Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032254.1 Gossypioides kirkii chromosome KI_12
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: 43711324
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 35 of 135
Found at i:13541450 original size:2 final size:2
Alignment explanation
Indices: 13541445--13541473 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
13541435 TATATATATA
13541445 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
13541474 AATCATACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:13545383 original size:2 final size:2
Alignment explanation
Indices: 13545376--13545408 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
13545366 TATCATACAT
13545376 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
13545409 GGGGGGGGGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:13547501 original size:18 final size:18
Alignment explanation
Indices: 13547478--13547515 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
13547468 AGAAGATACG
*
13547478 TTCGGATTTAGAAAGTTA
1 TTCGGATTTAAAAAGTTA
13547496 TTCGGATTTAAAAAGTTA
1 TTCGGATTTAAAAAGTTA
13547514 TT
1 TT
13547516 TAAATAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.34, C:0.05, G:0.18, T:0.42
Consensus pattern (18 bp):
TTCGGATTTAAAAAGTTA
Found at i:13555925 original size:11 final size:11
Alignment explanation
Indices: 13555908--13555971 Score: 74
Period size: 11 Copynumber: 5.8 Consensus size: 11
13555898 CAATGGTCAA
*
13555908 CGGTCAACGGT
1 CGGTCAACGCT
*
13555919 TGGTCAACGCT
1 CGGTCAACGCT
* *
13555930 CGATCAACGGT
1 CGGTCAACGCT
13555941 CGGTCAACGCT
1 CGGTCAACGCT
**
13555952 TAGTCAACGCT
1 CGGTCAACGCT
13555963 CGGTCAACG
1 CGGTCAACG
13555972 ATTTGGGTTT
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 42 1.00
ACGTcount: A:0.22, C:0.30, G:0.28, T:0.20
Consensus pattern (11 bp):
CGGTCAACGCT
Found at i:13555949 original size:33 final size:33
Alignment explanation
Indices: 13555908--13555971 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
13555898 CAATGGTCAA
* *
13555908 CGGTCAACGGTTGGTCAACGCTCGATCAACGGT
1 CGGTCAACGCTTAGTCAACGCTCGATCAACGGT
*
13555941 CGGTCAACGCTTAGTCAACGCTCGGTCAACG
1 CGGTCAACGCTTAGTCAACGCTCGATCAACG
13555972 ATTTGGGTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.22, C:0.30, G:0.28, T:0.20
Consensus pattern (33 bp):
CGGTCAACGCTTAGTCAACGCTCGATCAACGGT
Found at i:13556068 original size:16 final size:16
Alignment explanation
Indices: 13556047--13556096 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
13556037 TTGTTATTTT
13556047 AAAGGGTTTGGGTTTA
1 AAAGGGTTTGGGTTTA
* * *
13556063 AAAGGGTTATTGGATCA
1 AAAGGGTT-TGGGTTTA
*
13556080 AAATGGTTTGGGTTTA
1 AAAGGGTTTGGGTTTA
13556096 A
1 A
13556097 TATTGGGTCA
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
16 14 0.54
17 12 0.46
ACGTcount: A:0.30, C:0.02, G:0.32, T:0.36
Consensus pattern (16 bp):
AAAGGGTTTGGGTTTA
Found at i:13558669 original size:11 final size:11
Alignment explanation
Indices: 13558638--13558680 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
13558628 CCCAACTTGG
13558638 ATTTTAAATTA
1 ATTTTAAATTA
* *
13558649 AGTTTGAATTA
1 ATTTTAAATTA
*
13558660 ATTTTAAATTT
1 ATTTTAAATTA
*
13558671 GTTTTAAATT
1 ATTTTAAATT
13558681 TAAATACATT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (11 bp):
ATTTTAAATTA
Found at i:13562195 original size:35 final size:35
Alignment explanation
Indices: 13562149--13562220 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
13562139 AGCTCGAGAG
*
13562149 TAATAGGGATCCTTTTATAAAGGGCAAATGACCAC
1 TAATAGGGATCCTTTTATAAAGGCCAAATGACCAC
13562184 TAATAGGGATCCTTTTATAAAGGCCAAATGACCAC
1 TAATAGGGATCCTTTTATAAAGGCCAAATGACCAC
13562219 TA
1 TA
13562221 TCTTTTATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.26
Consensus pattern (35 bp):
TAATAGGGATCCTTTTATAAAGGCCAAATGACCAC
Found at i:13564153 original size:29 final size:28
Alignment explanation
Indices: 13564121--13564198 Score: 79
Period size: 29 Copynumber: 2.7 Consensus size: 28
13564111 AATTTCACCA
13564121 AAAATTACCTTTTTACCCTCGAACTTT-CC
1 AAAATTACCTTTTTACCC-CG-ACTTTCCC
*
13564150 AAAATT-CCATTTTTAACCCCGAGTTTCCCC
1 AAAATTACC-TTTTT-ACCCCGACTTT-CCC
*
13564180 AAAATTACATTTTTACCCC
1 AAAATTACCTTTTTACCCC
13564199 CGAGAGCCAA
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
28 6 0.14
29 18 0.43
30 17 0.40
31 1 0.02
ACGTcount: A:0.29, C:0.31, G:0.04, T:0.36
Consensus pattern (28 bp):
AAAATTACCTTTTTACCCCGACTTTCCC
Found at i:13564200 original size:30 final size:30
Alignment explanation
Indices: 13564098--13564202 Score: 101
Period size: 30 Copynumber: 3.5 Consensus size: 30
13564088 GATATCATTC
* *
13564098 CATTTTTAACCCC-AATTTCACCAAAAATTA
1 CATTTTTAACCCCGAGTTTC-CCCAAAATTA
* * *
13564128 CCTTTTT-ACCCTCGAACTTT--CCAAAATTC
1 CATTTTTAACCC-CG-AGTTTCCCCAAAATTA
13564157 CATTTTTAACCCCGAGTTTCCCCAAAATTA
1 CATTTTTAACCCCGAGTTTCCCCAAAATTA
*
13564187 CATTTTTACCCCCGAG
1 CATTTTTAACCCCGAG
13564203 AGCCAAAAAT
Statistics
Matches: 61, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
28 4 0.07
29 19 0.31
30 34 0.56
32 4 0.07
ACGTcount: A:0.30, C:0.31, G:0.05, T:0.34
Consensus pattern (30 bp):
CATTTTTAACCCCGAGTTTCCCCAAAATTA
Found at i:13564219 original size:59 final size:57
Alignment explanation
Indices: 13564094--13564219 Score: 139
Period size: 59 Copynumber: 2.1 Consensus size: 57
13564084 CAAAGATATC
* * *
13564094 ATTCCATTTTTAACCCCAATTTCACCAAAAATTACCTTTTTACCCTCGAACTTTCCAAA
1 ATTCCATTTTTAACCCCAATTTCACCAAAAATTACATTTTTACCCCCGAAC--TCAAAA
* *
13564153 ATTCCATTTTTAACCCCGAGTTTC-CCCAAAATTACATTTTTACCCCCGAGAGC-CAAAA
1 ATTCCATTTTTAACCCC-AATTTCACCAAAAATTACATTTTTACCCCCGA-A-CTCAAAA
13564211 ATTACCATT
1 ATT-CCATT
13564220 ATGCCCCCGT
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
58 7 0.12
59 44 0.76
60 6 0.10
61 1 0.02
ACGTcount: A:0.32, C:0.30, G:0.05, T:0.33
Consensus pattern (57 bp):
ATTCCATTTTTAACCCCAATTTCACCAAAAATTACATTTTTACCCCCGAACTCAAAA
Found at i:13567873 original size:29 final size:27
Alignment explanation
Indices: 13567803--13567879 Score: 75
Period size: 29 Copynumber: 2.7 Consensus size: 27
13567793 GTGACATGTG
*
13567803 ATATAAAAATGATAAAAATCAATCAAAA
1 ATATAAAAATTATAAAAATCAA-CAAAA
*
13567831 TTATAATAAATTATAACAAATACAA-AAAA
1 ATATAA-AAATTATAA-AAAT-CAACAAAA
13567860 ATATAAAAATTTATATAAAA
1 ATATAAAAA-TTATA-AAAA
13567880 ATATTCAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
28 8 0.20
29 25 0.61
30 5 0.12
31 3 0.07
ACGTcount: A:0.66, C:0.05, G:0.01, T:0.27
Consensus pattern (27 bp):
ATATAAAAATTATAAAAATCAACAAAA
Found at i:13567879 original size:20 final size:20
Alignment explanation
Indices: 13567856--13567901 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
13567846 ACAAATACAA
13567856 AAAAATATAAAAATTTATA-T
1 AAAAATATAAAAATTT-TACT
**
13567876 AAAAATATTCAAATTTTACT
1 AAAAATATAAAAATTTTACT
13567896 AAAAAT
1 AAAAAT
13567902 TAGAAAAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 2 0.09
20 21 0.91
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (20 bp):
AAAAATATAAAAATTTTACT
Found at i:13568167 original size:19 final size:19
Alignment explanation
Indices: 13568143--13568179 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
13568133 ATAAAGACTA
13568143 AAAAATTATA-AAAATATTG
1 AAAAA-TATAGAAAATATTG
13568162 AAAAATATAGAAAATATT
1 AAAAATATAGAAAATATT
13568180 TACAATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (19 bp):
AAAAATATAGAAAATATTG
Found at i:13568234 original size:10 final size:10
Alignment explanation
Indices: 13568142--13568227 Score: 52
Period size: 10 Copynumber: 8.6 Consensus size: 10
13568132 TATAAAGACT
13568142 AAAAA-ATTA
1 AAAAATATTA
*
13568151 TAAAAATATTG
1 -AAAAATATTA
13568162 AAAAATA-TA
1 AAAAATATTA
*
13568171 GAAAATATTTA
1 AAAAATA-TTA
* **
13568182 CAATTTATTA
1 AAAAATATTA
*
13568192 AAAAGT-TATA
1 AAAAATAT-TA
* *
13568202 ATAATTATTA
1 AAAAATATTA
13568212 AAAAATATTA
1 AAAAATATTA
13568222 AAAAAT
1 AAAAAT
13568228 CATAAAATTG
Statistics
Matches: 58, Mismatches: 13, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
9 8 0.14
10 40 0.69
11 10 0.17
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (10 bp):
AAAAATATTA
Found at i:13569327 original size:18 final size:18
Alignment explanation
Indices: 13569285--13569321 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
13569275 ATTAGGATTA
13569285 ATATTTAATATATTATTT
1 ATATTTAATATATTATTT
*
13569303 ATATTTAATTTA-TATTT
1 ATATTTAATATATTATTT
13569320 AT
1 AT
13569322 CTTTTAGGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
ATATTTAATATATTATTT
Found at i:13569333 original size:13 final size:14
Alignment explanation
Indices: 13569317--13569347 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
13569307 TTAATTTATA
13569317 TTTATCTTTTAG-G
