTTTGGTGTTGACCA-T-CAAATGGCCGACACCCCCTATTTCTCGAGAAAAAAATTTCAAAAT
*
1651273 TTTTTGGTGTTGGCCATCAAATACCCGACACCCTCTA-TTCTCGAGAAAAAAATTTTAAATT
64 TTTTTGGTGTTGGCCATCAAATACCCGACACCCCCTATTTCTCGAGAAAAAAATTTTAAA-T
* *
1651334 TTTTTTTGTGTTGACCATCAAATGGCCGGCACC
1 TTTTTTGGTGTTGACCATCAAATGGCCGACACC
1651367 AACTTCTCTT
Statistics
Matches: 238, Mismatches: 30, Indels: 20
0.83 0.10 0.07
Matches are distributed among these distances:
119 33 0.14
120 58 0.24
121 24 0.10
122 74 0.31
123 16 0.07
124 31 0.13
125 1 0.00
126 1 0.00
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.35
Consensus pattern (124 bp):
TTTTTTGGTGTTGACCATCAAATGGCCGACACCCCCTATTTCTCGAGAAAAAAATTTCAAAATTT
TTTGGTGTTGGCCATCAAATACCCGACACCCCCTATTTCTCGAGAAAAAAATTTTAAAT
Found at i:1651862 original size:62 final size:62
Alignment explanation
Indices: 1651765--1651900 Score: 263
Period size: 62 Copynumber: 2.2 Consensus size: 62
1651755 GACTTGGCCG
1651765 GGTATTCAGGCAATATGGACTCATATTAATTGAGGGTTAGAAGAATTTATTGAAGTCGATCA
1 GGTATTCAGGCAATATGGACTCATATTAATTGAGGGTTAGAAGAATTTATTGAAGTCGATCA
*
1651827 GGTATTCATGCAATATGGACTCATATTAATTGAGGGTTAGAAGAATTTATTGAAGTCGATCA
1 GGTATTCAGGCAATATGGACTCATATTAATTGAGGGTTAGAAGAATTTATTGAAGTCGATCA
1651889 GGTATTCAGGCA
1 GGTATTCAGGCA
1651901 GATGGACATT
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 72 1.00
ACGTcount: A:0.33, C:0.10, G:0.24, T:0.32
Consensus pattern (62 bp):
GGTATTCAGGCAATATGGACTCATATTAATTGAGGGTTAGAAGAATTTATTGAAGTCGATCA
Found at i:1656111 original size:6 final size:6
Alignment explanation
Indices: 1656100--1656128 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
1656090 TCTAGAGAGG
1656100 AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
1656129 GAGGAAACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:1670306 original size:7 final size:7
Alignment explanation
Indices: 1670291--1670384 Score: 61
Period size: 7 Copynumber: 13.4 Consensus size: 7
1670281 GTTTTATGCA
*
1670291 TAAGATT
1 TAAGGTT
1670298 TAAGGTT
1 TAAGGTT
*
1670305 TAGGGTTT
1 TAAGG-TT
1670313 TAA-GTT
1 TAAGGTT
1670319 TAAGGTT
1 TAAGGTT
1670326 TATA-GTT
1 TA-AGGTT
* *
1670333 CATGGTT
1 TAAGGTT
1670340 CTAA-GTT
1 -TAAGGTT
1670347 T-AGGATT
1 TAAGG-TT
*
1670354 TAAAGTT
1 TAAGGTT
1670361 TAAGGTT
1 TAAGGTT
*
1670368 TAAGTTT
1 TAAGGTT
*
1670375 TAGGGTT
1 TAAGGTT
1670382 TAA
1 TAA
1670385 TGTTATGAAA
Statistics
Matches: 66, Mismatches: 13, Indels: 16
0.69 0.14 0.17
Matches are distributed among these distances:
5 1 0.02
6 7 0.11
7 50 0.76
8 8 0.12
ACGTcount: A:0.29, C:0.02, G:0.23, T:0.46
Consensus pattern (7 bp):
TAAGGTT
Found at i:1670376 original size:28 final size:28
Alignment explanation
Indices: 1670294--1670384 Score: 87
Period size: 28 Copynumber: 3.2 Consensus size: 28
1670284 TTATGCATAA
* * *
1670294 GATTTAAGGTTTAGGGTTTTAAGTTTAAG
1 GATTTAAAGTTTAAGG-TTTAAGTTTTAG
* * *
1670323 G-TTTATAGTTCATGGTTCTAAG-TTTAG
1 GATTTAAAGTTTAAGGTT-TAAGTTTTAG
1670350 GATTTAAAGTTTAAGGTTTAAGTTTTAG
1 GATTTAAAGTTTAAGGTTTAAGTTTTAG
*
1670378 GGTTTAA
1 GATTTAA
1670385 TGTTATGAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 7
0.76 0.14 0.11
Matches are distributed among these distances:
27 11 0.22
28 38 0.76
29 1 0.02
ACGTcount: A:0.27, C:0.02, G:0.24, T:0.46
Consensus pattern (28 bp):
GATTTAAAGTTTAAGGTTTAAGTTTTAG
Found at i:1670607 original size:43 final size:43
Alignment explanation
Indices: 1670542--1670633 Score: 123
Period size: 43 Copynumber: 2.1 Consensus size: 43
1670532 TGAACTGCAC
* *
1670542 ATTTAATAACATGTCAAGATATTAATAAGAGTAAAGTAATATA
1 ATTTAATAACATGTCAACATATTAACAAGAGTAAAGTAATATA
* * *
1670585 ATTTAGTAACATG-CAACCATATTAACACGAGTCAAGTAATATA
1 ATTTAATAACATGTCAA-CATATTAACAAGAGTAAAGTAATATA
1670628 ATTTAA
1 ATTTAA
1670634 CATGTTAATG
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
42 3 0.07
43 39 0.93
ACGTcount: A:0.48, C:0.10, G:0.11, T:0.32
Consensus pattern (43 bp):
ATTTAATAACATGTCAACATATTAACAAGAGTAAAGTAATATA
Found at i:1671949 original size:17 final size:17
Alignment explanation
Indices: 1671929--1671978 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
1671919 ATGATGGGAT
1671929 ATTATTTTTGATAATTA
1 ATTATTTTTGATAATTA
1671946 ATTATTTTT-AT-ATT-
1 ATTATTTTTGATAATTA
*
1671960 A-TA-TTTTGGTAATTA
1 ATTATTTTTGATAATTA
1671975 ATTA
1 ATTA
1671979 GCTATGTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 9
0.74 0.03 0.24
Matches are distributed among these distances:
12 4 0.14
13 3 0.11
14 4 0.14
15 4 0.14
16 4 0.14
17 9 0.32
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (17 bp):
ATTATTTTTGATAATTA
Found at i:1672547 original size:20 final size:21
Alignment explanation
Indices: 1672522--1672564 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1672512 TACTTATTAC
1672522 TACTAAC-AACAAAATAAAAT
1 TACTAACTAACAAAATAAAAT
*
1672542 TACTAACTAACAAAATTAAAT
1 TACTAACTAACAAAATAAAAT
1672563 TA
1 TA
1672565 AAGTAAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.60, C:0.14, G:0.00, T:0.26
Consensus pattern (21 bp):
TACTAACTAACAAAATAAAAT
Found at i:1674493 original size:13 final size:13
Alignment explanation
Indices: 1674475--1674499 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1674465 TTTGGTCCAC
1674475 TTTGACAATTAAA
1 TTTGACAATTAAA
1674488 TTTGACAATTAA
1 TTTGACAATTAA
1674500 GTTTATTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (13 bp):
TTTGACAATTAAA
Found at i:1678802 original size:3 final size:3
Alignment explanation
Indices: 1678794--1678821 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1678784 AAAATTATAT
1678794 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1678822 AGGCCAGAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:1682049 original size:22 final size:20
Alignment explanation
Indices: 1682024--1682070 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
1682014 AGTTAAATTT
*
1682024 TTTTACATATTCTTTTTGAAAA
1 TTTTACAT-TT-TTTTTAAAAA
*
1682046 TTTTAGATTTTTTTTAAAAA
1 TTTTACATTTTTTTTAAAAA
1682066 TTTTA
1 TTTTA
1682071 TACTTTTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 14 0.61
21 2 0.09
22 7 0.30
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.60
Consensus pattern (20 bp):
TTTTACATTTTTTTTAAAAA
Found at i:1682077 original size:20 final size:20
Alignment explanation
Indices: 1682036--1682078 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1682026 TTACATATTC
* *
1682036 TTTTTGAAAATTTTAGATTT
1 TTTTTAAAAATTTTAGACTT
*
1682056 TTTTTAAAAATTTTATACTT
1 TTTTTAAAAATTTTAGACTT
1682076 TTT
1 TTT
1682079 GTCAGATAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.63
Consensus pattern (20 bp):
TTTTTAAAAATTTTAGACTT
Found at i:1689135 original size:3 final size:3
Alignment explanation
Indices: 1689127--1689151 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1689117 ACACTTTTAA
1689127 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
1689152 TGTTGGGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1694385 original size:31 final size:32
Alignment explanation
Indices: 1694335--1694394 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 32
1694325 AGATTTATTT
1694335 ATAGCAATTTATTGGGTAATTTTCAAGCTTTG
1 ATAGCAATTTATTGGGTAATTTTCAAGCTTTG
* *
1694367 ATAGCAGTTTGTT-GGTAATTTTCAAGCT
1 ATAGCAATTTATTGGGTAATTTTCAAGCT
1694395 CTATATTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 15 0.58
32 11 0.42
ACGTcount: A:0.27, C:0.10, G:0.20, T:0.43
Consensus pattern (32 bp):
ATAGCAATTTATTGGGTAATTTTCAAGCTTTG
Found at i:1697541 original size:16 final size:16
Alignment explanation
Indices: 1697516--1697551 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1697506 TAATTAAATC
1697516 TATTAACTAACTTTAT
1 TATTAACTAACTTTAT
* *
1697532 TATTATCTAACTTTTT
1 TATTAACTAACTTTAT
1697548 TATT
1 TATT
1697552 TGTGTGTGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.31, C:0.11, G:0.00, T:0.58
Consensus pattern (16 bp):
TATTAACTAACTTTAT
Found at i:1704281 original size:20 final size:21
Alignment explanation
Indices: 1704238--1704282 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
1704228 TCAAATCCAG
* *
1704238 CCTCTACAACCAACATAAAAA
1 CCTCTACAACCAAAAGAAAAA
*
1704259 CCTCTAC-ACCAAAAGAAACA
1 CCTCTACAACCAAAAGAAAAA
1704279 CCTC
1 CCTC
1704283 CAATTATTGC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.47, C:0.38, G:0.02, T:0.13
Consensus pattern (21 bp):
CCTCTACAACCAAAAGAAAAA
Found at i:1705427 original size:6 final size:6
Alignment explanation
Indices: 1705416--1705445 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
1705406 TTTTCTAAAA
1705416 TCAATT TCAATT TCAATT TCAATT T-AATT T
1 TCAATT TCAATT TCAATT TCAATT TCAATT T
1705446 GATTGTTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.33, C:0.13, G:0.00, T:0.53
Consensus pattern (6 bp):
TCAATT
Found at i:1715302 original size:29 final size:29
Alignment explanation
Indices: 1715247--1715302 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
1715237 TCCATTCAAA
* *
1715247 TAATTAATTTATTTAATGGAGTGAAATTT
1 TAATTAATTTATTTAAAGGAGTAAAATTT
*
1715276 TAATATAATTT-TTTAAAGGATTAAAAT
1 TAAT-TAATTTATTTAAAGGAGTAAAAT
