Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D13
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: 60343961
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 596159 characters in sequence are not A, C, G, or T
File 5 of 204
Found at i:1553748 original size:49 final size:49
Alignment explanation
Indices: 1553636--1553753 Score: 125
Period size: 51 Copynumber: 2.4 Consensus size: 49
1553626 ATTTTCCACG
* *
1553636 TTTTATAT-TATACTTATATATTTCATTTTTTGTAAATGCATGAATATA
1 TTTTATATATATATTTATATATTTCATTTTTTATAAATGCATGAATATA
* * *
1553684 TTTTATATGTATATATTTATAT-TTTCCTTGTTTTCATAAATGCAT-TATGTA
1 TTTTATA--TATATATTTATATATTTCATT-TTTT-ATAAATGCATGAATATA
*
1553735 TTTTATATATATATATATA
1 TTTTATATATATATTTATA
1553754 AGTTTTATAA
Statistics
Matches: 59, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
48 7 0.12
49 11 0.19
50 7 0.12
51 25 0.42
52 9 0.15
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.56
Consensus pattern (49 bp):
TTTTATATATATATTTATATATTTCATTTTTTATAAATGCATGAATATA
Found at i:1556160 original size:21 final size:19
Alignment explanation
Indices: 1556118--1556169 Score: 72
Period size: 21 Copynumber: 2.7 Consensus size: 19
1556108 TCACGTCAAC
1556118 AAATAATTTAAAAATTATA
1 AAATAATTTAAAAATTATA
1556137 AAATAAATATTAAAAATT-TA
1 AAAT-AAT-TTAAAAATTATA
1556157 AAA-AATTTAAAAA
1 AAATAATTTAAAAA
1556170 AATAACATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
17 7 0.23
18 3 0.10
19 4 0.13
20 8 0.26
21 9 0.29
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
AAATAATTTAAAAATTATA
Found at i:1556161 original size:22 final size:19
Alignment explanation
Indices: 1556118--1556162 Score: 54
Period size: 22 Copynumber: 2.2 Consensus size: 19
1556108 TCACGTCAAC
*
1556118 AAATAATTTAAAAATTATA
1 AAATAATTTAAAAATTAAA
1556137 AAATAAATATTAAAAATTTAAA
1 AAAT-AAT-TTAAAAA-TTAAA
1556159 AAAT
1 AAAT
1556163 TTAAAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 4 0.18
20 3 0.14
21 7 0.32
22 8 0.36
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
AAATAATTTAAAAATTAAA
Found at i:1558215 original size:41 final size:40
Alignment explanation
Indices: 1558158--1558245 Score: 167
Period size: 41 Copynumber: 2.2 Consensus size: 40
1558148 ATGACTCCTT
1558158 AAAGAAAATCGAGAAGAAAACTACTTCTAAAAATCATAAG
1 AAAGAAAATCGAGAAGAAAACTACTTCTAAAAATCATAAG
1558198 AAAAGAAAATCGAGAAGAAAACTACTTCTAAAAATCATAAG
1 -AAAGAAAATCGAGAAGAAAACTACTTCTAAAAATCATAAG
1558239 AAAGAAA
1 AAAGAAA
1558246 TCTTGCACAA
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
40 7 0.15
41 40 0.85
ACGTcount: A:0.60, C:0.11, G:0.12, T:0.16
Consensus pattern (40 bp):
AAAGAAAATCGAGAAGAAAACTACTTCTAAAAATCATAAG
Found at i:1571748 original size:31 final size:31
Alignment explanation
Indices: 1571713--1571774 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
1571703 GGTTAAGAAT
*
1571713 AAAATTT-TACCAACTTTTAAGGGACCTAAAA
1 AAAATTTCT-CCAACTTTTAAGGAACCTAAAA
*
1571744 AAAATTTCTCTAACTTTTAAGGAACCTAAAA
1 AAAATTTCTCCAACTTTTAAGGAACCTAAAA
1571775 CCCCATTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 27 0.96
32 1 0.04
ACGTcount: A:0.45, C:0.16, G:0.08, T:0.31
Consensus pattern (31 bp):
AAAATTTCTCCAACTTTTAAGGAACCTAAAA
Found at i:1573480 original size:19 final size:19
Alignment explanation
Indices: 1573444--1573486 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
1573434 ATTTTTATAA
*
1573444 AATTTTTATAATTTATTAT
1 AATTTTTATAATTTATTAC
*
1573463 AATTTTTA-ATTTTCATTAC
1 AATTTTTATAATTT-ATTAC
1573482 AATTT
1 AATTT
1573487 ATAGATTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (19 bp):
AATTTTTATAATTTATTAC
Found at i:1586257 original size:3 final size:3
Alignment explanation
Indices: 1586249--1586286 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
1586239 GCTTTTCTAT
1586249 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1586287 ATTTTCACAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:1593123 original size:23 final size:24
Alignment explanation
Indices: 1593097--1593143 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
1593087 GCAAGGCTCG
1593097 ATTCTAAAT-GATCGCATAATCTT
1 ATTCTAAATGGATCGCATAATCTT
*
1593120 ATTCTAAATGGGTCGCATAATCTT
1 ATTCTAAATGGATCGCATAATCTT
1593144 TTATATACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (24 bp):
ATTCTAAATGGATCGCATAATCTT
Found at i:1608013 original size:26 final size:26
Alignment explanation
Indices: 1607976--1608043 Score: 77
Period size: 26 Copynumber: 2.6 Consensus size: 26
1607966 TGAGAAGACA
1607976 ACAAGG-GAAGCTCGTAGACCTAGCTC
1 ACAAGGAG-AGCTCGTAGACCTAGCTC
* * *
1608002 GCAA-GAGGAGCTCATAGATCTAGCTC
1 ACAAGGA-GAGCTCGTAGACCTAGCTC
1608028 ACAAGGAGAGCTCGTA
1 ACAAGGAGAGCTCGTA
1608044 TGAACCAGGA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
25 1 0.03
26 30 0.88
27 3 0.09
ACGTcount: A:0.32, C:0.24, G:0.28, T:0.16
Consensus pattern (26 bp):
ACAAGGAGAGCTCGTAGACCTAGCTC
Found at i:1609999 original size:17 final size:18
Alignment explanation
Indices: 1609964--1610000 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
1609954 AGTATATTAC
1609964 TAATACATAATATAATAT
1 TAATACATAATATAATAT
*
1609982 TAATACAT-ATATAGTAT
1 TAATACATAATATAATAT
1609999 TA
1 TA
1610001 CATGATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (18 bp):
TAATACATAATATAATAT
Found at i:1613396 original size:10 final size:10
Alignment explanation
Indices: 1613381--1613405 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1613371 TGCATTACAT
1613381 ATTTACATAA
1 ATTTACATAA
1613391 ATTTACATAA
1 ATTTACATAA
1613401 ATTTA
1 ATTTA
1613406 AGATTTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (10 bp):
ATTTACATAA
Found at i:1613990 original size:6 final size:7
Alignment explanation
Indices: 1613973--1613998 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1613963 ATCCTCCAAT
1613973 TTTTTTA
1 TTTTTTA
1613980 TTTTTTA
1 TTTTTTA
1613987 TTTTTTA
1 TTTTTTA
1613994 TTTTT
1 TTTTT
1613999 GTAATTTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTA
Found at i:1624381 original size:40 final size:40
Alignment explanation
Indices: 1624321--1624399 Score: 149
Period size: 40 Copynumber: 2.0 Consensus size: 40
1624311 ATTATAAAAG
*
1624321 TACAGTTTTATATTAGAGTAATTGAATCAGTTCTTAAATA
1 TACAATTTTATATTAGAGTAATTGAATCAGTTCTTAAATA
1624361 TACAATTTTATATTAGAGTAATTGAATCAGTTCTTAAAT
1 TACAATTTTATATTAGAGTAATTGAATCAGTTCTTAAAT
1624400 GTAATAATTA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.38, C:0.08, G:0.11, T:0.43
Consensus pattern (40 bp):
TACAATTTTATATTAGAGTAATTGAATCAGTTCTTAAATA
Found at i:1630246 original size:26 final size:26
Alignment explanation
Indices: 1630217--1630295 Score: 70
Period size: 28 Copynumber: 3.0 Consensus size: 26
1630207 TTATGCTTAA
1630217 ATTTAAGATTTAATCCTTATACTTTT
1 ATTTAAGATTTAATCCTTATACTTTT
* ** * * *
1630243 ATTTCAA-TTTTAGCCACAATATGCTTAT
1 ATTT-AAGATTTAATC-C-TTATACTTTT
1630271 ATTTAAGATTTAATCCTTATACTTT
1 ATTTAAGATTTAATCCTTATACTTT
1630296 AATCTTTTAA
Statistics
Matches: 37, Mismatches: 12, Indels: 8
0.65 0.21 0.14
Matches are distributed among these distances:
26 15 0.41
27 6 0.16
28 16 0.43
ACGTcount: A:0.32, C:0.14, G:0.05, T:0.49
Consensus pattern (26 bp):
ATTTAAGATTTAATCCTTATACTTTT
Found at i:1630247 original size:49 final size:50
Alignment explanation
Indices: 1630174--1630298 Score: 164
Period size: 54 Copynumber: 2.5 Consensus size: 50
1630164 AATATGCTTG
* *
1630174 AGATTTAATTC-TATACTTTAATTTCAATTTTAG-TTATGCTTAAATTTA
1 AGATTTAATCCTTATACTTTAATTTCAATTTTAGCATATGCTTAAATTTA
* *
1630222 AGATTTAATCCTTATACTTTTATTTCAATTTTAGCCACAATATGCTTATATTTA
1 AGATTTAATCCTTATACTTTAATTTCAATTTTAG---C-ATATGCTTAAATTTA
1630276 AGATTTAATCCTTATACTTTAAT
1 AGATTTAATCCTTATACTTTAAT
1630299 CTTTTAACAT
Statistics
Matches: 66, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
48 10 0.15
49 21 0.32
54 35 0.53
ACGTcount: A:0.33, C:0.12, G:0.06, T:0.50
Consensus pattern (50 bp):
AGATTTAATCCTTATACTTTAATTTCAATTTTAGCATATGCTTAAATTTA
Found at i:1636027 original size:14 final size:14
Alignment explanation
Indices: 1636008--1636035 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1635998 TTTTAATAAT
1636008 TAAAAAAAAGAAAA
1 TAAAAAAAAGAAAA
1636022 TAAAAAAAAGAAAA
1 TAAAAAAAAGAAAA
1636036 GGATTGAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.86, C:0.00, G:0.07, T:0.07
Consensus pattern (14 bp):
TAAAAAAAAGAAAA
Found at i:1645447 original size:46 final size:46
Alignment explanation
Indices: 1645394--1645599 Score: 337
Period size: 46 Copynumber: 4.5 Consensus size: 46
1645384 AGTACTTCTA
*
1645394 ATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTG
1 ATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTG
* *
1645440 ATCAAGTGACAAAGTGATAAGTGGTAGCTTTAACTACACTTATCTG
1 ATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTG
*
1645486 ATCAAGTAACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTG
1 ATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTG
*
1645532 ATCAAGTGACAAAGTGATAAGTGATAGC-CTAGCTACACTTATCTG
1 ATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTG
*
1645577 ATC-AGGGAC-AAGTGATAAGTGAT
1 ATCAAGTGACAAAGTGATAAGTGAT
1645600 CATATGTAAG
Statistics
Matches: 153, Mismatches: 7, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
43 14 0.09
44 5 0.03
45 19 0.12
46 115 0.75
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (46 bp):
ATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTG
Found at i:1647516 original size:45 final size:46
Alignment explanation
Indices: 1647440--1647546 Score: 166
Period size: 46 Copynumber: 2.4 Consensus size: 46
1647430 TACGTATGAT
* *
1647440 CACTTATCAC-TTCTC-CTTGATCAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