1 TTTATCTTTTAGAG
13569330 TTTATCTTTTAGAG
1 TTTATCTTTTAGAG
13569344 TTTA
1 TTTA
13569348 AATTGGATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.19, C:0.06, G:0.13, T:0.61
Consensus pattern (14 bp):
TTTATCTTTTAGAG
Found at i:13578026 original size:24 final size:24
Alignment explanation
Indices: 13577996--13578049 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
13577986 CTGTGGAGAT
* *
13577996 TGATGATGCTT-TGGTGATTGAAGA
1 TGATGATACTTCTGATGA-TGAAGA
*
13578020 TGATGATATTTCTGATGATGAAGA
1 TGATGATACTTCTGATGATGAAGA
13578044 TGATGA
1 TGATGA
13578050 ACATGAAGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 21 0.81
25 5 0.19
ACGTcount: A:0.30, C:0.04, G:0.30, T:0.37
Consensus pattern (24 bp):
TGATGATACTTCTGATGATGAAGA
Found at i:13583206 original size:10 final size:10
Alignment explanation
Indices: 13583189--13583258 Score: 55
Period size: 9 Copynumber: 7.5 Consensus size: 10
13583179 GGATTTAATT
13583189 AATT-TTAAA
1 AATTATTAAA
13583198 AATTATTAAA
1 AATTATTAAA
*
13583208 AA-TAATAAA
1 AATTATTAAA
13583217 AA-TA--AAA
1 AATTATTAAA
13583224 AATTATATAAA
1 AATTAT-TAAA
*
13583235 AATGATT-AA
1 AATTATTAAA
13583244 AATTGA-TAAA
1 AATT-ATTAAA
13583254 AATTA
1 AATTA
13583259 AAAAAATATA
Statistics
Matches: 51, Mismatches: 3, Indels: 14
0.75 0.04 0.21
Matches are distributed among these distances:
7 5 0.10
8 2 0.04
9 21 0.41
10 15 0.29
11 8 0.16
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (10 bp):
AATTATTAAA
Found at i:13583224 original size:16 final size:18
Alignment explanation
Indices: 13583212--13583268 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
13583202 ATTAAAAATA
13583212 ATAAAAATAAAAAATTAT
1 ATAAAAATAAAAAATTAT
*
13583230 ATAAAAATGATTAAAATTGAT
1 ATAAAAAT-A-AAAAATT-AT
* *
13583251 A-AAAATTAAAAAAATAT
1 ATAAAAATAAAAAATTAT
13583268 A
1 A
13583269 GAATTTATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
17 3 0.09
18 13 0.41
19 2 0.06
20 11 0.34
21 3 0.09
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (18 bp):
ATAAAAATAAAAAATTAT
Found at i:13583412 original size:20 final size:20
Alignment explanation
Indices: 13583362--13583412 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
13583352 TATAATTTTC
* *
13583362 TAATTTTTACAATATTTTAA
1 TAATTTTTAAAAAATTTTAA
*
13583382 TAATTTATAAAAAATTTTAA
1 TAATTTTTAAAAAATTTTAA
**
13583402 TTTTTTTTAAA
1 TAATTTTTAAA
13583413 TTATACTTTT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (20 bp):
TAATTTTTAAAAAATTTTAA
Found at i:13583898 original size:27 final size:26
Alignment explanation
Indices: 13583851--13583907 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
13583841 TTGATATTAT
*
13583851 TTTTATAATATTTAATATTTTATAAGA
1 TTTTATAAAATTTAATATTTTATAA-A
* *
13583878 TTTTCTAAAATTT-ATATTTTTCTAAA
1 TTTTATAAAATTTAATA-TTTTATAAA
13583904 TTTT
1 TTTT
13583908 TCATGCAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 8 0.31
27 18 0.69
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.60
Consensus pattern (26 bp):
TTTTATAAAATTTAATATTTTATAAA
Found at i:13586743 original size:6 final size:7
Alignment explanation
Indices: 13586724--13586749 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
13586714 AGAAAGGAGA
13586724 AAGGGGG
1 AAGGGGG
13586731 AAGGGGG
1 AAGGGGG
13586738 AAGGGGG
1 AAGGGGG
13586745 AAGGG
1 AAGGG
13586750 AGAGGGGTGT
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:0.31, C:0.00, G:0.69, T:0.00
Consensus pattern (7 bp):
AAGGGGG
Found at i:13586755 original size:13 final size:14
Alignment explanation
Indices: 13586719--13586756 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
13586709 AAAGGAGAAA
13586719 GGAGAAAGGGGGAAG
1 GGAG-AAGGGGGAAG
*
13586734 GGGGAAGGGGGAAG
1 GGAGAAGGGGGAAG
13586748 GGAG-AGGGG
1 GGAGAAGGGG
13586757 TGTTTTTCCG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 5 0.24
14 13 0.62
15 3 0.14
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (14 bp):
GGAGAAGGGGGAAG
Found at i:13597336 original size:3 final size:3
Alignment explanation
Indices: 13597328--13597352 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
13597318 AAAATAATCC
13597328 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
13597353 TTCCTTCCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:13599554 original size:209 final size:209
Alignment explanation
Indices: 13599192--13599604 Score: 817
Period size: 209 Copynumber: 2.0 Consensus size: 209
13599182 TGCTTCAAGT
13599192 TGACTATCCTTCTTGGTGAAGGCACCTAAAACCAATCTGTTTCGACTATGGGCTAGTTTAGCATT
1 TGACTATCCTTCTTGGTGAAGGCACCTAAAACCAATCTGTTTCGACTATGGGCTAGTTTAGCATT
13599257 GCTTTTGGAAAGTGCTAAGAAAAAGTGACTTTGAAAAATGCTTTTGAAAGGTTTGGTTTAAGATC
66 GCTTTTGGAAAGTGCTAAGAAAAAGTGACTTTGAAAAATGCTTTTGAAAGGTTTGGTTTAAGATC
13599322 TAAGCATTCAGTATTGCTGTAAAAAAAGTGCATTTTTAGACATGATGTTGTAAAGTAAAAAATAT
131 TAAGCATTCAGTATTGCTGTAAAAAAAGTGCATTTTTAGACATGATGTTGTAAAGTAAAAAATAT
13599387 GCATTTAAAAAAAG
196 GCATTTAAAAAAAG
13599401 TGACTATCCTTCTTGGTGAAGGCACCTAAAACCAATCTGTTTCGACTATGGGCTAGTTTAGCATT
1 TGACTATCCTTCTTGGTGAAGGCACCTAAAACCAATCTGTTTCGACTATGGGCTAGTTTAGCATT
13599466 GCTTTTGGAAAGTGCTAAGAAAAAGTGACTTTGAAAAATGCTTTTGAAAGGTTTGGTTTAAGATC
66 GCTTTTGGAAAGTGCTAAGAAAAAGTGACTTTGAAAAATGCTTTTGAAAGGTTTGGTTTAAGATC
*
13599531 TAAGCATTCAGTATTGTTGTAAAAAAAGTGCATTTTTAGACATGATGTTGTAAAGTAAAAAATAT
131 TAAGCATTCAGTATTGCTGTAAAAAAAGTGCATTTTTAGACATGATGTTGTAAAGTAAAAAATAT
13599596 GCATTTAAA
196 GCATTTAAA
13599605 TGATGTTTAA
Statistics
Matches: 203, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
209 203 1.00
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.34
Consensus pattern (209 bp):
TGACTATCCTTCTTGGTGAAGGCACCTAAAACCAATCTGTTTCGACTATGGGCTAGTTTAGCATT
GCTTTTGGAAAGTGCTAAGAAAAAGTGACTTTGAAAAATGCTTTTGAAAGGTTTGGTTTAAGATC
TAAGCATTCAGTATTGCTGTAAAAAAAGTGCATTTTTAGACATGATGTTGTAAAGTAAAAAATAT
GCATTTAAAAAAAG
Found at i:13605012 original size:13 final size:13
Alignment explanation
Indices: 13604994--13605018 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13604984 CTAAATATTC
13604994 TTTTCTATTTTTA
1 TTTTCTATTTTTA
13605007 TTTTCTATTTTT
1 TTTTCTATTTTT
13605019 TAAAAAAAAA
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:0.12, C:0.08, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTCTATTTTTA
Found at i:13605114 original size:23 final size:23
Alignment explanation
Indices: 13605083--13605127 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
13605073 TAAAATTGTT
*
13605083 GTCTGTCTCGTTGACACACGCTC
1 GTCTCTCTCGTTGACACACGCTC
* *
13605106 GTCTCTCTCTTTGACACGCGCT
1 GTCTCTCTCGTTGACACACGCT
13605128 TCTCTGTATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.11, C:0.36, G:0.20, T:0.33
Consensus pattern (23 bp):
GTCTCTCTCGTTGACACACGCTC
Found at i:13605131 original size:21 final size:22
Alignment explanation
Indices: 13605088--13605132 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
13605078 TTGTTGTCTG
13605088 TCTCGTTGACACACGCTCGTCTC
1 TCTCGTTGACACACGCTC-TCTC
* *
13605111 TCTCTTTGACACGCGCT-TCTC
1 TCTCGTTGACACACGCTCTCTC
13605132 T
1 T
13605133 GTATTTTGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 5 0.25
23 15 0.75
ACGTcount: A:0.11, C:0.38, G:0.16, T:0.36
Consensus pattern (22 bp):
TCTCGTTGACACACGCTCTCTC
Found at i:13612626 original size:21 final size:22
Alignment explanation
Indices: 13612601--13612641 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
13612591 TAAAACCATG
*
13612601 AAAACCCAAT-ACCCAAACCTT
1 AAAACCAAATCACCCAAACCTT
13612622 AAAACCAAATCACCCAAACC
1 AAAACCAAATCACCCAAACC
13612642 CTAGACCCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.51, C:0.39, G:0.00, T:0.10
Consensus pattern (22 bp):
AAAACCAAATCACCCAAACCTT
Found at i:13613907 original size:3 final size:3
Alignment explanation
Indices: 13613833--13613890 Score: 93
Period size: 3 Copynumber: 20.0 Consensus size: 3
13613823 ACAGATTTAC
*
13613833 ATT ATT -TT A-T ATT ATT ATT ATT ATT ATT GTT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
13613879 ATT ATT ATT ATT
1 ATT ATT ATT ATT
13613891 TCGATTTTGG
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
2 4 0.08
3 47 0.92
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:13619602 original size:23 final size:22
Alignment explanation
Indices: 13619555--13619608 Score: 72
Period size: 23 Copynumber: 2.4 Consensus size: 22
13619545 CGTCTATCCT
* * *
13619555 TGCTGACTAGACTTTTGGAAGC
1 TGCTGACTGGACTTCTAGAAGC
13619577 TGCTGACTGGATCTTCTAGAAGC
1 TGCTGACTGGA-CTTCTAGAAGC
13619600 TGCTGACTG
1 TGCTGACTG
13619609 AATGTCACGT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 10 0.36
23 18 0.64
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.31
Consensus pattern (22 bp):
TGCTGACTGGACTTCTAGAAGC
Found at i:13628608 original size:29 final size:30
Alignment explanation
