Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold173
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: 2040036
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 14 of 16
Found at i:1798615 original size:27 final size:27
Alignment explanation
Indices: 1798582--1798655 Score: 121
Period size: 27 Copynumber: 2.7 Consensus size: 27
1798572 CCTAGCTGTA
*
1798582 CACATAGCTGTACACAACTCCTTACAG
1 CACATAGTTGTACACAACTCCTTACAG
* *
1798609 CATATAGTTATACACAACTCCTTACAG
1 CACATAGTTGTACACAACTCCTTACAG
1798636 CACATAGTTGTACACAACTC
1 CACATAGTTGTACACAACTC
1798656 ACAGCACCTA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.35, C:0.30, G:0.09, T:0.26
Consensus pattern (27 bp):
CACATAGTTGTACACAACTCCTTACAG
Found at i:1798649 original size:90 final size:90
Alignment explanation
Indices: 1798496--1798697 Score: 289
Period size: 90 Copynumber: 2.2 Consensus size: 90
1798486 GAATAGCACC
* * **
1798496 TAGCTGTACACAACTTCTCACAGCACATAGCTATACACAACCTAGTTGTACACATAGCTGTACAC
1 TAGCTGTACACAACTCCTCACAGCACATAGCTATACACAACCTACTTACACACATAGCTGTACAC
*
1798561 AACTCACAGCACCTAGCTGTACACA
66 AACTCACAGCACCTAGCTGCACACA
* * * * *
1798586 TAGCTGTACACAACTCCTTACAGCATATAGTTATACACAA-CTCCTTACAGCACATAGTTGTACA
1 TAGCTGTACACAACTCCTCACAGCACATAGCTATACACAACCTACTTACA-CACATAGCTGTACA
1798650 CAACTCACAGCACCTAGCTGCACACA
65 CAACTCACAGCACCTAGCTGCACACA
*
1798676 TAGCTGTACACAATTCCTCACA
1 TAGCTGTACACAACTCCTCACA
1798698 CTCCCTCTCA
Statistics
Matches: 99, Mismatches: 12, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
89 5 0.05
90 94 0.95
ACGTcount: A:0.34, C:0.31, G:0.11, T:0.23
Consensus pattern (90 bp):
TAGCTGTACACAACTCCTCACAGCACATAGCTATACACAACCTACTTACACACATAGCTGTACAC
AACTCACAGCACCTAGCTGCACACA
Found at i:1800642 original size:15 final size:15
Alignment explanation
Indices: 1800622--1800651 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1800612 CAGGTTCAGG
*
1800622 TGTAGAAACGGGTTC
1 TGTAGAAACAGGTTC
1800637 TGTAGAAACAGGTTC
1 TGTAGAAACAGGTTC
1800652 AGACACAGGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.13, G:0.30, T:0.27
Consensus pattern (15 bp):
TGTAGAAACAGGTTC
Found at i:1803260 original size:34 final size:34
Alignment explanation
Indices: 1803222--1803340 Score: 95
Period size: 34 Copynumber: 3.5 Consensus size: 34
1803212 AAAATGGTGA
1803222 TGGCAATAAAGGCCAAGAAACTTCACCAAATATT
1 TGGCAATAAAGGCCAAGAAACTTCACCAAATATT
* *
1803256 TGGCAATTAAGG-CAAGAAA----AACAGAATATGGT
1 TGGCAATAAAGGCCAAGAAACTTCACCA-AATAT--T
* * *
1803288 GATGGTAATAAAGGCCAAGAAACTTCACCAAATGTC
1 --TGGCAATAAAGGCCAAGAAACTTCACCAAATATT
*
1803324 TGGCAATTAAGGTCCAA
1 TGGCAATAAAGG-CCAA
1803341 AAAAAAAAAA
Statistics
Matches: 65, Mismatches: 9, Indels: 21
0.68 0.09 0.22
Matches are distributed among these distances:
29 3 0.05
30 5 0.08
32 1 0.02
33 7 0.11
34 31 0.48
35 11 0.17
38 4 0.06
39 3 0.05
ACGTcount: A:0.43, C:0.17, G:0.20, T:0.20
Consensus pattern (34 bp):
TGGCAATAAAGGCCAAGAAACTTCACCAAATATT
Found at i:1803344 original size:68 final size:68
Alignment explanation
Indices: 1803208--1803335 Score: 220
Period size: 68 Copynumber: 1.9 Consensus size: 68
1803198 CACTCTAGGG
*
1803208 ACAGAAAATGGTGATGGCAATAAAGGCCAAGAAACTTCACCAAATATTTGGCAATTAAGGCAAGA
1 ACAGAAAATGGTGATGGCAATAAAGGCCAAGAAACTTCACCAAATATCTGGCAATTAAGGCAAGA
1803273 AAA
66 AAA
* * *
1803276 ACAGAATATGGTGATGGTAATAAAGGCCAAGAAACTTCACCAAATGTCTGGCAATTAAGG
1 ACAGAAAATGGTGATGGCAATAAAGGCCAAGAAACTTCACCAAATATCTGGCAATTAAGG
1803336 TCCAAAAAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
68 56 1.00
ACGTcount: A:0.44, C:0.15, G:0.22, T:0.20
Consensus pattern (68 bp):
ACAGAAAATGGTGATGGCAATAAAGGCCAAGAAACTTCACCAAATATCTGGCAATTAAGGCAAGA
AAA
Found at i:1803603 original size:36 final size:36
Alignment explanation
Indices: 1803556--1803640 Score: 116
Period size: 36 Copynumber: 2.4 Consensus size: 36
1803546 ATACACAACC
* * * * *
1803556 TAGTTGTACACAACTTACAACACTTAGTTGTACGCA
1 TAGTTGTACACAACTCACAACACCTAGCTGCACACA
1803592 TAGTTGTACACAACTCACAACACCTAGCTGCACACA
1 TAGTTGTACACAACTCACAACACCTAGCTGCACACA
*
1803628 TAGCTGTACACAA
1 TAGTTGTACACAA
1803641 TTCCTCACAT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.35, C:0.27, G:0.13, T:0.25
Consensus pattern (36 bp):
TAGTTGTACACAACTCACAACACCTAGCTGCACACA
Found at i:1805107 original size:21 final size:21
Alignment explanation
Indices: 1805059--1805107 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
1805049 TCAGCCTCTA
* * *
1805059 CAGCAGCCGCAATCTCAGCCT
1 CAGCAGCCACAATCCCAGCCG
* *
1805080 CAACAGCCACAATCCCAGTCG
1 CAGCAGCCACAATCCCAGCCG
1805101 CAGCAGC
1 CAGCAGC
1805108 AGCCAACCAC
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.29, C:0.43, G:0.18, T:0.10
Consensus pattern (21 bp):
CAGCAGCCACAATCCCAGCCG
Found at i:1805883 original size:24 final size:25
Alignment explanation
Indices: 1805835--1805880 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
1805825 TTTATTATTC
1805835 TTAAATAAAATTTTTAATATTTTAT
1 TTAAATAAAATTTTTAATATTTTAT
1805860 TTAAAT-AAATTTTT-ATATTTT
1 TTAAATAAAATTTTTAATATTTT
1805881 TATCTGATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 7 0.33
24 8 0.38
25 6 0.29
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
TTAAATAAAATTTTTAATATTTTAT
Found at i:1805944 original size:29 final size:28
Alignment explanation
Indices: 1805891--1805946 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 28
1805881 TATCTGATTT
* * *
1805891 AAATAAATTTTAATTTTTAATTTATATC
1 AAATAAATTTAAAATTTTAAATTATATC
1805919 AAATAAATTTGAAAATTTTAAATTATAT
1 AAATAAATTT-AAAATTTTAAATTATAT
1805947 GTGAAAGTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 10 0.42
29 14 0.58
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (28 bp):
AAATAAATTTAAAATTTTAAATTATATC
Found at i:1806134 original size:31 final size:29
Alignment explanation
Indices: 1806071--1806134 Score: 69
Period size: 29 Copynumber: 2.1 Consensus size: 29
1806061 TAAAAAAATT
*
1806071 TAAAAATTATTTTTATAATTAAATTTAAA
1 TAAAAATTATTTTTATAATTAAATATAAA
1806100 TAAAAA-TATTTTTTATAAGATT-AATATAATA
1 TAAAAATTA-TTTTTAT-A-ATTAAATATAA-A
1806131 TAAA
1 TAAA
1806135 TATTTTAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
28 2 0.07
29 13 0.43
30 7 0.23
31 8 0.27
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (29 bp):
TAAAAATTATTTTTATAATTAAATATAAA
Found at i:1806271 original size:3 final size:3
Alignment explanation
Indices: 1806256--1806296 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
1806246 TTTCACTTTA
* *
1806256 AAT AAT AAG AAT AAT AAT AAT AAT AAT AAT AAC AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1806297 ATCATCAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:1806370 original size:16 final size:17
Alignment explanation
Indices: 1806345--1806385 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
1806335 TTAATTAAAA
1806345 TTTA-AAATTTA-TATT
1 TTTATAAATTTATTATT
1806360 TTTATAAATTTATTATT
1 TTTATAAATTTATTATT
*
1806377 CTTATAAAT
1 TTTATAAAT
1806386 CAGTTCTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 4 0.17
16 7 0.30
17 12 0.52
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTATAAATTTATTATT
Found at i:1806410 original size:15 final size:15
Alignment explanation
Indices: 1806390--1806442 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
1806380 ATAAATCAGT
1806390 TCTTATTAATAATTA
1 TCTTATTAATAATTA
*
1806405 TCTTATTAATTATCT-
1 TCTTATTAATAAT-TA
* *
1806420 TATTAATAATAATTA
1 TCTTATTAATAATTA
1806435 TCTTATTA
1 TCTTATTA
1806443 TTATGCTTAA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
14 1 0.03
15 28 0.93
16 1 0.03
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.55
Consensus pattern (15 bp):
TCTTATTAATAATTA
Found at i:1806416 original size:12 final size:12
Alignment explanation
Indices: 1806399--1806426 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1806389 TTCTTATTAA
1806399 TAATTATCTTAT
1 TAATTATCTTAT
1806411 TAATTATCTTAT
1 TAATTATCTTAT
1806423 TAAT
1 TAAT
1806427 AATAATTATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (12 bp):
TAATTATCTTAT
Found at i:1806495 original size:3 final size:3