1715303 AACACTGTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 17 0.74
30 6 0.26
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (29 bp):
TAATTAATTTATTTAAAGGAGTAAAATTT
Found at i:1717037 original size:29 final size:29
Alignment explanation
Indices: 1717004--1717064 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
1716994 GTTAGAACCA
*
1717004 AAATTT-TGAAACTCAAAAAGTAAAA-AACT
1 AAATTTCTAAAACT-AAAAA-TAAAATAACT
*
1717033 AAATTTCTAAAAGTAAAAATAAAATAACT
1 AAATTTCTAAAACTAAAAATAAAATAACT
1717062 AAA
1 AAA
1717065 ATTTAAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 5 0.18
29 18 0.64
30 5 0.18
ACGTcount: A:0.62, C:0.08, G:0.05, T:0.25
Consensus pattern (29 bp):
AAATTTCTAAAACTAAAAATAAAATAACT
Found at i:1736165 original size:21 final size:19
Alignment explanation
Indices: 1736105--1736161 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 19
1736095 CTAAGTTTAT
**
1736105 TTTTAATAATTATTTACGG
1 TTTTAATAATTATTTACAA
*
1736124 TTTTAAATAATGTTTTTACAA
1 TTTT-AATAAT-TATTTACAA
1736145 TATTTAATAATTATTTA
1 T-TTTAATAATTATTTA
1736162 ACAACTCTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
19 4 0.13
20 11 0.35
21 13 0.42
22 3 0.10
ACGTcount: A:0.37, C:0.04, G:0.05, T:0.54
Consensus pattern (19 bp):
TTTTAATAATTATTTACAA
Found at i:1736934 original size:42 final size:43
Alignment explanation
Indices: 1736887--1736971 Score: 136
Period size: 43 Copynumber: 2.0 Consensus size: 43
1736877 ATAGCCATTC
**
1736887 AACGTTCATCTTA-AATTTGAATTTTGAAAATTCAGACCGTTG
1 AACGTTCATCTTATAATTTGAATTTTGAAAAACCAGACCGTTG
*
1736929 AACGTTCATCTTATATTTTGAATTTTGAAAAACCAGACCGTTG
1 AACGTTCATCTTATAATTTGAATTTTGAAAAACCAGACCGTTG
1736972 CTCACCCCGT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
42 13 0.33
43 26 0.67
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (43 bp):
AACGTTCATCTTATAATTTGAATTTTGAAAAACCAGACCGTTG
Found at i:1737977 original size:12 final size:12
Alignment explanation
Indices: 1737962--1737994 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
1737952 CAAGAAGCTG
1737962 AGAAAGAAACCA
1 AGAAAGAAACCA
*
1737974 AGAAAAAAACCA
1 AGAAAGAAACCA
1737986 AGAAAGAAA
1 AGAAAGAAA
1737995 GGGATCCCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.73, C:0.12, G:0.15, T:0.00
Consensus pattern (12 bp):
AGAAAGAAACCA
Found at i:1739805 original size:18 final size:18
Alignment explanation
Indices: 1739746--1739805 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
1739736 ATTATTATTA
* *
1739746 TTTTATAATTTTTTACAAC
1 TTTTAT-ATTTTATACAAT
* **
1739765 TTTTAAATTTTAT-GTAT
1 TTTTATATTTTATACAAT
1739782 TCTTTATATTTTATACAAT
1 T-TTTATATTTTATACAAT
1739801 TTTTA
1 TTTTA
1739806 AAAACAAAAA
Statistics
Matches: 31, Mismatches: 8, Indels: 5
0.70 0.18 0.11
Matches are distributed among these distances:
17 2 0.06
18 21 0.68
19 8 0.26
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.62
Consensus pattern (18 bp):
TTTTATATTTTATACAAT
Found at i:1740370 original size:54 final size:54
Alignment explanation
Indices: 1740288--1740396 Score: 218
Period size: 54 Copynumber: 2.0 Consensus size: 54
1740278 GAAATGAATT
1740288 TGGCCAATATAAGAAAGTGGATTCAAAGGGTGATGTTACATAATGCACGAGGAA
1 TGGCCAATATAAGAAAGTGGATTCAAAGGGTGATGTTACATAATGCACGAGGAA
1740342 TGGCCAATATAAGAAAGTGGATTCAAAGGGTGATGTTACATAATGCACGAGGAA
1 TGGCCAATATAAGAAAGTGGATTCAAAGGGTGATGTTACATAATGCACGAGGAA
1740396 T
1 T
1740397 CTCACTTTTC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.39, C:0.11, G:0.28, T:0.23
Consensus pattern (54 bp):
TGGCCAATATAAGAAAGTGGATTCAAAGGGTGATGTTACATAATGCACGAGGAA
Found at i:1740749 original size:9 final size:9
Alignment explanation
Indices: 1740735--1740822 Score: 65
Period size: 9 Copynumber: 9.8 Consensus size: 9
1740725 CTTGCCATGG
1740735 AAAGAAGGA
1 AAAGAAGGA
1740744 AAAGAA-G-
1 AAAGAAGGA
* *
1740751 -ATGAAAGA
1 AAAGAAGGA
*
1740759 CAAGAAGGA
1 AAAGAAGGA
1740768 GAAAGACAAGGA
1 -AAAG--AAGGA
* *
1740780 CAGGAAGGA
1 AAAGAAGGA
*
1740789 AAAGAAAGA
1 AAAGAAGGA
*
1740798 AAAGAAAGA
1 AAAGAAGGA
1740807 AAAGAAGGA
1 AAAGAAGGA
1740816 AAAGAAG
1 AAAGAAG
1740823 ACTGAGAGCA
Statistics
Matches: 63, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
6 4 0.06
7 1 0.02
8 1 0.02
9 47 0.75
10 3 0.05
11 2 0.03
12 5 0.08
ACGTcount: A:0.65, C:0.03, G:0.31, T:0.01
Consensus pattern (9 bp):
AAAGAAGGA
Found at i:1740765 original size:15 final size:15
Alignment explanation
Indices: 1740753--1740820 Score: 52
Period size: 14 Copynumber: 4.4 Consensus size: 15
1740743 AAAAGAAGAT
1740753 GAAAGACAAGAAGGA
1 GAAAGACAAGAAGGA
1740768 GAAAGACAAGGACAGGAA
1 GAAAGACAA-GA-AGG-A
*
1740786 GGAAAAGA-AAGAA-AA
1 -G-AAAGACAAGAAGGA
*
1740801 GAAAGAAAAGAAGGA
1 GAAAGACAAGAAGGA
1740816 -AAAGA
1 GAAAGA
1740821 AGACTGAGAG
Statistics
Matches: 44, Mismatches: 2, Indels: 15
0.72 0.03 0.25
Matches are distributed among these distances:
13 5 0.11
14 11 0.25
15 11 0.25
16 2 0.05
17 4 0.09
18 3 0.07
19 3 0.07
20 5 0.11
ACGTcount: A:0.65, C:0.04, G:0.31, T:0.00
Consensus pattern (15 bp):
GAAAGACAAGAAGGA
Found at i:1743598 original size:13 final size:13
Alignment explanation
Indices: 1743580--1743604 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1743570 AACATAAAAT
1743580 AGAGTTTCCCTTA
1 AGAGTTTCCCTTA
1743593 AGAGTTTCCCTT
1 AGAGTTTCCCTT
1743605 GGCGCCAAAT
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:0.20, C:0.24, G:0.16, T:0.40
Consensus pattern (13 bp):
AGAGTTTCCCTTA
Found at i:1745729 original size:20 final size:18
Alignment explanation
Indices: 1745693--1745735 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
1745683 TAATTTAATG
*
1745693 TTAATTAACCTTGTTTAA
1 TTAATTAAACTTGTTTAA
*
1745711 TTAATTAAACTATGATTTAC
1 TTAATTAAACT-TG-TTTAA
1745731 TTAAT
1 TTAAT
1745736 ATAATTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 10 0.48
19 2 0.10
20 9 0.43
ACGTcount: A:0.37, C:0.09, G:0.05, T:0.49
Consensus pattern (18 bp):
TTAATTAAACTTGTTTAA
Found at i:1758118 original size:3 final size:3
Alignment explanation
Indices: 1758110--1758139 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1758100 TCAGCATCGG
1758110 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC
1758140 TATCACCATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.67, G:0.00, T:0.00
Consensus pattern (3 bp):
CAC
Found at i:1760902 original size:28 final size:27
Alignment explanation
Indices: 1760845--1760903 Score: 70
Period size: 26 Copynumber: 2.2 Consensus size: 27
1760835 AATTTATAAT
1760845 TAAT-TTTAAAATTTAATAGTGTAAAA
1 TAATATTTAAAATTTAATAGTGTAAAA
*
1760871 -AATATTTAATATTTAAGCTAGTG-AAAA
1 TAATATTTAAAATTTAA--TAGTGTAAAA
1760898 TAATAT
1 TAATAT
1760904 AAAAATTACA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
25 3 0.11
26 11 0.39
27 4 0.14
28 10 0.36
ACGTcount: A:0.49, C:0.02, G:0.08, T:0.41
Consensus pattern (27 bp):
TAATATTTAAAATTTAATAGTGTAAAA
Found at i:1762140 original size:13 final size:13
Alignment explanation
Indices: 1762095--1762141 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
1762085 TTTATAAAAA
1762095 ATAAAAAAATTAT
1 ATAAAAAAATTAT
*
1762108 GTAATAAACATATT-T
1 ATAA-AAA-A-ATTAT
1762123 ATAAAAAAATTAT
1 ATAAAAAAATTAT
1762136 ATAAAA
1 ATAAAA
1762142 TTAAATAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
12 3 0.11
13 11 0.39
14 6 0.21
15 5 0.18
16 3 0.11
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (13 bp):
ATAAAAAAATTAT
Found at i:1768362 original size:23 final size:24
Alignment explanation
Indices: 1768318--1768362 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
1768308 TTCTCAACAG
* *
1768318 TAAAAATTAATAATAATTTTAATA
1 TAAAAATCAATAATAATCTTAATA
*
1768342 TAAAAATCAA-AATACTCTTAA
1 TAAAAATCAATAATAATCTTAA
1768363 ATATTTTACC
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 9 0.50
24 9 0.50
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.36
Consensus pattern (24 bp):
TAAAAATCAATAATAATCTTAATA
Found at i:1769803 original size:16 final size:15
Alignment explanation
Indices: 1769761--1769803 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
1769751 CATTTTGAAG
1769761 TTTTTAAATTTTTTA
1 TTTTTAAATTTTTTA
**
1769776 TTTTTATTTTTTTGTA
1 TTTTTAAATTTTT-TA
*
1769792 TTTTTACATTTT
1 TTTTTAAATTTT
1769804 GTGAACAGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (15 bp):
TTTTTAAATTTTTTA
Found at i:1799900 original size:20 final size:20
Alignment explanation
Indices: 1799875--1799923 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 20
1799865 AAATAGATTT
1799875 ATTTAAAATAAAAATATTA-A
1 ATTTAAAATAAAAA-ATTATA
*
1799895 ATTTAAATTAAAAAATTATA
1 ATTTAAAATAAAAAATTATA
1799915 ATATTAAAA
1 AT-TTAAAA
1799924 ACACTTTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 4 0.16
20 16 0.64
21 5 0.20
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
ATTTAAAATAAAAAATTATA
Found at i:1799910 original size:14 final size:16
Alignment explanation
Indices: 1799893--1799924 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1799883 TAAAAATATT
1799893 AAATT-TAA-ATTAAA
1 AAATTATAATATTAAA
1799907 AAATTATAATATTAAA
1 AAATTATAATATTAAA
1799923 AA
1 AA