Indices: 13628576--13628646 Score: 99
Period size: 29 Copynumber: 2.4 Consensus size: 30
13628566 AAATCAAATT
*
13628576 TTCATGTATAAAATTGCACA-AAATTAAAG
1 TTCATGTATAAAATTGCACACAAACTAAAG
*
13628605 TTCATGTATAACATTGCACATCAAACTAAAG
1 TTCATGTATAAAATTGCACA-CAAACTAAAG
*
13628636 TTCAGGTATAA
1 TTCATGTATAA
13628647 TTTTGAGATT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 19 0.51
31 18 0.49
ACGTcount: A:0.44, C:0.14, G:0.11, T:0.31
Consensus pattern (30 bp):
TTCATGTATAAAATTGCACACAAACTAAAG
Found at i:13639191 original size:24 final size:24
Alignment explanation
Indices: 13639162--13639274 Score: 163
Period size: 24 Copynumber: 4.7 Consensus size: 24
13639152 TTTAGTTAAC
** *
13639162 ATAAACGAACATGTTTGCAAACAT
1 ATAAACGAACATGTTCACGAACAT
13639186 ATAAACGAACATGTTCACGAACAT
1 ATAAACGAACATGTTCACGAACAT
*
13639210 ATAAACGAATATGTTCACGAACAT
1 ATAAACGAACATGTTCACGAACAT
* * *
13639234 ATAAACGAGCATGTTCGCGAACGT
1 ATAAACGAACATGTTCACGAACAT
13639258 ATAAACGAACATGTTCA
1 ATAAACGAACATGTTCA
13639275 AACATGTTTG
Statistics
Matches: 79, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 79 1.00
ACGTcount: A:0.43, C:0.19, G:0.15, T:0.23
Consensus pattern (24 bp):
ATAAACGAACATGTTCACGAACAT
Found at i:13639196 original size:12 final size:12
Alignment explanation
Indices: 13639181--13639269 Score: 61
Period size: 12 Copynumber: 7.4 Consensus size: 12
13639171 CATGTTTGCA
13639181 AACATATAAACG
1 AACATATAAACG
* **
13639193 AACATGTTCACG
1 AACATATAAACG
13639205 AACATATAAACG
1 AACATATAAACG
* * **
13639217 AATATGTTCACG
1 AACATATAAACG
13639229 AACATATAAACG
1 AACATATAAACG
* * ***
13639241 AGCATGTTCGCG
1 AACATATAAACG
*
13639253 AACGTATAAACG
1 AACATATAAACG
13639265 AACAT
1 AACAT
13639270 GTTCAAACAT
Statistics
Matches: 51, Mismatches: 26, Indels: 0
0.66 0.34 0.00
Matches are distributed among these distances:
12 51 1.00
ACGTcount: A:0.45, C:0.19, G:0.15, T:0.21
Consensus pattern (12 bp):
AACATATAAACG
Found at i:13639538 original size:12 final size:12
Alignment explanation
Indices: 13639521--13639552 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
13639511 AAATATTATA
13639521 TATAAGGAGTTT
1 TATAAGGAGTTT
13639533 TATAAGGAGTTT
1 TATAAGGAGTTT
*
13639545 TATTAGGA
1 TATAAGGA
13639553 TTAAGTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.34, C:0.00, G:0.25, T:0.41
Consensus pattern (12 bp):
TATAAGGAGTTT
Found at i:13639960 original size:12 final size:12
Alignment explanation
Indices: 13639943--13639967 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
13639933 ATTGTTTAGA
13639943 ATCTGATTAAGG
1 ATCTGATTAAGG
13639955 ATCTGATTAAGG
1 ATCTGATTAAGG
13639967 A
1 A
13639968 ATAGAGAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.08, G:0.24, T:0.32
Consensus pattern (12 bp):
ATCTGATTAAGG
Found at i:13640263 original size:47 final size:46
Alignment explanation
Indices: 13640212--13640336 Score: 162
Period size: 47 Copynumber: 2.7 Consensus size: 46
13640202 GTTATTTTAT
* * *
13640212 GTTTATTCGAATTTGATGTCGATATTGATTGTGATTTTTGATTTAGG
1 GTTTATTCGATTTTGAT-TAGATTTTGATTGTGATTTTTGATTTAGG
* * *
13640259 GTTTATTCGATTTTAATTTGGATTTTGATTTTGATTTTTGATTTAGG
1 GTTTATTCGATTTTGA-TTAGATTTTGATTGTGATTTTTGATTTAGG
13640306 G-TTATTTCGATTTTGATTAGATTTTGATTGT
1 GTTTA-TTCGATTTTGATTAGATTTTGATTGT
13640337 TACTGTTTGA
Statistics
Matches: 68, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
46 16 0.24
47 51 0.75
48 1 0.01
ACGTcount: A:0.20, C:0.03, G:0.21, T:0.56
Consensus pattern (46 bp):
GTTTATTCGATTTTGATTAGATTTTGATTGTGATTTTTGATTTAGG
Found at i:13640403 original size:14 final size:14
Alignment explanation
Indices: 13640386--13640412 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
13640376 TTTTTTATTC
13640386 ACATATTTTGGTTA
1 ACATATTTTGGTTA
13640400 ACATATTTTGGTT
1 ACATATTTTGGTT
13640413 TAGGGTTATT
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:0.26, C:0.07, G:0.15, T:0.52
Consensus pattern (14 bp):
ACATATTTTGGTTA
Found at i:13652554 original size:43 final size:43
Alignment explanation
Indices: 13652506--13652601 Score: 167
Period size: 43 Copynumber: 2.2 Consensus size: 43
13652496 GTCGCAGTTT
13652506 GACCTGGATTTTCTTTTTCTTTTTTT-TATTTATTTTGGTAACA
1 GACCTGGATTTTCTTTTTCTTTTTTTAT-TTTATTTTGGTAACA
*
13652549 GACCTGGATTTTCTTTTTCTTTTTTTATTTTATTTTGGTAATA
1 GACCTGGATTTTCTTTTTCTTTTTTTATTTTATTTTGGTAACA
13652592 GACCTGGATT
1 GACCTGGATT
13652602 CTGGAATACA
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
43 50 0.98
44 1 0.02
ACGTcount: A:0.17, C:0.11, G:0.14, T:0.58
Consensus pattern (43 bp):
GACCTGGATTTTCTTTTTCTTTTTTTATTTTATTTTGGTAACA
Found at i:13655256 original size:14 final size:15
Alignment explanation
Indices: 13655224--13655256 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
13655214 AGTCTTTATA
*
13655224 TTTTAATTTTGATAT
1 TTTTAATCTTGATAT
13655239 TTTTAATCTTG-TAT
1 TTTTAATCTTGATAT
13655253 TTTT
1 TTTT
13655257 CGAATAGGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.21, C:0.03, G:0.06, T:0.70
Consensus pattern (15 bp):
TTTTAATCTTGATAT
Found at i:13660663 original size:41 final size:41
Alignment explanation
Indices: 13660618--13660695 Score: 113
Period size: 41 Copynumber: 1.9 Consensus size: 41
13660608 GTTGAGTGCA
*
13660618 GATTACTTCTATTTATCTG-ATGATGCACTATGTGCCAATAT
1 GATTACTTCGATTTATC-GAATGATGCACTATGTGCCAATAT
* *
13660659 GATTACTTCGATTTATCGAATTATGCAGTATGTGCCA
1 GATTACTTCGATTTATCGAATGATGCACTATGTGCCA
13660696 GTATATTTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 1 0.03
41 32 0.97
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.40
Consensus pattern (41 bp):
GATTACTTCGATTTATCGAATGATGCACTATGTGCCAATAT
Found at i:13663155 original size:2 final size:2
Alignment explanation
Indices: 13663148--13663197 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
13663138 TCTCTTTGGA
*
13663148 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CC CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
*
13663190 CT CC CT CT
1 CT CT CT CT
13663198 TTGGTAATTA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (2 bp):
CT
Found at i:13674962 original size:25 final size:23
Alignment explanation
Indices: 13674933--13674978 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
13674923 GTTGGATCCA
13674933 AATTAAATTCTAAAAAGATAATTTG
1 AATTAAA-TCTAAAAA-ATAATTTG
*
13674958 AATTAAATCTAAATAATAATT
1 AATTAAATCTAAAAAATAATT
13674979 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.37
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTTG
Found at i:13681058 original size:17 final size:18
Alignment explanation
Indices: 13681036--13681070 Score: 54
Period size: 17 Copynumber: 1.9 Consensus size: 18
13681026 TCTTAAAAAA
13681036 AAAAAATT-AAAATTTTG
1 AAAAAATTAAAAATTTTG
13681053 AAAAAATTCAAAAATTTT
1 AAAAAATT-AAAAATTTT
13681071 AAGGGATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
19 8 0.50
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (18 bp):
AAAAAATTAAAAATTTTG
Found at i:13681249 original size:24 final size:25
Alignment explanation
Indices: 13681214--13681277 Score: 67
Period size: 24 Copynumber: 2.5 Consensus size: 25
13681204 AGTAGTTTTT
* * *
13681214 TAAAATTTAAAAACATATAACAAA-
1 TAAAATTCAAAAACATAAAAAAAAG
*
13681238 TAAAATTCAAAAATATAAAAAAAAG
1 TAAAATTCAAAAACATAAAAAAAAG
13681263 TAAAATAGTCAAAAA
1 TAAAAT--TCAAAAA
13681278 AAATTTAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
24 20 0.61
25 6 0.18
27 7 0.21
ACGTcount: A:0.69, C:0.06, G:0.03, T:0.22
Consensus pattern (25 bp):
TAAAATTCAAAAACATAAAAAAAAG
Found at i:13681592 original size:58 final size:59
Alignment explanation
Indices: 13681447--13681601 Score: 170
Period size: 58 Copynumber: 2.6 Consensus size: 59
13681437 AAGCATATGT
* *
13681447 ACCAAATTAGAAAAAAATATCAAGTTC-AGATACCAAATTAGGTCCAAAAAAGTTTAGGT
1 ACCAAATTAGAAAAAAATATCAAGTTCAAG-TACCAAATTAGGTCCAAAAAAGTTTAAGA
* * * * * * *
13681506 ATCAAAGTAGGAAAAAGTGTCAAGTTCAAGTACCAAATTGGGT-TAAAAAAGTTTAAGA
1 ACCAAATTAGAAAAAAATATCAAGTTCAAGTACCAAATTAGGTCCAAAAAAGTTTAAGA
* * * *
13681564 ACCAAATTAAAAAAAAATATTAAATTCAAGTATCAAAT
1 ACCAAATTAGAAAAAAATATCAAGTTCAAGTACCAAAT
13681602 GTTATATTAA
Statistics
Matches: 77, Mismatches: 18, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
58 41 0.53
59 34 0.44
60 2 0.03
ACGTcount: A:0.51, C:0.11, G:0.14, T:0.25
Consensus pattern (59 bp):
ACCAAATTAGAAAAAAATATCAAGTTCAAGTACCAAATTAGGTCCAAAAAAGTTTAAGA
Found at i:13698734 original size:16 final size:16
Alignment explanation
Indices: 13698703--13698748 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
13698693 TAATTATCAT
*
13698703 TTTATAATTATATATAA
1 TTTAT-ATTTTATATAA
13698720 TTTATATTTTATATAA
1 TTTATATTTTATATAA
* *
13698736 TTGATATATTATA
1 TTTATATTTTATA
13698749 AAAATTAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