Alignment explanation
Indices: 1806487--1806514 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1806477 ATTATCTTAT
1806487 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1806515 TAAAATTGGA
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1807000 original size:35 final size:35
Alignment explanation
Indices: 1806961--1807036 Score: 134
Period size: 35 Copynumber: 2.1 Consensus size: 35
1806951 CAAAATTAGA
1806961 TATTTCTTCATCAGTTGAATTTTTGATTTCTTGTT
1 TATTTCTTCATCAGTTGAATTTTTGATTTCTTGTT
*
1806996 TATTTCTTCATTAGTTGAATTTTTGATTTCTTGTT
1 TATTTCTTCATCAGTTGAATTTTTGATTTCTTGTT
1807031 TGATTT
1 T-ATTT
1807037 TCTTTCTTAT
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
35 35 0.90
36 4 0.10
ACGTcount: A:0.17, C:0.09, G:0.12, T:0.62
Consensus pattern (35 bp):
TATTTCTTCATCAGTTGAATTTTTGATTTCTTGTT
Found at i:1807297 original size:63 final size:66
Alignment explanation
Indices: 1807190--1807314 Score: 202
Period size: 63 Copynumber: 1.9 Consensus size: 66
1807180 ATTTAATGTA
1807190 TTATAGTAATTTGATGATTTTTGATATATATTTTTTCCCATTGTTGTTTGTAAAATGTTGCTTCT
1 TTATAGTAATTTGATGATTTTTGATATATATTTTTTCCCATTGTTGTTTGTAAAATGTTGCTTCT
1807255 T
66 T
* * *
1807256 TTATAGTAATTTGA-GA-TTTTGGTATA-ATTTTTTCCCTTTGTTGTTTTTAAAATGTTGCT
1 TTATAGTAATTTGATGATTTTTGATATATATTTTTTCCCATTGTTGTTTGTAAAATGTTGCT
1807315 AGGATTTAAG
Statistics
Matches: 56, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
63 31 0.55
64 9 0.16
65 2 0.04
66 14 0.25
ACGTcount: A:0.22, C:0.07, G:0.14, T:0.56
Consensus pattern (66 bp):
TTATAGTAATTTGATGATTTTTGATATATATTTTTTCCCATTGTTGTTTGTAAAATGTTGCTTCT
T
Found at i:1814581 original size:2 final size:2
Alignment explanation
Indices: 1814576--1814607 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1814566 GGTTTTTTGA
1814576 AT 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
1814608 GTAAATGAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1815226 original size:18 final size:17
Alignment explanation
Indices: 1815199--1815290 Score: 61
Period size: 17 Copynumber: 5.5 Consensus size: 17
1815189 TATAATAAAA
*
1815199 ATATATATATCAAAATTT
1 ATATAAATAT-AAAATTT
*
1815217 ATATTAATAT-AAA-TT
1 ATATAAATATAAAATTT
1815232 AT-TAATATATTAAAATTT
1 ATATAA-ATA-TAAAATTT
*
1815250 ATATCAATATAAAATATT
1 ATATAAATATAAAAT-TT
*
1815268 -T-TAAATATAATAA-AT
1 ATATAAATATAA-AATTT
1815283 ATATAAAT
1 ATATAAAT
1815291 TACCAAATAT
Statistics
Matches: 59, Mismatches: 6, Indels: 19
0.70 0.07 0.23
Matches are distributed among these distances:
14 2 0.03
15 8 0.14
16 13 0.22
17 17 0.29
18 17 0.29
19 2 0.03
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
ATATAAATATAAAATTT
Found at i:1815247 original size:33 final size:33
Alignment explanation
Indices: 1815188--1815267 Score: 105
Period size: 33 Copynumber: 2.5 Consensus size: 33
1815178 TATAATTAAA
1815188 ATAT-AATA-AAAATA-T-ATATATCAAAATTT
1 ATATCAATATAAAATATTAATATATCAAAATTT
* * *
1815217 ATATTAATATAAATTATTAATATATTAAAATTT
1 ATATCAATATAAAATATTAATATATCAAAATTT
1815250 ATATCAATATAAAATATT
1 ATATCAATATAAAATATT
1815268 TTAAATATAA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
29 4 0.09
30 4 0.09
31 5 0.12
32 1 0.02
33 29 0.67
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (33 bp):
ATATCAATATAAAATATTAATATATCAAAATTT
Found at i:1816200 original size:13 final size:12
Alignment explanation
Indices: 1816170--1816211 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 12
1816160 ACCATATATC
1816170 AAAATTTTATTG
1 AAAATTTTATTG
*
1816182 AAAATTTTATTTT
1 AAAATTTTA-TTG
*
1816195 AAAATTTT-TTA
1 AAAATTTTATTG
1816206 AAAATT
1 AAAATT
1816212 ATATAACTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
11 8 0.30
12 9 0.33
13 10 0.37
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (12 bp):
AAAATTTTATTG
Found at i:1816482 original size:3 final size:3
Alignment explanation
Indices: 1816474--1816510 Score: 56
Period size: 3 Copynumber: 12.0 Consensus size: 3
1816464 ATAAGTCAGC
*
1816474 AAT AAT AAT AAT AAT AAT AAT ATAT AAC AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT
1816511 TTGGTAAGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1817655 original size:2 final size:2
Alignment explanation
Indices: 1817648--1817692 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1817638 ATGAAAAGTC
1817648 AT AT AT AT AT AT 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 AT AT AT
1817690 AT A
1 AT A
1817693 CTTCTTGCTG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1820278 original size:44 final size:44
Alignment explanation
Indices: 1820229--1820329 Score: 161
Period size: 44 Copynumber: 2.3 Consensus size: 44
1820219 AAGTATTAAA
*
1820229 AATATTTAAAATTATTTAAGTTTTAATCGA-TTCGAAATATGAAT
1 AATATTTAAAATTATTTAAGTTCTAATCGACTT-GAAATATGAAT
1820273 AATATTTAAAATTATTTAAGTTCTAATCGACTTGAAATATGAAT
1 AATATTTAAAATTATTTAAGTTCTAATCGACTTGAAATATGAAT
1820317 AGA-ATTTAAAATT
1 A-ATATTTAAAATT
1820330 TAAGTTGATC
Statistics
Matches: 54, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
44 51 0.94
45 3 0.06
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.42
Consensus pattern (44 bp):
AATATTTAAAATTATTTAAGTTCTAATCGACTTGAAATATGAAT
Found at i:1824287 original size:2 final size:2
Alignment explanation
Indices: 1824280--1824310 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1824270 ACGTTTTGAT
1824280 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1824311 GAATATCTTG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1824756 original size:2 final size:2
Alignment explanation
Indices: 1824749--1824782 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1824739 ATTTCGGTGT
1824749 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1824783 ACTTTTATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1825861 original size:15 final size:15
Alignment explanation
Indices: 1825841--1825871 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1825831 TGTCAAAGTT
1825841 TTGAATAAATTTGAG
1 TTGAATAAATTTGAG
*
1825856 TTGAATTAATTTGAG
1 TTGAATAAATTTGAG
1825871 T
1 T
1825872 ACGAATCATT
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:0.00, G:0.19, T:0.45
Consensus pattern (15 bp):
TTGAATAAATTTGAG
Found at i:1825968 original size:15 final size:16
Alignment explanation
Indices: 1825937--1825975 Score: 62
Period size: 15 Copynumber: 2.5 Consensus size: 16
1825927 TAAACGAATA
*
1825937 TTAAATTATTTTATAT
1 TTAAATTATCTTATAT
1825953 TTAAATTATCTT-TAT
1 TTAAATTATCTTATAT
1825968 TTAAATTA
1 TTAAATTA
1825976 ATTCGGATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (16 bp):
TTAAATTATCTTATAT
Found at i:1827107 original size:18 final size:18
Alignment explanation
Indices: 1827081--1827116 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1827071 AATAAAATAT
1827081 TTGAAAATTGATTAAAAA
1 TTGAAAATTGATTAAAAA
* *
1827099 TTGATAATTGGTTAAAAA
1 TTGAAAATTGATTAAAAA
1827117 ATATTTTCTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (18 bp):
TTGAAAATTGATTAAAAA
Found at i:1827893 original size:16 final size:17
Alignment explanation
Indices: 1827872--1827914 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
1827862 ACCAACAACT
*
1827872 AATTTAAGTATTT-TTA
1 AATTTAAGTATTTCCTA
1827888 AATTTAA-TATTTCCTA
1 AATTTAAGTATTTCCTA
1827904 AATTTATAGTA
1 AATTTA-AGTA
1827915 AAAATGATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 5 0.22
16 15 0.65
17 1 0.04
18 2 0.09
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.51
Consensus pattern (17 bp):
AATTTAAGTATTTCCTA
Found at i:1829564 original size:2 final size:2
Alignment explanation
Indices: 1829559--1829592 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1829549 TCTTTTTTTC
1829559 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1829593 ACTTCTTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1830000 original size:16 final size:16
Alignment explanation
Indices: 1829970--1830014 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
1829960 TAAAAAAGAT
*
1829970 ATTAAATTAT-TAAAA
1 ATTAAATTATAAAAAA
1829985 ATTAAATTTATAAAAAA
1 ATTAAA-TTATAAAAAA