1799925 CACTTTTCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.31
15 3 0.19
16 8 0.50
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
AAATTATAATATTAAA
Found at i:1800088 original size:14 final size:14
Alignment explanation
Indices: 1800065--1800119 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 14
1800055 TTAAATGTAC
1800065 TTTAAATATCAAAT
1 TTTAAATATCAAAT
*
1800079 TTTAAGTATCAAA-
1 TTTAAATATCAAAT
* *
1800092 TTGAAATAAAT-AAAA
1 TTTAAAT--ATCAAAT
1800107 TTTAAATATCAAA
1 TTTAAATATCAAA
1800120 ATAAAAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
13 7 0.21
14 18 0.55
15 8 0.24
ACGTcount: A:0.55, C:0.05, G:0.04, T:0.36
Consensus pattern (14 bp):
TTTAAATATCAAAT
Found at i:1800102 original size:42 final size:44
Alignment explanation
Indices: 1800032--1800119 Score: 108
Period size: 42 Copynumber: 2.0 Consensus size: 44
1800022 ACAAAAATAT
* ** *
1800032 ATTTTAAGTACCAATTTGAAAATTTAAATGTACTTTAAATATCAA
1 ATTTTAAGTACCAAATTGAAAA-TTAAATAAAATTTAAATATCAA
*
1800077 ATTTTAAGTATCAAATTG-AAA-TAAATAAAATTTAAATATCAA
1 ATTTTAAGTACCAAATTGAAAATTAAATAAAATTTAAATATCAA
1800119 A
1 A
1800120 ATAAAAAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
42 19 0.50
44 3 0.08
45 16 0.42
ACGTcount: A:0.50, C:0.07, G:0.06, T:0.38
Consensus pattern (44 bp):
ATTTTAAGTACCAAATTGAAAATTAAATAAAATTTAAATATCAA
Found at i:1801948 original size:16 final size:17
Alignment explanation
Indices: 1801921--1801953 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1801911 GATAATTTAT
1801921 TTTAATAATATAAAATA
1 TTTAATAATATAAAATA
*
1801938 TTTAA-AATATATAATA
1 TTTAATAATATAAAATA
1801954 AAAAAATTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TTTAATAATATAAAATA
Found at i:1804382 original size:17 final size:18
Alignment explanation
Indices: 1804344--1804384 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1804334 ATTTACTTTT
* *
1804344 ATTTTATTTTACCACTGA
1 ATTTTATTTTAACACAGA
1804362 ATTTTATTTTAACA-AGA
1 ATTTTATTTTAACACAGA
1804379 ATTTTA
1 ATTTTA
1804385 GTCACCCAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.34, C:0.10, G:0.05, T:0.51
Consensus pattern (18 bp):
ATTTTATTTTAACACAGA
Found at i:1813827 original size:26 final size:25
Alignment explanation
Indices: 1813798--1813888 Score: 78
Period size: 26 Copynumber: 3.5 Consensus size: 25
1813788 TTTTTTATTC
1813798 TTAAAAGTTAAAATTTTTTAGGCTTT
1 TTAAAAGTTAAAATTTTTT-GGCTTT
* *
1813824 TTAAAAATTGGTAAAA-TTTTTGAC-TT
1 TT-AAAA--GTTAAAATTTTTTGGCTTT
* *
1813850 TTAAAAGTTAAATTTTTTTGGGTTTT
1 TTAAAAGTTAAAATTTTTT-GGCTTT
*
1813876 TTAAAAATTAAAA
1 TTAAAAGTTAAAA
1813889 AGTAATATTT
Statistics
Matches: 51, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
23 5 0.10
24 5 0.10
25 5 0.10
26 19 0.37
27 6 0.12
28 5 0.10
29 6 0.12
ACGTcount: A:0.38, C:0.02, G:0.11, T:0.48
Consensus pattern (25 bp):
TTAAAAGTTAAAATTTTTTGGCTTT
Found at i:1827553 original size:25 final size:23
Alignment explanation
Indices: 1827525--1827582 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 23
1827515 TTTTTTAAAA
*
1827525 AATATTTATATATTTTTTAAAAATT
1 AATATTT-TA-ATTTTTTAAAAATG
1827550 AATACTTTTAATTTTTTAAAAATG
1 AATA-TTTTAATTTTTTAAAAATG
1827574 AATGATTTT
1 AAT-ATTTT
1827583 TTTTCTTGCC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
24 20 0.67
25 7 0.23
26 3 0.10
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.53
Consensus pattern (23 bp):
AATATTTTAATTTTTTAAAAATG
Found at i:1827962 original size:18 final size:20
Alignment explanation
Indices: 1827939--1827977 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1827929 ATTTAATAAT
1827939 TATTATT-TT-TTATCATTA
1 TATTATTGTTATTATCATTA
*
1827957 TATTATTGTTATTATTATTA
1 TATTATTGTTATTATCATTA
1827977 T
1 T
1827978 TAAGAAAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 2 0.11
20 9 0.50
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (20 bp):
TATTATTGTTATTATCATTA
Found at i:1830798 original size:13 final size:13
Alignment explanation
Indices: 1830764--1830798 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
1830754 AGAGAAACAA
*
1830764 AAAACAAGGGAAT
1 AAAACAAGTGAAT
1830777 AAAACAAGTGAAT
1 AAAACAAGTGAAT
*
1830790 AATACAAGT
1 AAAACAAGT
1830799 CTTTTTCATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.60, C:0.09, G:0.17, T:0.14
Consensus pattern (13 bp):
AAAACAAGTGAAT
Found at i:1843158 original size:24 final size:24
Alignment explanation
Indices: 1843130--1843188 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
1843120 TAGAGTAATA
*
1843130 AGAGTTTGACTCAAACAAATAAAC
1 AGAGTTTAACTCAAACAAATAAAC
* *
1843154 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTCAAACAAATAAAC
*
1843178 AGAATTTAACT
1 AGAGTTTAACT
1843189 GAAAGATTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.51, C:0.12, G:0.12, T:0.25
Consensus pattern (24 bp):
AGAGTTTAACTCAAACAAATAAAC
Found at i:1843191 original size:24 final size:24
Alignment explanation
Indices: 1843142--1843192 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
1843132 AGTTTGACTC
* *
1843142 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAATTTAACTG
1843166 AAACAAATAAACAGAATTTAACTG
1 AAACAAATAAACAGAATTTAACTG
1843190 AAA
1 AAA
1843193 GATTATTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.22
Consensus pattern (24 bp):
AAACAAATAAACAGAATTTAACTG
Found at i:1845247 original size:30 final size:29
Alignment explanation
Indices: 1845211--1845276 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 29
1845201 GTGATTTGTG
*
1845211 AAAATTAAATC-AAATTAAAATTTCATGTAT
1 AAAATTAAA-CAAAATCAAAATTT-ATGTAT
*
1845241 AAAATTACACAAAATCAAAATTTATGTAT
1 AAAATTAAACAAAATCAAAATTTATGTAT
*
1845270 AATATTA
1 AAAATTA
1845277 CACATTGAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 13 0.41
30 19 0.59
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.35
Consensus pattern (29 bp):
AAAATTAAACAAAATCAAAATTTATGTAT
Found at i:1845268 original size:29 final size:30
Alignment explanation
Indices: 1845222--1845280 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
1845212 AAATTAAATC
*
1845222 AAATTAAAATTTCATGTATAAAATTACACA
1 AAATCAAAATTTCATGTATAAAATTACACA
*
1845252 AAATCAAAATTT-ATGTATAATATTACACA
1 AAATCAAAATTTCATGTATAAAATTACACA
1845281 TTGAATCAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 16 0.59
30 11 0.41
ACGTcount: A:0.53, C:0.10, G:0.03, T:0.34
Consensus pattern (30 bp):
AAATCAAAATTTCATGTATAAAATTACACA
Found at i:1850712 original size:21 final size:23
Alignment explanation
Indices: 1850679--1850720 Score: 70
Period size: 21 Copynumber: 1.9 Consensus size: 23
1850669 TTTGATGTGC
1850679 AAATGTATATAATAAATTATTGT
1 AAATGTATATAATAAATTATTGT
1850702 AAAT-TAT-TAATAAATTATT
1 AAATGTATATAATAAATTATT
1850721 TATATAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 12 0.63
22 3 0.16
23 4 0.21
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (23 bp):
AAATGTATATAATAAATTATTGT
Found at i:1850717 original size:11 final size:11
Alignment explanation
Indices: 1850688--1850720 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
1850678 CAAATGTATA
1850688 TAATAAATTAT
1 TAATAAATTAT
*
1850699 T-GTAAATTAT
1 TAATAAATTAT
1850709 TAATAAATTAT
1 TAATAAATTAT
1850720 T
1 T
1850721 TATATAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (11 bp):
TAATAAATTAT
Found at i:1858604 original size:32 final size:32
Alignment explanation
Indices: 1858542--1858604 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 32
1858532 ATTTTGATAA
* **
1858542 TATTTATATTTTTTTTATATAATATTTAAAAT
1 TATTTATATTTTTTTAATATAATAAATAAAAT
*
1858574 TATTTATAATTTTTTTAAT-TCATAAATAAAA
1 TATTTAT-ATTTTTTTAATATAATAAATAAAA
1858605 AGATAATACA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
32 16 0.62
33 10 0.38
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (32 bp):
TATTTATATTTTTTTAATATAATAAATAAAAT
Found at i:1862255 original size:22 final size:22
Alignment explanation
Indices: 1862230--1862290 Score: 56
Period size: 21 Copynumber: 2.9 Consensus size: 22
1862220 TAATGGATTC
1862230 AATTGATTAAAATTAAAATTAA
1 AATTGATTAAAATTAAAATTAA
* *
1862252 AATT--TTAAAAATATAAACTAA
1 AATTGATTAAAATTA-AAATTAA
* *
1862273 AAATGAGT-AAATTAAAAT
1 AATTGATTAAAATTAAAAT
1862291 ATCTATCTAT
Statistics
Matches: 30, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
20 8 0.27
21 12 0.40
22 9 0.30
23 1 0.03
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.33
Consensus pattern (22 bp):
AATTGATTAAAATTAAAATTAA
Found at i:1862273 original size:21 final size:20
Alignment explanation
Indices: 1862236--1862274 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1862226 ATTCAATTGA
* *
1862236 TTAAAATTAAAATTAAAATT
1 TTAAAAATAAAACTAAAATT
1862256 TTAAAAATATAAACTAAAA
1 TTAAAAATA-AAACTAAAA
1862275 ATGAGTAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (20 bp):
TTAAAAATAAAACTAAAATT
Found at i:1863049 original size:21 final size:21
Alignment explanation
Indices: 1863021--1863061 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
1863011 TTAACAATAC
1863021 TTTAATTAT-TATTTAAAAAT
1 TTTAATTATATATTTAAAAAT
1863041 TTTATATTATAATATTTAAAA