1647483 CACTTATCACTTTGTCACTTGCTCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1647529 CACTTATCACTTTGTCAC
1 CACTTATCACTTTGTCAC
1647547 CACTTATCAC
Statistics
Matches: 58, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
43 10 0.17
44 4 0.07
45 20 0.34
46 24 0.41
ACGTcount: A:0.26, C:0.26, G:0.14, T:0.34
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:1647540 original size:46 final size:45
Alignment explanation
Indices: 1647440--1647662 Score: 200
Period size: 45 Copynumber: 4.6 Consensus size: 45
1647430 TACGTATGAT
* *
1647440 CACTTATCAC-TTCTC-CTTGATCAGATAAGTGTAGCTAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTAC
*
1647483 CACTTATCACTTTGTCACTTGCTCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AAGCTAC
* *
1647529 CACTTATCACTTTGTCACCACTT-ATCACTTGTTCCTGATCAGATAAGTGTAGCTAAAACTAC
1 CACTTATCACTTTGT---CACTTGATCA---------GATAAG-T--G--TAGCT-AAGCTAC
*
1647591 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTAC
1647636 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
1647663 AGTACTCAAA
Statistics
Matches: 150, Mismatches: 9, Indels: 40
0.75 0.05 0.20
Matches are distributed among these distances:
43 10 0.07
44 4 0.03
45 52 0.35
46 26 0.17
48 4 0.03
49 5 0.03
50 1 0.01
51 5 0.03
57 5 0.03
58 1 0.01
59 5 0.03
60 5 0.03
62 27 0.18
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.34
Consensus pattern (45 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTAC
Found at i:1647580 original size:62 final size:64
Alignment explanation
Indices: 1647481--1647608 Score: 208
Period size: 62 Copynumber: 2.0 Consensus size: 64
1647471 TAGCTAGGCT
* *
1647481 ACCACTTATCACTTTGTCACTTGCTCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTC
1 ACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAACTACCACTTATCACTTTGTC
1647545 ACCACTTATCAC-TTGTTC-C-TGATCAGATAAGTGTAGCTAAAACTACCACTTATCACTTTGTC
1 ACCACTTATCACTTTG-TCACTTGATCAGATAAGTGTAGCTAAAACTACCACTTATCACTTTGTC
1647607 AC
1 AC
1647609 TTGATCAGAT
Statistics
Matches: 61, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
62 43 0.70
63 4 0.07
64 14 0.23
ACGTcount: A:0.28, C:0.27, G:0.12, T:0.34
Consensus pattern (64 bp):
ACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAACTACCACTTATCACTTTGTC
Found at i:1647640 original size:107 final size:107
Alignment explanation
Indices: 1647440--1647653 Score: 351
Period size: 107 Copynumber: 2.0 Consensus size: 107
1647430 TACGTATGAT
** *
1647440 CACTTATCACTTCTCCTTGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTGTCACTTGC
1 CACTTATCACTTCTCCTTGATCAGATAAGTGTAGCTAAACTACCACTTATCACTTTGTCACTTGA
1647505 TCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCAC
66 TCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCAC
*
1647547 CACTTATCACTTGTTCC-TGATCAGATAAGTGTAGCTAAAACTACCACTTATCACTTTGTCACTT
1 CACTTATCACTT-CTCCTTGATCAGATAAGTGTAGCT-AAACTACCACTTATCACTTTGTCACTT
*
1647611 GATCAGATAAGTGTAGCT-AAGCTATCACTTATCACTTTGTCAC
64 GATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCAC
1647654 TTGATCAGAA
Statistics
Matches: 100, Mismatches: 5, Indels: 4
0.92 0.05 0.04
Matches are distributed among these distances:
107 55 0.55
108 45 0.45
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.34
Consensus pattern (107 bp):
CACTTATCACTTCTCCTTGATCAGATAAGTGTAGCTAAACTACCACTTATCACTTTGTCACTTGA
TCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCAC
Found at i:1657336 original size:17 final size:17
Alignment explanation
Indices: 1657314--1657347 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1657304 ATCCACTAAT
*
1657314 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
1657331 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
1657348 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:1661975 original size:17 final size:17
Alignment explanation
Indices: 1661953--1661986 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1661943 ATCCACTAAT
*
1661953 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
1661970 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
1661987 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:1663171 original size:18 final size:19
Alignment explanation
Indices: 1663131--1663176 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
1663121 CATTAATTAT
1663131 ATTTTAAATATGTATTTAG
1 ATTTTAAATATGTATTTAG
1663150 ATTTT-AATAGTGTATTTA-
1 ATTTTAAATA-TGTATTTAG
1663168 ATTTATAAA
1 ATTT-TAAA
1663177 AAAAATTATC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 8 0.33
19 14 0.58
20 2 0.08
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (19 bp):
ATTTTAAATATGTATTTAG
Found at i:1673904 original size:15 final size:15
Alignment explanation
Indices: 1673884--1673914 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1673874 ATTTTAAATG
*
1673884 TTTAATTACTTTTAA
1 TTTAATTAATTTTAA
1673899 TTTAATTAATTTTAA
1 TTTAATTAATTTTAA
1673914 T
1 T
1673915 GTTTAATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTAATTAATTTTAA
Found at i:1676845 original size:16 final size:15
Alignment explanation
Indices: 1676824--1676857 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
1676814 GAATTGAATA
1676824 ATTGTATGATATAGTT
1 ATTGTATGATATA-TT
*
1676840 ATTGTATGTTATATT
1 ATTGTATGATATATT
1676855 ATT
1 ATT
1676858 TTACTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.29, C:0.00, G:0.15, T:0.56
Consensus pattern (15 bp):
ATTGTATGATATATT
Found at i:1688832 original size:11 final size:11
Alignment explanation
Indices: 1688816--1688840 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1688806 GTAAAAATAA
1688816 AAATTATTTTT
1 AAATTATTTTT
1688827 AAATTATTTTT
1 AAATTATTTTT
1688838 AAA
1 AAA
1688841 ATAAGTACAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
AAATTATTTTT
Found at i:1689210 original size:14 final size:14
Alignment explanation
Indices: 1689191--1689217 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1689181 TTTCTAATAT
1689191 TTTTTTATAAATTA
1 TTTTTTATAAATTA
1689205 TTTTTTATAAATT
1 TTTTTTATAAATT
1689218 TGTTATGGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTTTTATAAATTA
Found at i:1689336 original size:28 final size:28
Alignment explanation
Indices: 1689305--1689362 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
1689295 AAAATTTAAC
1689305 AAATATTAATATTTTTA-ATTTTTTTTAT
1 AAAT-TTAATATTTTTATATTTTTTTTAT
* *
1689333 AAATTTTATATTTTTATGTTTTTTTTAT
1 AAATTTAATATTTTTATATTTTTTTTAT
1689361 AA
1 AA
1689363 TTCCAAAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 11 0.41
28 16 0.59
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (28 bp):
AAATTTAATATTTTTATATTTTTTTTAT
Found at i:1689919 original size:44 final size:44
Alignment explanation
Indices: 1689843--1689932 Score: 146
Period size: 44 Copynumber: 2.0 Consensus size: 44
1689833 CCGAATTTAA
1689843 TTTAATTGTTTTATTTTTTATTTTAAAGCAAATAAGATTATATTT
1 TTTAATTGTTTTATTTTTTATTTTAAAGCAAATAAGATTAT-TTT
* *
1689888 TTTAATTGTTTTA-TTTTTATTTTGAAGCAAATAATATTATTTT
1 TTTAATTGTTTTATTTTTTATTTTAAAGCAAATAAGATTATTTT
1689931 TT
1 TT
1689933 GAGTTTAGAA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
43 5 0.12
44 25 0.58
45 13 0.30
ACGTcount: A:0.31, C:0.02, G:0.07, T:0.60
Consensus pattern (44 bp):
TTTAATTGTTTTATTTTTTATTTTAAAGCAAATAAGATTATTTT
Found at i:1695424 original size:13 final size:13
Alignment explanation
Indices: 1695403--1695446 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
1695393 GTAGAGCTAA
*
1695403 TTATGGATGATTT
1 TTATTGATGATTT
1695416 TTATTGATGATTACTT
1 TTATTGATGA-T--TT
1695432 TTATTGATGATTT
1 TTATTGATGATTT
1695445 TT
1 TT
1695447 CTAGAAAAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
13 13 0.48
14 1 0.04
15 1 0.04
16 12 0.44
ACGTcount: A:0.23, C:0.02, G:0.16, T:0.59
Consensus pattern (13 bp):
TTATTGATGATTT
Found at i:1709384 original size:3 final size:3
Alignment explanation
Indices: 1709378--1709404 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1709368 CTCCTCCTCC
1709378 TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT
1709405 AATTTTACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:1711058 original size:24 final size:22
Alignment explanation
Indices: 1711027--1711108 Score: 78
Period size: 22 Copynumber: 3.6 Consensus size: 22
1711017 TTTTCACAAA
1711027 AAAAATTCAATATCAATATCC-TTC
1 AAAAATTC--TATCAAT-TCCGTTC
*
1711051 AAAAATTCTCTCAATTCCGTTC
1 AAAAATTCTATCAATTCCGTTC
* *
1711073 AAAAATTCTCTCAAATTCCTTTC
1 AAAAATTCTATC-AATTCCGTTC
*
1711096 -AAAATTCTCTCAA
1 AAAAATTCTATCAA
1711109 ACTCTCAAAT
Statistics
Matches: 54, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
21 5 0.09
22 32 0.59
23 9 0.17
24 8 0.15
ACGTcount: A:0.39, C:0.24, G:0.01, T:0.35
Consensus pattern (22 bp):
AAAAATTCTATCAATTCCGTTC
Found at i:1711073 original size:22 final size:21
Alignment explanation
Indices: 1711039--1711108 Score: 97
Period size: 22 Copynumber: 3.2 Consensus size: 21
1711029 AAATTCAATA
1711039 TCAATATCCTTCAAAAATTCTC
1 TCAAT-TCCTTCAAAAATTCTC
1711061 TCAATTCCGTTCAAAAATTCTC
1 TCAATTCC-TTCAAAAATTCTC
1711083 TCAAATTCCTTTC-AAAATTCTC
1 TC-AATTCC-TTCAAAAATTCTC
1711105 TCAA
1 TCAA
1711109 ACTCTCAAAT
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
21 5 0.11
22 31 0.69
23 9 0.20
ACGTcount: A:0.34, C:0.27, G:0.01, T:0.37
Consensus pattern (21 bp):
TCAATTCCTTCAAAAATTCTC
Found at i:1711109 original size:22 final size:23
Alignment explanation
Indices: 1711048--1711109 Score: 101
Period size: 22 Copynumber: 2.8 Consensus size: 23
1711038 ATCAATATCC
1711048 TTCAAAAATTCTCTC-AATTCCG
1 TTCAAAAATTCTCTCAAATTCCG
*
1711070 TTCAAAAATTCTCTCAAATTCCT
1 TTCAAAAATTCTCTCAAATTCCG
1711093 TTC-AAAATTCTCTCAAA
1 TTCAAAAATTCTCTCAAA
1711110 CTCTCAAATT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
22 29 0.76
23 9 0.24