16 21 0.81
17 5 0.19
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (16 bp):
TTTATATTTTATATAA
Found at i:13702238 original size:17 final size:18
Alignment explanation
Indices: 13702204--13702242 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
13702194 CTATTATCGA
**
13702204 TTTTATTAATTTATTTAT
1 TTTTATTAAAATATTTAT
13702222 TTTTATTAAAATA-TTAT
1 TTTTATTAAAATATTTAT
13702239 TTTT
1 TTTT
13702243 TATAGTTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTTATTAAAATATTTAT
Found at i:13706039 original size:29 final size:31
Alignment explanation
Indices: 13706007--13706074 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 31
13705997 AAAAATTCGT
*
13706007 GTTTAATTTTTTAAATT-TTAAAATT-TTAA
1 GTTTAATTTGTTAAATTATTAAAATTATTAA
* *
13706036 GTTTAA-TTGTTATATTATTAAAATTATTAT
1 GTTTAATTTGTTAAATTATTAAAATTATTAA
*
13706066 GTTAAATTT
1 GTTTAATTT
13706075 ACGTTTATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
28 8 0.25
29 14 0.44
30 8 0.25
31 2 0.06
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (31 bp):
GTTTAATTTGTTAAATTATTAAAATTATTAA
Found at i:13707490 original size:20 final size:20
Alignment explanation
Indices: 13707467--13707515 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
13707457 TTTACTAATG
13707467 TTTCAAAGGCTTTACCATCA
1 TTTCAAAGGCTTTACCATCA
* * * *
13707487 TTTCTAAGTCTTTATCATTA
1 TTTCAAAGGCTTTACCATCA
13707507 TTTCTAAAG
1 TTTC-AAAG
13707516 ATTTCTCTGT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
20 20 0.87
21 3 0.13
ACGTcount: A:0.29, C:0.18, G:0.08, T:0.45
Consensus pattern (20 bp):
TTTCAAAGGCTTTACCATCA
Found at i:13707630 original size:19 final size:20
Alignment explanation
Indices: 13707571--13707705 Score: 69
Period size: 20 Copynumber: 6.7 Consensus size: 20
13707561 GACAGCGTGG
* *
13707571 AAATCTTTAGAAATTGTGGT
1 AAATCTTTAAAAATTTTGGT
* * * *
13707591 AAAACTTTAGAAATATAGGT
1 AAATCTTTAAAAATTTTGGT
13707611 AAATC-TTAAAAATTTTGGT
1 AAATCTTTAAAAATTTTGGT
* * *
13707630 ATAATC-TTCAAATTTTTAGT
1 A-AATCTTTAAAAATTTTGGT
** **
13707650 AAAT-TGTTAGAATTTCTTTTTT
1 AAATCT-TTA-AAAAT-TTTGGT
*
13707672 AAATCTTTAAAAGTTTTGGT
1 AAATCTTTAAAAATTTTGGT
*
13707692 AAATTATTTAAAAA
1 AAA-TCTTTAAAAA
13707706 AATTGTATTG
Statistics
Matches: 87, Mismatches: 21, Indels: 13
0.72 0.17 0.11
Matches are distributed among these distances:
19 15 0.17
20 45 0.52
21 15 0.17
22 11 0.13
23 1 0.01
ACGTcount: A:0.40, C:0.05, G:0.11, T:0.44
Consensus pattern (20 bp):
AAATCTTTAAAAATTTTGGT
Found at i:13713436 original size:3 final size:3
Alignment explanation
Indices: 13713428--13713532 Score: 95
Period size: 3 Copynumber: 35.0 Consensus size: 3
13713418 TCTTCACTGC
* * * * * **
13713428 CAT CAT CAT CAT CGT CTT CAT CAA CCT CAT TAT CAT TGT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
* ** *
13713476 CAT CAT CAT CAT CAT CAT CAT CGT TGT CAT CAT CAT CAT CAG CAT CAAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C-AT
13713525 -AT CAT CAT
1 CAT CAT CAT
13713533 AAACATCATG
Statistics
Matches: 81, Mismatches: 19, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
2 2 0.02
3 77 0.95
4 2 0.02
ACGTcount: A:0.30, C:0.30, G:0.05, T:0.35
Consensus pattern (3 bp):
CAT
Found at i:13717867 original size:10 final size:10
Alignment explanation
Indices: 13717849--13717881 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
13717839 GTAAAATATT
*
13717849 TTATAAAATA
1 TTATTAAATA
13717859 TTATTAAATA
1 TTATTAAATA
13717869 TTATTAAATA
1 TTATTAAATA
13717879 TTA
1 TTA
13717882 AAAATAATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (10 bp):
TTATTAAATA
Found at i:13732846 original size:12 final size:12
Alignment explanation
Indices: 13732829--13732867 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
13732819 TTACAGAATC
13732829 ATAGGCTGATTT
1 ATAGGCTGATTT
* *
13732841 ATAGGCTAATTA
1 ATAGGCTGATTT
*
13732853 ATAGGTTGATTT
1 ATAGGCTGATTT
13732865 ATA
1 ATA
13732868 TTGTATTTAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.33, C:0.05, G:0.21, T:0.41
Consensus pattern (12 bp):
ATAGGCTGATTT
Found at i:13741821 original size:120 final size:118
Alignment explanation
Indices: 13741666--13741909 Score: 305
Period size: 120 Copynumber: 2.1 Consensus size: 118
13741656 TTTCACAGGC
* * * *
13741666 AAGCCTACAAGAAAATTGCTAACTGATTCCATCTTTATGTTTC-ATGTATTAACAA-ATATTTCC
1 AAGCCTACAAGAAAATAGCTAACTGATTCCATCTTTA-GGTTCAATGTATTAACAAGAAAGTTCC
* *
13741729 TTTAATCTTTCACTAATCTTT-TACACCATTTTTTTCTCATTCATTACCTTCAGAATT
65 TTTAATCTTTCACTAATCTTTCGA-ACC---TTTTTCTCATTCATTACCTTCAGAAAT
* * * *
13741786 AAGCCTGCAAGTAAATAGCTAATTGGTTCCATCTTTAGGTTCAATGTATTAACAAGAAAGTTCCT
1 AAGCCTACAAGAAAATAGCTAACTGATTCCATCTTTAGGTTCAATGTATTAACAAGAAAGTTCCT
* * *
13741851 TTAATCTTTCATTAATCTTTCGAACCTTTTTCTCATTCATTACTTTCATAAAT
66 TTAATCTTTCACTAATCTTTCGAACCTTTTTCTCATTCATTACCTTCAGAAAT
13741904 AAGCCT
1 AAGCCT
13741910 TACTTCCAAT
Statistics
Matches: 108, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
118 30 0.28
119 4 0.04
120 44 0.41
121 29 0.27
122 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.08, T:0.41
Consensus pattern (118 bp):
AAGCCTACAAGAAAATAGCTAACTGATTCCATCTTTAGGTTCAATGTATTAACAAGAAAGTTCCT
TTAATCTTTCACTAATCTTTCGAACCTTTTTCTCATTCATTACCTTCAGAAAT
Found at i:13744762 original size:19 final size:19
Alignment explanation
Indices: 13744740--13744779 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
13744730 TTTTACTTTT
*
13744740 ATTATACTTTTCT-ATTCTA
1 ATTAAACTTTT-TGATTCTA
13744759 ATTAAACTTTTTGATTCTA
1 ATTAAACTTTTTGATTCTA
13744778 AT
1 AT
13744780 AATAATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 1 0.05
19 18 0.95
ACGTcount: A:0.30, C:0.12, G:0.03, T:0.55
Consensus pattern (19 bp):
ATTAAACTTTTTGATTCTA
Found at i:13745790 original size:15 final size:15
Alignment explanation
Indices: 13745766--13745799 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
13745756 GGATTTTTTG
* *
13745766 ACATTCTAATTCCGT
1 ACATTATAATTCCAT
13745781 ACATTATAATTCCAT
1 ACATTATAATTCCAT
13745796 ACAT
1 ACAT
13745800 AGACATAACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.24, G:0.03, T:0.38
Consensus pattern (15 bp):
ACATTATAATTCCAT
Found at i:13752014 original size:13 final size:13
Alignment explanation
Indices: 13751992--13752062 Score: 83
Period size: 13 Copynumber: 5.5 Consensus size: 13
13751982 TTGAAATGAC
13751992 TATATG-AATGGT
1 TATATGAAATGGT
13752004 TATATGAAATGGT
1 TATATGAAATGGT
13752017 TATATG-AATCGGT
1 TATATGAAAT-GGT
**
13752030 TATATGGAAATAAT
1 TATAT-GAAATGGT
*
13752044 TATATGAAATGTT
1 TATATGAAATGGT
13752057 TATATG
1 TATATG
13752063 GATAGATATG
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
12 9 0.18
13 32 0.63
14 7 0.14
15 3 0.06
ACGTcount: A:0.38, C:0.01, G:0.20, T:0.41
Consensus pattern (13 bp):
TATATGAAATGGT
Found at i:13752046 original size:27 final size:26
Alignment explanation
Indices: 13751992--13752064 Score: 94
Period size: 27 Copynumber: 2.8 Consensus size: 26
13751982 TTGAAATGAC
**
13751992 TATATGAATGGTTATAT-GAAATGGT
1 TATATGAATGGTTATATGGAAATAAT
13752017 TATATGAATCGGTTATATGGAAATAAT
1 TATATGAAT-GGTTATATGGAAATAAT
*
13752044 TATATGAAATGTTTATATGGA
1 TATATG-AATGGTTATATGGA
13752065 TAGATATGTA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
25 9 0.21
26 8 0.19
27 22 0.52
28 3 0.07
ACGTcount: A:0.38, C:0.01, G:0.21, T:0.40
Consensus pattern (26 bp):
TATATGAATGGTTATATGGAAATAAT
Found at i:13752197 original size:25 final size:25
Alignment explanation
Indices: 13752169--13752228 Score: 102
Period size: 25 Copynumber: 2.4 Consensus size: 25
13752159 TTTATACTTG
*
13752169 TATATGTTTTATGAGATAATAGAGT
1 TATAAGTTTTATGAGATAATAGAGT
*
13752194 TATAAGTTTTATGAGATAATAGGGT
1 TATAAGTTTTATGAGATAATAGAGT
13752219 TATAAGTTTT
1 TATAAGTTTT
13752229 GTATATGTGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.35, C:0.00, G:0.20, T:0.45
Consensus pattern (25 bp):
TATAAGTTTTATGAGATAATAGAGT
Found at i:13752972 original size:34 final size:34
Alignment explanation
Indices: 13752927--13752997 Score: 106
Period size: 34 Copynumber: 2.1 Consensus size: 34
13752917 TTTCATCTCT
* *
13752927 CTTGACTTTTAACATTTCATTTTCCTTAACCTTC
1 CTTGACCTTTAACATTTCATCTTCCTTAACCTTC
* *
13752961 CTTGACCTTTAACCTTTCATCTTCCTTAACTTTC
1 CTTGACCTTTAACATTTCATCTTCCTTAACCTTC
13752995 CTT
1 CTT
13752998 ATTCTTGTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.18, C:0.30, G:0.03, T:0.49
Consensus pattern (34 bp):
CTTGACCTTTAACATTTCATCTTCCTTAACCTTC
Found at i:13753711 original size:18 final size:18
Alignment explanation
Indices: 13753676--13753711 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
13753666 AAGATTCCCT
*
13753676 AAGATTACAAAATCTTCA
1 AAGATTACAAAATATTCA
*
13753694 AAGATTACAATATATTCA
1 AAGATTACAAAATATTCA
13753712 CCTTGATAAA