1 TTTA-ATTAT-ATATTTAAAA
1863062 TGATAAGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 5 0.28
23 9 0.50
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TTTAATTATATATTTAAAAAT
Found at i:1869382 original size:47 final size:47
Alignment explanation
Indices: 1869331--1869535 Score: 340
Period size: 47 Copynumber: 4.4 Consensus size: 47
1869321 GTTGTAGATG
* * *
1869331 TAGGACTCTTAATTAAAGTTGTTTTATTGTATTTAGGATAAGTTAGA
1 TAGGACTCTTAATAAAAGTTGTTTTATTATTTTTAGGATAAGTTAGA
*
1869378 TAGGACTCTTAATAAAAGTTGTTTTATTATTTTTAGGATAACTTAGA
1 TAGGACTCTTAATAAAAGTTGTTTTATTATTTTTAGGATAAGTTAGA
1869425 TAGGACTCTTAATAAAAGTTGTTTTATTATTTTTAGGATAAGTTAGA
1 TAGGACTCTTAATAAAAGTTGTTTTATTATTTTTAGGATAAGTTAGA
* *
1869472 TAAGACTCTTAATAAAAGTTGTTTTATTATTTTTAGGAGAAGTTATG-
1 TAGGACTCTTAATAAAAGTTGTTTTATTATTTTTAGGATAAGTTA-GA
1869519 TAGGACTCTTAATAAAA
1 TAGGACTCTTAATAAAA
1869536 TAAGATTCTT
Statistics
Matches: 149, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
47 148 0.99
48 1 0.01
ACGTcount: A:0.35, C:0.05, G:0.17, T:0.43
Consensus pattern (47 bp):
TAGGACTCTTAATAAAAGTTGTTTTATTATTTTTAGGATAAGTTAGA
Found at i:1873958 original size:29 final size:28
Alignment explanation
Indices: 1873884--1873958 Score: 64
Period size: 29 Copynumber: 2.6 Consensus size: 28
1873874 AAAAAAAGCT
*
1873884 TTGTTTTATTT-ATTTATTTTTAAAACA
1 TTGTTTTATTTAATTTATTATTAAAACA
* * * *
1873911 TTATTTT-TATTAAGATTATTATTAGAATA
1 TTGTTTTAT-TTAA-TTTATTATTAAAACA
1873940 TTGTTTATATTTAATTTAT
1 TTGTTT-TATTTAATTTAT
1873959 ATTTTCCATG
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
26 1 0.03
27 8 0.22
28 1 0.03
29 20 0.56
30 5 0.14
31 1 0.03
ACGTcount: A:0.32, C:0.01, G:0.05, T:0.61
Consensus pattern (28 bp):
TTGTTTTATTTAATTTATTATTAAAACA
Found at i:1879462 original size:15 final size:16
Alignment explanation
Indices: 1879430--1879465 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
1879420 TAATCTTTTA
*
1879430 AAAATAATAAAATTAT
1 AAAATAATAAAATGAT
1879446 AAAATAAT-AAATGAT
1 AAAATAATAAAATGAT
1879461 AAAAT
1 AAAAT
1879466 TATCATTCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (16 bp):
AAAATAATAAAATGAT
Found at i:1881968 original size:21 final size:25
Alignment explanation
Indices: 1881920--1881969 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 25
1881910 TAATTTCAGA
*
1881920 TATTTTATTTGAAGAGAAGAAACTC
1 TATTTTATTTGAAGAGAAGAAACAC
1881945 TATTTT-TTTG-A-AGAA-AAACAC
1 TATTTTATTTGAAGAGAAGAAACAC
1881966 TATT
1 TATT
1881970 CCTTTTATCT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 9 0.38
22 4 0.17
23 1 0.04
24 4 0.17
25 6 0.25
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (25 bp):
TATTTTATTTGAAGAGAAGAAACAC
Found at i:1882259 original size:14 final size:15
Alignment explanation
Indices: 1882231--1882270 Score: 64
Period size: 14 Copynumber: 2.7 Consensus size: 15
1882221 AATTATTATT
*
1882231 AATAATAATGGTAAA
1 AATAATAATGATAAA
1882246 AATAA-AATGATAAA
1 AATAATAATGATAAA
1882260 AATAATAATGA
1 AATAATAATGA
1882271 GATGTGTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.57
15 10 0.43
ACGTcount: A:0.65, C:0.00, G:0.10, T:0.25
Consensus pattern (15 bp):
AATAATAATGATAAA
Found at i:1884387 original size:14 final size:14
Alignment explanation
Indices: 1884368--1884404 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
1884358 AGGTTGTTTA
1884368 TGTTGCTTTAGATT
1 TGTTGCTTTAGATT
1884382 TGTTGCTTTAGATT
1 TGTTGCTTTAGATT
1884396 TGTTG-TTTA
1 TGTTGCTTTA
1884405 TGTTGCTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 4 0.17
14 19 0.83
ACGTcount: A:0.14, C:0.05, G:0.22, T:0.59
Consensus pattern (14 bp):
TGTTGCTTTAGATT
Found at i:1887614 original size:95 final size:95
Alignment explanation
Indices: 1887451--1887637 Score: 374
Period size: 95 Copynumber: 2.0 Consensus size: 95
1887441 TATTTCTTGC
1887451 TAATTTTTTTAAGTTGATCTAGAAATTAAGATGTTGAACTAATTGAATGAAGATGTGAAATTTGG
1 TAATTTTTTTAAGTTGATCTAGAAATTAAGATGTTGAACTAATTGAATGAAGATGTGAAATTTGG
1887516 AGACAAGGCTCCAAACATATCTGTGGATCT
66 AGACAAGGCTCCAAACATATCTGTGGATCT
1887546 TAATTTTTTTAAGTTGATCTAGAAATTAAGATGTTGAACTAATTGAATGAAGATGTGAAATTTGG
1 TAATTTTTTTAAGTTGATCTAGAAATTAAGATGTTGAACTAATTGAATGAAGATGTGAAATTTGG
1887611 AGACAAGGCTCCAAACATATCTGTGGA
66 AGACAAGGCTCCAAACATATCTGTGGA
1887638 GCTTTTATGG
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
95 92 1.00
ACGTcount: A:0.36, C:0.09, G:0.20, T:0.34
Consensus pattern (95 bp):
TAATTTTTTTAAGTTGATCTAGAAATTAAGATGTTGAACTAATTGAATGAAGATGTGAAATTTGG
AGACAAGGCTCCAAACATATCTGTGGATCT
Found at i:1887927 original size:26 final size:24
Alignment explanation
Indices: 1887872--1887931 Score: 59
Period size: 25 Copynumber: 2.4 Consensus size: 24
1887862 TATATTTTTA
*
1887872 AAAATGTATTTTTATATATAAATTT
1 AAAAT-TATTTTTATATATAAATAT
* *
1887897 TAAATTATTTTTACTATTTTAAATAT
1 AAAATTATTTTTA-TA-TATAAATAT
1887923 AAAA-TATTT
1 AAAATTATTT
1887932 ATTTTTACAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
24 8 0.28
25 11 0.38
26 10 0.34
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (24 bp):
AAAATTATTTTTATATATAAATAT
Found at i:1889499 original size:122 final size:122
Alignment explanation
Indices: 1889308--1889551 Score: 416
Period size: 122 Copynumber: 2.0 Consensus size: 122
1889298 TTTATTGTTA
** *
1889308 AAATTAATCTTTGTATGTCAACATAATATACACATGACACGTTACGTATCACTGTCTAATTATTC
1 AAATTAATCTTTGTATGTCAACATAATATACACATGACACCCTACGTATCACTATCTAATTATTC
*
1889373 TATCAAATACTAATTTTTAAAAATACAAATAAAAAAATTCTTAACAAAAAAACTAAT
66 TATCAAATACTAATTTTTAAAAATACAAATAAAAAAACTCTTAACAAAAAAACTAAT
* * *
1889430 AAATTGATTTTTGTATGTTAACATAATATACACATGACACCCTACGTATCACTATCTAATTATTC
1 AAATTAATCTTTGTATGTCAACATAATATACACATGACACCCTACGTATCACTATCTAATTATTC
*
1889495 TATCAAATACTAATTTTTAAAAATACAAATAGAAAAACTCTTAACAAAAAAACTAAT
66 TATCAAATACTAATTTTTAAAAATACAAATAAAAAAACTCTTAACAAAAAAACTAAT
1889552 TTACTCTTTA
Statistics
Matches: 114, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
122 114 1.00
ACGTcount: A:0.46, C:0.15, G:0.05, T:0.34
Consensus pattern (122 bp):
AAATTAATCTTTGTATGTCAACATAATATACACATGACACCCTACGTATCACTATCTAATTATTC
TATCAAATACTAATTTTTAAAAATACAAATAAAAAAACTCTTAACAAAAAAACTAAT
Found at i:1898885 original size:108 final size:108
Alignment explanation
Indices: 1898696--1898914 Score: 393
Period size: 108 Copynumber: 2.0 Consensus size: 108
1898686 GCACTGACAA
**
1898696 CAAATATTTCTCAGGCTTGCTGCTCAAGATTTTTGAATCAGAGTGGCAATCACTTTCTGACAAAT
1 CAAATATTTCTCAGGCTTGCTGCTCAAGATTTTTGAATCAGAGTCACAATCACTTTCTGACAAAT
*
1898761 CTTTCTTCTCAATGGCATCACATGCTACCTGCACCATCGAATC
66 CTTTCTTCCCAATGGCATCACATGCTACCTGCACCATCGAATC
* *
1898804 CAAATATTTCTCAGGCTTGCTGCTCAAGATTTTTGAATCGGGGTCACAATCACTTTCTGACAAAT
1 CAAATATTTCTCAGGCTTGCTGCTCAAGATTTTTGAATCAGAGTCACAATCACTTTCTGACAAAT
1898869 CTTTCTTCCCAATGGCATCACATGCTACCTGCACCATCGAATC
66 CTTTCTTCCCAATGGCATCACATGCTACCTGCACCATCGAATC
1898912 CAA
1 CAA
1898915 GTTATCCAAC
Statistics
Matches: 106, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
108 106 1.00
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.32
Consensus pattern (108 bp):
CAAATATTTCTCAGGCTTGCTGCTCAAGATTTTTGAATCAGAGTCACAATCACTTTCTGACAAAT
CTTTCTTCCCAATGGCATCACATGCTACCTGCACCATCGAATC
Found at i:1901582 original size:22 final size:23
Alignment explanation
Indices: 1901539--1901582 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
1901529 ACTTCAACCA
* *
1901539 CAAACATAACAACAAGACGAAAT
1 CAAACATAACAACAAAAAGAAAT
*
1901562 CAAAC-TAAGAACAAAAAGAAA
1 CAAACATAACAACAAAAAGAAA
1901583 ACCAAAGAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.66, C:0.18, G:0.09, T:0.07
Consensus pattern (23 bp):
CAAACATAACAACAAAAAGAAAT
Found at i:1903519 original size:29 final size:29
Alignment explanation
Indices: 1903486--1903541 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
1903476 GATATAAACA
*
1903486 TTATTATCAATATAAATTAAATTCTAACT
1 TTATTATCAATACAAATTAAATTCTAACT
* *
1903515 TTATTATCAATGCAGATTAAATTCTAA
1 TTATTATCAATACAAATTAAATTCTAA
1903542 TTCAATTGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.43, C:0.11, G:0.04, T:0.43
Consensus pattern (29 bp):
TTATTATCAATACAAATTAAATTCTAACT
Found at i:1915232 original size:18 final size:20
Alignment explanation
Indices: 1915186--1915232 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 20
1915176 TTTAACTTAA
1915186 TTTAAATT-TAATTAAATTG
1 TTTAAATTATAATTAAATTG
*
1915205 CTTAAA--ATAATT-AATT-
1 TTTAAATTATAATTAAATTG
1915221 TTTAAATTATAA
1 TTTAAATTATAA
1915233 ACAAACATCT
Statistics
Matches: 23, Mismatches: 2, Indels: 7
0.72 0.06 0.22
Matches are distributed among these distances:
16 5 0.22
17 4 0.17
18 9 0.39
19 5 0.22
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (20 bp):
TTTAAATTATAATTAAATTG
Found at i:1923478 original size:27 final size:27
Alignment explanation
Indices: 1923447--1923526 Score: 74
Period size: 27 Copynumber: 3.0 Consensus size: 27
1923437 TTTTTATTAG
*
1923447 TTTTAAAATATATTTTACATATTTTAA
1 TTTTAAAATATATTTTAAATATTTTAA
* *
1923474 TTTTAAAAT-T-GTTAAATATATTTTAA
1 TTTTAAAATATATTTTAA-ATATTTTAA
* * * *
1923500 TTGTCAAGTATATTTTAAATTTTTTAA
1 TTTTAAAATATATTTTAAATATTTTAA