1830002 ATT-AATTA-AAAAA
1 ATTAAATTATAAAAA
1830015 TAAAATATGG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 5 0.19
15 9 0.33
16 6 0.22
17 7 0.26
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
ATTAAATTATAAAAAA
Found at i:1830171 original size:15 final size:15
Alignment explanation
Indices: 1830151--1830184 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
1830141 GTTGAAAGCG
1830151 CACTCTTAATCTTAA
1 CACTCTTAATCTTAA
1830166 CACTCTTAATCTTAA
1 CACTCTTAATCTTAA
1830181 CACT
1 CACT
1830185 TTTACAGTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.38
Consensus pattern (15 bp):
CACTCTTAATCTTAA
Found at i:1830735 original size:4 final size:4
Alignment explanation
Indices: 1830726--1830750 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1830716 TAATATATGA
1830726 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
1830751 TTACAACCGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:1831292 original size:3 final size:3
Alignment explanation
Indices: 1831284--1831321 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
1831274 ACTAAACAAA
1831284 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1831322 AGAAATTGTT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1832697 original size:47 final size:47
Alignment explanation
Indices: 1832635--1832730 Score: 174
Period size: 47 Copynumber: 2.0 Consensus size: 47
1832625 CATAGAGATC
* *
1832635 AAGTTAATTAATTTTCTTATTTTAAATTTGGAGATTGATATATAGAA
1 AAGTTAATTAATTTTCTTACTTTAAATTTAGAGATTGATATATAGAA
1832682 AAGTTAATTAATTTTCTTACTTTAAATTTAGAGATTGATATATAGAA
1 AAGTTAATTAATTTTCTTACTTTAAATTTAGAGATTGATATATAGAA
1832729 AA
1 AA
1832731 TAAGAATTAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.41, C:0.03, G:0.11, T:0.45
Consensus pattern (47 bp):
AAGTTAATTAATTTTCTTACTTTAAATTTAGAGATTGATATATAGAA
Found at i:1834102 original size:18 final size:18
Alignment explanation
Indices: 1834071--1834105 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1834061 ATTTTTTTAT
*
1834071 ATTTTTATTAATTATTAG
1 ATTTTTATCAATTATTAG
*
1834089 ATTTTTATCGATTATTA
1 ATTTTTATCAATTATTA
1834106 AAGTTTCATT
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:0.31, C:0.03, G:0.06, T:0.60
Consensus pattern (18 bp):
ATTTTTATCAATTATTAG
Found at i:1835814 original size:15 final size:14
Alignment explanation
Indices: 1835785--1835823 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
1835775 TTGAATAAAA
*
1835785 GCATGCATGTGTAT
1 GCATGTATGTGTAT
1835799 GCATGTATGATGTAT
1 GCATGTATG-TGTAT
*
1835814 GCATATATGT
1 GCATGTATGT
1835824 TGTCGTTGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.26, C:0.10, G:0.26, T:0.38
Consensus pattern (14 bp):
GCATGTATGTGTAT
Found at i:1837048 original size:16 final size:16
Alignment explanation
Indices: 1837027--1837057 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1837017 AAGTCTTATC
1837027 AAATCAAGTAATATTT
1 AAATCAAGTAATATTT
*
1837043 AAATCAAGTTATATT
1 AAATCAAGTAATATT
1837058 CGTATTGAGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.39
Consensus pattern (16 bp):
AAATCAAGTAATATTT
Found at i:1840659 original size:20 final size:20
Alignment explanation
Indices: 1840614--1840659 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
1840604 GTTAACAGCC
*
1840614 CATGATTCATGCATTTTAAG
1 CATGTTTCATGCATTTTAAG
1840634 CTATGTTTCATGCA-TTTACAG
1 C-ATGTTTCATGCATTTTA-AG
1840655 CATGT
1 CATGT
1840660 CCAGTACCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.41
Consensus pattern (20 bp):
CATGTTTCATGCATTTTAAG
Found at i:1843159 original size:28 final size:28
Alignment explanation
Indices: 1843128--1843194 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 28
1843118 ATTTTTAATC
**
1843128 TTATATTTTAAATAATACTTCATTTTTA
1 TTATATTTTAAATAATACTTCATTTAAA
*
1843156 TTATA--TTAAA-AATACTTTATTTAAA
1 TTATATTTTAAATAATACTTCATTTAAA
*
1843181 TTA-ATTATAAATAA
1 TTATATTTTAAATAA
1843195 ATATAATATA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
24 1 0.03
25 15 0.47
26 9 0.28
27 2 0.06
28 5 0.16
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (28 bp):
TTATATTTTAAATAATACTTCATTTAAA
Found at i:1843431 original size:2 final size:2
Alignment explanation
Indices: 1843424--1843466 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
1843414 CACTTTTGTT
1843424 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1843465 TA
1 TA
1843467 ATTATTTACT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1843470 original size:6 final size:7
Alignment explanation
Indices: 1843423--1843471 Score: 55
Period size: 8 Copynumber: 6.6 Consensus size: 7
1843413 CCACTTTTGT
1843423 TTATATA
1 TTATATA
1843430 TATATATA
1 T-TATATA
1843438 TATATATA
1 T-TATATA
1843446 TATATATA
1 T-TATATA
1843454 TATATATA
1 T-TATATA
1843462 TTATA-A
1 TTATATA
1843468 TTAT
1 TTAT
1843472 TTACTTAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
6 5 0.12
7 5 0.12
8 31 0.76
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (7 bp):
TTATATA
Found at i:1844189 original size:2 final size:2
Alignment explanation
Indices: 1844184--1844219 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1844174 CTTTTTCTAA
1844184 AT AT AT 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
1844220 CTAACTTCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1844516 original size:26 final size:27
Alignment explanation
Indices: 1844473--1844527 Score: 71
Period size: 25 Copynumber: 2.1 Consensus size: 27
1844463 AGATTAGTTG
1844473 TTTCTAATATAATATATGTTAATTTTATA
1 TTTCTAATATAATATATG-TAATTTT-TA
1844502 TTTCT-ATAT-AT-TATGTAATTTTTA
1 TTTCTAATATAATATATGTAATTTTTA
1844526 TT
1 TT
1844528 ATAAAGAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
24 4 0.15
25 7 0.27
26 4 0.15
27 2 0.08
28 4 0.15
29 5 0.19
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.60
Consensus pattern (27 bp):
TTTCTAATATAATATATGTAATTTTTA
Found at i:1844624 original size:17 final size:16
Alignment explanation
Indices: 1844598--1844644 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 16
1844588 TTTTAAAACT
1844598 TTTA-AAAAATATTAAA
1 TTTATAAAAA-ATTAAA
*
1844614 -TTATTAAAAATTAAA
1 TTTATAAAAAATTAAA
1844629 TTTATAAAAAAATTAA
1 TTTAT-AAAAAATTAA
1844645 TTAAAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 9 0.35
16 8 0.31
17 9 0.35
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TTTATAAAAAATTAAA
Found at i:1844628 original size:15 final size:17
Alignment explanation
Indices: 1844600--1844644 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
1844590 TTAAAACTTT
1844600 TAAAAAATATTAAA-TTA
1 TAAAAAA-ATTAAATTTA
*
1844617 T-TAAAAATTAAATTTA
1 TAAAAAAATTAAATTTA
1844633 TAAAAAAATTAA
1 TAAAAAAATTAA
1844645 TTAAAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 6 0.25
16 8 0.33
17 10 0.42
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TAAAAAAATTAAATTTA
Found at i:1844646 original size:16 final size:16
Alignment explanation
Indices: 1844600--1844646 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
1844590 TTAAAACTTT
*
1844600 TAAAAAATATTAAATTA
1 TAAAAAA-ATTAATTTA
*
1844617 T-TAAAAATTAAATTTA
1 TAAAAAAATT-AATTTA
1844633 TAAAAAAATTAATT
1 TAAAAAAATTAATT
1844647 AAAAAATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
15 3 0.12
16 14 0.56
17 8 0.32
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TAAAAAAATTAATTTA
Found at i:1844661 original size:27 final size:27
Alignment explanation
Indices: 1844611--1844662 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
1844601 AAAAAATATT
* *
1844611 AAATTATTAAAAATTAAATTTATAAAA
1 AAATTATTAAAAAATAAATATATAAAA
1844638 AAATTAATTAAAAAATAAA-ATATAA
1 AAATT-ATTAAAAAATAAATATATAA
1844663 GCAAGCTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 10 0.45
28 12 0.55
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (27 bp):
AAATTATTAAAAAATAAATATATAAAA
Found at i:1844718 original size:21 final size:20
Alignment explanation
Indices: 1844694--1844758 Score: 51
Period size: 20 Copynumber: 3.1 Consensus size: 20
1844684 TACCAATTTA
*
1844694 AAAATATAAATTAATTTGAAT
1 AAAAT-TAAATTAATTTAAAT