ACGTcount: A:0.35, C:0.26, G:0.02, T:0.37
Consensus pattern (23 bp):
TTCAAAAATTCTCTCAAATTCCG
Found at i:1711115 original size:30 final size:30
Alignment explanation
Indices: 1711080--1711138 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
1711070 TTCAAAAATT
* *
1711080 CTCTCAAATTCCTTTCAAAATTCTCTCAAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAAA
1711110 CTCTCAAATTCCTTCCAAAATCCTCTCAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAA
1711139 TTTCCTTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.32, C:0.34, G:0.00, T:0.34
Consensus pattern (30 bp):
CTCTCAAATTCCTTCCAAAATCCTCTCAAA
Found at i:1711149 original size:21 final size:22
Alignment explanation
Indices: 1711110--1711151 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1711100 TTCTCTCAAA
1711110 CTCTCAAATTCCTTCCAAAATC
1 CTCTCAAATTCCTTCCAAAATC
* *
1711132 CTCTCAATTTCCTTCAAAAA
1 CTCTCAAATTCCTTCCAAAA
1711152 ATCTCCAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (22 bp):
CTCTCAAATTCCTTCCAAAATC
Found at i:1711257 original size:29 final size:29
Alignment explanation
Indices: 1711197--1711257 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
1711187 AATTTCATTA
* *
1711197 TTTTAAGAAAATTTTAAAATTTTTTATTT
1 TTTTAAGAAAATTTTAAAATTTTTAATAT
1711226 TTTTAA-AATAATTTTAAAATTTTTAATAT
1 TTTTAAGAA-AATTTTAAAATTTTTAATAT
1711255 TTT
1 TTT
1711258 CAACAATGGC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 2 0.07
29 27 0.93
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (29 bp):
TTTTAAGAAAATTTTAAAATTTTTAATAT
Found at i:1711377 original size:14 final size:15
Alignment explanation
Indices: 1711348--1711381 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1711338 AAATTTTAAA
1711348 TTTTATTTAAGATAT
1 TTTTATTTAAGATAT
*
1711363 TTTTATTTATG-TAT
1 TTTTATTTAAGATAT
1711377 TTTTA
1 TTTTA
1711382 GATATTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (15 bp):
TTTTATTTAAGATAT
Found at i:1713015 original size:18 final size:18
Alignment explanation
Indices: 1712982--1713016 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1712972 AGGTATGTTT
* *
1712982 CCTAACCCTTATATGTAC
1 CCTAACCCGTACATGTAC
1713000 CCTAACCCGTACATGTA
1 CCTAACCCGTACATGTA
1713017 TCCTTTTCCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.34, G:0.09, T:0.29
Consensus pattern (18 bp):
CCTAACCCGTACATGTAC
Found at i:1713519 original size:28 final size:28
Alignment explanation
Indices: 1713473--1714073 Score: 653
Period size: 28 Copynumber: 22.4 Consensus size: 28
1713463 TTTTGACATT
*
1713473 ATTTGATTAAAAACCCTAACCTAACTTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
*
1713501 ATATAATTAAAAA--CT---CTAACTTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
* *
1713524 ACTTAATTAAAAACCCTAACCTAACCTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
*
1713552 ATTTAATTAAAAACCCTAACCTAATTTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
1713580 ATTTAATTAAAAACCCTAA-C--A--TA
1 ATTTAATTAAAAACCCTAACCTAACTTA
*
1713603 ATTTAATTAAAAACCCTAACCTAATTTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
*
1713631 ATTTAATTAAATTAAAAACCCTAACCTAATTTA
1 A--T--TT-AATTAAAAACCCTAACCTAACTTA
*
1713664 ATTTAATTAAAAACCCTAACCTAACCTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
*
1713692 ATTTAATTAAAAACCCTAACCTAATTTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
1713720 ATTTAATTAAAAACCCTAA-C--A--TA
1 ATTTAATTAAAAACCCTAACCTAACTTA
*
1713743 ATTTAATTAAAAACCCTAACCTAACCTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
* *
1713771 ATTTAATTAAAACCCCTAACCTAATTTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
1713799 ATTTAATTAAAAACCCTAA-C--A--TA
1 ATTTAATTAAAAACCCTAACCTAACTTA
*
1713822 ATTTAATTAAAAACCCTAACCCTAACCTA
1 ATTTAATTAAAAACCCTAA-CCTAACTTA
* *
1713851 ATTTAATTAAAATCCCTAACTCTAACCTA
1 ATTTAATTAAAAACCCTAAC-CTAACTTA
*
1713880 ATTTAATTAAAAA-CCT----TAACCTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
* *
1713903 GTTTAGTTAAAAACCCTAACCCTAA-TCTA
1 ATTTAATTAAAAACCCTAA-CCTAACT-TA
*
1713932 ATTTAATTAAAAACCCTAACCCTAACCTA
1 ATTTAATTAAAAACCCTAA-CCTAACTTA
*
1713961 ATTTAATTAAAAACCCTAACCTAATTTA
1 ATTTAATTAAAAACCCTAACCTAACTTA
1713989 ATTTAATTAAAAACCCTAA-C---C-TA
1 ATTTAATTAAAAACCCTAACCTAACTTA
*
1714012 ATTTAATTAAAAACCATAA-C---C-TA
1 ATTTAATTAAAAACCCTAACCTAACTTA
*
1714035 ATTTAATTAAAAACCCTAACTCTAACCTA
1 ATTTAATTAAAAACCCTAAC-CTAACTTA
1714064 ATTTAATTAA
1 ATTTAATTAA
1714074 TGTAAAAACC
Statistics
Matches: 503, Mismatches: 29, Indels: 81
0.82 0.05 0.13
Matches are distributed among these distances:
23 142 0.28
24 5 0.01
25 7 0.01
26 4 0.01
27 5 0.01
28 208 0.41
29 103 0.20
30 1 0.00
31 1 0.00
32 2 0.00
33 25 0.05
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (28 bp):
ATTTAATTAAAAACCCTAACCTAACTTA
Found at i:1713523 original size:23 final size:23
Alignment explanation
Indices: 1713493--1713633 Score: 120
Period size: 23 Copynumber: 5.7 Consensus size: 23
1713483 AAACCCTAAC
*
1713493 CTAACTTAATATAATTAAAAACT
1 CTAACTTAATTTAATTAAAAACT
*
1713516 CTAACTTAACTTAATTAAAAACCCT
1 CTAACTTAATTTAATTAAAAA--CT
*
1713541 AACCTAACCTAATTTAATTAAAAACCCT
1 ---CTAACTTAATTTAATTAAAAA--CT
* *
1713569 AACCTAATTTAATTTAATTAAAAACC
1 ---CTAACTTAATTTAATTAAAAACT
* *
1713595 CTAACATAATTTAATTAAAAACC
1 CTAACTTAATTTAATTAAAAACT
*
1713618 CTAACCTAATTTAATT
1 CTAACTTAATTTAATT
1713634 TAATTAAATT
Statistics
Matches: 103, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
23 55 0.53
25 2 0.02
26 1 0.01
28 45 0.44
ACGTcount: A:0.48, C:0.19, G:0.00, T:0.33
Consensus pattern (23 bp):
CTAACTTAATTTAATTAAAAACT
Found at i:1713559 original size:51 final size:52
Alignment explanation
Indices: 1713473--1714073 Score: 486
Period size: 51 Copynumber: 11.2 Consensus size: 52
1713463 TTTTGACATT
* * * *
1713473 ATTTGATTAAAAACCCTAACCTAACTTAATATAATTAAAAACT-CTAACTTA
1 ATTTAATTAAAAACCCTAACCTAACCTAATTTAATTAAAAACTACTAACCTA
* *
1713524 ACTTAATTAAAAACCCTAACCTAACCTAATTTAATTAAAAAC-CCTAACCTA
1 ATTTAATTAAAAACCCTAACCTAACCTAATTTAATTAAAAACTACTAACCTA
* **
1713575 ATTTAATTTAATTAAA----AACCCTAACATAATTTAATTAAAAACCCTAACCTAATTTA
1 ATTTAA-TTAA--AAACCCTAA-CCTAACCTAATTTAATTAAAAA--CT-A-CTAACCTA
**
1713631 ATTTAATTAAATTAAAAACCCTAACCTAATTTAATTTAATTAAAAACCCTAACCTAACCTA
1 A--T--TT-AATTAAAAACCCTAACCTAACCTAATTTAATTAAAAA--CT-A-CTAACCTA
** * *
1713692 ATTTAATTAAAAACCCTAACCTAATTTAATTTAATTAAAAAC-CCTAACATA
1 ATTTAATTAAAAACCCTAACCTAACCTAATTTAATTAAAAACTACTAACCTA
**
1713743 ATTTAATTAAAAACCCTAACCTAACCTAATTTAATT-AAAACCCCTAACCTA
1 ATTTAATTAAAAACCCTAACCTAACCTAATTTAATTAAAAACTACTAACCTA
*
1713794 ATTTAATTTAATTAAA----AACCCTAACATAATTTAATTAAAAACCCTAACCCTAACCTA
1 ATTTAA-TTAA--AAACCCTAA-CCTAACCTAATTTAATTAAAAA--CT-A--CTAACCTA
*
1713851 ATTTAATTAAAATCCCTAACTCTAACCTAATTTAATTAAAAAC--CTTAACCTA
1 ATTTAATTAAAAACCCTAAC-CTAACCTAATTTAATTAAAAACTAC-TAACCTA
* * *
1713903 GTTTAGTTAAAAACCCTAACCCTAATCTAATTTAATTAAAAACCCTAACCCTAACCTA
1 ATTTAATTAAAAACCCTAA-CCTAACCTAATTTAATTAAAAA--CT-A--CTAACCTA
** *
1713961 ATTTAATTAAAAACCCTAACCTAATTTAATTTAATTAAAAAC-CCTAACCTA
1 ATTTAATTAAAAACCCTAACCTAACCTAATTTAATTAAAAACTACTAACCTA
1714012 ATTTAATTAAAAA-CC--A--TAACCTAATTTAATTAAAAACCCTAACTCTAACCTA
1 ATTTAATTAAAAACCCTAACCTAACCTAATTTAATTAAAAA--CT-A--CTAACCTA
1714064 ATTTAATTAA
1 ATTTAATTAA
1714074 TGTAAAAACC
Statistics
Matches: 465, Mismatches: 35, Indels: 99
0.78 0.06 0.17
Matches are distributed among these distances:
46 18 0.04
48 2 0.00
50 11 0.02
51 164 0.35
52 73 0.16
53 2 0.00
54 11 0.02
55 1 0.00
56 49 0.11
57 38 0.08
58 50 0.11
59 2 0.00
60 6 0.01
61 36 0.08
62 2 0.00
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (52 bp):
ATTTAATTAAAAACCCTAACCTAACCTAATTTAATTAAAAACTACTAACCTA
Found at i:1714053 original size:18 final size:20
Alignment explanation
Indices: 1713987--1714049 Score: 72
Period size: 23 Copynumber: 2.9 Consensus size: 20
1713977 TAACCTAATT
1713987 TAATTTAATTAAAAACCCTAACC
1 TAATTTAATTAAAAA-CC--ACC
1714010 TAATTTAATTAAAAACCATAACC
1 TAATTTAATTAAAAACC---ACC
1714033 TAATTTAATTAAAAACC
1 TAATTTAATTAAAAACC
1714050 CTAACTCTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
22 2 0.05
23 37 0.95
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.32
Consensus pattern (20 bp):
TAATTTAATTAAAAACCACC
Found at i:1717557 original size:124 final size:124
Alignment explanation
Indices: 1717292--1717557 Score: 408
Period size: 124 Copynumber: 2.1 Consensus size: 124
1717282 CCACGAGGGC
* *
1717292 GCGATTTGACACTATTTACTCAGAAACGTCAAAAAAAATTATTTCCTACATGACCAACTGTAGCG
1 GCGATTTCACACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCCTACATGACCAACTGTAGCG
* * * * **
1717357 AAATCGCGTCCACGAGGGCGCGATTTTACAATTTCTTCTCATATAGCATCCTGGTATCA
66 AAATCGCGTCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAA
* * *
1717416 GCGATTTTATACTATTTGCTCAGAAAACGTCAAAAAAAATTATTTCTTACATGACC-ACTGTAGC
1 GCGATTTCACACTATTTGCTCAG-AAACGTCAAAAAAAATTATTTCCTACATGACCAACTGTAGC
1717480 GAAATCGCGTCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAA
65 GAAATCGCGTCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAA
*
1717540 GCGATTTCCCACTATTTG
1 GCGATTTCACACTATTTG
1717558 ACCAGATACA
Statistics
Matches: 128, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
124 97 0.76
125 31 0.24
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (124 bp):
GCGATTTCACACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCCTACATGACCAACTGTAGCG
AAATCGCGTCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAA
Found at i:1723124 original size:25 final size:26
Alignment explanation
Indices: 1723084--1723132 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
1723074 ATATAACATA
*
1723084 ATACTACAATATTGTTCATACCAATG
1 ATACTACAATATTGTTCAAACCAATG
1723110 ATACTAC-ATATTGTTCAAACCAA
1 ATACTACAATATTGTTCAAACCAA