1923527 AACATAATTT
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
25 3 0.07
26 16 0.39
27 18 0.44
28 4 0.10
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.55
Consensus pattern (27 bp):
TTTTAAAATATATTTTAAATATTTTAA
Found at i:1923498 original size:20 final size:20
Alignment explanation
Indices: 1923473--1923518 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 20
1923463 ACATATTTTA
*
1923473 ATTTTAAAATTGTTAAATAT
1 ATTTTAAAATTGTCAAATAT
*
1923493 ATTTT--AATTGTCAAGTAT
1 ATTTTAAAATTGTCAAATAT
1923511 ATTTTAAA
1 ATTTTAAA
1923519 TTTTTTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 16 0.73
20 6 0.27
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (20 bp):
ATTTTAAAATTGTCAAATAT
Found at i:1935295 original size:19 final size:20
Alignment explanation
Indices: 1935260--1935297 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
1935250 CACCATATTT
1935260 GTTACTTTAAAATAAATATG
1 GTTACTTTAAAATAAATATG
1935280 GTTA-TTTAATAA-AAATAT
1 GTTACTTTAA-AATAAATAT
1935298 TAATAAGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.42
Consensus pattern (20 bp):
GTTACTTTAAAATAAATATG
Found at i:1939363 original size:8 final size:9
Alignment explanation
Indices: 1939344--1939381 Score: 51
Period size: 10 Copynumber: 4.1 Consensus size: 9
1939334 CAATTACAAA
1939344 ATATATATT
1 ATATATATT
1939353 -TATATTATT
1 ATATA-TATT
1939362 ATATATATAT
1 ATATATAT-T
1939372 ATATATATT
1 ATATATATT
1939381 A
1 A
1939382 AACAAATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
8 4 0.15
9 9 0.35
10 13 0.50
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (9 bp):
ATATATATT
Found at i:1955347 original size:11 final size:12
Alignment explanation
Indices: 1955323--1955355 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1955313 AATAAAAGTA
1955323 ATTTAAAAATAT
1 ATTTAAAAATAT
1955335 ATTTAAATAATAT
1 ATTTAAA-AATAT
1955348 -TTTAAAAA
1 ATTTAAAAA
1955356 AAGTAATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 2 0.10
12 13 0.65
13 5 0.25
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
ATTTAAAAATAT
Found at i:1959801 original size:16 final size:16
Alignment explanation
Indices: 1959775--1959819 Score: 67
Period size: 15 Copynumber: 2.9 Consensus size: 16
1959765 TTTTATATTA
1959775 TATAA-TTAAATTTTT
1 TATAATTTAAATTTTT
1959790 TATAATTTAAATTTTT
1 TATAATTTAAATTTTT
*
1959806 TA-ATTTTAAATTTT
1 TATAATTTAAATTTT
1959820 AAATTTCAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
15 16 0.57
16 12 0.43
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TATAATTTAAATTTTT
Found at i:1960825 original size:19 final size:19
Alignment explanation
Indices: 1960801--1960838 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1960791 TTATGTCCTT
1960801 GCTTTAAAGTTTAATCCCC
1 GCTTTAAAGTTTAATCCCC
1960820 GCTTTAAAGTTTAATCCCC
1 GCTTTAAAGTTTAATCCCC
1960839 ACTTGGTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.26, G:0.11, T:0.37
Consensus pattern (19 bp):
GCTTTAAAGTTTAATCCCC
Found at i:1987502 original size:339 final size:339
Alignment explanation
Indices: 1986877--1988236 Score: 2292
Period size: 339 Copynumber: 4.0 Consensus size: 339
1986867 TTCAACAGCA
* * *
1986877 CATCCAGAAGCTCAATTTTCCTAAAATTATCATTCAATCCGCTTGCATTTGTATCTGAATGGACT
1 CATCCAGAAGCTTAATTTTCCTAAAATTATCATTCAATCTGCTTGCATTTGTATCCGAATGGACT
* * * * *
1986942 GCCCCAGTTTCGTTAACATTCGGTTCCTCATCAGCTTTCTCACCATCCTCCGGTTTGCCCTTAGA
66 GTCCCGGTTTCATTAACATTCGGTTCTTCATCAGCTTTCTCACCATCCTCCGCTTTGCCCTTAGA
* *
1987007 CAATGAAGGCAACTCTGTTTCAAAATCCAACGGCTGTGAAGGCAATACCCGTTTCTTCTTAGTGC
131 CAATGAAGGCAACTCTGCTTCAAAATCCAACGGCTGTGAAGGCAATACCCGTTCCTTCTTAGTGC
* * * *
1987072 CATCTGGATTCGAAGTGCTTTTAATCTTCTTCGCCGAATCAACTTCCTCCTCAGAAAATCCTGAA
196 CATCTGGATTCGAAGTGCTTTTAATCTTCCTCGCCAAATCAACTTCCTCCTCAGAAAACCCTAAA
* * *
1987137 TCTGTATCCTTTCCCAAATTAACTGCCCTCCTACTGTCAGCACTAACAGTTCTTCCG-CTGTGAT
261 TCTGTATCCTTTCCCAAATCAACTGCCCTCCTAGTGTCAGCACTAACAGTTTTTCCGCCT-TGAT
1987201 TGTCGATCATTTCAT
325 TGTCGATCATTTCAT
* *
1987216 CATCCAGAAGCTTAATTTTCCTAAAATTATCATTCATTCTGCTTGCATTTGTATCCAAATGGACT
1 CATCCAGAAGCTTAATTTTCCTAAAATTATCATTCAATCTGCTTGCATTTGTATCCGAATGGACT
* *
1987281 GTTCCGGTTTCATTAACATACGGTTCTTCATCAGCTTTCTCACCATCCTCCGCTTTGCCCTTAGA
66 GTCCCGGTTTCATTAACATTCGGTTCTTCATCAGCTTTCTCACCATCCTCCGCTTTGCCCTTAGA
*
1987346 CAATGAAGGCAACTCTG-TATCAAAATCCAACGGCTGTGAAGGCAATACCCGTTTCTTCTTAGTG
131 CAATGAAGGCAACTCTGCT-TCAAAATCCAACGGCTGTGAAGGCAATACCCGTTCCTTCTTAGTG
*
1987410 CCATCTGGATTCGAAGTGCTTTTAATCTTCCTGGCCAAATCAACTTCCTCCTCAGAAAACCCTAA
195 CCATCTGGATTCGAAGTGCTTTTAATCTTCCTCGCCAAATCAACTTCCTCCTCAGAAAACCCTAA
* * *
1987475 ATCCGTATCCTTTCCCAAATCAACTGCCCTCCTAGTGTCAGCACTAACAATTTTTCCGCCGTGAT
260 ATCTGTATCCTTTCCCAAATCAACTGCCCTCCTAGTGTCAGCACTAACAGTTTTTCCGCCTTGAT
1987540 TGTCGATCATTTCAT
325 TGTCGATCATTTCAT
* * **
1987555 CATCCAGAAGCTTAGTTTTCCTAAAATTATCATTCAATCTGCCTGCATTTGTATCCGAATGTCCT
1 CATCCAGAAGCTTAATTTTCCTAAAATTATCATTCAATCTGCTTGCATTTGTATCCGAATGGACT
* *
1987620 GTCCCGGTTTCAGTAACATTCGGTTCTTCATCAGCTTTCTCACCATCCTCCGCTTTGCCGTTAGA
66 GTCCCGGTTTCATTAACATTCGGTTCTTCATCAGCTTTCTCACCATCCTCCGCTTTGCCCTTAGA
1987685 CAATGAAGGCAACTCTGCTTCAAAATCCAACGGCTGTGAAGGCAATACCCGTTCCTTCTTAGTGC
131 CAATGAAGGCAACTCTGCTTCAAAATCCAACGGCTGTGAAGGCAATACCCGTTCCTTCTTAGTGC
* *
1987750 CATCTGGATTCGAAGTGCTTTTTATCTTCCTGGCCAAATCAACTTCCTCCTCAGAAAACCCTAAA
196 CATCTGGATTCGAAGTGCTTTTAATCTTCCTCGCCAAATCAACTTCCTCCTCAGAAAACCCTAAA
1987815 TCTGTATCCTTTCCCAAATCAACTGCCCTCCTAGTGTCAGCACTAACAGTTTTTCCGCCTTGATT
261 TCTGTATCCTTTCCCAAATCAACTGCCCTCCTAGTGTCAGCACTAACAGTTTTTCCGCCTTGATT
1987880 GTCGATCATTTCAT
326 GTCGATCATTTCAT
*
1987894 CATCCAGAAGCTTAGTTTTCCTAAAATTATCATTCAATCTGCTTGCATTTGTATCCGAATGGACT
1 CATCCAGAAGCTTAATTTTCCTAAAATTATCATTCAATCTGCTTGCATTTGTATCCGAATGGACT
* * *
1987959 GTCCCGGTTTCATTAACATTCGGTTTTTCATGAGCTTTCTCACCATCCTCCGCTTTGCCGTTAGA
66 GTCCCGGTTTCATTAACATTCGGTTCTTCATCAGCTTTCTCACCATCCTCCGCTTTGCCCTTAGA
1988024 CAATGAAGGCAACTCTGCTTCAAAATCCAACGGCTGTGAAGGCAATACCCGTTCCTTCTTAGTGC
131 CAATGAAGGCAACTCTGCTTCAAAATCCAACGGCTGTGAAGGCAATACCCGTTCCTTCTTAGTGC
* * * *
1988089 CATCTGGATTCGAAGTGCTTTTCATCTTCCTCGACGAATCAACTTCCCCCTCAGAAAACCCTAAA
196 CATCTGGATTCGAAGTGCTTTTAATCTTCCTCGCCAAATCAACTTCCTCCTCAGAAAACCCTAAA
* *
1988154 TCTGTTTCCTTTCCCAAATCAACTGCCCTCCTAGTGTCAGCACTAACAGTATTTCCGCCTTGATT
261 TCTGTATCCTTTCCCAAATCAACTGCCCTCCTAGTGTCAGCACTAACAGTTTTTCCGCCTTGATT
1988219 GTCGATCATTTCAT
326 GTCGATCATTTCAT
1988233 CATC
1 CATC
1988237 ATTGCAATCA
Statistics
Matches: 967, Mismatches: 51, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
338 1 0.00
339 964 1.00
340 2 0.00
ACGTcount: A:0.24, C:0.28, G:0.15, T:0.33
Consensus pattern (339 bp):
CATCCAGAAGCTTAATTTTCCTAAAATTATCATTCAATCTGCTTGCATTTGTATCCGAATGGACT
GTCCCGGTTTCATTAACATTCGGTTCTTCATCAGCTTTCTCACCATCCTCCGCTTTGCCCTTAGA
CAATGAAGGCAACTCTGCTTCAAAATCCAACGGCTGTGAAGGCAATACCCGTTCCTTCTTAGTGC
CATCTGGATTCGAAGTGCTTTTAATCTTCCTCGCCAAATCAACTTCCTCCTCAGAAAACCCTAAA
TCTGTATCCTTTCCCAAATCAACTGCCCTCCTAGTGTCAGCACTAACAGTTTTTCCGCCTTGATT
GTCGATCATTTCAT
Found at i:1996078 original size:15 final size:15
Alignment explanation
Indices: 1996051--1996096 Score: 76
Period size: 15 Copynumber: 3.1 Consensus size: 15
1996041 TTAAAATTAA
1996051 TTATTTT-TAAAATT
1 TTATTTTATAAAATT
1996065 TTATTTTATAAAATT
1 TTATTTTATAAAATT
*
1996080 TTATTTTAAAAAATT
1 TTATTTTATAAAATT
1996095 TT
1 TT
1996097 CACACTATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
14 7 0.23
15 23 0.77
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TTATTTTATAAAATT
Found at i:1996449 original size:29 final size:30
Alignment explanation
Indices: 1996404--1996462 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
1996394 TAAACACACT
1996404 TTTACAAAATTGATTTATTCTAGTAAATAA
1 TTTACAAAATTGATTTATTCTAGTAAATAA
* * *
1996434 TTTACAATA-TGATTTATTTTTGTAAATAA
1 TTTACAAAATTGATTTATTCTAGTAAATAA
1996463 AATAAAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 18 0.69
30 8 0.31
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.47
Consensus pattern (30 bp):
TTTACAAAATTGATTTATTCTAGTAAATAA
Found at i:2009066 original size:21 final size:22
Alignment explanation
Indices: 2009042--2009091 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
2009032 GTATATATGC
2009042 ATAAAAAATAT-AAATAAATAT
1 ATAAAAAATATAAAATAAATAT
* *
2009063 ATAAAAAAATTTAAAATATATAT
1 AT-AAAAAATATAAAATAAATAT
2009086 ATAAAA
1 ATAAAA
2009092 TTTAGAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 2 0.08
22 12 0.48
23 11 0.44
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (22 bp):
ATAAAAAATATAAAATAAATAT
Found at i:2009070 original size:23 final size:23
Alignment explanation
Indices: 2009044--2009091 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
2009034 ATATATGCAT
2009044 AAAAAATAT-AAATAAATATATA
1 AAAAAATATAAAATAAATATATA
* *
2009066 AAAAAATTTAAAATATATATATA
1 AAAAAATATAAAATAAATATATA
2009089 AAA
1 AAA
2009092 TTTAGAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (23 bp):
AAAAAATATAAAATAAATATATA
Found at i:2013626 original size:5 final size:6
Alignment explanation