* * **
1844715 AAAATTTAA-TACTTTTATTT
1 AAAATTAAATTA-ATTTAAAT
1844735 AAAATTAAATTAAATTTAAAT
1 AAAATTAAATT-AATTTAAAT
1844756 AAA
1 AAA
1844759 TATAAATAAT
Statistics
Matches: 32, Mismatches: 9, Indels: 6
0.68 0.19 0.13
Matches are distributed among these distances:
19 2 0.06
20 15 0.47
21 14 0.44
22 1 0.03
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (20 bp):
AAAATTAAATTAATTTAAAT
Found at i:1845195 original size:16 final size:17
Alignment explanation
Indices: 1845153--1845196 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
1845143 ATGAGTAAAA
1845153 TTAATTTAAATTATAAT
1 TTAATTTAAATTATAAT
**
1845170 TTTTTTTAAATT-TAAT
1 TTAATTTAAATTATAAT
*
1845186 TTAATATAAAT
1 TTAATTTAAAT
1845197 CAAATTAAGT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTAATTTAAATTATAAT
Found at i:1846368 original size:24 final size:24
Alignment explanation
Indices: 1846341--1846393 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
1846331 TTGTCTTGAA
* *
1846341 ATATGTGTGTGTGTATATATATAT
1 ATATATGTGTGTGCATATATATAT
1846365 ATATATGTGTGTGCATATATATAT
1 ATATATGTGTGTGCATATATATAT
1846389 ATATA
1 ATATA
1846394 AATTTTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.34, C:0.02, G:0.17, T:0.47
Consensus pattern (24 bp):
ATATATGTGTGTGCATATATATAT
Found at i:1846391 original size:22 final size:22
Alignment explanation
Indices: 1846348--1846392 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1846338 GAAATATGTG
*
1846348 TGTGTGTATATATATATATATA
1 TGTGTGTACATATATATATATA
*
1846370 TGTGTGTGCATATATATATATA
1 TGTGTGTACATATATATATATA
1846392 T
1 T
1846393 AAATTTTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (22 bp):
TGTGTGTACATATATATATATA
Found at i:1847089 original size:18 final size:18
Alignment explanation
Indices: 1847041--1847093 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
1847031 TATATATTTT
1847041 AAAATTTATAT-AATAT-
1 AAAATTTATATAAATATA
*
1847057 -AAA-TTAT-TGATATATA
1 AAAATTTATAT-AAATATA
1847073 AAAATTTATATAAATATA
1 AAAATTTATATAAATATA
1847091 AAA
1 AAA
1847094 TATCTTAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
13 1 0.03
14 4 0.14
15 7 0.24
17 3 0.10
18 13 0.45
19 1 0.03
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (18 bp):
AAAATTTATATAAATATA
Found at i:1847120 original size:16 final size:16
Alignment explanation
Indices: 1847101--1847139 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
1847091 AAATATCTTA
1847101 AATATAAT-TATAATAT
1 AATATAATGTATAA-AT
*
1847117 AATAAAATGTATAAAT
1 AATATAATGTATAAAT
1847133 AATATAA
1 AATATAA
1847140 ATATTATTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (16 bp):
AATATAATGTATAAAT
Found at i:1847518 original size:15 final size:16
Alignment explanation
Indices: 1847492--1847523 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
1847482 CTATCATTTT
1847492 AAATTCTTTTAATTAA
1 AAATTCTTTTAATTAA
1847508 AAATT-TTTTAATTAA
1 AAATTCTTTTAATTAA
1847523 A
1 A
1847524 TTATATATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (16 bp):
AAATTCTTTTAATTAA
Found at i:1847589 original size:16 final size:16
Alignment explanation
Indices: 1847568--1847599 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1847558 TATGATAACG
*
1847568 TTATAATTAGTTAAAT
1 TTATAATTAATTAAAT
1847584 TTATAATTAATTAAAT
1 TTATAATTAATTAAAT
1847600 ATGTAGTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (16 bp):
TTATAATTAATTAAAT
Found at i:1852357 original size:21 final size:20
Alignment explanation
Indices: 1852329--1852368 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
1852319 ATTTTTATTT
1852329 AAATTTAATTATAAA-ATATA
1 AAATTTAA-TATAAACATATA
1852349 AAATATTAATATAAACATAT
1 AAAT-TTAATATAAACATAT
1852369 TTTAAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (20 bp):
AAATTTAATATAAACATATA
Found at i:1853285 original size:225 final size:227
Alignment explanation
Indices: 1852891--1853303 Score: 564
Period size: 225 Copynumber: 1.8 Consensus size: 227
1852881 GTATGGGATG
*
1852891 CGATCTTTTCAATATTTAAAATTAGAAAAGACATGTCTTGATTATACATCAATATAACTCATATA
1 CGATCTTATCAATATTTAAAATTAGAAAAGACATGTCTTGATTATACATCAATATAACTCATATA
* * * * *** **
1852956 AAATAAAGAGTCAGTTGTTAGATCTTATTAGTCATGATAAGATTTGGGTTTGAATTAGATTAAAC
66 AAACAAAAAGTCA-TTGTTAGATCTTACTAGTCATAATAAGATTTGAACTCAAATTAGATTAAAC
* * * *
1853021 TAGTATTAAAAAGATTTAAAGTTGTTTAGGTTTTAATTGACTTGAAATATAAAAAGTTTTTACAC
130 TAATATTAAAAAGATTTAAAATTATTTAGGTTTTAATTGACTCGAAATATAAAAAGTTTTTACAC
1853086 TTTATGTGACGTCTTTACAAATAATGCAAGATA
195 TTTATGTGACGTCTTTACAAATAATGCAAGATA
* * * *
1853119 CGATCTTATCAATATTTAAAAATTA-AAATGACATGTCTTGGTTGTACATCAATATAGCTCATAT
1 CGATCTTATCAATATTT-AAAATTAGAAAAGACATGTCTTGATTATACATCAATATAACTCATAT
** *
1853183 AAGGCAAAAAG-C-TTGTTAGATCTTACTAGTCATAATTAGATTTGAACTCAAATTAGATTAAA-
65 AAAACAAAAAGTCATTGTTAGATCTTACTAGTCATAATAAGATTTGAACTCAAATTAGATTAAAC
* *
1853245 TAAATATTAAAAAGTTTTAAAATTATTTAGGTTTTAATTGACTCGAAATATGAAAAGTT
130 T-AATATTAAAAAGATTTAAAATTATTTAGGTTTTAATTGACTCGAAATATAAAAAGTT
1853304 GTCATATTCG
Statistics
Matches: 160, Mismatches: 23, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
224 1 0.01
225 93 0.58
227 1 0.01
228 58 0.36
229 7 0.04
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (227 bp):
CGATCTTATCAATATTTAAAATTAGAAAAGACATGTCTTGATTATACATCAATATAACTCATATA
AAACAAAAAGTCATTGTTAGATCTTACTAGTCATAATAAGATTTGAACTCAAATTAGATTAAACT
AATATTAAAAAGATTTAAAATTATTTAGGTTTTAATTGACTCGAAATATAAAAAGTTTTTACACT
TTATGTGACGTCTTTACAAATAATGCAAGATA
Found at i:1854167 original size:228 final size:228
Alignment explanation
Indices: 1853731--1854865 Score: 1171
Period size: 228 Copynumber: 5.0 Consensus size: 228
1853721 ATTATAAAAT
* * * * * * * * * *
1853731 AGTTTTCACGCTTTGTGTCACATCTTAACAAATAGTATGAGATGCGATCTTTTCAATATTT-AAA
1 AGTTTTCACACTTTATGTGACGTCTTCACAAATAATGTAAGATGTGATCTTATCAATATTTAAAA
* * * * * *
1853795 ATTAAAAAAGACATTTCTTGATTATACATCAATATAACTCATATAAAACAAAGAGCCAGTTGTTA
66 ATT-AAAAAGACATGTCTTGATTGTACACCAATATAGCTCATATAAGACAAAGAGTCAGTTGTTA
* *
1853860 GATCTTACTAGTCAT-GATAAGATTTAGG-TTTGAATTAGATTAAACTAGTATTAAAAAGATTTA
130 GATCTTACTAGTCATAG-TTAGATTT-GGATTTGAATTAGATTAAACAAGTATTAAAAAGATTTA
* * * * *
1853923 AAGTTGTTTAGGTTTTAATTGACTTGAAATATGAAA
193 AAATTATTTAGGTTCTAATCGACTCGAAATATGAAA
* * * * *
1853959 AGTTTTTACACTTTATGTAACGTCTTCGCAAATAATGCAAGATGCGATCTTATCAATATTTAAAA
1 AGTTTTCACACTTTATGTGACGTCTTCACAAATAATGTAAGATGTGATCTTATCAATATTTAAAA
* * * * *
1854024 ATTAAAATGACATGTTTTGGTTGTACATCAATATAGCTCATATAAGGCAGAA-AGTCAGTTGTTA
66 ATTAAAAAGACATGTCTTGATTGTACACCAATATAGCTCATATAAGACA-AAGAGTCAGTTGTTA
* * * ** * *
1854088 GATCTTATTAGTCATAATTAGATTTGGACTCAAATTAGATTAAATAAGTATTAAAAAGTTTTAAA
130 GATCTTACTAGTCATAGTTAGATTTGGATTTGAATTAGATTAAACAAGTATTAAAAAGATTTAAA
* * *
1854153 ATTATTTGGGTTTTAATTGACTCGAAATATGAAA
195 ATTATTTAGGTTCTAATCGACTCGAAATATGAAA
* * * * * * *
1854187 AGTTTTCATATTTTATGTGACATCTTCACAAATAATATGAGATGTGATCTCATTAATATTTAAAA
1 AGTTTTCACACTTTATGTGACGTCTTCACAAATAATGTAAGATGTGATCTTATCAATATTTAAAA
* ** *
1854252 ATTAAAAAGACATGTCTTGATTGTACACCAATATAGCCCATATAA-ACGGA-AGCCAGTTGTTCA
66 ATTAAAAAGACATGTCTTGATTGTACACCAATATAGCTCATATAAGACAAAGAGTCAGTTGTT-A
* *
1854315 -ATCTTACTAGTCATAGTTGGATTT-GAGTTTGAATTAGATTAAACAAGTATTAAAGAGATTTAA
130 GATCTTACTAGTCATAGTTAGATTTGGA-TTTGAATTAGATTAAACAAGTATTAAAAAGATTTAA
* * * *
1854378 AATTGTTTAGGTTCTAATCGATTCAAAATTTGAAA
194 AATTATTTAGGTTCTAATCGACTCGAAATATGAAA
* * * * * * * *
1854413 AGTTTTCACACTCTAAGTGATGTTTTCACAAAAAAAAGTAGGCTGTGATCTTATCAATATTT---
1 AGTTTTCACACTTTATGTGACGTCTTCAC-AAATAATGTAAGATGTGATCTTATCAATATTTAAA
* * * * *
1854475 AATTAAAAAGACATGTCTTGGTTATACACCAATATAGCTTATATACGACAAAGAGTCGGTTGTTA
65 AATTAAAAAGACATGTCTTGATTGTACACCAATATAGCTCATATAAGACAAAGAGTCAGTTGTTA
* * * * * *
1854540 GATCTTACTAGTCATAGTT-GAATTT-TAGTTCGAAATAAATTAAACAAGTAATAAAAAAATTTA
130 GATCTTACTAGTCATAGTTAG-ATTTGGA-TTTGAATTAGATTAAACAAGTATTAAAAAGATTTA
* ** * *
1854603 AGATTAAATAAGTTCTAATCAACTCGAAATATGAAA
193 AAATTATTTAGGTTCTAATCGACTCGAAATATGAAA
* * * * *
1854639 AGTTTTCACAATTTATGGGACGTCTTTAGAAATAATGTGAGATGTGATCTTATCAATATTTAAAA
1 AGTTTTCACACTTTATGTGACGTCTTCACAAATAATGTAAGATGTGATCTTATCAATATTTAAAA