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:0.14, G:0.06, T:0.31
Consensus pattern (18 bp):
AAGATTACAAAATATTCA
Found at i:13761823 original size:17 final size:17
Alignment explanation
Indices: 13761801--13761835 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
13761791 CTCCACATTG
* *
13761801 ACAAGAATTCTCTACGA
1 ACAAGAACTCTCAACGA
13761818 ACAAGAACTCTCAACGA
1 ACAAGAACTCTCAACGA
13761835 A
1 A
13761836 AAGTTCTCCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.46, C:0.26, G:0.11, T:0.17
Consensus pattern (17 bp):
ACAAGAACTCTCAACGA
Found at i:13762472 original size:21 final size:21
Alignment explanation
Indices: 13762448--13762488 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
13762438 GCATGACGGT
13762448 ACCAAATGAATTAAAATTGAC
1 ACCAAATGAATTAAAATTGAC
13762469 ACCAAATGAATTAAAATTGA
1 ACCAAATGAATTAAAATTGA
13762489 GTTACATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.54, C:0.12, G:0.10, T:0.24
Consensus pattern (21 bp):
ACCAAATGAATTAAAATTGAC
Found at i:13763986 original size:30 final size:29
Alignment explanation
Indices: 13763930--13763988 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
13763920 AAAATAGATG
13763930 TATTATAAATTATTTTATTATAAAAAACA
1 TATTATAAATTATTTTATTATAAAAAACA
*
13763959 TATTAATAATTTATTATT-TTATTAAAAAAC
1 TATT-ATAAATTATT-TTATTA-TAAAAAAC
13763989 GACATTCAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 4 0.15
30 12 0.46
31 10 0.38
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.47
Consensus pattern (29 bp):
TATTATAAATTATTTTATTATAAAAAACA
Found at i:13778100 original size:32 final size:30
Alignment explanation
Indices: 13778060--13778162 Score: 95
Period size: 32 Copynumber: 3.4 Consensus size: 30
13778050 AAAAAAGCTT
13778060 AGGTATCAAATTAGGAAAAAAATGTTAAGTTC
1 AGGTATCAAATTAGGAAAAAAA-G-TAAGTTC
* *
13778092 AGGTATCAAA-TAGGGTAAAAAA--AAGTTT
1 AGGTATCAAATTA-GGAAAAAAAGTAAGTTC
* *
13778120 AGGTACCAAATTAGAAAAAAAAAGTCAAGTTC
1 AGGTATCAAATTAG-GAAAAAAAGT-AAGTTC
*
13778152 AGATATCAAAT
1 AGGTATCAAAT
13778163 GTTATATTAA
Statistics
Matches: 57, Mismatches: 8, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
28 15 0.26
29 8 0.14
31 2 0.04
32 32 0.56
ACGTcount: A:0.50, C:0.08, G:0.17, T:0.24
Consensus pattern (30 bp):
AGGTATCAAATTAGGAAAAAAAGTAAGTTC
Found at i:13778130 original size:60 final size:60
Alignment explanation
Indices: 13778049--13778162 Score: 174
Period size: 60 Copynumber: 1.9 Consensus size: 60
13778039 AATTCAAACT
* * * * *
13778049 AAAAAAAGCTTAGGTATCAAATTAGGAAAAAAATGTTAAGTTCAGGTATCAAATAGGGTA
1 AAAAAAAGCTTAGGTACCAAATTAGAAAAAAAAAGTCAAGTTCAGATATCAAATAGGGTA
*
13778109 AAAAAAAGTTTAGGTACCAAATTAGAAAAAAAAAGTCAAGTTCAGATATCAAAT
1 AAAAAAAGCTTAGGTACCAAATTAGAAAAAAAAAGTCAAGTTCAGATATCAAAT
13778163 GTTATATTAA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 48 1.00
ACGTcount: A:0.52, C:0.08, G:0.17, T:0.24
Consensus pattern (60 bp):
AAAAAAAGCTTAGGTACCAAATTAGAAAAAAAAAGTCAAGTTCAGATATCAAATAGGGTA
Found at i:13784040 original size:17 final size:18
Alignment explanation
Indices: 13784013--13784046 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
13784003 TTTATGAAAG
13784013 TTGGATTTATTGAGTGTC
1 TTGGATTTATTGAGTGTC
*
13784031 TTGG-TTTATTGGGTGT
1 TTGGATTTATTGAGTGT
13784047 TAAAAAACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.12, C:0.03, G:0.32, T:0.53
Consensus pattern (18 bp):
TTGGATTTATTGAGTGTC
Found at i:13787511 original size:42 final size:42
Alignment explanation
Indices: 13787453--13787548 Score: 183
Period size: 42 Copynumber: 2.3 Consensus size: 42
13787443 GTAATAAAAA
*
13787453 TATTATTTAAATTATCATTTGGATTGAAATAATGTTATTTTT
1 TATTATTTAAATTATCATTTGAATTGAAATAATGTTATTTTT
13787495 TATTATTTAAATTATCATTTGAATTGAAATAATGTTATTTTT
1 TATTATTTAAATTATCATTTGAATTGAAATAATGTTATTTTT
13787537 TATTATTTAAAT
1 TATTATTTAAAT
13787549 CATTTTAAAA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.35, C:0.02, G:0.07, T:0.55
Consensus pattern (42 bp):
TATTATTTAAATTATCATTTGAATTGAAATAATGTTATTTTT
Found at i:13791140 original size:9 final size:9
Alignment explanation
Indices: 13791126--13791151 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
13791116 TAAATAGTTC
13791126 GAGTTATTT
1 GAGTTATTT
13791135 GAGTTATTT
1 GAGTTATTT
13791144 GAGTTATT
1 GAGTTATT
13791152 CGGATCAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.54
Consensus pattern (9 bp):
GAGTTATTT
Found at i:13791750 original size:20 final size:20
Alignment explanation
Indices: 13791727--13791771 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
13791717 TTTGTCATAT
13791727 TTTATAAACTGCACAGGATG
1 TTTATAAACTGCACAGGATG
*
13791747 TTTATAAACTGCATAGGATG
1 TTTATAAACTGCACAGGATG
13791767 TTTAT
1 TTTAT
13791772 CTATAACCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.38
Consensus pattern (20 bp):
TTTATAAACTGCACAGGATG
Found at i:13796642 original size:78 final size:79
Alignment explanation
Indices: 13796512--13796667 Score: 287
Period size: 78 Copynumber: 2.0 Consensus size: 79
13796502 ATTTTCAACT
*
13796512 ACTCTCCCATTTAGATTTATTGTTTATAGGATAGTATATTTTGGTGCTTTAATCTGACTGCATAG
1 ACTCTCCCATTTAGATTTATTGTTTATAGGATAGTATATTTTGGTGCCTTAATCTGACTGCATAG
*
13796577 C-CTAAATTCATTC
66 CAATAAATTCATTC
13796590 ACTCTCCCATTTAGATTTATTGTTTATAGGATAGTATATTTTGGTGCCTTAATCTGACTGCATAG
1 ACTCTCCCATTTAGATTTATTGTTTATAGGATAGTATATTTTGGTGCCTTAATCTGACTGCATAG
13796655 CAATAAATTCATT
66 CAATAAATTCATT
13796668 GATGAATGAA
Statistics
Matches: 75, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
78 65 0.87
79 10 0.13
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (79 bp):
ACTCTCCCATTTAGATTTATTGTTTATAGGATAGTATATTTTGGTGCCTTAATCTGACTGCATAG
CAATAAATTCATTC
Found at i:13801833 original size:3 final size:3
Alignment explanation
Indices: 13801825--13801856 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
13801815 GAAGATGGTG
*
13801825 AGA AGA AGA AGA AGA AGA AGA AGG AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
13801857 GGATTGAAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:13801857 original size:9 final size:9
Alignment explanation
Indices: 13801811--13801857 Score: 51
Period size: 9 Copynumber: 5.3 Consensus size: 9
13801801 AAGAAGAGAT
13801811 AGGAGAAGA
1 AGGAGAAGA
* *
13801820 TGGTG-AGA
1 AGGAGAAGA
*
13801828 AGAAGAAGA
1 AGGAGAAGA
*
13801837 AGAAGAAGA
1 AGGAGAAGA
13801846 AGGAGAAGA
1 AGGAGAAGA
13801855 AGG
1 AGG
13801858 GATTGAAGGA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
8 5 0.16
9 26 0.84
ACGTcount: A:0.53, C:0.00, G:0.43, T:0.04
Consensus pattern (9 bp):
AGGAGAAGA
Found at i:13803811 original size:32 final size:32
Alignment explanation
Indices: 13803766--13803884 Score: 83
Period size: 32 Copynumber: 3.9 Consensus size: 32
13803756 GTACCAACTT
*
13803766 AAAAAAGTGTCAAGTTTAGGTACCAAATTAGAA
1 AAAAAAATGTCAAGTTTAGGTACCAAATT-GAA
* * *
13803799 AAAAAAAT-TCAAGTTT-GACTATCAAATTGGAC
1 AAAAAAATGTCAAGTTTAG-GTACCAAATT-GAA
* *
13803831 CAAAAAA--T-AA-TTTAAGTACCAAATT--A
1 AAAAAAATGTCAAGTTTAGGTACCAAATTGAA
* *
13803857 AGAAAAATGTCAAGTTCAGGTACCAAAT
1 AAAAAAATGTCAAGTTTAGGTACCAAAT
13803885 GTTATATTAA
Statistics
Matches: 66, Mismatches: 14, Indels: 15
0.69 0.15 0.16
Matches are distributed among these distances:
26 5 0.08
28 1 0.02
29 13 0.20
30 14 0.21
31 2 0.03
32 24 0.36
33 7 0.11
ACGTcount: A:0.50, C:0.12, G:0.13, T:0.25
Consensus pattern (32 bp):
AAAAAAATGTCAAGTTTAGGTACCAAATTGAA
Found at i:13804352 original size:2 final size:2
Alignment explanation
Indices: 13804345--13804390 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
13804335 ATAAACGTAA
13804345 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
13804387 AT AT
1 AT AT
13804391 TTACAGATTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13805937 original size:20 final size:20
Alignment explanation
Indices: 13805912--13805955 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
13805902 TTTTTCAAAT
13805912 AATTAT-AAAATAATATTAAA
1 AATTATAAAAAT-ATATTAAA
*
13805932 AATTATAAAAATATTTTAAA
1 AATTATAAAAATATATTAAA
13805952 AATT
1 AATT
13805956 GAAAATATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
AATTATAAAAATATATTAAA
Found at i:13805946 original size:18 final size:18
Alignment explanation
Indices: 13805912--13805972 Score: 54
Period size: 20 Copynumber: 3.3 Consensus size: 18
13805902 TTTTTCAAAT
13805912 AATTATAAAATAATATTAAA
1 AATTAT-AAA-AATATTAAA
13805932 AATTATAAAAATATTTTAAA
1 AATTATAAAAATA--TTAAA
* *
13805952 AA-T-TGAAAATATTTAA
1 AATTATAAAAATATTAAA
13805968 AATTA
1 AATTA
13805973 ATCTTAATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
16 6 0.17
17 1 0.03
18 11 0.31
19 4 0.11
20 13 0.37
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (18 bp):
AATTATAAAAATATTAAA
Found at i:13816151 original size:11 final size:11