Indices: 2013609--2013634 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2013599 AGGAAAAATT
2013609 ATAAAA ATAAAA ATAAAA ATAAAA AT
1 ATAAAA ATAAAA ATAAAA ATAAAA AT
2013635 GGGTTAGCTA
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:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
ATAAAA
Found at i:2027556 original size:78 final size:78
Alignment explanation
Indices: 2027427--2027581 Score: 310
Period size: 78 Copynumber: 2.0 Consensus size: 78
2027417 CAGAGTTGCT
2027427 GTCATAAACAGATTTTCCATAACAAAACAAAAAGTTTTGGGTTTCAAAAATTTATAATAACATGC
1 GTCATAAACAGATTTTCCATAACAAAACAAAAAGTTTTGGGTTTCAAAAATTTATAATAACATGC
2027492 TGATCTTAATTTG
66 TGATCTTAATTTG
2027505 GTCATAAACAGATTTTCCATAACAAAACAAAAAGTTTTGGGTTTCAAAAATTTATAATAACATGC
1 GTCATAAACAGATTTTCCATAACAAAACAAAAAGTTTTGGGTTTCAAAAATTTATAATAACATGC
2027570 TGATCTTAATTT
66 TGATCTTAATTT
2027582 TGCATATTTA
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 77 1.00
ACGTcount: A:0.41, C:0.13, G:0.11, T:0.35
Consensus pattern (78 bp):
GTCATAAACAGATTTTCCATAACAAAACAAAAAGTTTTGGGTTTCAAAAATTTATAATAACATGC
TGATCTTAATTTG
Found at i:2034335 original size:29 final size:28
Alignment explanation
Indices: 2034295--2034514 Score: 211
Period size: 29 Copynumber: 7.5 Consensus size: 28
2034285 ACCCGAGGGC
2034295 AAAATGGTAATTTTGGTGAAATCGGGGTT
1 AAAATGG-AATTTTGGTGAAATCGGGGTT
* *
2034324 AAAAATGGAATTTTGG-GAAGTTTAGGGG-T
1 -AAAATGGAATTTTGGTGAA--ATCGGGGTT
2034353 AAAATGGTAATTTTGGTGAAATCGGGGTT
1 AAAATGG-AATTTTGGTGAAATCGGGGTT
2034382 AAAATGGAATTTT-G-GAAAGTTCGAGGG-T
1 AAAATGGAATTTTGGTGAAA--TCG-GGGTT
*
2034410 AAAATCGTAATTTTTGGTGAAATCGGGGTT
1 AAAAT-GGAA-TTTTGGTGAAATCGGGGTT
*
2034440 AAAAATGGAATTTT-G-GAAAGTTCGGGGGT
1 -AAAATGGAATTTTGGTGAAA--TCGGGGTT
2034469 AAAATGGTAAGTTTTGGTGAAATCGGGGTT
1 AAAATGG-AA-TTTTGGTGAAATCGGGGTT
2034499 AAAAATGGAATTTTGG
1 -AAAATGGAATTTTGG
2034515 AAAGTTTGGG
Statistics
Matches: 161, Mismatches: 8, Indels: 43
0.76 0.04 0.20
Matches are distributed among these distances:
26 4 0.02
27 5 0.03
28 38 0.24
29 53 0.33
30 39 0.24
31 14 0.09
32 8 0.05
ACGTcount: A:0.33, C:0.03, G:0.31, T:0.32
Consensus pattern (28 bp):
AAAATGGAATTTTGGTGAAATCGGGGTT
Found at i:2034463 original size:59 final size:58
Alignment explanation
Indices: 2034253--2034541 Score: 404
Period size: 59 Copynumber: 5.0 Consensus size: 58
2034243 GGAGGAATGA
** * * ** *
2034253 TGAAATCGGGGTTGAAAACGGGACTTTTGGATA-CCCGAGGGCAAAATGGTAATTTTGG
1 TGAAATCGGGGTT-AAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTGG
* *
2034311 TGAAATCGGGGTTAAAAATGGAATTTTGGGAAGTT-TAGGGGTAAAATGGTAATTTTGG
1 TGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGA-GGGTAAAATGGTAATTTTGG
*
2034369 TGAAATCGGGGTT-AAAATGGAATTTTGGAAAGTTCGAGGGTAAAATCGTAATTTTTGG
1 TGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAA-TTTTGG
*
2034427 TGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAAGTTTTGG
1 TGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAA-TTTTGG
* *
2034486 TGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGTAAAATGGTAATTTT
1 TGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTT
2034542 TGAAAGTTTT
Statistics
Matches: 210, Mismatches: 16, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
57 48 0.23
58 69 0.33
59 93 0.44
ACGTcount: A:0.32, C:0.05, G:0.32, T:0.31
Consensus pattern (58 bp):
TGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTGG
Found at i:2034525 original size:29 final size:28
Alignment explanation
Indices: 2034295--2034570 Score: 203
Period size: 29 Copynumber: 9.5 Consensus size: 28
2034285 ACCCGAGGGC
2034295 AAAATGGTAATTTTGGTGAAA--TCGGGGTT
1 AAAATGG-AATTTT-G-GAAAGTTCGGGGTT
* *
2034324 AAAAATGGAATTTTGGGAAGTTTAGGGG-T
1 -AAAATGGAATTTTGGAAAG-TTCGGGGTT
2034353 AAAATGGTAATTTTGGTGAAA--TCGGGGTT
1 AAAATGG-AATTTT-G-GAAAGTTCGGGGTT
2034382 AAAATGGAATTTTGGAAAGTTCGAGGG-T
1 AAAATGGAATTTTGGAAAGTTCG-GGGTT
*
2034410 AAAATCGTAATTTTTGGTGAAA--TCGGGGTT
1 AAAAT-GGAA-TTTT-G-GAAAGTTCGGGGTT
*
2034440 AAAAATGGAATTTTGGAAAGTTCGGGGGT
1 -AAAATGGAATTTTGGAAAGTTCGGGGTT
2034469 AAAATGGTAAGTTTTGGTGAAA--TCGGGGTT
1 AAAATGG-AA-TTTT-G-GAAAGTTCGGGGTT
* *
2034499 AAAAATGGAATTTTGGAAAGTTTGGGGGT
1 -AAAATGGAATTTTGGAAAGTTCGGGGTT
* * *
2034528 AAAATGGTAATTTTTGAAAGTTTTGGGGTC
1 AAAATGG-AATTTTGGAAAG-TTCGGGGTT
*
2034558 AAAATGTAATTTT
1 AAAATGGAATTTT
2034571 TTAAAATTTT
Statistics
Matches: 205, Mismatches: 14, Indels: 55
0.75 0.05 0.20
Matches are distributed among these distances:
26 4 0.02
27 12 0.06
28 44 0.21
29 70 0.34
30 50 0.24
31 17 0.08
32 8 0.04
ACGTcount: A:0.33, C:0.03, G:0.30, T:0.34
Consensus pattern (28 bp):
AAAATGGAATTTTGGAAAGTTCGGGGTT
Found at i:2034527 original size:30 final size:28
Alignment explanation
Indices: 2034316--2034603 Score: 175
Period size: 29 Copynumber: 9.8 Consensus size: 28
2034306 TTTGGTGAAA
*
2034316 TCGGGGTTAAAAATGGAATTTTGGGAAGTT
1 TCGGGG-T-AAAATGGAATTTTGGAAAGTT
*
2034346 TAGGGGTAAAATGGTAATTTTGGTGAAA---
1 TCGGGGTAAAATGG-AATTTT-G-GAAAGTT
2034374 TCGGGGTTAAAATGGAATTTTGGAAAG-T
1 TCGGGG-TAAAATGGAATTTTGGAAAGTT
*
2034402 TCGAGGGTAAAATCGTAATTTTTGGTGAAA---
1 TCG-GGGTAAAAT-GGAA-TTTT-G-GAAAGTT
2034432 TCGGGGTTAAAAATGGAATTTTGGAAAG-T
1 TCGGGG-T-AAAATGGAATTTTGGAAAGTT
2034461 TCGGGGGTAAAATGGTAAGTTTTGGTGAAA---
1 TC-GGGGTAAAATGG-AA-TTTT-G-GAAAGTT
2034491 TCGGGGTTAAAAATGGAATTTTGGAAAGTT
1 TCGGGG-T-AAAATGGAATTTTGGAAAGTT
* *
2034521 TGGGGGTAAAATGGTAATTTTTGAAAGTT
1 TCGGGGTAAAATGG-AATTTTGGAAAGTT
* * ** *
2034550 TTGGGGTCAAAATGTAATTTTTTAAAATT
1 TCGGGGT-AAAATGGAATTTTGGAAAGTT
* *
2034579 TTGGGGTCAAAATGCAATTTCTGGA
1 TCGGGGT-AAAATGGAATTT-TGGA
2034604 CTATTTGGGG
Statistics
Matches: 216, Mismatches: 14, Indels: 56
0.76 0.05 0.20
Matches are distributed among these distances:
26 4 0.02
27 9 0.04
28 43 0.20
29 92 0.43
30 43 0.20
31 17 0.08
32 8 0.04
ACGTcount: A:0.32, C:0.04, G:0.30, T:0.34
Consensus pattern (28 bp):
TCGGGGTAAAATGGAATTTTGGAAAGTT
Found at i:2034543 original size:59 final size:58
Alignment explanation
Indices: 2034295--2034541 Score: 415
Period size: 59 Copynumber: 4.2 Consensus size: 58
2034285 ACCCGAGGGC
* **
2034295 AAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGGAAGTTTAGGGGT
1 AAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGT
*
2034353 AAAATGGTAATTTTGGTGAAATCGGGGTT-AAAATGGAATTTTGGAAAGTTCGAGGGT
1 AAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGT
*
2034410 AAAATCGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGT
1 AAAATGGTAA-TTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGT
*
2034469 AAAATGGTAAGTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGT
1 AAAATGGTAA-TTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGT
2034528 AAAATGGTAATTTT
1 AAAATGGTAATTTT
2034542 TGAAAGTTTT
Statistics
Matches: 178, Mismatches: 9, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
57 33 0.19
58 52 0.29
59 93 0.52
ACGTcount: A:0.33, C:0.03, G:0.31, T:0.33
Consensus pattern (58 bp):
AAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGT
Found at i:2036566 original size:16 final size:17
Alignment explanation
Indices: 2036530--2036593 Score: 67
Period size: 17 Copynumber: 3.8 Consensus size: 17
2036520 TTTTGAATTT
2036530 ATTTAAATTTAAAACAA
1 ATTTAAATTTAAAACAA
* *
2036547 ATTTAAA-TTCAAATAA
1 ATTTAAATTTAAAACAA
* **
2036563 ATTTAAAATTAATTCAA
1 ATTTAAATTTAAAACAA
*
2036580 ACTTAAATTTAAAA
1 ATTTAAATTTAAAA
2036594 ATCCCAGTTA
Statistics
Matches: 36, Mismatches: 10, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
16 14 0.39
17 22 0.61
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (17 bp):
ATTTAAATTTAAAACAA
Found at i:2036571 original size:23 final size:22
Alignment explanation
Indices: 2036552--2036593 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
2036542 AACAAATTTA
2036552 AATTCAAA-TAAATTTAAAATT
1 AATTCAAACTAAATTTAAAATT
2036573 AATTCAAACTTAAATTTAAAA
1 AATTCAAAC-TAAATTTAAAA
2036594 ATCCCAGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 8 0.42
23 11 0.58
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (22 bp):
AATTCAAACTAAATTTAAAATT
Found at i:2037841 original size:31 final size:31
Alignment explanation
Indices: 2037806--2037864 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
2037796 TAAAATGATA
*
2037806 ATTGAATTA-TTCAAAATTTTTTATTTAAATT
1 ATTGAATCATTTCAAAA-TTTTTATTTAAATT
*
2037837 ATTGAATCATTTGAAAATTTTTATTTAA
1 ATTGAATCATTTCAAAATTTTTATTTAA
2037865 GTCACTAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 19 0.76
32 6 0.24
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.53
Consensus pattern (31 bp):
ATTGAATCATTTCAAAATTTTTATTTAAATT
Found at i:2041446 original size:26 final size:25
Alignment explanation
Indices: 2041411--2041500 Score: 72
Period size: 26 Copynumber: 3.3 Consensus size: 25
2041401 AAATCTGAAA
2041411 AAAAAATTATAAAAGTATAAATATAT
1 AAAAAATTATAAAA-TATAAATATAT
* * *
2041437 AAAAAATTATTAAATATTTAATAAAT
1 AAAAAATTATAAAATA-TAAATATAT
*
2041463 ATGAAAATTGATATAAACTTATAAATATTAT
1 A-AAAAATT-ATA-AAA--TATAAATA-TAT
2041494 AAAAAAT
1 AAAAAAT
2041501 GTATTAGTAT
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