1723133 ATAATCATAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.41, C:0.20, G:0.06, T:0.33
Consensus pattern (26 bp):
ATACTACAATATTGTTCAAACCAATG
Found at i:1723291 original size:13 final size:13
Alignment explanation
Indices: 1723273--1723299 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1723263 ACTTTTTTTG
1723273 TTTAAAAATTGTT
1 TTTAAAAATTGTT
1723286 TTTAAAAATTGTT
1 TTTAAAAATTGTT
1723299 T
1 T
1723300 ATACTTCAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (13 bp):
TTTAAAAATTGTT
Found at i:1731239 original size:53 final size:53
Alignment explanation
Indices: 1731171--1731274 Score: 172
Period size: 53 Copynumber: 2.0 Consensus size: 53
1731161 CTTCTAAGAG
* *
1731171 GTTTTTGGACATCCAAATTAATTCTGAGTCGATAGAATTCTTCACTAATTTTA
1 GTTTCTGGACATCCAAATTAATTCTGAGTCGACAGAATTCTTCACTAATTTTA
* *
1731224 GTTTCTGGACATCCAAATTAATTCTGTGTCGACAGAATTCTTTACTAATTT
1 GTTTCTGGACATCCAAATTAATTCTGAGTCGACAGAATTCTTCACTAATTT
1731275 CAGATCTGAG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 47 1.00
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.41
Consensus pattern (53 bp):
GTTTCTGGACATCCAAATTAATTCTGAGTCGACAGAATTCTTCACTAATTTTA
Found at i:1739898 original size:154 final size:154
Alignment explanation
Indices: 1739618--1740305 Score: 1160
Period size: 154 Copynumber: 4.5 Consensus size: 154
1739608 AAATTCAACA
*
1739618 GGGTCTATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAACCCGGTT
1 GGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAACCCGGTT
** * * * *
1739683 GGGCCCTAATTTTACCTATTTTTGCCAAGTCCGTCCAAAATTTCCATCGTTTATACATGTAGTAA
66 GGGCCCTGCTTTTACTTAATTTTGCCAAGTCCGTCCAAAACTTCCATAGTTTATACATGTAGTAA
**
1739748 CCAAAGTATCATTGCTTCTCAATG
131 CCAAAGTAAAATTGCTTCTCAATG
*
1739772 GGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCAACGGTTCGAACCCGGTT
1 GGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAACCCGGTT
*
1739837 GGGCCCTGCTTTTACTTAATTTTGCCAAGTCCGTCCTAAACTTCCATAGTTTATACATGTAGTAA
66 GGGCCCTGCTTTTACTTAATTTTGCCAAGTCCGTCCAAAACTTCCATAGTTTATACATGTAGTAA
* * * * *
1739902 CCAAAGTAGAATAGTTTATGAATG
131 CCAAAGTAAAATTGCTTCTCAATG
1739926 GGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAACCCGGTT
1 GGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAACCCGGTT
*
1739991 GGGCCCTGCTTTTACTTAATTTTGCCAAGTCCGTCCTAAACTTCCATAGTTTATACATGTAGTAA
66 GGGCCCTGCTTTTACTTAATTTTGCCAAGTCCGTCCAAAACTTCCATAGTTTATACATGTAGTAA
*
1740056 CCAAAGTAAAATTGCTTCTCAACG
131 CCAAAGTAAAATTGCTTCTCAATG
1740080 GGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAACCCGGTT
1 GGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAACCCGGTT
*
1740145 GGGCCCTGCTTTTACTTAATTTTGCCAAGTCCGTCCAAAACTTCCATAGTTTATACATGTAGTAG
66 GGGCCCTGCTTTTACTTAATTTTGCCAAGTCCGTCCAAAACTTCCATAGTTTATACATGTAGTAA
* *
1740210 CCAAAGTAAAATTGCCTCTCAATA
131 CCAAAGTAAAATTGCTTCTCAATG
* * *
1740234 GGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATTAAGAGGTCTCCGGTTCGAACCTGGTT
1 GGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAACCCGGTT
1740299 GGGCCCT
66 GGGCCCT
1740306 CTATATTTTT
Statistics
Matches: 504, Mismatches: 30, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
154 504 1.00
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (154 bp):
GGGTCCATAGCTCAGTGGTAGAGCATTTGACTGCAGATCAAGAGGTCACCGGTTCGAACCCGGTT
GGGCCCTGCTTTTACTTAATTTTGCCAAGTCCGTCCAAAACTTCCATAGTTTATACATGTAGTAA
CCAAAGTAAAATTGCTTCTCAATG
Found at i:1742488 original size:20 final size:20
Alignment explanation
Indices: 1742452--1742504 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
1742442 AATGTTATAG
*
1742452 TAAATATCTATTTATTATCA
1 TAAATATATATTTATTATCA
*
1742472 TAAATATAT-TTTAATTATTA
1 TAAATATATATTT-ATTATCA
*
1742492 TTTAATATATATT
1 -TAAATATATATT
1742505 ATAAACTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 3 0.11
20 14 0.52
21 8 0.30
22 2 0.07
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.55
Consensus pattern (20 bp):
TAAATATATATTTATTATCA
Found at i:1746066 original size:8 final size:8
Alignment explanation
Indices: 1746047--1746082 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
1746037 GGACTTAGAG
1746047 TTTTCTTCT
1 TTTTCTT-T
*
1746056 TTTTTTTT
1 TTTTCTTT
1746064 TTTTCTTT
1 TTTTCTTT
1746072 TTTTCTTT
1 TTTTCTTT
1746080 TTT
1 TTT
1746083 GGGGTTGGCG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
8 19 0.76
9 6 0.24
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTTCTTT
Found at i:1746069 original size:14 final size:14
Alignment explanation
Indices: 1746047--1746082 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
1746037 GGACTTAGAG
*
1746047 TTTTCTTCTTTTTT
1 TTTTTTTCTTTTTT
1746061 TTTTTTTCTTTTTT
1 TTTTTTTCTTTTTT
1746075 TCTTTTTT
1 T-TTTTTT
1746083 GGGGTTGGCG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 14 0.70
15 6 0.30
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (14 bp):
TTTTTTTCTTTTTT
Found at i:1746754 original size:18 final size:17
Alignment explanation
Indices: 1746731--1746764 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1746721 AATTTGGTAC
*
1746731 TTTCCTTTTTCTCTTTTT
1 TTTCCTTATTCT-TTTTT
1746749 TTTCCTTATTCTTTTT
1 TTTCCTTATTCTTTTT
1746765 CTTGCTTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTCCTTATTCTTTTTT
Found at i:1749897 original size:22 final size:21
Alignment explanation
Indices: 1749857--1749899 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1749847 TTTTTGGAAA
*
1749857 TTTTTTGAACTTTTAATTAAT
1 TTTTTTGAAATTTTAATTAAT
*
1749878 TTTTTTGAAATTTCTCATTAAT
1 TTTTTTGAAATTT-TAATTAAT
1749900 CTCACAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.28, C:0.07, G:0.05, T:0.60
Consensus pattern (21 bp):
TTTTTTGAAATTTTAATTAAT
Found at i:1750171 original size:14 final size:15
Alignment explanation
Indices: 1750146--1750183 Score: 55
Period size: 13 Copynumber: 2.7 Consensus size: 15
1750136 TGTAAATACG
1750146 TATTATTTTATTTAA
1 TATTATTTTATTTAA
1750161 TATTA-TTTATTT-A
1 TATTATTTTATTTAA
1750174 T-TTATTTTAT
1 TATTATTTTAT
1750184 CTAGCATCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 3 0.14
13 7 0.32
14 7 0.32
15 5 0.23
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TATTATTTTATTTAA
Found at i:1752188 original size:18 final size:17
Alignment explanation
Indices: 1752165--1752203 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
1752155 AACAAGAACC
* *
1752165 ATATATATGATGAAAAAG
1 ATATATATCAT-AAAAAA
1752183 ATATATATCATAAAAAA
1 ATATATATCATAAAAAA
1752200 ATAT
1 ATAT
1752204 TGATAAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.59, C:0.03, G:0.08, T:0.31
Consensus pattern (17 bp):
ATATATATCATAAAAAA
Found at i:1755683 original size:24 final size:25
Alignment explanation
Indices: 1755624--1755685 Score: 74
Period size: 24 Copynumber: 2.5 Consensus size: 25
1755614 ATTTTAAAAA
*
1755624 AATA-TTTTAAAAATTAAAAATCATT
1 AATATTTTTAAAAAATAAAAA-CATT
* *
1755649 AACATTATTAAAAAATAAAAA-ATT
1 AATATTTTTAAAAAATAAAAACATT
1755673 AATATTTTTAAAA
1 AATATTTTTAAAA
1755686 TTTAATTAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
24 14 0.45
25 3 0.10
26 14 0.45
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (25 bp):
AATATTTTTAAAAAATAAAAACATT
Found at i:1758659 original size:19 final size:19
Alignment explanation
Indices: 1758635--1758704 Score: 63
Period size: 19 Copynumber: 3.6 Consensus size: 19
1758625 TAAATATATT
1758635 TATTTTTTAAATTTTAAAA
1 TATTTTTTAAATTTTAAAA
**
1758654 TATTTTTTACATACTTTT-TGA
1 TATTTTTTA-A-A-TTTTAAAA
*
1758675 T-TTTTTTTAATTTTAAAA
1 TATTTTTTAAATTTTAAAA
*
1758693 TATTTTTAAAAT
1 TATTTTTTAAAT
1758705 ACTTTTTTTA
Statistics
Matches: 39, Mismatches: 7, Indels: 10
0.70 0.12 0.18
Matches are distributed among these distances:
17 4 0.10
18 3 0.08
19 18 0.46
20 7 0.18
21 3 0.08
22 4 0.10
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.61
Consensus pattern (19 bp):
TATTTTTTAAATTTTAAAA
Found at i:1758683 original size:40 final size:40
Alignment explanation
Indices: 1758636--1758817 Score: 258
Period size: 40 Copynumber: 4.5 Consensus size: 40
1758626 AAATATATTT
* * * *
1758636 ATTTTTTAAATTTTAAAATATTTTTTACATAC-TTTTTGA
1 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTA
*
1758675 TTTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAA
1 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTT-A
*
1758716 ATTTTTTTAATTTAAAAATATTTTTAAAATACTTTTTTTA
1 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTA
*
1758756 ATTTTTTTAATTTTAAAATATTTCTAAAATACTTTTTTTA
1 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTA
*
1758796 ATTTTTTAAAATTTTTAAAATA
1 ATTTTTT-TAA-TTTTAAAATA
1758818 AAAATGGGCC
Statistics
Matches: 129, Mismatches: 10, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
39 28 0.22
40 51 0.40
41 40 0.31
42 10 0.08
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (40 bp):
ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTA
Found at i:1758751 original size:12 final size:11
Alignment explanation
Indices: 1758685--1758817 Score: 58
Period size: 11 Copynumber: 12.9 Consensus size: 11
1758675 TTTTTTTTAA
1758685 TTTTAAAATAT
1 TTTTAAAATAT
1758696 TTTTAAAATACTT
1 TTTTAAAATA--T
*
1758709 TTTTTAAAT-T
1 TTTTAAAATAT
*
1758719 TTTT----TAA
1 TTTTAAAATAT
*
1758726 TTTAAAAATAT
1 TTTTAAAATAT
1758737 TTTTAAAATACT
1 TTTTAAAATA-T
**
1758749 TTTTTTAAT-T
1 TTTTAAAATAT
*
1758759 TTTT----TAA
1 TTTTAAAATAT
1758766 TTTTAAAATAT
1 TTTTAAAATAT
*
1758777 TTCTAAAATACT
1 TTTTAAAATA-T
**
1758789 TTTTTTAAT-T
1 TTTTAAAATAT
1758799 TTTT-AAA-AT
1 TTTTAAAATAT
1758808 TTTTAAAATA
1 TTTTAAAATA
1758818 AAAATGGGCC
Statistics
Matches: 91, Mismatches: 14, Indels: 34
0.65 0.10 0.24
Matches are distributed among these distances:
6 2 0.02
7 7 0.08
9 7 0.08
10 18 0.20
11 33 0.36
12 15 0.16
13 9 0.10