Alignment explanation
Indices: 13816137--13816227 Score: 60
Period size: 11 Copynumber: 7.9 Consensus size: 11
13816127 AATGTTTTGC
*
13816137 TATTCTTTTAT
1 TATTATTTTAT
* *
13816148 TATTATATTAC
1 TATTATTTTAT
13816159 TATTATTTTAT
1 TATTATTTTAT
13816170 TATTATTATT-T
1 TATTATT-TTAT
* * *
13816181 GGA-TACTGTATAAA
1 -TATTA-T-T-TTAT
13816195 TATTATTTTAT
1 TATTATTTTAT
13816206 TATTAATTTTAT
1 TATT-ATTTTAT
13816218 TATTATTTTA
1 TATTATTTTA
13816228 GAGACATTTA
Statistics
Matches: 62, Mismatches: 11, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
11 39 0.63
12 16 0.26
13 5 0.08
14 2 0.03
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (11 bp):
TATTATTTTAT
Found at i:13816164 original size:14 final size:14
Alignment explanation
Indices: 13816145--13816179 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
13816135 GCTATTCTTT
13816145 TATTATTATATTAC
1 TATTATTATATTAC
* *
13816159 TATTATTTTATTAT
1 TATTATTATATTAC
13816173 TATTATT
1 TATTATT
13816180 TGGATACTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (14 bp):
TATTATTATATTAC
Found at i:13816216 original size:12 final size:11
Alignment explanation
Indices: 13816195--13816227 Score: 57
Period size: 12 Copynumber: 2.9 Consensus size: 11
13816185 ACTGTATAAA
13816195 TATTATTTTAT
1 TATTATTTTAT
13816206 TATTAATTTTAT
1 TATT-ATTTTAT
13816218 TATTATTTTA
1 TATTATTTTA
13816228 GAGACATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
TATTATTTTAT
Found at i:13817816 original size:17 final size:18
Alignment explanation
Indices: 13817794--13817835 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
13817784 TGTTTAGCAT
*
13817794 TGCTTTTGGT-TCAAAAG
1 TGCTTTTGATGTCAAAAG
*
13817811 TGCTTTTTATGTCAAAAG
1 TGCTTTTGATGTCAAAAG
13817829 TGCTTTT
1 TGCTTTT
13817836 AAAAATCACT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.21, C:0.12, G:0.19, T:0.48
Consensus pattern (18 bp):
TGCTTTTGATGTCAAAAG
Found at i:13826911 original size:32 final size:33
Alignment explanation
Indices: 13826875--13826936 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
13826865 GTTTTTTGTC
*
13826875 AATTTGATA-CTCAAACTTGACA-TTTTTTTCCT
1 AATTTAATACCTC-AACTTGACACTTTTTTTCCT
13826907 AATTTAATACCTCAACTTGACACTTTTTTT
1 AATTTAATACCTCAACTTGACACTTTTTTT
13826937 AAGTTGGTAC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
32 17 0.63
33 10 0.37
ACGTcount: A:0.29, C:0.19, G:0.05, T:0.47
Consensus pattern (33 bp):
AATTTAATACCTCAACTTGACACTTTTTTTCCT
Found at i:13827332 original size:59 final size:58
Alignment explanation
Indices: 13827161--13827341 Score: 211
Period size: 58 Copynumber: 3.1 Consensus size: 58
13827151 ATTTAGGTAT
* * **
13827161 CAAATTGAATCCAAAAAAACCTTAGGTACCAAATT-AGGAAAAATGTCAAGTTCAAGTAC
1 CAAATTGAGT-CAAAAAAA-TTTAGGTACCAAATTAAAAAAAAATGTCAAGTTCAAGTAC
** * * * * *
13827220 CATTTTGGGTCAAAAAAATTTAAGTACCGAATTAGAAAAAAATGTCAAGTTCAAATAC
1 CAAATTGAGTCAAAAAAATTTAGGTACCAAATTAAAAAAAAATGTCAAGTTCAAGTAC
* *
13827278 CAAATTGAGTCAAAAAAATTTAGGTACTAAATTAAAAAAAAAGTGTCAAATTCAAGTAC
1 CAAATTGAGTCAAAAAAATTTAGGTACCAAATTAAAAAAAAA-TGTCAAGTTCAAGTAC
13827337 CAAAT
1 CAAAT
13827342 ATTATATTAA
Statistics
Matches: 100, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
57 12 0.12
58 63 0.63
59 25 0.25
ACGTcount: A:0.49, C:0.13, G:0.13, T:0.25
Consensus pattern (58 bp):
CAAATTGAGTCAAAAAAATTTAGGTACCAAATTAAAAAAAAATGTCAAGTTCAAGTAC
Found at i:13830072 original size:13 final size:13
Alignment explanation
Indices: 13830054--13830078 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13830044 TGTTAAAAAA
13830054 TAAAATAGAGAGG
1 TAAAATAGAGAGG
13830067 TAAAATAGAGAG
1 TAAAATAGAGAG
13830079 TTCTATGGGG
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:0.28, T:0.16
Consensus pattern (13 bp):
TAAAATAGAGAGG
Found at i:13838246 original size:34 final size:35
Alignment explanation
Indices: 13838190--13838291 Score: 129
Period size: 34 Copynumber: 3.0 Consensus size: 35
13838180 GTGTCATTTC
* *
13838190 TACATACTAA-TTCTTCAATTTGAAAACTTA-AAA
1 TACATACTAATTTCTTGAGTTTGAAAACTTACAAA
13838223 TACATACTAATTTCTTGAGTTTGAAAACTTACAAA
1 TACATACTAATTTCTTGAGTTTGAAAACTTACAAA
* * * *
13838258 -ACATATTGATTTCTTGCGCTTGAAAACTTACAAA
1 TACATACTAATTTCTTGAGTTTGAAAACTTACAAA
13838292 GTGAGTTGTG
Statistics
Matches: 61, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
33 10 0.16
34 48 0.79
35 3 0.05
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (35 bp):
TACATACTAATTTCTTGAGTTTGAAAACTTACAAA
Found at i:13839905 original size:32 final size:31
Alignment explanation
Indices: 13839826--13839910 Score: 100
Period size: 31 Copynumber: 2.7 Consensus size: 31
13839816 AAAGTTAGAG
* * **
13839826 AAAT-TTTTTTAAACCCTTAAAAGTTGGTAA
1 AAATATTTTTTAACCCCTTAAAAGCTGAAAA
**
13839856 AAATATTTTTGGACCCCTTAAAAGCTGAAAA
1 AAATATTTTTTAACCCCTTAAAAGCTGAAAA
13839887 AAATATTTTTTAAGCCCCTTAAAA
1 AAATATTTTTTAA-CCCCTTAAAA
13839911 TTTTTAAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
30 4 0.09
31 31 0.69
32 10 0.22
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.35
Consensus pattern (31 bp):
AAATATTTTTTAACCCCTTAAAAGCTGAAAA
Found at i:13840111 original size:18 final size:18
Alignment explanation
Indices: 13840076--13840111 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
13840066 AAGATTCCCT
*
13840076 AAGATTACAAAATCTTCA
1 AAGATTACAAAATATTCA
*
13840094 AAGATTACAATATATTCA
1 AAGATTACAAAATATTCA
13840112 CCTTGATAAA
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:0.14, G:0.06, T:0.31
Consensus pattern (18 bp):
AAGATTACAAAATATTCA
Found at i:13840951 original size:34 final size:34
Alignment explanation
Indices: 13840906--13840976 Score: 106
Period size: 34 Copynumber: 2.1 Consensus size: 34
13840896 TTTCATCTCT
* *
13840906 CTTGACTTTTAACATTTCATTTTCCTTAACCTTC
1 CTTGACCTTTAACATTTCATCTTCCTTAACCTTC
* *
13840940 CTTGACCTTTAACCTTTCATCTTCCTTAACTTTC
1 CTTGACCTTTAACATTTCATCTTCCTTAACCTTC
13840974 CTT
1 CTT
13840977 ATTCTTGTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.18, C:0.30, G:0.03, T:0.49
Consensus pattern (34 bp):
CTTGACCTTTAACATTTCATCTTCCTTAACCTTC
Found at i:13846423 original size:3 final size:3
Alignment explanation
Indices: 13846415--13846462 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
13846405 TAAGTACACC
13846415 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
13846463 AGGAACAATA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:13858837 original size:58 final size:58
Alignment explanation
Indices: 13858767--13858880 Score: 210
Period size: 58 Copynumber: 2.0 Consensus size: 58
13858757 CTTGCACCTC
13858767 ACTTCCAGGCCCTTGCGGAACGGGCACACTATTTGCTGCTCCCTGATATGAAGAGGCA
1 ACTTCCAGGCCCTTGCGGAACGGGCACACTATTTGCTGCTCCCTGATATGAAGAGGCA
* *
13858825 ACTTCCAGGCCCTTGCGGAATGGGCACACTATTTGCTGCTCCCTGATCTGAAGAGG
1 ACTTCCAGGCCCTTGCGGAACGGGCACACTATTTGCTGCTCCCTGATATGAAGAGG
13858881 GAACGTTACT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
58 54 1.00
ACGTcount: A:0.21, C:0.29, G:0.26, T:0.24
Consensus pattern (58 bp):
ACTTCCAGGCCCTTGCGGAACGGGCACACTATTTGCTGCTCCCTGATATGAAGAGGCA
Found at i:13860110 original size:19 final size:20
Alignment explanation
Indices: 13860086--13860125 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
13860076 AGATTAAACT
*
13860086 TTAATTAATT-ATAATTAAC
1 TTAATTAATTAACAATTAAC
13860105 TTAATTAATTAACAATTAAC
1 TTAATTAATTAACAATTAAC
13860125 T
1 T
13860126 AATGTTAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.45
Consensus pattern (20 bp):
TTAATTAATTAACAATTAAC
Found at i:13875804 original size:20 final size:20
Alignment explanation
Indices: 13875770--13875822 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
13875760 TTTTTATAAA
*
13875770 TATTTTGAA-TTTTGAAAGT
1 TATTTTGAATTTTTGAAAAT
*
13875789 TATTTTAAATTTTTGAAAAT
1 TATTTTGAATTTTTGAAAAT
13875809 TATTTTGAATTTTT
1 TATTTTGAATTTTT
13875823 TTGTAATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 8 0.27
20 22 0.73
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.58
Consensus pattern (20 bp):
TATTTTGAATTTTTGAAAAT
Found at i:13877684 original size:31 final size:30
Alignment explanation
Indices: 13877618--13877689 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
13877608 GTTACATTTA
* *
13877618 ACAAAACAGTCACTCAACTTTGAAAATTTG
1 ACAAAACAGTCACTAAACTTTGAAAATGTG
*
13877648 ACAAAACAGTCACTAAAGTTATCGAAAA-GTG
1 ACAAAACAGTCACTAAACTT-T-GAAAATGTG
*
13877679 ACAAAATAGTC
1 ACAAAACAGTC
13877690 CTCTACTTAC
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 18 0.50
31 13 0.36
32 5 0.14
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.22
Consensus pattern (30 bp):
ACAAAACAGTCACTAAACTTTGAAAATGTG
Found at i:13878639 original size:28 final size:28
Alignment explanation
Indices: 13878591--13878824 Score: 140
Period size: 29 Copynumber: 8.2 Consensus size: 28