25 2 0.04
26 21 0.43
27 6 0.12
28 2 0.04
29 3 0.06
30 10 0.20
31 5 0.10
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.34
Consensus pattern (25 bp):
AAAAAATTATAAAATATAAATATAT
Found at i:2041452 original size:19 final size:20
Alignment explanation
Indices: 2041428--2041506 Score: 69
Period size: 19 Copynumber: 4.1 Consensus size: 20
2041418 TATAAAAGTA
2041428 TAAATA-TATAAAAAATTAT
1 TAAATATTATAAAAAATTAT
*
2041447 TAAATATT-TAATAAA-TAT
1 TAAATATTATAAAAAATTAT
* * *
2041465 GAAA-ATTGATATAAACTTA-
1 TAAATATT-ATAAAAAATTAT
2041484 TAAATATTATAAAAAATGTAT
1 TAAATATTATAAAAAAT-TAT
2041505 TA
1 TA
2041507 GTATTCTTAA
Statistics
Matches: 45, Mismatches: 8, Indels: 12
0.69 0.12 0.18
Matches are distributed among these distances:
17 3 0.07
18 6 0.13
19 26 0.58
20 8 0.18
21 2 0.04
ACGTcount: A:0.57, C:0.01, G:0.04, T:0.38
Consensus pattern (20 bp):
TAAATATTATAAAAAATTAT
Found at i:2041537 original size:56 final size:57
Alignment explanation
Indices: 2041426--2041547 Score: 139
Period size: 56 Copynumber: 2.2 Consensus size: 57
2041416 ATTATAAAAG
*
2041426 TATAAATA-TATAAAAAATTATTAAATATTTAATAAATATGAAAATTGATATAAACT
1 TATAAATATTATAAAAAATTATTAAATATTTAATAAATATGAAAAATGATATAAACT
*
2041482 TATAAATATTATAAAAAATGTATT-AGTATTCTTAA-AAATAAT-AAAAATG-TA-AAACT
1 TATAAATATTATAAAAAAT-TATTAAATA-T-TTAATAAAT-ATGAAAAATGATATAAACT
*
2041538 TATTAATATT
1 TATAAATATT
2041548 TTATTAAAAT
Statistics
Matches: 58, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
56 22 0.38
57 15 0.26
58 15 0.26
59 6 0.10
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.39
Consensus pattern (57 bp):
TATAAATATTATAAAAAATTATTAAATATTTAATAAATATGAAAAATGATATAAACT
Found at i:2042072 original size:19 final size:19
Alignment explanation
Indices: 2042003--2042074 Score: 60
Period size: 19 Copynumber: 3.8 Consensus size: 19
2041993 AGTTTATATC
*
2042003 AATTTTAAT-ACTTTTAATA
1 AATTTTAATGA-TTTTTATA
* *
2042022 AATTTTATTGA-TGTTATA
1 AATTTTAATGATTTTTATA
* *
2042040 ATTTTTTATGATTTTTATA
1 AATTTTAATGATTTTTATA
2042059 GAATTTTAAT-ATTTTT
1 -AATTTTAATGATTTTT
2042075 TTTATAAAAT
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
18 13 0.32
19 20 0.49
20 8 0.20
ACGTcount: A:0.33, C:0.01, G:0.06, T:0.60
Consensus pattern (19 bp):
AATTTTAATGATTTTTATA
Found at i:2042092 original size:23 final size:22
Alignment explanation
Indices: 2042046--2042098 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
2042036 TATAATTTTT
* * *
2042046 TATGATTTTTATAGAATTTTAA
1 TATGTTTTTTATAAAATTTAAA
*
2042068 TATTTTTTTTATAAAATTCTAAA
1 TATGTTTTTTATAAAATT-TAAA
2042091 TATGTTTT
1 TATGTTTT
2042099 ATTTCTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 15 0.60
23 10 0.40
ACGTcount: A:0.34, C:0.02, G:0.06, T:0.58
Consensus pattern (22 bp):
TATGTTTTTTATAAAATTTAAA
Found at i:2042166 original size:18 final size:17
Alignment explanation
Indices: 2042116--2042166 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 17
2042106 TAATAAATTT
2042116 TTTTTATAATTTATTAGA
1 TTTTTATAATTTA-TAGA
2042134 TTTTTATAATTTATA-A
1 TTTTTATAATTTATAGA
2042150 CTTTTTATAAGTTTATA
1 -TTTTTATAA-TTTATA
2042167 TCAATTTTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
16 1 0.03
17 11 0.35
18 19 0.61
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (17 bp):
TTTTTATAATTTATAGA
Found at i:2042223 original size:17 final size:15
Alignment explanation
Indices: 2042191--2042234 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 15
2042181 TTTAATGTGT
2042191 TTTTAATATTTTATAA
1 TTTT-ATATTTTATAA
2042207 TTTTATAATTTTGATAA
1 TTTTAT-ATTTT-ATAA
2042224 TTTTATATTTT
1 TTTTATATTTT
2042235 TTTACAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
15 2 0.08
16 14 0.54
17 10 0.38
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (15 bp):
TTTTATATTTTATAA
Found at i:2042235 original size:17 final size:16
Alignment explanation
Indices: 2042199--2042256 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 16
2042189 GTTTTTAATA
2042199 TTTTATAATTTTATAAT
1 TTTTATAATTTTAT-AT
*
2042216 TTTGATAATTTTATATTT
1 TTTTATAATTTTATA--T
*
2042234 TTTTACAATTTTAATAT
1 TTTTATAATTTT-ATAT
2042251 TTTTAT
1 TTTTAT
2042257 GAGAAATATA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
16 1 0.03
17 19 0.56
18 11 0.32
19 3 0.09
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (16 bp):
TTTTATAATTTTATAT
Found at i:2042246 original size:8 final size:8
Alignment explanation
Indices: 2042198--2042234 Score: 58
Period size: 8 Copynumber: 4.6 Consensus size: 8
2042188 TGTTTTTAAT
2042198 ATTTTATA
1 ATTTTATA
2042206 ATTTTATA
1 ATTTTATA
2042214 ATTTTGATA
1 ATTTT-ATA
2042223 ATTTTAT-
1 ATTTTATA
2042230 ATTTT
1 ATTTT
2042235 TTTACAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 5 0.18
8 15 0.54
9 8 0.29
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (8 bp):
ATTTTATA
Found at i:2042400 original size:15 final size:15
Alignment explanation
Indices: 2042380--2042415 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
2042370 AATTGATTAT
*
2042380 TTTAATTAGCAAGAA
1 TTTAATTAACAAGAA
*
2042395 TTTAATTAACACGAA
1 TTTAATTAACAAGAA
2042410 TTTAAT
1 TTTAAT
2042416 ATAAAAACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.39
Consensus pattern (15 bp):
TTTAATTAACAAGAA
Found at i:2042683 original size:7 final size:7
Alignment explanation
Indices: 2042671--2042704 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
2042661 GGGAACGGAG
2042671 TAAAAAA
1 TAAAAAA
2042678 TAAAAAA
1 TAAAAAA
2042685 TAAAAAA
1 TAAAAAA
*
2042692 GTAAAAAG
1 -TAAAAAA
2042700 TAAAA
1 TAAAA
2042705 TCTCCGGCTC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
7 19 0.76
8 6 0.24
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (7 bp):
TAAAAAA
Found at i:2042690 original size:14 final size:15
Alignment explanation
Indices: 2042671--2042704 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
2042661 GGGAACGGAG
2042671 TAAAAAA-TAAAAAA
1 TAAAAAAGTAAAAAA
*
2042685 TAAAAAAGTAAAAAG
1 TAAAAAAGTAAAAAA
2042700 TAAAA
1 TAAAA
2042705 TCTCCGGCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (15 bp):
TAAAAAAGTAAAAAA
Found at i:2044844 original size:29 final size:29
Alignment explanation
Indices: 2044810--2044882 Score: 73
Period size: 29 Copynumber: 2.6 Consensus size: 29
2044800 ATAATTAGAC
* *
2044810 CTAAATTTTGAAATTTGAAAGTAGAGAGA
1 CTAAATTTTGAAATTTGAAAGTACAAAGA
2044839 CTAAATTATTAGAAA--TGAAAGTACAAAGA
1 CTAAATT-TT-GAAATTTGAAAGTACAAAGA
2044868 -TAAAATTTT-AAATTT
1 CT-AAATTTTGAAATTT
2044883 ATGAAGAGTA
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
26 3 0.08
28 4 0.11
29 24 0.65
30 2 0.05
31 4 0.11
ACGTcount: A:0.49, C:0.04, G:0.14, T:0.33
Consensus pattern (29 bp):
CTAAATTTTGAAATTTGAAAGTACAAAGA
Found at i:2052412 original size:25 final size:25
Alignment explanation
Indices: 2052358--2052414 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
2052348 GAATAAAATA
***
2052358 AAAT-ATTTAAAATATATATTTCTT
1 AAATAATTTAAAATATATATTTAAC
*
2052382 ACATAATTTAAAATATATATTTAAC
1 AAATAATTTAAAATATATATTTAAC
2052407 AAATAATT
1 AAATAATT
2052415 AATTTTATGT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
24 3 0.11
25 24 0.89
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (25 bp):
AAATAATTTAAAATATATATTTAAC
Found at i:2054600 original size:10 final size:10
Alignment explanation
Indices: 2054585--2054628 Score: 61
Period size: 10 Copynumber: 4.4 Consensus size: 10
2054575 GTCACTGTTC
*
2054585 TATACATACA
1 TATACATATA
2054595 TATACATATA
1 TATACATATA
*
2054605 TATATATATA
1 TATACATATA
*
2054615 TATATATATA
1 TATACATATA
2054625 TATA
1 TATA
2054629 TGTCTCAACC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
10 32 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (10 bp):
TATACATATA
Found at i:2054607 original size:2 final size:2
Alignment explanation
Indices: 2054594--2054629 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2054584 CTATACATAC
*
2054594 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2054630 GTCTCAACCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2055176 original size:30 final size:31
Alignment explanation
Indices: 2055127--2055194 Score: 102
Period size: 30 Copynumber: 2.2 Consensus size: 31
2055117 TTACAATTTG
* *
2055127 GTCACTAAACAATTCAAAAGTTTTCATTTAA
1 GTCACTGAACAATTCAAAAGATTTCATTTAA
*
2055158 GTCACTGAACTATT-AAAAGATTTCATTTAA
1 GTCACTGAACAATTCAAAAGATTTCATTTAA
2055188 GTCACTG
1 GTCACTG
2055195 GTTGTTAAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 22 0.65
31 12 0.35
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.35
Consensus pattern (31 bp):
GTCACTGAACAATTCAAAAGATTTCATTTAA
Found at i:2055943 original size:22 final size:19
Alignment explanation
Indices: 2055918--2055966 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 19
2055908 TCATTATTGT
2055918 TTTTTTTTTTATAATTTAGATG
1 TTTTTTTTTT-TAA--TAGATG
*
2055940 TTTTTATTTTTTAATATATG
1 TTTTT-TTTTTTAATAGATG
2055960 TTTTTTT
1 TTTTTTT
2055967 ATAGAATATC
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 2 0.08
20 10 0.40
22 8 0.32
23 5 0.20