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:1758795 original size:31 final size:30
Alignment explanation
Indices: 1758757--1758817 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 30
1758747 CTTTTTTTAA
1758757 TTTTTTTAA-TTTTAAAATATTTCTAAAATAC
1 TTTTTTTAATTTTTAAAAT-TTT-TAAAATAC
1758788 TTTTTTTAATTTTTTAAAATTTTTAAAATA
1 TTTTTTTAA-TTTTTAAAATTTTTAAAATA
1758818 AAAATGGGCC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
31 16 0.57
32 3 0.11
33 9 0.32
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (30 bp):
TTTTTTTAATTTTTAAAATTTTTAAAATAC
Found at i:1758809 original size:81 final size:80
Alignment explanation
Indices: 1758636--1758805 Score: 261
Period size: 81 Copynumber: 2.1 Consensus size: 80
1758626 AAATATATTT
* * * * *
1758636 ATTTTTTAAATTTTAAAATATTTTTTACATACTTTTTGATTTTTTTTAATTTTAAAATATTTTTA
1 ATTTTTTAAATTTAAAAATATTTTTAAAATACTTTTTGAATTTTTTTAATTTTAAAATATTTCTA
1758701 AAATACTTTTTTTAA
66 AAATACTTTTTTTAA
* *
1758716 ATTTTTTTAATTTAAAAATATTTTTAAAATACTTTTTTTAATTTTTTTAATTTTAAAATATTTCT
1 ATTTTTTAAATTTAAAAATATTTTTAAAATAC-TTTTTGAATTTTTTTAATTTTAAAATATTTCT
1758781 AAAATACTTTTTTT-A
65 AAAATACTTTTTTTAA
1758796 ATTTTTTAAA
1 ATTTTTTAAA
1758806 ATTTTTAAAA
Statistics
Matches: 81, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
80 38 0.47
81 43 0.53
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.61
Consensus pattern (80 bp):
ATTTTTTAAATTTAAAAATATTTTTAAAATACTTTTTGAATTTTTTTAATTTTAAAATATTTCTA
AAATACTTTTTTTAA
Found at i:1759381 original size:14 final size:15
Alignment explanation
Indices: 1759357--1759386 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1759347 ATTTAGAGTT
1759357 TTTTTAGAATTTTTA
1 TTTTTAGAATTTTTA
1759372 TTTTTA-AATTTTTA
1 TTTTTAGAATTTTTA
1759386 T
1 T
1759387 AATTTAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (15 bp):
TTTTTAGAATTTTTA
Found at i:1759421 original size:19 final size:18
Alignment explanation
Indices: 1759397--1759456 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 18
1759387 AATTTAAAAA
1759397 AAATATTTGAAATTTTTAT
1 AAATATTTG-AATTTTTAT
* *
1759416 AAATATTTGGATTTTTAA
1 AAATATTTGAATTTTTAT
1759434 AAATTATTTTGAATTTTT-T
1 AAA-TA-TTTGAATTTTTAT
1759453 AAAT
1 AAAT
1759457 TTGTTTAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
18 11 0.31
19 14 0.40
20 10 0.29
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (18 bp):
AAATATTTGAATTTTTAT
Found at i:1759457 original size:19 final size:20
Alignment explanation
Indices: 1759402--1759470 Score: 65
Period size: 19 Copynumber: 3.5 Consensus size: 20
1759392 AAAAAAAATA
1759402 TTTGAAATTTTTATAAA-TA-
1 TTTG-AATTTTTATAAATTAT
* *
1759421 TTTGGATTTTTAAAAATTAT
1 TTTGAATTTTTATAAATTAT
1759441 TTTGAATTTTT-TAAATT-T
1 TTTGAATTTTTATAAATTAT
*
1759459 GTTTAAATTTTT
1 -TTTGAATTTTT
1759471 TGTTGATTAG
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
18 11 0.26
19 21 0.50
20 10 0.24
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.59
Consensus pattern (20 bp):
TTTGAATTTTTATAAATTAT
Found at i:1762423 original size:19 final size:19
Alignment explanation
Indices: 1762401--1762444 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
1762391 TTCTAATACT
*
1762401 TTTTTAAATTTTATTA-AAA
1 TTTTCAAATTTT-TTAGAAA
*
1762420 TTTTCATATTTTTTAGAAA
1 TTTTCAAATTTTTTAGAAA
1762439 TTTTCA
1 TTTTCA
1762445 TTTTTAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (19 bp):
TTTTCAAATTTTTTAGAAA
Found at i:1762445 original size:19 final size:19
Alignment explanation
Indices: 1762408--1762450 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
1762398 ACTTTTTTAA
1762408 ATTTTATTAAAATTTTCAT
1 ATTTTATTAAAATTTTCAT
1762427 ATTTT-TTAGAAATTTTCAT
1 ATTTTATTA-AAATTTTCAT
1762446 -TTTTA
1 ATTTTA
1762451 AAATTTTATG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (19 bp):
ATTTTATTAAAATTTTCAT
Found at i:1762464 original size:16 final size:16
Alignment explanation
Indices: 1762408--1762473 Score: 64
Period size: 16 Copynumber: 3.9 Consensus size: 16
1762398 ACTTTTTTAA
1762408 ATTTTATTAAAATTTTC
1 ATTTT-TTAAAATTTTC
1762425 ATATTTTTTAGAAATTTTC
1 --ATTTTTTA-AAATTTTC
1762444 A-TTTTTAAAATTTT-
1 ATTTTTTAAAATTTTC
*
1762458 ATGTTTTTATAATTTT
1 AT-TTTTTAAAATTTT
1762474 TAATTAATTT
Statistics
Matches: 43, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
14 1 0.02
15 7 0.16
16 18 0.42
17 1 0.02
18 3 0.07
19 13 0.30
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (16 bp):
ATTTTTTAAAATTTTC
Found at i:1762799 original size:14 final size:15
Alignment explanation
Indices: 1762780--1762808 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1762770 TTTAAAAATT
1762780 TTAAAAAAT-ATAGC
1 TTAAAAAATAATAGC
1762794 TTAAAAAATAATAGC
1 TTAAAAAATAATAGC
1762809 ATGTGGCCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.59, C:0.07, G:0.07, T:0.28
Consensus pattern (15 bp):
TTAAAAAATAATAGC
Found at i:1787036 original size:22 final size:22
Alignment explanation
Indices: 1787011--1787061 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
1787001 AAATTAAATT
*
1787011 ATATATTTTTACTATTGTAAAA
1 ATATATTTTCACTATTGTAAAA
* * *
1787033 ATATAATTTCATTATTTTAAAA
1 ATATATTTTCACTATTGTAAAA
1787055 ATATATT
1 ATATATT
1787062 AATTTTTAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (22 bp):
ATATATTTTCACTATTGTAAAA
Found at i:1790679 original size:12 final size:12
Alignment explanation
Indices: 1790632--1790680 Score: 57
Period size: 11 Copynumber: 4.2 Consensus size: 12
1790622 TCATTTAATA
1790632 TTAAAAA-ATTT
1 TTAAAAATATTT
*
1790643 TAAAAAATATTT
1 TTAAAAATATTT
* *
1790655 TT-ATAATCTTT
1 TTAAAAATATTT
1790666 TTAAAAATATTT
1 TTAAAAATATTT
1790678 TTA
1 TTA
1790681 CCAATAATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
11 15 0.50
12 15 0.50
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (12 bp):
TTAAAAATATTT
Found at i:1790691 original size:24 final size:23
Alignment explanation
Indices: 1790638--1790693 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
1790628 AATATTAAAA
*
1790638 AATTTTAAAAAATATTTTTATAAT
1 AATTTT-AAAAATATTTTTACAAT
**
1790662 CTTTTTAAAAATATTTTTACCAAT
1 AATTTTAAAAATATTTTTA-CAAT
1790686 AATTTTAA
1 AATTTTAA
1790694 TATAAAAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
23 13 0.50
24 13 0.50
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (23 bp):
AATTTTAAAAATATTTTTACAAT
Found at i:1793630 original size:22 final size:22
Alignment explanation
Indices: 1793605--1793649 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
1793595 TCTACCATTG
1793605 TCCTTCAGATCTCAAAACTTGC
1 TCCTTCAGATCTCAAAACTTGC
1793627 TCCTTCAGATCTCAAAACTTGC
1 TCCTTCAGATCTCAAAACTTGC
1793649 T
1 T
1793650 GGACCCTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.31, G:0.09, T:0.33
Consensus pattern (22 bp):
TCCTTCAGATCTCAAAACTTGC
Found at i:1801626 original size:19 final size:19
Alignment explanation
Indices: 1801602--1801638 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
1801592 TTATGTGTTC
1801602 ATCGTTGAGGTTGAAAATT
1 ATCGTTGAGGTTGAAAATT
1801621 ATCGTTGAGGTTGAAAAT
1 ATCGTTGAGGTTGAAAAT
1801639 CAGTTTTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.05, G:0.27, T:0.35
Consensus pattern (19 bp):
ATCGTTGAGGTTGAAAATT
Found at i:1812361 original size:114 final size:114
Alignment explanation
Indices: 1812161--1812384 Score: 412
Period size: 114 Copynumber: 2.0 Consensus size: 114
1812151 AAGACAACAA
* *
1812161 GGCCAAAAAGAGCAAGGCATAAAGACTCAAGCTGCTCGAGGTGGTGTAATGGAAACAAAACCGTT
1 GGCCAAAAAGAACAAGGCATAAAGACTCAAGCTGCTCGAGGTGGTGTAATGGAAACAAAACCATT
1812226 GAACATGTCTTGTTATTTTGTCCATTTGCAAGTGTAGTGTGGGAGACAT
66 GAACATGTCTTGTTATTTTGTCCATTTGCAAGTGTAGTGTGGGAGACAT
*
1812275 GGCCAAAAAGAACAAGGCATAAAGACTCAAGGTGCTCGAGGTGGTGTAATGGAAACAAAACCATT
1 GGCCAAAAAGAACAAGGCATAAAGACTCAAGCTGCTCGAGGTGGTGTAATGGAAACAAAACCATT
*
1812340 GAACATGTCTTGTTCTTTTGTCCATTTGCAAGTGTAGTGTGGGAG
66 GAACATGTCTTGTTATTTTGTCCATTTGCAAGTGTAGTGTGGGAG
1812385 GCTTGTAGTC
Statistics
Matches: 106, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
114 106 1.00
ACGTcount: A:0.32, C:0.16, G:0.27, T:0.25
Consensus pattern (114 bp):
GGCCAAAAAGAACAAGGCATAAAGACTCAAGCTGCTCGAGGTGGTGTAATGGAAACAAAACCATT
GAACATGTCTTGTTATTTTGTCCATTTGCAAGTGTAGTGTGGGAGACAT
Found at i:1814414 original size:3 final size:3
Alignment explanation
Indices: 1814406--1814454 Score: 57
Period size: 3 Copynumber: 16.3 Consensus size: 3
1814396 ATGAAAACCC
*
1814406 TAA TAA TAA -AA TTAA TTAA TGA TAA TAA TAA TAA TAA TAA TAA T-A
1 TAA TAA TAA TAA -TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1814451 TAA T
1 TAA T
1814455 TACCAAATAA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 4 0.10
3 31 0.76
4 6 0.15
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:1817305 original size:17 final size:16
Alignment explanation
Indices: 1817261--1817307 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 16
1817251 AAAAAAACTA
1817261 AAATATATATATTTTT
1 AAATATATATATTTTT
*
1817277 AAAT-TCTCATATGTTTT
1 AAATATAT-ATAT-TTTT
1817294 AAATATATATATTT
1 AAATATATATATTT
1817308 AACTACTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 2 0.08
16 10 0.38
17 12 0.46
18 2 0.08
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.53
Consensus pattern (16 bp):
AAATATATATATTTTT
Found at i:1822475 original size:31 final size:29
Alignment explanation
Indices: 1822434--1822509 Score: 73
Period size: 29 Copynumber: 2.5 Consensus size: 29
1822424 CCCTTGAAAC
**
1822434 TTTTAGAAAATTTTAACTAAGCTCTCTTA-AA
1 TTTTA-AAAATTTTAACTAA--TCTCACAGAA
* *
1822465 TTTTTAAAAATTATCACTAATCTCACAGAA
1 -TTTTAAAAATTTTAACTAATCTCACAGAA
1822495 TTTTAAAAATTTTAA
1 TTTTAAAAATTTTAA
1822510 TTAGACCCCA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
29 18 0.49