* * * * **
1854704 ATTGAAAAGGCATGTCTTGTTTGTACACTAATATAGCTCATATAAGACAAAGAGTTGGTTGTTAG
66 ATTAAAAAGACATGTCTTGATTGTACACCAATATAGCTCATATAAGACAAAGAGTCAGTTGTTAG
* * * *
1854769 ATCTTACTAGTCGTAGTTGGATTTGGGTTTGAATTAGATTAAACAAGTATTAAAATGATTTAAAA
131 ATCTTACTAGTCATAGTTAGATTTGGATTTGAATTAGATTAAACAAGTATTAAAAAGATTTAAAA
* * * *
1854834 TTATTTAAGCTCTAATCGACCCAAAATATGAA
196 TTATTTAGGTTCTAATCGACTCGAAATATGAA
1854866 TAGAATTTAA
Statistics
Matches: 743, Mismatches: 148, Indels: 32
0.80 0.16 0.03
Matches are distributed among these distances:
224 41 0.06
225 34 0.05
226 222 0.30
227 28 0.04
228 409 0.55
229 9 0.01
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (228 bp):
AGTTTTCACACTTTATGTGACGTCTTCACAAATAATGTAAGATGTGATCTTATCAATATTTAAAA
ATTAAAAAGACATGTCTTGATTGTACACCAATATAGCTCATATAAGACAAAGAGTCAGTTGTTAG
ATCTTACTAGTCATAGTTAGATTTGGATTTGAATTAGATTAAACAAGTATTAAAAAGATTTAAAA
TTATTTAGGTTCTAATCGACTCGAAATATGAAA
Found at i:1856227 original size:2 final size:2
Alignment explanation
Indices: 1856220--1856266 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1856210 TGCTAACTTG
1856220 AT AT AT AT AT AT 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 AT AT AT
1856262 AT AT A
1 AT AT A
1856267 CACGTATGTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1860132 original size:15 final size:16
Alignment explanation
Indices: 1860096--1860135 Score: 57
Period size: 14 Copynumber: 2.6 Consensus size: 16
1860086 TAAAATTTAA
1860096 TAAAAAATTAAATTAT
1 TAAAAAATTAAATTAT
*
1860112 TAAAAACTT-AATT-T
1 TAAAAAATTAAATTAT
1860126 TAAAAAATTA
1 TAAAAAATTA
1860136 TTAAAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
14 9 0.43
15 4 0.19
16 8 0.38
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (16 bp):
TAAAAAATTAAATTAT
Found at i:1866987 original size:2 final size:2
Alignment explanation
Indices: 1866974--1867036 Score: 117
Period size: 2 Copynumber: 31.5 Consensus size: 2
1866964 TTTTTGAATG
*
1866974 AT AT AC AT AT AT 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 AT AT AT
1867016 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
1867037 CTCTTGTTAA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1869186 original size:30 final size:30
Alignment explanation
Indices: 1869152--1869211 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
1869142 GTAAGATTTC
1869152 ATGTTTAGCTATCTGAAATTAACCACAAAA
1 ATGTTTAGCTATCTGAAATTAACCACAAAA
1869182 ATGTTTAGCTATCTGAAATTAACCACAAAA
1 ATGTTTAGCTATCTGAAATTAACCACAAAA
1869212 CAAAAAGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.43, C:0.17, G:0.10, T:0.30
Consensus pattern (30 bp):
ATGTTTAGCTATCTGAAATTAACCACAAAA
Found at i:1871052 original size:24 final size:24
Alignment explanation
Indices: 1871025--1871070 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1871015 AATAAAAATT
1871025 AGCCACCAATTTTGACAAACAACA
1 AGCCACCAATTTTGACAAACAACA
* *
1871049 AGCCACCATTTTTTACAAACAA
1 AGCCACCAATTTTGACAAACAA
1871071 AAATAACCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.43, C:0.28, G:0.07, T:0.22
Consensus pattern (24 bp):
AGCCACCAATTTTGACAAACAACA
Found at i:1873072 original size:21 final size:22
Alignment explanation
Indices: 1873034--1873079 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
1873024 ATCTGTTGAA
* **
1873034 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGCGGAGTACT
1873055 ACTCCACCTGCTGCGGAGTACT
1 ACTCCACCTGCTGCGGAGTACT
1873077 ACT
1 ACT
1873080 TGTTTGAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (22 bp):
ACTCCACCTGCTGCGGAGTACT
Found at i:1875688 original size:30 final size:30
Alignment explanation
Indices: 1875652--1875736 Score: 170
Period size: 30 Copynumber: 2.8 Consensus size: 30
1875642 AAACAAAAAT
1875652 AACCACCATATTTGACAAATACAAAAAGGA
1 AACCACCATATTTGACAAATACAAAAAGGA
1875682 AACCACCATATTTGACAAATACAAAAAGGA
1 AACCACCATATTTGACAAATACAAAAAGGA
1875712 AACCACCATATTTGACAAATACAAA
1 AACCACCATATTTGACAAATACAAA
1875737 GAGTGATATT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 55 1.00
ACGTcount: A:0.53, C:0.21, G:0.08, T:0.18
Consensus pattern (30 bp):
AACCACCATATTTGACAAATACAAAAAGGA
Found at i:1877145 original size:15 final size:15
Alignment explanation
Indices: 1877108--1877147 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
1877098 GGATAATATG
*
1877108 AATATTAAATAATTT
1 AATATAAAATAATTT
1877123 AA-AGTAAAATAATTT
1 AATA-TAAAATAATTT
1877138 AATATAAAAT
1 AATATAAAAT
1877148 TTAATATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 1 0.05
15 20 0.91
16 1 0.05
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (15 bp):
AATATAAAATAATTT
Found at i:1878109 original size:24 final size:24
Alignment explanation
Indices: 1878081--1878148 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 24
1878071 AGGACTAAAA
*
1878081 ATAATCATGGTAAAATTAATTATT
1 ATAATAATGGTAAAATTAATTATT
* *
1878105 ATAATGAT-G--AAATTAAATATT
1 ATAATAATGGTAAAATTAATTATT
1878126 ATAATAATGAGATTAAAATTAAT
1 ATAATAATG-G--TAAAATTAAT
1878149 AGTAAAACAT
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
21 18 0.53
23 2 0.06
24 7 0.21
27 7 0.21
ACGTcount: A:0.51, C:0.01, G:0.09, T:0.38
Consensus pattern (24 bp):
ATAATAATGGTAAAATTAATTATT
Found at i:1878118 original size:21 final size:21
Alignment explanation
Indices: 1878093--1878146 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
1878083 AATCATGGTA
* *
1878093 AAATTAATTATTATAATGATG
1 AAATTAAATATTATAATAATG
1878114 AAATTAAATATTATAATAATG
1 AAATTAAATATTATAATAATG
*
1878135 AGATTAAA-ATTA
1 AAATTAAATATTA
1878147 ATAGTAAAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 4 0.13
21 26 0.87
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (21 bp):
AAATTAAATATTATAATAATG
Found at i:1878357 original size:24 final size:22
Alignment explanation
Indices: 1878311--1878381 Score: 67
Period size: 21 Copynumber: 3.2 Consensus size: 22
1878301 CATTGTTGTT
* *
1878311 AAATAATA-ATTAAAATTTAATA
1 AAATTATATATTAAAA-ATAATA
1878333 AAATTATAT-TTATATTAAATAATA
1 AAATTATATATTA-A--AAATAATA
1878357 AAA-TATATATTAAAAATAATA
1 AAATTATATATTAAAAATAATA
1878378 AAAT
1 AAAT
1878382 AAAAATAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
21 11 0.27
22 10 0.24
23 7 0.17
24 11 0.27
25 2 0.05
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
AAATTATATATTAAAAATAATA
Found at i:1878383 original size:64 final size:64
Alignment explanation
Indices: 1878234--1878383 Score: 146
Period size: 64 Copynumber: 2.4 Consensus size: 64
1878224 ATTAAAATGT
* * *
1878234 TATATA-TATAAAA-AAT-AAATAGTTAAAAATTATTAAAATTATATTTATATCACATAATAAAA
1 TATATATTA-AAAATAATAAAATAATTAAAAATTAATAAAATTATATTTATATCAAATAATAAAA
* ***** * * *
1878296 TATTACATTGTTGTTAA-ATAATAATTAAAATTTAATAAAATTATATTTATATTAAATAATAAAA
1 TA-TATATTAAAAATAATAAAATAATTAAAAATTAATAAAATTATATTTATATCAAATAATAAAA
1878360 TATATATTAAAAATAATAAAATAA
1 TATATATTAAAAATAATAAAATAA
1878384 AAATAAAAAA
Statistics
Matches: 64, Mismatches: 19, Indels: 8
0.70 0.21 0.09
Matches are distributed among these distances:
62 2 0.03
63 11 0.17
64 51 0.80
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (64 bp):
TATATATTAAAAATAATAAAATAATTAAAAATTAATAAAATTATATTTATATCAAATAATAAAA
Found at i:1878392 original size:21 final size:21
Alignment explanation
Indices: 1878349--1878396 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
1878339 TATTTATATT
* * *
1878349 AAATAATAAAATATATATTAA
1 AAATAATAAAATAAAAATAAA
1878370 AAATAATAAAATAAAAATAAA
1 AAATAATAAAATAAAAATAAA
1878391 AAATAA
1 AAATAA
1878397 AAGAGGTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (21 bp):
AAATAATAAAATAAAAATAAA
Found at i:1878393 original size:13 final size:14
Alignment explanation
Indices: 1878367--1878398 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
1878357 AAATATATAT
1878367 TAAAAATAATAAAA
1 TAAAAATAATAAAA
1878381 TAAAAATAA-AAAA
1 TAAAAATAATAAAA
1878394 TAAAA
1 TAAAA
1878399 GAGGTAAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (14 bp):
TAAAAATAATAAAA
Found at i:1878551 original size:2 final size:2
Alignment explanation