ACGTcount: A:0.20, C:0.00, G:0.06, T:0.73
Consensus pattern (19 bp):
TTTTTTTTTTTAATAGATG
Found at i:2055967 original size:22 final size:22
Alignment explanation
Indices: 2055915--2055968 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
2055905 TCCTCATTAT
*
2055915 TGTTTTTTT-TTTTATAATTTA
1 TGTTTTTTTATTTTATAATATA
* *
2055936 -GATGTTTTTATTTTTTAATATA
1 TG-TTTTTTTATTTTATAATATA
2055958 TGTTTTTTTAT
1 TGTTTTTTTAT
2055969 AGAATATCTA
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
20 1 0.04
21 6 0.23
22 18 0.69
23 1 0.04
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.72
Consensus pattern (22 bp):
TGTTTTTTTATTTTATAATATA
Found at i:2060428 original size:28 final size:27
Alignment explanation
Indices: 2060384--2060436 Score: 63
Period size: 28 Copynumber: 1.9 Consensus size: 27
2060374 ATACTTAAAT
*
2060384 TTTAAAGTTAAAAAAAAAACTAAATGCC
1 TTTAAAGTAAAAAAAAAAAC-AAATGCC
*
2060412 TTTAAA-TAAAAATAAAATACAAATG
1 TTTAAAGTAAAAA-AAAAAACAAATG
2060437 TACAAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
27 10 0.45
28 12 0.55
ACGTcount: A:0.60, C:0.08, G:0.06, T:0.26
Consensus pattern (27 bp):
TTTAAAGTAAAAAAAAAAACAAATGCC
Found at i:2064339 original size:44 final size:44
Alignment explanation
Indices: 2064289--2064379 Score: 182
Period size: 44 Copynumber: 2.1 Consensus size: 44
2064279 TTTGTAGATT
2064289 GTAAATACCAAATTTATCATAAGATGAATAATCTTCTGTTGAGA
1 GTAAATACCAAATTTATCATAAGATGAATAATCTTCTGTTGAGA
2064333 GTAAATACCAAATTTATCATAAGATGAATAATCTTCTGTTGAGA
1 GTAAATACCAAATTTATCATAAGATGAATAATCTTCTGTTGAGA
2064377 GTA
1 GTA
2064380 CATAGAATCT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.34
Consensus pattern (44 bp):
GTAAATACCAAATTTATCATAAGATGAATAATCTTCTGTTGAGA
Found at i:2070843 original size:163 final size:163
Alignment explanation
Indices: 2070556--2070883 Score: 568
Period size: 163 Copynumber: 2.0 Consensus size: 163
2070546 TAACGAATCG
2070556 TTCCTATGTCGTTTCCTCCCGGAATAGAACAAAATCCTTTTGTCTTTAATCCTCATCCTGTTTTC
1 TTCCTATGTCGTTTCCTCCCGGAATAGAACAAAATCCTTTTGTCTTTAATCCTCATCCTGTTTTC
*
2070621 TGGCTCTGCATTTAATGTATTTGATCTGTAATTTTGAAAAAACGACAAATTCCGGGAACTATTTG
66 TGGCTCTGCATTTAATGTATTTGATCTGTAATTTTGAAAAAACGACAAATTCCGGGAACTATTCG
*
2070686 CTAATCAAAGACACGTTTTTGTTGAGTTTTTAC
131 CTAATCAAAAACACGTTTTTGTTGAGTTTTTAC
* *
2070719 TTCCTATGTCGTTTCCTCTCGGAATAGAATAAAATCCTTTTGTCTTTAATCCTCATCCTGTTTTC
1 TTCCTATGTCGTTTCCTCCCGGAATAGAACAAAATCCTTTTGTCTTTAATCCTCATCCTGTTTTC
* * *
2070784 TGGTTCTGCATTTAATGTATTTGATCTGTAATTTTGAAAAGCACGACAAATT-TGGGAACTATTC
66 TGGCTCTGCATTTAATGTATTTGATCTGTAATTTTGAAAA-AACGACAAATTCCGGGAACTATTC
*
2070848 GCTAATGAAAAACACGTTTTTGTTGAGTTTTTAC
130 GCTAATCAAAAACACGTTTTTGTTGAGTTTTTAC
2070882 TT
1 TT
2070884 GTATACGTAA
Statistics
Matches: 156, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
163 146 0.94
164 10 0.06
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (163 bp):
TTCCTATGTCGTTTCCTCCCGGAATAGAACAAAATCCTTTTGTCTTTAATCCTCATCCTGTTTTC
TGGCTCTGCATTTAATGTATTTGATCTGTAATTTTGAAAAAACGACAAATTCCGGGAACTATTCG
CTAATCAAAAACACGTTTTTGTTGAGTTTTTAC
Found at i:2078222 original size:23 final size:21
Alignment explanation
Indices: 2078155--2078223 Score: 68
Period size: 21 Copynumber: 3.1 Consensus size: 21
2078145 TAAAAATACG
*
2078155 TAAATATTTTAAATATATATAA
1 TAAATATTTTAAA-ACATATAA
* *
2078177 TAAAT-TTTAAAAACATAAAAA
1 TAAATATTTTAAAACAT-ATAA
2078198 TAAATATTTTCAAAACAATATAA
1 TAAATATTTT-AAAAC-ATATAA
2078221 TAA
1 TAA
2078224 TAATAATTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
20 3 0.08
21 14 0.37
22 8 0.21
23 11 0.29
24 2 0.05
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.36
Consensus pattern (21 bp):
TAAATATTTTAAAACATATAA
Found at i:2078232 original size:26 final size:26
Alignment explanation
Indices: 2078166--2078236 Score: 73
Period size: 26 Copynumber: 2.9 Consensus size: 26
2078156 AAATATTTTA
2078166 AATAT-AT-ATAATAAATTTTAAAAAC
1 AATATAATAATAAT-AATTTTAAAAAC
*
2078191 -ATA-AA-AATAA-ATATTTTCAAAAC
1 AATATAATAATAATA-ATTTTAAAAAC
2078214 AATATAATAATAATAATTTTAAA
1 AATATAATAATAATAATTTTAAA
2078237 TATGTATTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 13
0.71 0.04 0.25
Matches are distributed among these distances:
22 1 0.03
23 10 0.27
24 11 0.30
25 2 0.05
26 12 0.32
27 1 0.03
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (26 bp):
AATATAATAATAATAATTTTAAAAAC
Found at i:2081195 original size:56 final size:55
Alignment explanation
Indices: 2081062--2081290 Score: 230
Period size: 57 Copynumber: 4.1 Consensus size: 55
2081052 AATACAAATA
* * *
2081062 AAAAATATTTTTTGAAGTGTTTGCCACTTAATGGTCTACACCACCTTTTCCAAATTT
1 AAAAATATTTTTT-TAGTGTTTGTCAC-CAATGGTCTACACCACCTTTTCCAAATTT
*
2081119 AAAAATATTTTTTTGAGTGTTTGTCATCCAATGG-CTTACACCACCTTTCCCAAATTT
1 AAAAATATTTTTTT-AGTGTTTGTCA-CCAATGGTC-TACACCACCTTTTCCAAATTT
* * * *
2081176 AAAAATATTTTTTTAGTGTTCGTCACCCAATGATCTACACCGCTTTTTCCAAATTT
1 AAAAATATTTTTTTAGTGTTTGTCA-CCAATGGTCTACACCACCTTTTCCAAATTT
* * *** ** *
2081232 AAAAATATTGTTTTGAGTATTTGT--CCAATAACCTACACCATATTTTCAAAATTT
1 AAAAATATT-TTTTTAGTGTTTGTCACCAATGGTCTACACCACCTTTTCCAAATTT
2081286 AAAAA
1 AAAAA
2081291 AATAATTCAA
Statistics
Matches: 148, Mismatches: 19, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
54 29 0.20
56 44 0.30
57 74 0.50
58 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.09, T:0.40
Consensus pattern (55 bp):
AAAAATATTTTTTTAGTGTTTGTCACCAATGGTCTACACCACCTTTTCCAAATTT
Found at i:2081336 original size:26 final size:28
Alignment explanation
Indices: 2081307--2081374 Score: 88
Period size: 26 Copynumber: 2.5 Consensus size: 28
2081297 TCAAGTTTAA
2081307 ATAATTAAAACATGATTTAAA-AA-TTT
1 ATAATTAAAACATGATTTAAATAATTTT
2081333 ATAATTGAAAA-ATGATTTAAATAATTTT
1 ATAATT-AAAACATGATTTAAATAATTTT
*
2081361 TTAAATTAAAACAT
1 AT-AATTAAAACAT
2081375 TACAATTGAT
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
26 16 0.44
27 6 0.17
28 8 0.22
29 6 0.17
ACGTcount: A:0.53, C:0.03, G:0.04, T:0.40
Consensus pattern (28 bp):
ATAATTAAAACATGATTTAAATAATTTT
Found at i:2087744 original size:23 final size:24
Alignment explanation
Indices: 2087718--2087764 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
2087708 TTTTTAAGGA
*
2087718 AATAA-AATTAAAT-TATATATTTT
1 AATAATAATAAAATATATA-ATTTT
2087741 AATAATAATAAAATATATAATTTT
1 AATAATAATAAAATATATAATTTT
2087765 TTCAATTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 5 0.24
24 12 0.57
25 4 0.19
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
AATAATAATAAAATATATAATTTT
Found at i:2087794 original size:23 final size:21
Alignment explanation
Indices: 2087752--2087795 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
2087742 ATAATAATAA
*
2087752 AATATATAATTTTTTCAATTT
1 AATATATAATTTTTTAAATTT
*
2087773 AATATTTATATTTTTATAAATTT
1 AATATATA-ATTTTT-TAAATTT
2087796 TAAAATATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 7 0.37
22 6 0.32
23 6 0.32
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (21 bp):
AATATATAATTTTTTAAATTT
Found at i:2113150 original size:32 final size:32
Alignment explanation
Indices: 2113114--2113176 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
2113104 TTCTAATAAA
*
2113114 TCCTAATTTCTTCAAGGGTTTGTATTAATCAG
1 TCCTAATTTCTTCAAGGATTTGTATTAATCAG
** *
2113146 TCCTAATTTCTTTGAGTATTTGTATTAATCA
1 TCCTAATTTCTTCAAGGATTTGTATTAATCA
2113177 ACCTCTAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.25, C:0.14, G:0.13, T:0.48
Consensus pattern (32 bp):
TCCTAATTTCTTCAAGGATTTGTATTAATCAG
Found at i:2123577 original size:6 final size:6
Alignment explanation
Indices: 2123567--2123610 Score: 61
Period size: 6 Copynumber: 7.3 Consensus size: 6
2123557 ACTTCCATAT
* * *
2123567 CCTCCA GCTCCA CCTCCA CCACCA CCACCA CCTCCA CCTCCA CC
1 CCTCCA CCTCCA CCTCCA CCTCCA CCTCCA CCTCCA CCTCCA CC
2123611 ACCTCCATGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.20, C:0.66, G:0.02, T:0.11
Consensus pattern (6 bp):
CCTCCA
Found at i:2123578 original size:21 final size:21
Alignment explanation
Indices: 2123545--2123584 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2123535 AGCCACTTCC
*
2123545 TCCTCCACTTCCACTTCCATA
1 TCCTCCACTTCCACCTCCATA
2123566 TCCTCCAGC-TCCACCTCCA
1 TCCTCCA-CTTCCACCTCCA
2123585 CCACCACCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.17, C:0.53, G:0.03, T:0.28
Consensus pattern (21 bp):
TCCTCCACTTCCACCTCCATA
Found at i:2123588 original size:9 final size:9
Alignment explanation
Indices: 2123576--2123660 Score: 55
Period size: 9 Copynumber: 9.1 Consensus size: 9
2123566 TCCTCCAGCT
2123576 CCACCTCCA
1 CCACCTCCA
*
2123585 CCACCACCA
1 CCACCTCCA
2123594 CCACCTCCA
1 CCACCTCCA
* *
2123603 CCTCCACCA
1 CCACCTCCA
*
2123612 CCTCCATGTCCA
1 CCACC---TCCA
*
2123624 CCACCAT-TA
1 CCACC-TCCA
*
2123633 CCAGCTCCA
1 CCACCTCCA
*
2123642 CCACCTTCA
1 CCACCTCCA
*
2123651 CCACTTCCA
1 CCACCTCCA
2123660 C
1 C
2123661 TTCCACTTCC
Statistics
Matches: 58, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
8 1 0.02
9 49 0.84
10 1 0.02
12 7 0.12
ACGTcount: A:0.24, C:0.59, G:0.02, T:0.15
Consensus pattern (9 bp):
CCACCTCCA
Done.