30 2 0.05
31 12 0.32
32 5 0.14
ACGTcount: A:0.42, C:0.12, G:0.04, T:0.42
Consensus pattern (29 bp):
TTTTAAAAATTTTAACTAATCTCACAGAA
Found at i:1824072 original size:29 final size:29
Alignment explanation
Indices: 1824005--1824073 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 29
1823995 ATGGGTACAT
**
1824005 GTCGTTTTCTTTCTAATATTTATGATTTAA
1 GTCGTTTT-TTTCTAATATTTATGAAATAA
1824035 G-CGTCTTTTTTCTAATATTTATGAGAATAA
1 GTCGT-TTTTTTCTAATATTTATGA-AATAA
1824065 GTCGTTTTT
1 GTCGTTTTT
1824074 CGAGAGATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
29 19 0.56
30 12 0.35
31 3 0.09
ACGTcount: A:0.23, C:0.10, G:0.13, T:0.54
Consensus pattern (29 bp):
GTCGTTTTTTTCTAATATTTATGAAATAA
Found at i:1825284 original size:21 final size:21
Alignment explanation
Indices: 1825256--1825297 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
1825246 GGCAAAAATT
1825256 ATAATATA-TATTTGTTATAA
1 ATAATATATTATTTGTTATAA
*
1825276 ATAAGTATATTATTTTTTATAA
1 ATAA-TATATTATTTGTTATAA
1825298 TATATAGCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 4 0.21
22 11 0.58
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (21 bp):
ATAATATATTATTTGTTATAA
Found at i:1825497 original size:3 final size:3
Alignment explanation
Indices: 1825489--1825523 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1825479 AGTTTTGGGT
1825489 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1825524 ATCTAATTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:1828117 original size:24 final size:24
Alignment explanation
Indices: 1828089--1828140 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
1828079 TTAGTAGGTC
* *
1828089 AAATAAACTATGCTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
1828113 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
1828137 AAAT
1 AAAT
1828141 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:1828671 original size:13 final size:13
Alignment explanation
Indices: 1828653--1828678 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1828643 TAAATAAACC
1828653 ATTAATAGAATCA
1 ATTAATAGAATCA
1828666 ATTAATAGAATCA
1 ATTAATAGAATCA
1828679 GACACTGCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.31
Consensus pattern (13 bp):
ATTAATAGAATCA
Found at i:1840776 original size:6 final size:6
Alignment explanation
Indices: 1840767--1840801 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
1840757 GTGGCTGTGG
* *
1840767 CGGTCA CGGTCA CGGTTA CGGTTA CGGTTA CGGTT
1 CGGTTA CGGTTA CGGTTA CGGTTA CGGTTA CGGTT
1840802 CGCACTTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.14, C:0.23, G:0.34, T:0.29
Consensus pattern (6 bp):
CGGTTA
Found at i:1841510 original size:13 final size:13
Alignment explanation
Indices: 1841492--1841517 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1841482 CTCGTCTCAA
1841492 ATTTTATTTTATT
1 ATTTTATTTTATT
1841505 ATTTTATTTTATT
1 ATTTTATTTTATT
1841518 TTGAAATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
ATTTTATTTTATT
Found at i:1844574 original size:11 final size:11
Alignment explanation
Indices: 1844558--1844585 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
1844548 AGTTCTCCAT
1844558 GACCCGCGCGC
1 GACCCGCGCGC
1844569 GACCCGCGCGC
1 GACCCGCGCGC
1844580 GACCCG
1 GACCCG
1844586 ATCCGCTCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.11, C:0.54, G:0.36, T:0.00
Consensus pattern (11 bp):
GACCCGCGCGC
Found at i:1845267 original size:16 final size:16
Alignment explanation
Indices: 1845246--1845278 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1845236 TTTAATTTAT
1845246 TTATTTATATAT-ATTG
1 TTATTT-TATATGATTG
1845262 TTATTTTATATGATTG
1 TTATTTTATATGATTG
1845278 T
1 T
1845279 AGGTATGACT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.27, C:0.00, G:0.09, T:0.64
Consensus pattern (16 bp):
TTATTTTATATGATTG
Found at i:1857454 original size:44 final size:44
Alignment explanation
Indices: 1857344--1857546 Score: 154
Period size: 46 Copynumber: 4.7 Consensus size: 44
1857334 ATTATACAGG
* * ** *
1857344 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGA-ATTTCAGA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTAAAGACA---GAGA
* * *
1857390 TCTTATCTCCCTGAGGTTACAGCGGAGCAGATTGAAGCCAGAGA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTAAAGACAGAGA
* *
1857434 TCTTATCTCCCTGAGATTACAGC-GAGCAGA-TCAAGACATA-A
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTAAAGACAGAGA
* * * *
1857475 TCCTATCT-CCTGA-ATTACAGTGGAGCGGATTAAA-ATA-AGGA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTAAAGACAGA-GA
* * *
1857516 TCTTATCTCTCTGAG-TTACAGCAGAGTAGAT
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGAT
1857547 CGCATCAGTC
Statistics
Matches: 127, Mismatches: 23, Indels: 18
0.76 0.14 0.11
Matches are distributed among these distances:
39 8 0.06
40 13 0.10
41 19 0.15
42 23 0.18
43 7 0.06
44 25 0.20
46 31 0.24
47 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.27
Consensus pattern (44 bp):
TCTTATCTCCCTGAGATTACAGCGGAGCAGATTAAAGACAGAGA
Found at i:1857921 original size:86 final size:86
Alignment explanation
Indices: 1857825--1858107 Score: 259
Period size: 86 Copynumber: 3.3 Consensus size: 86
1857815 TTAAAATAAG
* * * * * * *
1857825 GATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCACCAGGTCTTATCTCCTTGAGATATAGT
1 GATCTTATCTCCCTGAAGTTACAGCAGAGTAGATCGCAACAAGTCTTATCTCCCTGAGTTACAGT
1857890 GGAGCAGACCGAAGAATTTCA
66 GGAGCAGACCGAAGAATTTCA
* * * * * *
1857911 GATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGACATAATCCTATCTCCCTGAAGTTAC
1 GATCTTATCTCCCTGAAGTTACAGCAGAGTAGATCGCA-ACA-AGTCTTATCTCCCTG-AGTTAC
** * **
1857976 AGTGGAGC-G---GATTAAATAAA
63 AGTGGAGCAGACCGAAGAATTTCA
* ** *
1857996 GGATCTTATCTCTCTGAAGTTACAGCAGAGTAGATCGCGTCAAGTCTTATTTCCCTGAGGTTACA
1 -GATCTTATCTCCCTGAAGTTACAGCAGAGTAGATCGCAACAAGTCTTATCTCCCTGA-GTTACA
*
1858061 GTGGAACAGACCGAAGAATTTCA
64 GTGGAGCAGACCGAAGAATTTCA
* **
1858084 GATCTTACCTCCCTGTGGTTACAG
1 GATCTTATCTCCCTGAAGTTACAG
1858108 TGGAGTACAT
Statistics
Matches: 150, Mismatches: 38, Indels: 17
0.73 0.19 0.08
Matches are distributed among these distances:
83 1 0.01
84 24 0.16
85 9 0.06
86 64 0.43
87 22 0.15
88 18 0.12
89 12 0.08
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (86 bp):
GATCTTATCTCCCTGAAGTTACAGCAGAGTAGATCGCAACAAGTCTTATCTCCCTGAGTTACAGT
GGAGCAGACCGAAGAATTTCA
Found at i:1857949 original size:46 final size:45
Alignment explanation
Indices: 1857868--1858112 Score: 163
Period size: 43 Copynumber: 5.6 Consensus size: 45
1857858 TCGCACCAGG
* * * *
1857868 TCTTATCTCCTTGA-GATATAGTGGAGCAGACCGAAGAATTTCAGA
1 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATCGAAGAA-TTCAGA
*
1857913 TCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGACA-T-A-A
1 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATCGAAGA-ATTCAGA
* * * * **
1857956 TCCTATCTCCCTGAAGTTACAGTGGAGCGGAT--TA-AATAAAGGA
1 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATCGAAGAATTCA-GA
* * ** * *
1857999 TCTTATCTCTCTGAAGTTACAGCAGAGTAGATCG-CG---TCA-A
1 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATCGAAGAATTCAGA
* * *
1858039 GTCTTATTTCCCTGAGGTTACAGTGGAACAGACCGAAGAATTTCAGA
1 -TCTTATCTCCCTGAGGTTACAGTGGAGCAGATCGAAGAA-TTCAGA
* *
1858086 TCTTACCTCCCTGTGGTTACAGTGGAG
1 TCTTATCTCCCTGAGGTTACAGTGGAG
1858113 TACATTGAAG
Statistics
Matches: 151, Mismatches: 33, Indels: 31
0.70 0.15 0.14
Matches are distributed among these distances:
39 1 0.01
40 2 0.01
41 28 0.19
42 2 0.01
43 56 0.37
44 1 0.01
45 14 0.09
46 45 0.30
47 2 0.01
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.28
Consensus pattern (45 bp):
TCTTATCTCCCTGAGGTTACAGTGGAGCAGATCGAAGAATTCAGA
Found at i:1858006 original size:43 final size:42
Alignment explanation
Indices: 1857787--1858020 Score: 150
Period size: 43 Copynumber: 5.5 Consensus size: 42
1857777 ATATGAGTCC
* * *
1857787 TATCTCCCTGAAGTTATAGTGGAGCGGATTAAAATAAGGATCT
1 TATCTCCCTGAAGTTACAGTGGAGCGGATCAAAA-CAGGATCT
* * ** ** *
1857830 TATCTCTCTGAAGTTACAGTAGAGTAGATCGCACCAGG-TCT
1 TATCTCCCTGAAGTTACAGTGGAGCGGATCAAAACAGGATCT
* * * * *
1857871 TATCTCCTTG-AGATATAGTGGAGCAGACCGAAGAATTTCA-GATCT
1 TATCTCCCTGAAGTTACAGTGGAGCGGATC-AA-AA---CAGGATCT
* * * * ** *
1857916 TATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGACATAATCC
1 TATCTCCCTGAAGTTACAGTGGAGCGGATC-AAAACAGGATCT
* *
1857959 TATCTCCCTGAAGTTACAGTGGAGCGGATTAAATAAAGGATCT
1 TATCTCCCTGAAGTTACAGTGGAGCGGATCAAA-ACAGGATCT
*
1858002 TATCTCTCTGAAGTTACAG
1 TATCTCCCTGAAGTTACAG
1858021 CAGAGTAGAT
Statistics
Matches: 143, Mismatches: 39, Indels: 18
0.71 0.19 0.09
Matches are distributed among these distances:
40 14 0.10
41 11 0.08
42 8 0.06
43 77 0.54
44 1 0.01
45 15 0.10
46 17 0.12
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.28
Consensus pattern (42 bp):
TATCTCCCTGAAGTTACAGTGGAGCGGATCAAAACAGGATCT
Found at i:1859644 original size:3 final size:3
Alignment explanation
Indices: 1859636--1859671 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
1859626 GATTTAGTCC
1859636 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1859672 CTACTTATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1861416 original size:304 final size:305
Alignment explanation
Indices: 1860857--1861467 Score: 1066
Period size: 305 Copynumber: 2.0 Consensus size: 305
1860847 GGTGTCAACA
* *
1860857 ATGAGCATATGTTGTTTTCTACCGTAACTCGGCAGTCTTCGGATGCCGATTTCAGGTATATTCGA
1 ATGAGCATATGTTGTTTTCTACCGTAACTCGGCAATCTTCGGATGCCGATTTCAGGTATATTCAA
* *
1860922 GCTCCATTTTCATTTAAAATTTCATTTTTATTTTGATGATTTTTTTTTTGTGATCAAGATCTTAT
66 GCTCCATTTTCATTGAAAATTTCATTTTTATTTTGATGA-GTTTTTTTTGTGATCAAGATCTTAT
1860987 TGAATTTCATCACGGTTTGGTTTAGTAATAGGATTGTGCTATCTGGTTGCTAGCGATTTAATTTT
130 TGAATTTCATCACGGTTTGGTTTAGTAATAGGATTGTGCTATCTGGTTGCTAGCGATTTAATTTT