Indices: 1878544--1878570 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1878534 CAAATAAAAC
1878544 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1878571 ATCAAATCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1879349 original size:15 final size:15
Alignment explanation
Indices: 1879331--1879363 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1879321 TAATGTATTT
1879331 TTTAAAAATTTAATA
1 TTTAAAAATTTAATA
*
1879346 TTTAATAATTTAATA
1 TTTAAAAATTTAATA
1879361 TTT
1 TTT
1879364 TTCTTTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTAAAAATTTAATA
Found at i:1881438 original size:22 final size:22
Alignment explanation
Indices: 1881397--1881439 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1881387 TTAATAAGAA
*
1881397 ATATTTTTATATTAATATTTAT
1 ATATTTTTATAGTAATATTTAT
1881419 ATATTTTTATAAGTAA-ATTTA
1 ATATTTTTAT-AGTAATATTTA
1881440 AATTAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (22 bp):
ATATTTTTATAGTAATATTTAT
Found at i:1881889 original size:34 final size:34
Alignment explanation
Indices: 1881832--1882050 Score: 289
Period size: 34 Copynumber: 6.5 Consensus size: 34
1881822 ATATGTATAT
*
1881832 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
1881865 ATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
1881899 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* **
1881933 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
1881967 ATTATTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
1882001 ATTGTTGACTAAAT-GGTAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGT-GATTTGGTAGCTTACC
1882035 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
1882051 TGGTTTTTAC
Statistics
Matches: 162, Mismatches: 21, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
33 17 0.10
34 144 0.89
35 1 0.01
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.41
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
Found at i:1881975 original size:102 final size:101
Alignment explanation
Indices: 1881832--1882050 Score: 348
Period size: 102 Copynumber: 2.2 Consensus size: 101
1881822 ATATGTATAT
** * * * *
1881832 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
1881897 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
66 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1881933 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTT
1 ATTGTTGATTAAATG-GAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTT
* * *
1881998 ACCATTGTTGACTAAATGGTAGATTTGGTAGGTTGCC
65 ACCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1882035 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
1882051 TGGTTTTTAC
Statistics
Matches: 108, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
101 16 0.15
102 92 0.85
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.41
Consensus pattern (101 bp):
ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
Found at i:1886518 original size:34 final size:34
Alignment explanation
Indices: 1886461--1886679 Score: 289
Period size: 34 Copynumber: 6.5 Consensus size: 34
1886451 AAGTGGGAGA
*
1886461 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
1886494 ATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
1886528 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* **
1886562 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
1886596 ATTATTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
1886630 ATTGTTGACTAAAT-GGTAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGT-GATTTGGTAGCTTACC
1886664 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
1886680 TGGTTTTTAT
Statistics
Matches: 162, Mismatches: 21, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
33 17 0.10
34 144 0.89
35 1 0.01
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.41
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
Found at i:1886604 original size:102 final size:101
Alignment explanation
Indices: 1886461--1886679 Score: 348
Period size: 102 Copynumber: 2.2 Consensus size: 101
1886451 AAGTGGGAGA
** * * * *
1886461 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
1886526 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
66 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1886562 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTT
1 ATTGTTGATTAAATG-GAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTT
* * *
1886627 ACCATTGTTGACTAAATGGTAGATTTGGTAGGTTGCC
65 ACCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1886664 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
1886680 TGGTTTTTAT
Statistics
Matches: 108, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
101 16 0.15
102 92 0.85
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.41
Consensus pattern (101 bp):
ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
Found at i:1888281 original size:39 final size:39
Alignment explanation
Indices: 1888238--1888377 Score: 151
Period size: 39 Copynumber: 3.6 Consensus size: 39
1888228 TATTTGAATC
* * *
1888238 GTATTTGATTAGATGTATCGTGTATATTATATTATTTTT
1 GTATTTAATTAAATGTGTCGTGTATATTATATTATTTTT
** *
1888277 GTATTTAATTAAACATGTCATGTATATTATA-TAGTTTTT
1 GTATTTAATTAAATGTGTCGTGTATATTATATTA-TTTTT
*
1888316 GTATTTAATTAAATGTGTTGTG-ATATTATATTA-TTTT
1 GTATTTAATTAAATGTGTCGTGTATATTATATTATTTTT
* * * *
1888353 GTATATGATTAAACGTGTCGAGTAT
1 GTATTTAATTAAATGTGTCGTGTAT
1888378 GTGTTGTATT
Statistics
Matches: 83, Mismatches: 15, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
37 21 0.25
38 12 0.14
39 50 0.60
ACGTcount: A:0.30, C:0.04, G:0.15, T:0.51
Consensus pattern (39 bp):
GTATTTAATTAAATGTGTCGTGTATATTATATTATTTTT
Found at i:1888964 original size:2 final size:2
Alignment explanation
Indices: 1888957--1888981 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1888947 AGATTGCTTA
1888957 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 A
1888982 AATTTTTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1890585 original size:3 final size:3
Alignment explanation
Indices: 1890579--1890627 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
1890569 TTTTTTTTGC
1890579 TAT TAT TAT TAT 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 TAT TAT TAT TAT
1890627 T
1 T
1890628 TGGGTATGAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1891260 original size:2 final size:2
Alignment explanation
Indices: 1891253--1891313 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
1891243 TAACTTTTTC
1891253 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1891295 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
1891314 TCTTTGAATT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1891584 original size:20 final size:20
Alignment explanation
Indices: 1891559--1891600 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 20
1891549 TTAATTTTAC
1891559 TTTTTTTTAT-T-TTGTATAT
1 TTTTTTTTATATATT-TATAT
1891578 TTTTTTTTATATATTTATAT
1 TTTTTTTTATATATTTATAT
1891598 TTT
1 TTT
1891601 ATTCATGTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 10 0.48
20 9 0.43
21 2 0.10
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (20 bp):
TTTTTTTTATATATTTATAT
Found at i:1891585 original size:14 final size:15
Alignment explanation
Indices: 1891562--1891602 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
1891552 ATTTTACTTT
*
1891562 TTTTTATTTTGTATA
1 TTTTTATTTTATATA
1891577 TTTTT-TTTTATATA
1 TTTTTATTTTATATA
*
1891591 TTTATATTTTAT
1 TTTTTATTTTAT
1891603 TCATGTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (15 bp):
TTTTTATTTTATATA
Found at i:1891690 original size:32 final size:32
Alignment explanation
Indices: 1891649--1891710 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
1891639 TTATATATTA
*
1891649 ATATAAATTTTGATGCGTTAATAATTTATTTT
1 ATATAAATTTTGATACGTTAATAATTTATTTT
1891681 ATATAAATTTTGATACGTTAATAATTTATT
1 ATATAAATTTTGATACGTTAATAATTTATT
1891711 CAATCTAACT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.37, C:0.03, G:0.08, T:0.52
Consensus pattern (32 bp):
ATATAAATTTTGATACGTTAATAATTTATTTT
Found at i:1892479 original size:22 final size:20