13878581 AAAGGGGTCG
* * *
13878591 AAAATG-AAGTTTCGGAGAGTTTGGGGTT
1 AAAATGTAA-TTTTGGAAAGTTTGGGGTA
*
13878619 AAAATGTAATTTTGGAAAGTTTTAGGGATA
1 AAAATGTAATTTTGGAAAG-TTT-GGGGTA
* * * *
13878649 AAAATATCATTTTGGGAGAGTTCGGGGTA
1 AAAATGTAATTTT-GGAAAGTTTGGGGTA
* *
13878678 AAAATGTAATTTTTGAGAAGTTCGGGG--
1 AAAATGTAATTTTGGA-AAGTTTGGGGTA
*
13878705 AAAATGTGATTTTTGG-AAGTTTGAGGG-A
1 AAAATGT-AATTTTGGAAAGTTTG-GGGTA
*
13878733 AAAATGTAATTTTTGG-AAGTTCGGGGGTA
1 AAAATGTAA-TTTTGGAAAGTT-TGGGGTA
* * * *
13878762 AAAATATGATTTTTGAAA-TTTCAGGGGCA
1 AAAATGTAATTTTGGAAAGTTT--GGGGTA
* * *
13878791 AAAATATAATTTTGGAAAAGTTTAGGGTC
1 AAAATGTAATTTTGG-AAAGTTTGGGGTA
13878820 AAAAT
1 AAAAT
13878825 ATGATTTTCG
Statistics
Matches: 162, Mismatches: 28, Indels: 31
0.73 0.13 0.14
Matches are distributed among these distances:
26 6 0.04
27 11 0.07
28 50 0.31
29 67 0.41
30 20 0.12
31 8 0.05
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.34
Consensus pattern (28 bp):
AAAATGTAATTTTGGAAAGTTTGGGGTA
Found at i:13878823 original size:29 final size:28
Alignment explanation
Indices: 13878757--13878832 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 28
13878747 GGAAGTTCGG
* *
13878757 GGGTAAAAATATGATTTTTGAAATTTCA
1 GGGTCAAAATATGATTTTGGAAATTTCA
* *
13878785 GGGGCAAAAATATAATTTTGGAAAAGTTT-A
1 GGGTC-AAAATATGATTTTGG-AAA-TTTCA
13878815 GGGTCAAAATATGATTTT
1 GGGTCAAAATATGATTTT
13878833 CGGATAGCTC
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
28 3 0.08
29 25 0.64
30 8 0.21
31 3 0.08
ACGTcount: A:0.39, C:0.04, G:0.21, T:0.36
Consensus pattern (28 bp):
GGGTCAAAATATGATTTTGGAAATTTCA
Found at i:13880591 original size:6 final size:6
Alignment explanation
Indices: 13880582--13880683 Score: 63
Period size: 6 Copynumber: 17.8 Consensus size: 6
13880572 TAATTTTTAA
** *
13880582 TTAAAT TTAAAT TTAAA- ACAAAT TTAAAT TTAGAA- -TGAAT TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTA-AAT TTAAAT TTAAAT
* * * * * *
13880628 TCAAA- ATAAAT TTAAAT TCAAA- ATAAAT TTAAAT TTATA- CTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
*
13880673 TTAAAC TTAAA
1 TTAAAT TTAAA
13880684 AATAAATTAA
Statistics
Matches: 70, Mismatches: 19, Indels: 14
0.68 0.18 0.14
Matches are distributed among these distances:
4 2 0.03
5 13 0.19
6 53 0.76
7 2 0.03
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (6 bp):
TTAAAT
Found at i:13880604 original size:17 final size:17
Alignment explanation
Indices: 13880583--13880691 Score: 137
Period size: 17 Copynumber: 6.4 Consensus size: 17
13880573 AATTTTTAAT
13880583 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
* *
13880600 CAAATTTAAATTTAGAA
1 TAAATTTAAATTTAAAA
* *
13880617 TGAATTTAAATTCAAAA
1 TAAATTTAAATTTAAAA
*
13880634 TAAATTTAAATTCAAAA
1 TAAATTTAAATTTAAAA
* *
13880651 TAAATTTAAATTTATAC
1 TAAATTTAAATTTAAAA
*
13880668 TAAATTTAAACTTAAAAA
1 TAAATTTAAA-TTTAAAA
13880686 TAAATT
1 TAAATT
13880692 AAAAATAGGT
Statistics
Matches: 78, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
17 68 0.87
18 10 0.13
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.39
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:13880608 original size:34 final size:33
Alignment explanation
Indices: 13880570--13880664 Score: 100
Period size: 34 Copynumber: 2.8 Consensus size: 33
13880560 TAGACTCTCT
*
13880570 TTTAATTTTTAATTAAATTTAAATTTAAAACAAA
1 TTTAA-TTTTAAATAAATTTAAATTTAAAACAAA
* * * *
13880604 TTTAAATTTAGAATGAATTTAAATTCAAAATAAA
1 TTTAATTTTA-AATAAATTTAAATTTAAAACAAA
**
13880638 TTTAAATTCAAAATAAATTTAAATTTA
1 TTT-AATTTTAAATAAATTTAAATTTA
13880665 TACTAAATTT
Statistics
Matches: 49, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
33 4 0.08
34 41 0.84
35 4 0.08
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (33 bp):
TTTAATTTTAAATAAATTTAAATTTAAAACAAA
Found at i:13880694 original size:51 final size:51
Alignment explanation
Indices: 13880583--13880691 Score: 155
Period size: 51 Copynumber: 2.1 Consensus size: 51
13880573 AATTTTTAAT
* * *
13880583 TAAATTTAAATTTAAAACAAATTTAAATTTAGAATGAATTTAAATTCAAAA
1 TAAATTTAAATTCAAAACAAATTTAAATTTAGAATAAATTTAAATTAAAAA
* * *
13880634 TAAATTTAAATTCAAAATAAATTTAAATTTATACTAAATTTAAACTTAAAAA
1 TAAATTTAAATTCAAAACAAATTTAAATTTAGAATAAATTTAAA-TTAAAAA
13880686 TAAATT
1 TAAATT
13880692 AAAAATAGGT
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
51 39 0.76
52 12 0.24
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.39
Consensus pattern (51 bp):
TAAATTTAAATTCAAAACAAATTTAAATTTAGAATAAATTTAAATTAAAAA
Found at i:13881204 original size:39 final size:38
Alignment explanation
Indices: 13881161--13881567 Score: 126
Period size: 39 Copynumber: 10.4 Consensus size: 38
13881151 ACTGATAATG
13881161 ATCTGCCCTAAGCTCGAGGTAGAAGATCGAATGGTAGCA
1 ATCTGCCCTAAGCTCGAGGTA-AAGATCGAATGGTAGCA
* * ** * **
13881200 ATCTG-CCTCAAGCTCGGGGTAAGAGATTGGTTGATAGTG
1 ATCTGCCCT-AAGCTCGAGGTAA-AGATCGAATGGTAGCA
*
13881239 ATCTGCCCCAAGCTC-AGGGTAAAAGATCGAATGGCT-GCA
1 ATCTGCCCTAAGCTCGA-GGT-AAAGATCGAATGG-TAGCA
* *
13881278 ATCTGCCCTAAGCTCGGGGTAAGAGATTTACTAATGGT-G--
1 ATCTGCCCTAAGCTCGAGGTAA-AGA--T-CGAATGGTAGCA
*
13881317 ATCTG-CCTCAGGCTC-AGGGTAAGAGATCGAATGGCTA-CA
1 ATCTGCCCT-AAGCTCGA-GGTAA-AGATCGAATGG-TAGCA
* * * * ** * * **
13881356 ATCTGCCCCAGGATCGAGGTAAGAGATTGGCTGATGGTG
1 ATCTGCCCTAAGCTCGAGGTAA-AGATCGAATGGTAGCA
* * * *
13881395 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTAATGAT-G--
1 ATCTGCCCTAAGCTCGAGGTAA-AGA-T--CGAATGGTAGCA
* * *
13881434 ATCTGCCCCAAGCTCGGGGTAAGAGATTGAATGGCT-GCA
1 ATCTGCCCTAAGCTCGAGGTAA-AGATCGAATGG-TAGCA
* * * * * **
13881473 ATCTGCCCTAGGCTCGGGGTAAGAGAT-TAACTGATGGTG
1 ATCTGCCCTAAGCTCGAGGTAA-AGATCGAA-TGGTAGCA
* * *
13881512 ATCTACCCCAAGCTCGAGGTAAGAGATCGAATGGCT-GCT
1 ATCTGCCCTAAGCTCGAGGTAA-AGATCGAATGG-TAGCA
13881551 ATCTG-CCTCAAGCTCGA
1 ATCTGCCCT-AAGCTCGA
13881568 AGGCTGGCTG
Statistics
Matches: 281, Mismatches: 56, Indels: 62
0.70 0.14 0.16
Matches are distributed among these distances:
36 10 0.04
37 4 0.01
38 16 0.06
39 225 0.80
40 12 0.04
41 4 0.01
42 10 0.04
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.23
Consensus pattern (38 bp):
ATCTGCCCTAAGCTCGAGGTAAAGATCGAATGGTAGCA
Found at i:13881241 original size:78 final size:78
Alignment explanation
Indices: 13881120--13881959 Score: 638
Period size: 78 Copynumber: 10.9 Consensus size: 78
13881110 CGAATGATTA
* * * ** *
13881120 CAATCTGCCCCATGATCGGGGTAAGAGATTGACTGATAATGATCTGCCCTAAGCTCGAGGT-AGA
1 CAATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCTAAGCTCGGGGTAAG-
13881184 AGATCGAATGG-TAG
65 AGATCGAATGGCT-G
* * * * * *
13881198 CAATCTGCCTCAAGCTCGGGGTAAGAGATTGGTTGATAGTGATCTGCCCCAAGCTCAGGGTAAAA
1 CAATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCTAAGCTCGGGGTAAGA
13881263 GATCGAATGGCTG
66 GATCGAATGGCTG
* ** * * *
13881276 CAATCTGCCCTAAGCTCGGGGTAAGAGATTTACTAATGGTGATCTG-CCTCAGGCTCAGGGTAAG
1 CAATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCT-AAGCTCGGGGTAAG
*
13881340 AGATCGAATGGCTA
65 AGATCGAATGGCTG
* * * *
13881354 CAATCTGCCCCAGGATCGAGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGGGGTAAGA
1 CAATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCTAAGCTCGGGGTAAGA
* *
13881419 GATTGGCTAAT-GATG
66 GA-T--CGAATGGCTG
* *
13881434 --ATCTGCCCCAAGCTCGGGGTAAGAGATT-G--AATGGCTGCAATCTGCCCTAGGCTCGGGGTA
1 CAATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGG-TG--ATCTGCCCTAAGCTCGGGGTA
13881494 AGAGATTAACTG-ATGG-TG
63 AGAGA-T--C-GAATGGCTG
* * * ** * *
13881512 --ATCTACCCCAAGCTCGAGGTAAGAGATCGAATGGCTGCT-ATCTG-CCTCAAGCTC---G-AA
1 CAATCTGCCCCAAGCTCGGGGTAAGAGATTGGCT-GATGGTGATCTGCCCT-AAGCTCGGGGTAA
13881569 G-G--C---TGGCTG
64 GAGATCGAATGGCTG
* * * * * ** *
13881578 TAATCTGTCTCAGGCTCGGGGTAAGAGATTGACTGATGGTGATCTG-CCTCGGGCTCGGGATAAG
1 CAATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCT-AAGCTCGGGGTAAG
*
13881642 AGATCGAATGGCTA
65 AGATCGAATGGCTG
* * * * ** * *
13881656 CAATTTGCCCTAGGATCAAGGTAAGAGATTGG-TAGATGGTGATCTACCCCAAGCTCGGGGTAAG
1 CAATCTGCCCCAAGCTCGGGGTAAGAGATTGGCT-GATGGTGATCTGCCCTAAGCTCGGGGTAAG
13881720 AGATCGAATGGCTG
65 AGATCGAATGGCTG
* * * * * * *
13881734 TAATCTGCCCCAAGCACGAGGTAAGAGATTGGTTGATGGTGATTTGCCCCAAGCTCGGGGTAAAA
1 CAATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCTAAGCTCGGGGTAAGA
13881799 GATCGAATGGCTG
66 GATCGAATGGCTG
* * * * * * *
13881812 TAATCTGCCTCAGGCTCGGGGTAAGAGATTAGCTAATGGTGATCTG-TCTTAGACTCGGGGTAAG
1 CAATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCTAAG-CTCGGGGTAAG
13881876 AGATCGAATGGCTG
65 AGATCGAATGGCTG
* * ** * ** *** *
13881890 CAATATACCATAAGCTTGGGAAAAGAGATTGGCTGATGGTGATCTGCCCCGTGCTCAGGGTAAGA
1 CAATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCTAAGCTCGGGGTAAGA
13881955 GATCG
66 GATCG
13881960 GAATCTTCAA
Statistics
Matches: 609, Mismatches: 117, Indels: 72