* *
1861052 GTTTGTTTGTTTGTTTTTATGAGAACGTTGTTTGAAGTTTGTGATCTTTCATTGAG-AAAAAAAA
195 GTTTGTTTATTTATTTTTATGAGAACGTTGTTTGAAGTTTGTGATCTTTCATTGAGAAAAAAAAA
* * *
1861116 GTTTCATGGAACCTGGTGTGATATTTGTCCAAATTGAGTGGAAAAT
260 GTTTCATGGAACCCGGTATGATATTTGTCCAAATTGAGCGGAAAAT
1861162 ATGAGCATATGTTGTTTTCTACCGTAACTCGGCAATCTTCGGATGCCGATTTCAGGTATATTCAA
1 ATGAGCATATGTTGTTTTCTACCGTAACTCGGCAATCTTCGGATGCCGATTTCAGGTATATTCAA
* *
1861227 GCTTCATTTTCATTGAAATTTTCATTTTTATTTTGATG-GTTTTTTTTGTGATCAAGATCTTATT
66 GCTCCATTTTCATTGAAAATTTCATTTTTATTTTGATGAGTTTTTTTTGTGATCAAGATCTTATT
1861291 GAATTTCATCACGGTTTGG-TTAGTAATCGAGGATTGTGCTATCTGGTTGCTAGCGATTTAATTT
131 GAATTTCATCACGGTTTGGTTTAGTAAT--AGGATTGTGCTATCTGGTTGCTAGCGATTTAATTT
*
1861355 TGTTTGTTTATTTATTTTTATGAGAACGTTGTTTGAAGTTTGTGATCTTTCGTTGAGAAAAAAAA
194 TGTTTGTTTATTTATTTTTATGAGAACGTTGTTTGAAGTTTGTGATCTTTCATTGAGAAAAAAAA
1861420 AGTTTCATGGAACCCGGTATGATATTTGTCCAAATTGAGCGGAAAAT
259 AGTTTCATGGAACCCGGTATGATATTTGTCCAAATTGAGCGGAAAAT
1861467 A
1 A
1861468 GTGATAATAA
Statistics
Matches: 291, Mismatches: 12, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
302 8 0.03
303 44 0.15
304 89 0.31
305 150 0.52
ACGTcount: A:0.25, C:0.12, G:0.20, T:0.44
Consensus pattern (305 bp):
ATGAGCATATGTTGTTTTCTACCGTAACTCGGCAATCTTCGGATGCCGATTTCAGGTATATTCAA
GCTCCATTTTCATTGAAAATTTCATTTTTATTTTGATGAGTTTTTTTTGTGATCAAGATCTTATT
GAATTTCATCACGGTTTGGTTTAGTAATAGGATTGTGCTATCTGGTTGCTAGCGATTTAATTTTG
TTTGTTTATTTATTTTTATGAGAACGTTGTTTGAAGTTTGTGATCTTTCATTGAGAAAAAAAAAG
TTTCATGGAACCCGGTATGATATTTGTCCAAATTGAGCGGAAAAT
Found at i:1873249 original size:2 final size:2
Alignment explanation
Indices: 1873242--1873272 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1873232 ACCTATACTA
1873242 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1873273 AAGCTTTGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1876684 original size:88 final size:88
Alignment explanation
Indices: 1876535--1876711 Score: 345
Period size: 88 Copynumber: 2.0 Consensus size: 88
1876525 TTGTATTGTT
1876535 AAAATTTGACAAGGTTGATGGAATAACTAGACAGTGAAATGTGGCGTGTCATGAGTAACTCATAT
1 AAAATTTGACAAGGTTGATGGAATAACTAGACAGTGAAATGTGGCGTGTCATGAGTAACTCATAT
1876600 TGATTTACAGGAATCAATTTTTA
66 TGATTTACAGGAATCAATTTTTA
1876623 AAAATTTGACAAGGTTGATGGAATAACTAGACAGTGAAATGTGGCGTGTCATGAGTAACTCATAT
1 AAAATTTGACAAGGTTGATGGAATAACTAGACAGTGAAATGTGGCGTGTCATGAGTAACTCATAT
*
1876688 TGATTTACAGGAATCGATTTTTA
66 TGATTTACAGGAATCAATTTTTA
1876711 A
1 A
1876712 CAGAAAGACC
Statistics
Matches: 88, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
88 88 1.00
ACGTcount: A:0.36, C:0.10, G:0.22, T:0.32
Consensus pattern (88 bp):
AAAATTTGACAAGGTTGATGGAATAACTAGACAGTGAAATGTGGCGTGTCATGAGTAACTCATAT
TGATTTACAGGAATCAATTTTTA
Found at i:1878145 original size:34 final size:34
Alignment explanation
Indices: 1878107--1878172 Score: 82
Period size: 34 Copynumber: 1.9 Consensus size: 34
1878097 TATATATAAT
*
1878107 ATATAAATTAATAAAA-AA-TAAAAATTTACAAAAA
1 ATATAAA-T-ATAAAAGAATTAAAAAATTACAAAAA
*
1878141 ATATATATATAAAAGAATTAAAAAATTACAAA
1 ATATAAATATAAAAGAATTAAAAAATTACAAA
1878173 TTTATAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
32 6 0.21
33 3 0.11
34 19 0.68
ACGTcount: A:0.68, C:0.03, G:0.02, T:0.27
Consensus pattern (34 bp):
ATATAAATATAAAAGAATTAAAAAATTACAAAAA
Found at i:1878151 original size:42 final size:42
Alignment explanation
Indices: 1878100--1878189 Score: 112
Period size: 42 Copynumber: 2.2 Consensus size: 42
1878090 ATTGTTTTAT
**
1878100 ATATAATATATAAATTAA-TAAAAAA-TAAAAATTTACAAAAA
1 ATAT-ATATATAAAAGAATTAAAAAATTAAAAATTTACAAAAA
* *
1878141 ATATATATATAAAAGAATTAAAAAATTACAAATTTATAAAAA
1 ATATATATATAAAAGAATTAAAAAATTAAAAATTTACAAAAA
*
1878183 AAATATA
1 ATATATA
1878190 AACAATAATT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
40 11 0.26
41 11 0.26
42 20 0.48
ACGTcount: A:0.67, C:0.02, G:0.01, T:0.30
Consensus pattern (42 bp):
ATATATATATAAAAGAATTAAAAAATTAAAAATTTACAAAAA
Found at i:1885698 original size:306 final size:308
Alignment explanation
Indices: 1885080--1885704 Score: 1085
Period size: 306 Copynumber: 2.0 Consensus size: 308
1885070 CCATTTTCCG
*
1885080 CTCAATTTGGACAAATATCACACCGGATTCCATGAAACTTTTTTTTCTCAATGAAAGATCACAAA
1 CTCAATTTGGACAAATATCACACCGGATTCCATGAAACTTTTTTTTATCAATGAAAGATCACAAA
* * *
1885145 CTTCAAACAACGTACTCATAAAAATAAATAAACAAACAAAATTAAATCGCTAGCTACCAGATAGC
66 CTTCAAACAACGTACTCATAAAAACAAACAAACAAACAAAATTAAATCGCTAGCAACCAGATAGC
1885210 ACAATCCTCGATTACTAAACCAAACCGTGATGAAATTCAATAAGATCTTGATCACAAAAAAAAAA
131 ACAATCCTCGATTACTAAACCAAACCGTGATGAAATTCAATAAGATCTTGATCAC-AAAAAAAAA
* *
1885275 AATCATCAAACTAAAAATGAAAATTTCAATGAAAATGGAGCTTGAATATACCTGAAATCGGCATC
195 AATCATCAAAATAAAAATGAAAATTTCAATGAAAATGGAGCTCGAATATACCTGAAATCGGCATC
* *
1885340 CGAAGATTGCCGAGTTACGGTAGAAAACAACATATGCTCATATTTTCCA
260 CGAAGATTGCCGAGTTACGGTAGAAAACAACACATGCTCATATTTGCCA
*
1885389 CTCAATTTGGACAAATATCACTCCAGG-TTCCATGAAACTTTTTTTTATCAATGAAAGATCACAA
1 CTCAATTTGGACAAATATCACACC-GGATTCCATGAAACTTTTTTTTATCAATGAAAGATCACAA
* * *
1885453 ACTTGAAACAAC-TTCTCATAAAAACAAGCAAACAAACAAAATTAAATCGCTAGCAACCAGATAG
65 ACTTCAAACAACGTACTCATAAAAACAAACAAACAAACAAAATTAAATCGCTAGCAACCAGATAG
*
1885517 CACAATCCTCGATTACTAAACCAACCCGTGATGAAATTCAATAAGATCTTGATCAC-AAAAAAAA
130 CACAATCCTCGATTACTAAACCAAACCGTGATGAAATTCAATAAGATCTTGATCACAAAAAAAAA
1885581 AATCATCAAAATAAAAATGAAAATTTCAATGAAAATGGAGCTCGAATATACCTGAAATCGGCATC
195 AATCATCAAAATAAAAATGAAAATTTCAATGAAAATGGAGCTCGAATATACCTGAAATCGGCATC
1885646 CGAAGATTGCCGAGTTACGGTAGAAAACAACACATGCTCATATTTGCCA
260 CGAAGATTGCCGAGTTACGGTAGAAAACAACACATGCTCATATTTGCCA
1885695 CTCAAATTTG
1 CTC-AATTTG
1885705 TTTTCAAAAG
Statistics
Matches: 301, Mismatches: 13, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
306 121 0.40
307 6 0.02
308 102 0.34
309 70 0.23
310 2 0.01
ACGTcount: A:0.44, C:0.20, G:0.12, T:0.24
Consensus pattern (308 bp):
CTCAATTTGGACAAATATCACACCGGATTCCATGAAACTTTTTTTTATCAATGAAAGATCACAAA
CTTCAAACAACGTACTCATAAAAACAAACAAACAAACAAAATTAAATCGCTAGCAACCAGATAGC
ACAATCCTCGATTACTAAACCAAACCGTGATGAAATTCAATAAGATCTTGATCACAAAAAAAAAA
ATCATCAAAATAAAAATGAAAATTTCAATGAAAATGGAGCTCGAATATACCTGAAATCGGCATCC
GAAGATTGCCGAGTTACGGTAGAAAACAACACATGCTCATATTTGCCA
Found at i:1891570 original size:17 final size:18
Alignment explanation
Indices: 1891548--1891589 Score: 50
Period size: 20 Copynumber: 2.3 Consensus size: 18
1891538 ATGATAAGGG
1891548 TTCATACATA-TTTGACT
1 TTCATACATATTTTGACT
*
1891565 TTCATATATATATTTTGACT
1 TTC--ATACATATTTTGACT
1891585 TTCAT
1 TTCAT
1891590 TTTCCTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
17 3 0.14
18 2 0.10
19 6 0.29
20 10 0.48
ACGTcount: A:0.29, C:0.14, G:0.05, T:0.52
Consensus pattern (18 bp):
TTCATACATATTTTGACT
Found at i:1900827 original size:40 final size:40
Alignment explanation
Indices: 1900772--1900854 Score: 166
Period size: 40 Copynumber: 2.1 Consensus size: 40
1900762 AATTTACTCC
1900772 AAATGGTGTGAAGTTCCATTCTGGTTTACAAAATAATTGT
1 AAATGGTGTGAAGTTCCATTCTGGTTTACAAAATAATTGT
1900812 AAATGGTGTGAAGTTCCATTCTGGTTTACAAAATAATTGT
1 AAATGGTGTGAAGTTCCATTCTGGTTTACAAAATAATTGT
1900852 AAA
1 AAA
1900855 GCCAGATCAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.36
Consensus pattern (40 bp):
AAATGGTGTGAAGTTCCATTCTGGTTTACAAAATAATTGT
Found at i:1913727 original size:87 final size:91
Alignment explanation
Indices: 1913479--1913733 Score: 455
Period size: 91 Copynumber: 2.8 Consensus size: 91
1913469 TTAAATGTAC
1913479 AAATTATATATCATTATTAAATTATATTTAATATTAATTATTTTAAATTATATAAATTCATATAA
1 AAATTATATATCATTATTAAATTATATTTAATATTAATTATTTTAAATTATATAAATTCATATAA
1913544 GAAAATTTATTATCAAGAATTTTATG
66 GAAAATTTATTATCAAGAATTTTATG
1913570 AAATTATATATCATTATTAAATTATATTTAATATTAATTATTTTAAATTATATAAATTCATATAA
1 AAATTATATATCATTATTAAATTATATTTAATATTAATTATTTTAAATTATATAAATTCATATAA
*
1913635 TAAAATTT-TTATCAAGAATTTTATG
66 GAAAATTTATTATCAAGAATTTTATG
* *
1913660 AAA-T-TATAT-ATTATTAAATTATATTTAATAATAATTATTTTAAAATATATAAATTCATATAA
1 AAATTATATATCATTATTAAATTATATTTAATATTAATTATTTTAAATTATATAAATTCATATAA
1913722 GAAAATTTATTA
66 GAAAATTTATTA
1913734 GGTATAATTA
Statistics
Matches: 159, Mismatches: 4, Indels: 5
0.95 0.02 0.03
Matches are distributed among these distances:
87 58 0.36
88 8 0.05
89 1 0.01
90 20 0.13
91 72 0.45
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.47
Consensus pattern (91 bp):
AAATTATATATCATTATTAAATTATATTTAATATTAATTATTTTAAATTATATAAATTCATATAA
GAAAATTTATTATCAAGAATTTTATG
Found at i:1913813 original size:59 final size:58
Alignment explanation
Indices: 1913750--1913928 Score: 152
Period size: 59 Copynumber: 3.0 Consensus size: 58
1913740 ATTATTTTAA
1913750 ATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTAT
1 ATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTATTT-AAATTAT
* * * ** *
1913809 ATTTTA-TAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTAATTA-TT-AA-GA
1 ATTTTATTA-AATCATATATT-TTA-ATTA--AAA-T-ATAT-TTAATATTAATTATTTAAATTA
1913870 -
58 T
* * *
1913870 ATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTAT
1 ATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTAAATTAT
1913929 CTATATTATG
Statistics
Matches: 91, Mismatches: 15, Indels: 28
0.68 0.11 0.21
Matches are distributed among these distances:
54 10 0.11
55 4 0.04
56 3 0.03
57 4 0.04
58 3 0.03
59 19 0.21
60 4 0.04
61 18 0.20
62 3 0.03
63 5 0.05
64 1 0.01
65 6 0.07
66 11 0.12
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.51
Consensus pattern (58 bp):
ATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTATTTAAATTAT
Found at i:1913866 original size:37 final size:35
Alignment explanation
Indices: 1913825--1913994 Score: 109
Period size: 38 Copynumber: 4.7 Consensus size: 35
1913815 TAGTATCATA