Alignment explanation
Indices: 1892454--1892493 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1892444 GAATCCATGC
1892454 CAATAACAAGATTAGCAAAATG
1 CAAT-ACAAGA-TAGCAAAATG
*
1892476 CAATACGAGATAGCAAAA
1 CAATACAAGATAGCAAAA
1892494 ACTTCAAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 5 0.29
22 4 0.24
ACGTcount: A:0.55, C:0.15, G:0.15, T:0.15
Consensus pattern (20 bp):
CAATACAAGATAGCAAAATG
Found at i:1892688 original size:16 final size:16
Alignment explanation
Indices: 1892663--1892698 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
1892653 GTTTACTCGA
1892663 GTTT-GATTATTTTGT
1 GTTTGGATTATTTTGT
*
1892678 TTTTGGATTATTTTGT
1 GTTTGGATTATTTTGT
1892694 GTTTG
1 GTTTG
1892699 AATAATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
15 3 0.17
16 15 0.83
ACGTcount: A:0.11, C:0.00, G:0.22, T:0.67
Consensus pattern (16 bp):
GTTTGGATTATTTTGT
Found at i:1892875 original size:59 final size:59
Alignment explanation
Indices: 1892801--1892914 Score: 174
Period size: 59 Copynumber: 1.9 Consensus size: 59
1892791 ATTCTAACCC
* * *
1892801 ATATCCATGACCCTAAAAGAGGTAAAAACACTCCACTAATAAAACATTACAATTTGTAA
1 ATATCCATGACCCTAAAAAACGTAAAAACACTCCACTAATAAAACATTAAAATTTGTAA
* * *
1892860 ATATCTATGATCCTAAAAAACGTAAAAACACTTCACTAATAAAACATTAAAATTT
1 ATATCCATGACCCTAAAAAACGTAAAAACACTCCACTAATAAAACATTAAAATTT
1892915 ATAATTTTTA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
59 49 1.00
ACGTcount: A:0.49, C:0.18, G:0.06, T:0.26
Consensus pattern (59 bp):
ATATCCATGACCCTAAAAAACGTAAAAACACTCCACTAATAAAACATTAAAATTTGTAA
Found at i:1892980 original size:47 final size:47
Alignment explanation
Indices: 1892929--1893018 Score: 135
Period size: 47 Copynumber: 1.9 Consensus size: 47
1892919 TTTTTACACA
* * *
1892929 GATAAAATTATAAACCCTTCTCATAAATAACTTATAACTTTTGTGTG
1 GATAAAAATACAAACCCTTCTCACAAATAACTTATAACTTTTGTGTG
* *
1892976 GATAAAAATACAAACCCTTTTCACAAATAATTTATAACTTTTG
1 GATAAAAATACAAACCCTTCTCACAAATAACTTATAACTTTTG
1893019 CATTGTTAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 38 1.00
ACGTcount: A:0.41, C:0.16, G:0.07, T:0.37
Consensus pattern (47 bp):
GATAAAAATACAAACCCTTCTCACAAATAACTTATAACTTTTGTGTG
Found at i:1893035 original size:47 final size:47
Alignment explanation
Indices: 1892929--1893040 Score: 134
Period size: 47 Copynumber: 2.4 Consensus size: 47
1892919 TTTTTACACA
* * **
1892929 GATAAAATTATAAACCCTTCTCATAAATAACTTATAACTTTTGTGTG
1 GATAAAATTACAAACCCTTCTCACAAATAACTTATAACTTTTGCATG
* * * *
1892976 GATAAAAATACAAACCCTTTTCACAAATAATTTATAACTTTTGCATT
1 GATAAAATTACAAACCCTTCTCACAAATAACTTATAACTTTTGCATG
* *
1893023 GTTAAAGTTACAAACCCT
1 GATAAAATTACAAACCCT
1893041 CCAACAAACA
Statistics
Matches: 54, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
47 54 1.00
ACGTcount: A:0.40, C:0.17, G:0.07, T:0.36
Consensus pattern (47 bp):
GATAAAATTACAAACCCTTCTCACAAATAACTTATAACTTTTGCATG
Found at i:1899002 original size:18 final size:18
Alignment explanation
Indices: 1898978--1899025 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
1898968 AGAAAACAAA
*
1898978 CAAAAGAAAAGGCAAAAG
1 CAAAAGAAAAGGAAAAAG
* *
1898996 TAAAAGAAAAAGAAAAAG
1 CAAAAGAAAAGGAAAAAG
1899014 CAAAAGAGAAAG
1 CAAAAGA-AAAG
1899026 CATGAAGTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
18 21 0.88
19 3 0.12
ACGTcount: A:0.71, C:0.06, G:0.21, T:0.02
Consensus pattern (18 bp):
CAAAAGAAAAGGAAAAAG
Found at i:1899018 original size:7 final size:6
Alignment explanation
Indices: 1898965--1899025 Score: 50
Period size: 6 Copynumber: 9.8 Consensus size: 6
1898955 TTCATTAATT
* * * * *
1898965 AAAAGA AAACAAA CAAAAGA AAAGGC AAAAGT AAAAGA AAAAGA AAAAGC
1 AAAAGA AAA-AGA -AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
*
1899015 AAAAGA GAAAG
1 AAAAGA AAAAG
1899026 CATGAAGTAA
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
6 36 0.84
7 4 0.09
8 3 0.07
ACGTcount: A:0.74, C:0.07, G:0.18, T:0.02
Consensus pattern (6 bp):
AAAAGA
Found at i:1899424 original size:2 final size:2
Alignment explanation
Indices: 1899417--1899456 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1899407 CCTTACTTGC
1899417 AT AT AT AT AT 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 AT AT
1899457 GTATGATCAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1900172 original size:20 final size:21
Alignment explanation
Indices: 1900149--1900195 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
1900139 CTACATTTAA
*
1900149 TATTTATTCAATA-TTAAAAT
1 TATTTAATCAATATTTAAAAT
*
1900169 TATTTAATCTATATTTAAAAT
1 TATTTAATCAATATTTAAAAT
1900190 T-TTTAA
1 TATTTAA
1900196 AATTAAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (21 bp):
TATTTAATCAATATTTAAAAT
Found at i:1900393 original size:4 final size:4
Alignment explanation
Indices: 1900386--1900414 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
1900376 TGTTACAGGA
1900386 AATT AATT AATT AATT AATT AATT AATT A
1 AATT AATT AATT AATT AATT AATT AATT A
1900415 TCATTGCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
AATT
Found at i:1900566 original size:22 final size:22
Alignment explanation
Indices: 1900538--1900583 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
1900528 TTATTTGTTT
*
1900538 TTGAATATGTTTATGTTTATTA
1 TTGAATATGTTTATGTTCATTA
1900560 TTGAATATGTTTATGTTCATTA
1 TTGAATATGTTTATGTTCATTA
1900582 TT
1 TT
1900584 TTTTAAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.26, C:0.02, G:0.13, T:0.59
Consensus pattern (22 bp):
TTGAATATGTTTATGTTCATTA
Found at i:1900824 original size:38 final size:37
Alignment explanation
Indices: 1900782--1900864 Score: 96
Period size: 38 Copynumber: 2.2 Consensus size: 37
1900772 AGAAAAGAGT
1900782 AAAATAAAAATATTATTA-TAAATAAATGAAATAAACAA
1 AAAATAAAAATATTATTATTAAAT-AAT-AAATAAACAA
* * * *
1900820 AAAATAATATTATTATTATTAAATTATAATTAAACAA
1 AAAATAAAAATATTATTATTAAATAATAAATAAACAA
*
1900857 TAAATAAA
1 AAAATAAA
1900865 CTCTAAATAA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
37 15 0.39
38 18 0.47
39 5 0.13
ACGTcount: A:0.64, C:0.02, G:0.01, T:0.33
Consensus pattern (37 bp):
AAAATAAAAATATTATTATTAAATAATAAATAAACAA
Found at i:1900864 original size:22 final size:22
Alignment explanation
Indices: 1900839--1900905 Score: 55
Period size: 22 Copynumber: 3.0 Consensus size: 22
1900829 TTATTATTAT
*
1900839 TAAATTATAATTAAACAATAAA
1 TAAATTATAAATAAACAATAAA
* * **
1900861 TAAACTCTAAATAAACTTTAAA
1 TAAATTATAAATAAACAATAAA
**
1900883 TAAATTTATTCATAAAC-ATAAA
1 TAAA-TTATAAATAAACAATAAA
1900905 T
1 T
1900906 GAACTGAATA
Statistics
Matches: 34, Mismatches: 10, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
22 26 0.76
23 8 0.24
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (22 bp):
TAAATTATAAATAAACAATAAA
Found at i:1909925 original size:52 final size:52
Alignment explanation
Indices: 1909847--1909974 Score: 224
Period size: 52 Copynumber: 2.5 Consensus size: 52
1909837 CGAAATATGA
*
1909847 AAATTTGCCTGCATGTATCGATACA-TTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTAA-AATGTATCGATACATCTGGGC
1909899 AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
1909951 AAA-TTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
1909975 AAGATCAGTG
Statistics
Matches: 74, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
51 21 0.28
52 48 0.65
53 5 0.07
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
Found at i:1910001 original size:13 final size:13
Alignment explanation
Indices: 1909983--1910007 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1909973 CAAAGATCAG
1909983 TGTATCGATACAA
1 TGTATCGATACAA
1909996 TGTATCGATACA
1 TGTATCGATACA
1910008 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1910085 original size:33 final size:33
Alignment explanation
Indices: 1910048--1910114 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1910038 AGTAGCTTAA
1910048 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
1910081 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1910114 A
1 A
1910115 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:1910088 original size:13 final size:13
Alignment explanation
Indices: 1910070--1910094 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1910060 CAAAAAAATA
1910070 TGTATCGATACAT
1 TGTATCGATACAT
1910083 TGTATCGATACA
1 TGTATCGATACA
1910095 ACATTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1911860 original size:34 final size:34
Alignment explanation
Indices: 1911820--1911908 Score: 142
Period size: 34 Copynumber: 2.6 Consensus size: 34
1911810 TAGGTGAAGC
* *
1911820 ATATTAGATGTATTAGGTAATGTATTTGGTGAGA
1 ATATTAGGTGTGTTAGGTAATGTATTTGGTGAGA
*
1911854 ATATTAGGTGTGTTAGGTGATGTATTTGGTGAGA
1 ATATTAGGTGTGTTAGGTAATGTATTTGGTGAGA
*
1911888 ATGTTAGGTGTGTTAGGTAAT
1 ATATTAGGTGTGTTAGGTAAT
1911909 ATGTTAGGTG
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 50 1.00
ACGTcount: A:0.27, C:0.00, G:0.31, T:0.42
Consensus pattern (34 bp):
ATATTAGGTGTGTTAGGTAATGTATTTGGTGAGA
Found at i:1911919 original size:34 final size:34
Alignment explanation
Indices: 1911809--1911920 Score: 134
Period size: 34 Copynumber: 3.3 Consensus size: 34
1911799 GTTAAGTGTG
* * *
1911809 TTAGGTGAAGCATATTAGATGTATTAGGTAATGTA
1 TTAGGTG-AGAATATTAGGTGTGTTAGGTAATGTA
* *
1911844 TTTGGTGAGAATATTAGGTGTGTTAGGTGATGTA
1 TTAGGTGAGAATATTAGGTGTGTTAGGTAATGTA
* * * *
1911878 TTTGGTGAGAATGTTAGGTGTGTTAGGTAATATG
1 TTAGGTGAGAATATTAGGTGTGTTAGGTAATGTA
1911912 TTAGGTGAG
1 TTAGGTGAG
1911921 TAAGATATTT
Statistics
Matches: 67, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
34 61 0.91
35 6 0.09
ACGTcount: A:0.27, C:0.01, G:0.33, T:0.39
Consensus pattern (34 bp):
TTAGGTGAGAATATTAGGTGTGTTAGGTAATGTA
Found at i:1912247 original size:19 final size:19
Alignment explanation
Indices: 1912225--1912280 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 19
1912215 TTGTATTATA
1912225 CATAATTTTATATTATATT
1 CATAATTTTATATTATATT
* * * *
1912244 CATATTTTTTTATTTTAAT
1 CATAATTTTATATTATATT
*
1912263 AAT-ATTATTATATTATAT
1 CATAATT-TTATATTATAT
1912281 ATTTATATAA
Statistics
Matches: 27, Mismatches: 9, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
18 2 0.07
19 25 0.93
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.61
Consensus pattern (19 bp):
CATAATTTTATATTATATT
Found at i:1912336 original size:25 final size:26
Alignment explanation
Indices: 1912308--1912371 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 26
1912298 CATGTAAATA
1912308 ATTTATATTATATAAATT-TTTATAT
1 ATTTATATTATATAAATTATTTATAT
* ** *
1912333 ATTTATATCATA-ATTTTATTTATTT
1 ATTTATATTATATAAATTATTTATAT
1912358 ATGTTATATTATAT
1 AT-TTATATTATAT
1912372 TTTATAAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
24 3 0.10
25 19 0.61
26 9 0.29
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (26 bp):
ATTTATATTATATAAATTATTTATAT
Found at i:1912365 original size:78 final size:80
Alignment explanation
Indices: 1912226--1912375 Score: 177
Period size: 78 Copynumber: 1.9 Consensus size: 80
1912216 TGTATTATAC
* *
1912226 ATAATTTTATATTATATTCATATTTTTTTATTTTAATAATATTATTATATTATATATTTATA-TA
1 ATAATTTTATATTATATTCAAATTTTTATATTTTAATAATATTATTATATTATATATTTATATTA
1912290 AATTTTAACATGTAA
66 AATTTTAACATGTAA
* *
1912305 ATAA-TTTATATTATA-T-AAATTTTTATATATTTATATCATAATT-TTAT-TTATTTATGTTAT
1 ATAATTTTATATTATATTCAAATTTTTATAT-TTTA-ATAAT-ATTATTATATTATATAT-TTAT
*
1912365 ATTATATTTTA
62 ATTAAATTTTA
1912376 TAAATTACTT
Statistics
Matches: 61, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
76 10 0.16
77 12 0.20
78 24 0.39
79 15 0.25
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.59
Consensus pattern (80 bp):
ATAATTTTATATTATATTCAAATTTTTATATTTTAATAATATTATTATATTATATATTTATATTA
AATTTTAACATGTAA
Found at i:1912683 original size:2 final size:2
Alignment explanation
Indices: 1912676--1912705 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1912666 AATGTTTTAT
1912676 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1912706 ACGAACATAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1913068 original size:21 final size:19
Alignment explanation
Indices: 1913048--1913086 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
1913038 TTTATAATTA
1913048 AATTTAAATAAAAATATATT
1 AATTTAAATAAAAA-ATATT
* *
1913068 ATTTTAATTAAAAAATATT
1 AATTTAAATAAAAAATATT
1913087 GTTTCAAGCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
AATTTAAATAAAAAATATT
Found at i:1913767 original size:14 final size:14
Alignment explanation
Indices: 1913750--1913798 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
1913740 TTTTATAATT
1913750 AAATTTAAATTTAA
1 AAATTTAAATTTAA
**
1913764 AAATTTTTA-TTAA
1 AAATTTAAATTTAA
1913777 TTAAATTTAAATTTAA
1 --AAATTTAAATTTAA
1913793 AAATTT
1 AAATTT
1913799 TTATTAATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
13 4 0.14
14 13 0.46
15 7 0.25
16 4 0.14
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
AAATTTAAATTTAA
Found at i:1913824 original size:35 final size:29
Alignment explanation
Indices: 1913737--1913811 Score: 143
Period size: 29 Copynumber: 2.6 Consensus size: 29
1913727 ATTTTTATAT
1913737 AATTTTTA-TAATTAAATTTAAATTTAAA
1 AATTTTTATTAATTAAATTTAAATTTAAA
1913765 AATTTTTATTAATTAAATTTAAATTTAAA
1 AATTTTTATTAATTAAATTTAAATTTAAA
1913794 AATTTTTATTAATTAAAT
1 AATTTTTATTAATTAAAT
1913812 AATAATTTAA
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
28 8 0.17
29 38 0.83
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (29 bp):
AATTTTTATTAATTAAATTTAAATTTAAA
Found at i:1913840 original size:20 final size:17
Alignment explanation
Indices: 1913804--1913845 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 17
1913794 AATTTTTATT
1913804 AATTAAATAATAATTTA
1 AATTAAATAATAATTTA
1913821 AATTAAATTAAATCAATTTA
1 AATTAAA-T-AAT-AATTTA
1913841 AATTA
1 AATTA
1913846 CAAAACTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 7 0.32
18 1 0.05
19 3 0.14
20 11 0.50
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (17 bp):
AATTAAATAATAATTTA
Found at i:1915186 original size:20 final size:21
Alignment explanation
Indices: 1915148--1915189 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
1915138 TCAAATATAT
*
1915148 ATATATAATTATATTATAAAA
1 ATATATAATTATATAATAAAA
*
1915169 ATATA-AATTTTATAATAAAA
1 ATATATAATTATATAATAAAA
1915189 A
1 A
1915190 GCCTAGTTCG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
ATATATAATTATATAATAAAA
Found at i:1916338 original size:3 final size:3
Alignment explanation
Indices: 1916330--1916373 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
1916320 TTTTCTTTGT
1916330 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1916374 TTGGGGTATG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1921119 original size:2 final size:2
Alignment explanation
Indices: 1921112--1921141 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1921102 CATCAAAATT
1921112 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1921142 CTTAAATACA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1922211 original size:29 final size:26
Alignment explanation
Indices: 1922136--1922211 Score: 62
Period size: 29 Copynumber: 2.7 Consensus size: 26
1922126 ATTTAAAATT
* *
1922136 AATTATAATTATTAATATAAAAATAA
1 AATTTTAATTATTAAAATAAAAATAA
*
1922162 AATTTTAATATTATTTTAAATAATAATATAA
1 AATTTT-A-ATTA-TTAAAATAA-AA-ATAA
*
1922193 ATTTTTAATCTATTAAAAT
1 AATTTTAAT-TATTAAAAT
1922212 TTAATTTAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
26 5 0.13
27 1 0.03
28 4 0.10
29 15 0.38
30 5 0.13
31 9 0.23
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (26 bp):
AATTTTAATTATTAAAATAAAAATAA
Found at i:1922638 original size:30 final size:29
Alignment explanation
Indices: 1922585--1922669 Score: 109
Period size: 29 Copynumber: 2.9 Consensus size: 29
1922575 CGGTTTATTT
*
1922585 AATATAAATTAAAAGTTAAAATTTATATG
1 AATATAAATTAAAAATTAAAATTTATATG
* * *
1922614 AATATAAATAAAAAATAAAAAATTTAGTTTG
1 AATATAAATTAAAAAT-TAAAATTTA-TATG
1922645 -ATATAAATTAAAAATTAAAATTTAT
1 AATATAAATTAAAAATTAAAATTTAT
1922670 TTAAGCACAA
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
28 1 0.02
29 22 0.46
30 22 0.46
31 3 0.06
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (29 bp):
AATATAAATTAAAAATTAAAATTTATATG
Done.