1913825 TATTATGATTTTAGTAAATTCATATAAGAATATTAAT
1 TATTATGATTTTAGTAAATT-ATATAA-AATATTAAT
* * *
1913862 TATTAAGAATTTTATTAAATTATAT---ATTTTAAT
1 TATTATG-ATTTTAGTAAATTATATAAAATATTAAT
* * * *
1913895 TATAAT-ATATTTAATAATAATTATGTTAAATTATCT-A-
1 TATTATGAT-TTTAGT-A-AATTAT-ATAAAATAT-TAAT
*
1913932 TATTATGATTTGAGTAAATTCATATAAGAATATTAAT
1 TATTATGATTTTAGTAAATT-ATATAA-AATATTAAT
* *
1913969 TATTAATAATTTTATTAAATTATATA
1 TATT-ATGATTTTAGTAAATTATATA
1913995 TTTTAATTAT
Statistics
Matches: 101, Mismatches: 17, Indels: 30
0.68 0.11 0.20
Matches are distributed among these distances:
31 2 0.02
32 5 0.05
33 12 0.12
34 6 0.06
35 9 0.09
36 8 0.08
37 28 0.28
38 30 0.30
39 1 0.01
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (35 bp):
TATTATGATTTTAGTAAATTATATAAAATATTAAT
Found at i:1913904 original size:16 final size:16
Alignment explanation
Indices: 1913883--1913928 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
1913873 TTATTAAATT
1913883 ATATATTTTAATTATA
1 ATATATTTTAATTATA
*
1913899 ATATA-TTTAATAATA
1 ATATATTTTAATTATA
*
1913914 AT-TATGTTAAATTAT
1 ATATAT-TTTAATTAT
1913929 CTATATTATG
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
14 2 0.08
15 11 0.44
16 12 0.48
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATTATA
Found at i:1913935 original size:107 final size:109
Alignment explanation
Indices: 1913818--1914033 Score: 400
Period size: 107 Copynumber: 2.0 Consensus size: 109
1913808 TATTTTATAG
*
1913818 TATCATATATTATGATTTTAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
1 TATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
1913883 ATATATTTTAATTATAATATATTTAATAATAATTATG-TTAAAT
66 ATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAAT
*
1913926 TATC-TATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAATAATTTTATTAAATT
1 TATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
1913990 ATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAAT
66 ATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAAT
1914034 ATGATTAAAT
Statistics
Matches: 105, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
107 95 0.90
108 10 0.10
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.50
Consensus pattern (109 bp):
TATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
ATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAAT
Found at i:1914010 original size:18 final size:18
Alignment explanation
Indices: 1913964--1914011 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
1913954 TATAAGAATA
*
1913964 TTAATTATTA-ATA-ATT
1 TTAATTATAATATATATT
1913980 TT-ATTA-AATTATATATT
1 TTAATTATAA-TATATATT
1913997 TTAATTATAATATAT
1 TTAATTATAATATAT
1914012 TTAATAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
14 1 0.04
15 4 0.15
16 5 0.19
17 5 0.19
18 9 0.35
19 2 0.08
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTAATTATAATATATATT
Found at i:1914011 original size:16 final size:16
Alignment explanation
Indices: 1913964--1914031 Score: 54
Period size: 16 Copynumber: 4.2 Consensus size: 16
1913954 TATAAGAATA
1913964 TTAATTATTAATA-ATT
1 TTAATTA-TAATATATT
*
1913980 TT-ATTAAATTATATATT
1 TTAATT--ATAATATATT
1913997 TTAATTATAATATA-T
1 TTAATTATAATATATT
*
1914012 TTAATAATAAT-TATGT
1 TTAATTATAATATAT-T
1914028 TTAA
1 TTAA
1914032 ATATGATTAA
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
14 2 0.05
15 14 0.33
16 18 0.42
17 6 0.14
18 3 0.07
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (16 bp):
TTAATTATAATATATT
Found at i:1914241 original size:44 final size:45
Alignment explanation
Indices: 1914176--1914266 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
1914166 ACCTCTATTC
* * *
1914176 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
1914220 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
1914265 CA
1 CA
1914267 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:1914268 original size:16 final size:16
Alignment explanation
Indices: 1914247--1914282 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
1914237 GATTAGCTAT
1914247 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
1914263 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
1914279 TACA
1 TACA
1914283 GCGAACCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:1921636 original size:34 final size:35
Alignment explanation
Indices: 1921582--1921648 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
1921572 CAAACAGCAG
* *
1921582 AAAATATTTTCTAGTAAATCATTTCACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTCACAGAAAAGT
* *
1921617 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTCACAGAAAA
1921649 TATTTTCTGG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 16 0.57
35 12 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTCACAGAAAAGT
Found at i:1921653 original size:14 final size:15
Alignment explanation
Indices: 1921631--1921673 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
1921621 CATTTTCCAG
1921631 AAATCATTTTAC-GGA
1 AAAT-ATTTTACTGGA
1921646 AAATATTTT-CTGGA
1 AAATATTTTACTGGA
*
1921660 AAATGTTTTACTGG
1 AAATATTTTACTGG
1921674 CAATCAAACA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
13 1 0.04
14 16 0.64
15 8 0.32
ACGTcount: A:0.35, C:0.09, G:0.16, T:0.40
Consensus pattern (15 bp):
AAATATTTTACTGGA
Found at i:1922786 original size:12 final size:12
Alignment explanation
Indices: 1922769--1922795 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1922759 TTACTGATGT
1922769 GATTGCCACATG
1 GATTGCCACATG
1922781 GATTGCCACATG
1 GATTGCCACATG
1922793 GAT
1 GAT
1922796 GACACGTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (12 bp):
GATTGCCACATG
Found at i:1923670 original size:20 final size:20
Alignment explanation
Indices: 1923631--1923670 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1923621 TACTTGACTC
**
1923631 GACTCGACTCGAAATTTTTT
1 GACTCGACTCGAAAAATTTT
*
1923651 GACTCGATTCGAAAAATTTT
1 GACTCGACTCGAAAAATTTT
1923671 AATTTGAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (20 bp):
GACTCGACTCGAAAAATTTT
Found at i:1923956 original size:26 final size:28
Alignment explanation
Indices: 1923926--1923980 Score: 78
Period size: 26 Copynumber: 2.0 Consensus size: 28
1923916 TCCTGAAAAA
*
1923926 AAATTTAAATTTTTTTTA-TTTTT-TTT
1 AAATTGAAATTTTTTTTACTTTTTCTTT
*
1923952 AAATTGAGATTTTTTTTACTTTTTCTTT
1 AAATTGAAATTTTTTTTACTTTTTCTTT
1923980 A
1 A
1923981 TTTTATTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 16 0.64
27 5 0.20
28 4 0.16
ACGTcount: A:0.25, C:0.04, G:0.04, T:0.67
Consensus pattern (28 bp):
AAATTGAAATTTTTTTTACTTTTTCTTT
Found at i:1924271 original size:13 final size:13
Alignment explanation
Indices: 1924255--1924279 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1924245 TTAATTTTTA
1924255 TTTAAAAATATAT
1 TTTAAAAATATAT
1924268 TTTAAAAATATA
1 TTTAAAAATATA
1924280 ATACAGTAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTAAAAATATAT
Found at i:1924405 original size:32 final size:32
Alignment explanation
Indices: 1924369--1924431 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
1924359 AAACACTACC
*
1924369 ATAAATATAATAAATGTTTTATTATATTAAAA
1 ATAAATATAATAAATATTTTATTATATTAAAA
*
1924401 ATAAATATAATAAATATTTTATTGTATTAAA
1 ATAAATATAATAAATATTTTATTATATTAAA
1924432 TATAGTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.44
Consensus pattern (32 bp):
ATAAATATAATAAATATTTTATTATATTAAAA
Found at i:1926133 original size:14 final size:16
Alignment explanation
Indices: 1926112--1926150 Score: 55
Period size: 14 Copynumber: 2.6 Consensus size: 16
1926102 ATCATTTATT
1926112 AAATATTTTT-ATA-A
1 AAATATTTTTAATATA
*
1926126 ATATATTTTTAATATA
1 AAATATTTTTAATATA
1926142 AAATATTTT
1 AAATATTTT
1926151 CATTTCCTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 9 0.43
15 3 0.14
16 9 0.43
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
AAATATTTTTAATATA
Found at i:1928987 original size:96 final size:96
Alignment explanation
Indices: 1928815--1929008 Score: 363
Period size: 96 Copynumber: 2.0 Consensus size: 96
1928805 TCAAGGAGAG
1928815 TGGTTTTGAAAAATAATGCTTAAAATTAAATGTTTAAATTGAGCACAAGATTTTGAACACTTCCT
1 TGGTTTTGAAAAATAATGCTTAAAATTAAATGTTTAAATTGAGCACAAGATTTTGAACACTTCCT
1928880 TACTTTTACACTTTCAACCAATCCACATTAA
66 TACTTTTACACTTTCAACCAATCCACATTAA
*
1928911 TGGTTTTGAAAAATAATGCTTAAAATTAAATGTTTAAATTGAGCACAATATTTTGAACACTTCCT
1 TGGTTTTGAAAAATAATGCTTAAAATTAAATGTTTAAATTGAGCACAAGATTTTGAACACTTCCT
1928976 TA-TTTTCACACTTTCAACCAATCCACATTAA
66 TACTTTT-ACACTTTCAACCAATCCACATTAA
1929007 TG
1 TG
1929009 ACCAAATATG
Statistics
Matches: 96, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
95 4 0.04
96 92 0.96
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.37
Consensus pattern (96 bp):
TGGTTTTGAAAAATAATGCTTAAAATTAAATGTTTAAATTGAGCACAAGATTTTGAACACTTCCT
TACTTTTACACTTTCAACCAATCCACATTAA
Found at i:1933988 original size:17 final size:17
Alignment explanation
Indices: 1933966--1933998 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1933956 CACACGATAC
*
1933966 TAATATAATATAATGAT
1 TAATATAATAAAATGAT
1933983 TAATATAATAAAATGA
1 TAATATAATAAAATGA
1933999 ATTTAAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (17 bp):
TAATATAATAAAATGAT
Found at i:1934579 original size:14 final size:14
Alignment explanation
Indices: 1934562--1934618 Score: 53
Period size: 14 Copynumber: 4.1 Consensus size: 14
1934552 TTGCATCATG
1934562 AATCTTAAACCCCA
1 AATCTTAAACCCCA
* *
1934576 AATCTTAAACACTA
1 AATCTTAAACCCCA
* * *
1934590 AATCATAAATCCTA
1 AATCTTAAACCCCA
*
1934604 AA-CTTAAAACCCA
1 AATCTTAAACCCCA
1934617 AA
1 AA
1934619 ACATGAATCA
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
13 10 0.29
14 25 0.71
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (14 bp):
AATCTTAAACCCCA
Done.