0.76 0.15 0.09
Matches are distributed among these distances:
65 3 0.00
66 2 0.00
67 4 0.01
68 39 0.06
72 3 0.00
73 2 0.00
74 3 0.00
75 6 0.01
76 2 0.00
77 10 0.02
78 515 0.85
79 11 0.02
80 2 0.00
81 5 0.01
82 2 0.00
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (78 bp):
CAATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCTAAGCTCGGGGTAAGA
GATCGAATGGCTG
Found at i:13881555 original size:117 final size:116
Alignment explanation
Indices: 13881120--13881891 Score: 497
Period size: 117 Copynumber: 6.7 Consensus size: 116
13881110 CGAATGATTA
* * * ** *
13881120 CAATCTGCCCCATGATCGGGGTAAGAGATTGACTGATAATGATCTGCCCTAAGCTCGAGGT-AGA
1 CAATCTGCCCCAGGCTCGGGGTAAGAGATTAACTGATGGTGATCTGCCCCAAGCTCGAGGTAAG-
* * * *
13881184 AGATCGAATGG-TAGCAATCTGCCTCAAGCTCGGGGTAAGAGATTG-GTTGATAG
65 AGATCGAATGGCT-GC-ATCTGCCCCAAGCTCGGGGTAAGAGATTGAATGGCT-G
** * * * * *
13881237 TGATCTGCCCCAAGCTCAGGGTAAAAGA-T--C-GAATGGCTGCAATCTGCCCTAAGCTCGGGGT
1 CAATCTGCCCCAGGCTCGGGGTAAGAGATTAACTG-ATGG-TG--ATCTGCCCCAAGCTCGAGGT
* * * * * *
13881298 AAGAGATTTACTAATGG-TG-ATCTGCCTCAGGCTCAGGGTAAGAGATCGAATGGCTA
62 AAGAGA--T-CGAATGGCTGCATCTGCCCCAAGCTCGGGGTAAGAGATTGAATGGCTG
* * ** *
13881354 CAATCTGCCCCAGGATCGAGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGGGGTAAGA
1 CAATCTGCCCCAGGCTCGGGGTAAGAGATTAACTGATGGTGATCTGCCCCAAGCTCGAGGTAAGA
* *
13881419 GATTGGCTAAT-GATG-ATCTGCCCCAAGCTCGGGGTAAGAGATTGAATGGCTG
66 GA-T--CGAATGGCTGCATCTGCCCCAAGCTCGGGGTAAGAGATTGAATGGCTG
* *
13881471 CAATCTGCCCTAGGCTCGGGGTAAGAGATTAACTGATGGTGATCTACCCCAAGCTCGAGGTAAGA
1 CAATCTGCCCCAGGCTCGGGGTAAGAGATTAACTGATGGTGATCTGCCCCAAGCTCGAGGTAAGA
* *
13881536 GATCGAATGGCTGCTATCTGCCTCAAGCTC---G--A-AG---G-CTGGCTG
66 GATCGAATGGCTGC-ATCTGCCCCAAGCTCGGGGTAAGAGATTGAATGGCTG
* * * * * **
13881578 TAATCTGTCTCAGGCTCGGGGTAAGAGATTGACTGATGGTGATCTGCCTCGGGCTCG-GGATAAG
1 CAATCTGCCCCAGGCTCGGGGTAAGAGATTAACTGATGGTGATCTGCCCCAAGCTCGAGG-TAAG
* * * * * **
13881642 AGATCGAATGGCTACAATTTGCCCTAGGATCAAGGTAAGAGATTGGTAGATGG-TG
65 AGATCGAATGGCTGC-ATCTGCCCCAAGCTCGGGGTAAGAGATT-G-A-ATGGCTG
* * * * * *
13881697 --ATCTACCCCAAGCTCGGGGTAAGAGATCGAA-TGGCT-GTAATCTGCCCCAAGCACGAGGTAA
1 CAATCTGCCCCAGGCTCGGGGTAAGAGAT-TAACT-GATGGTGATCTGCCCCAAGCTCGAGGTAA
* * * * *
13881758 GAGATTGGTTGATGG-TG-ATTTGCCCCAAGCTCGGGGTAAAAGATCGAATGGCTG
64 GAGA-TCG--AATGGCTGCATCTGCCCCAAGCTCGGGGTAAGAGATTGAATGGCTG
* * * * * ** *
13881812 TAATCTGCCTCAGGCTCGGGGTAAGAGATTAGCTAATGGTGATCTG-TCTTAGACTCGGGGTAAG
1 CAATCTGCCCCAGGCTCGGGGTAAGAGATTAACTGATGGTGATCTGCCCCAAG-CTCGAGGTAAG
13881876 AGATCGAATGGCTGCA
65 AGATCGAATGGCTGCA
13881892 ATATACCATA
Statistics
Matches: 513, Mismatches: 96, Indels: 93
0.73 0.14 0.13
Matches are distributed among these distances:
106 2 0.00
107 82 0.16
108 1 0.00
110 1 0.00
111 2 0.00
112 2 0.00
113 3 0.01
114 16 0.03
115 10 0.02
116 14 0.03
117 340 0.66
118 13 0.03
119 7 0.01
120 19 0.04
121 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (116 bp):
CAATCTGCCCCAGGCTCGGGGTAAGAGATTAACTGATGGTGATCTGCCCCAAGCTCGAGGTAAGA
GATCGAATGGCTGCATCTGCCCCAAGCTCGGGGTAAGAGATTGAATGGCTG
Found at i:13881718 original size:39 final size:38
Alignment explanation
Indices: 13881675--13881879 Score: 159
Period size: 39 Copynumber: 5.3 Consensus size: 38
13881665 CTAGGATCAA
*
13881675 GGTAAGAGATTGGTAGATGGTGATCTACCCCAAGCTCGG
1 GGTAAGAGATTGGTA-ATGGTGATCTGCCCCAAGCTCGG
* * *
13881714 GGTAAGAGA-TCG-AATGGCTGTAATCTGCCCCAAGCACGA
1 GGTAAGAGATTGGTAATGG-TG--ATCTGCCCCAAGCTCGG
* *
13881753 GGTAAGAGATTGGTTGATGGTGATTTGCCCCAAGCTCGG
1 GGTAAGAGATTGG-TAATGGTGATCTGCCCCAAGCTCGG
* * * *
13881792 GGTAAAAGA-TCG-AATGGCTGTAATCTGCCTCAGGCTCGG
1 GGTAAGAGATTGGTAATGG-TG--ATCTGCCCCAAGCTCGG
* * **
13881831 GGTAAGAGATTAGCTAATGGTGATCTG-TCTTAGACTCGG
1 GGTAAGAGATT-GGTAATGGTGATCTGCCCCAAG-CTCGG
13881870 GGTAAGAGAT
1 GGTAAGAGAT
13881880 CGAATGGCTG
Statistics
Matches: 130, Mismatches: 23, Indels: 26
0.73 0.13 0.15
Matches are distributed among these distances:
36 8 0.06
37 5 0.04
38 5 0.04
39 96 0.74
40 3 0.02
41 4 0.03
42 9 0.07
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.24
Consensus pattern (38 bp):
GGTAAGAGATTGGTAATGGTGATCTGCCCCAAGCTCGG
Found at i:13881720 original size:185 final size:185
Alignment explanation
Indices: 13881406--13881748 Score: 501
Period size: 185 Copynumber: 1.9 Consensus size: 185
13881396 TCTGCCCCAA
* * * *
13881406 GCTCGGGGTAAGAGATTGGCTAATGATGATCTGCCCCAAGCTCGGGGTAAGAGATTGAATGGCTG
1 GCTCGGGGTAAGAGATTGACTAATGATGATCTGCCCCAAGCTCGGGATAAGAGATCGAATGGCTA
* **
13881471 CAATCTGCCCTAGGCTCGGGGTAAGAGATTAACTGATGGTGATCTACCCCAAGCTCGAGGTAAGA
66 CAATCTGCCCTAGGATCAAGGTAAGAGATTAACTGATGGTGATCTACCCCAAGCTCGAGGTAAGA
*
13881536 GATCGAATGGCTGCT-ATCTGCCTCAAGCTCGAAGGCTGGCTGTAATCTGTCTCAG
131 GATCGAATGGCTG-TAATCTGCCCCAAGCTCGAAGGCTGGCTGTAATCTGTCTCAG
* * * **
13881591 GCTCGGGGTAAGAGATTGACTGATGGTGATCTGCCTCGGGCTCGGGATAAGAGATCGAATGGCTA
1 GCTCGGGGTAAGAGATTGACTAATGATGATCTGCCCCAAGCTCGGGATAAGAGATCGAATGGCTA
* ** *
13881656 CAATTTGCCCTAGGATCAAGGTAAGAGATT-GGTAGATGGTGATCTACCCCAAGCTCGGGGTAAG
66 CAATCTGCCCTAGGATCAAGGTAAGAGATTAACT-GATGGTGATCTACCCCAAGCTCGAGGTAAG
13881720 AGATCGAATGGCTGTAATCTGCCCCAAGC
130 AGATCGAATGGCTGTAATCTGCCCCAAGC
13881749 ACGAGGTAAG
Statistics
Matches: 139, Mismatches: 17, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
184 2 0.01
185 137 0.99
ACGTcount: A:0.25, C:0.21, G:0.31, T:0.23
Consensus pattern (185 bp):
GCTCGGGGTAAGAGATTGACTAATGATGATCTGCCCCAAGCTCGGGATAAGAGATCGAATGGCTA
CAATCTGCCCTAGGATCAAGGTAAGAGATTAACTGATGGTGATCTACCCCAAGCTCGAGGTAAGA
GATCGAATGGCTGTAATCTGCCCCAAGCTCGAAGGCTGGCTGTAATCTGTCTCAG
Found at i:13884220 original size:3 final size:3
Alignment explanation
Indices: 13884212--13884238 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
13884202 AGTCATCCCT
13884212 TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC
13884239 AATATCATAA
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):
TTC
Found at i:13885657 original size:13 final size:13
Alignment explanation
Indices: 13885639--13885665 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
13885629 CACTGTGGCC
13885639 CTTTGATAAGTTA
1 CTTTGATAAGTTA
13885652 CTTTGATAAGTTA
1 CTTTGATAAGTTA
13885665 C
1 C
13885666 CCCTACATTT
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:0.30, C:0.11, G:0.15, T:0.44
Consensus pattern (13 bp):
CTTTGATAAGTTA
Found at i:13885910 original size:103 final size:103
Alignment explanation
Indices: 13885726--13885934 Score: 382
Period size: 103 Copynumber: 2.0 Consensus size: 103
13885716 ATAGTGCGAC
13885726 AAACATGGTTTTCTCCATATCTTCGGGATCCATCCTTATTTGGTTATACCCGGAGAAACCATCTA
1 AAACATGGTTTTCTCCATATCTTCGGGATCCATCCTTATTTGGTTATACCCGGAGAAACCATCTA
* *
13885791 TGAATGAGAATAAGGAGTGACCTATTGTATTCTCTATT
66 TGAATGACAATAAGGAGTGACCTATTGTATTATCTATT
*
13885829 AAACGTGGTTTTCTCCATATCTTCGGGATCCATCCTTATTTGGTTATACCCGGAGAAACCATCTA
1 AAACATGGTTTTCTCCATATCTTCGGGATCCATCCTTATTTGGTTATACCCGGAGAAACCATCTA
*
13885894 TGAATGACAATAAGGAGTGACCTGTTGTATTATCTATT
66 TGAATGACAATAAGGAGTGACCTATTGTATTATCTATT
13885932 AAA
1 AAA
13885935 GTGTCGATAT
Statistics
Matches: 102, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 102 1.00
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (103 bp):
AAACATGGTTTTCTCCATATCTTCGGGATCCATCCTTATTTGGTTATACCCGGAGAAACCATCTA
TGAATGACAATAAGGAGTGACCTATTGTATTATCTATT
Found at i:13888785 original size:18 final size:18
Alignment explanation
Indices: 13888762--13888810 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 18
13888752 TATGATGATA
13888762 TATATGTGATGAACAATG
1 TATATGTGATGAACAATG
13888780 TATATGTGAAATATGAACAATG
1 TATATGTG----ATGAACAATG
13888802 TATATGTGA
1 TATATGTGA
13888811 AATATTATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
18 9 0.33
22 18 0.67
ACGTcount: A:0.41, C:0.04, G:0.20, T:0.35
Consensus pattern (18 bp):
TATATGTGATGAACAATG
Found at i:13888795 original size:22 final size:22
Alignment explanation
Indices: 13888770--13888815 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
13888760 TATATATGTG
13888770 ATGAACAATGTATATGTGAAAT
1 ATGAACAATGTATATGTGAAAT
13888792 ATGAACAATGTATATGTGAAAT
1 ATGAACAATGTATATGTGAAAT
13888814 AT
1 AT
13888816 TATATGTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.46, C:0.04, G:0.17, T:0.33
Consensus pattern (22 bp):
ATGAACAATGTATATGTGAAAT
Found at i:13896605 original size:29 final size:29
Alignment explanation
Indices: 13896554--13896803 Score: 143
Period size: 29 Copynumber: 8.6 Consensus size: 29
13896544 GAAATTGAAG
* * *
13896554 TTTTGGAGAGTTT-GGGGTTAAAATATAA
1 TTTTGGAAAGTTTAGGGGTAAAAATGTAA
*
13896582 TTTTGGAAAGTTTTAGGGGTAAAAATGTGA
1 TTTTGGAAAG-TTTAGGGGTAAAAATGTAA
** * * * * *
13896612 TTTTTTAAAG-CTCGAGGGCAAAATTTTAA
1 TTTTGGAAAGTTTAG-GGGTAAAAATGTAA
** *
13896641 TTTTTGG-AAGTTCGGGGGTAAAAATGTGAT
1 -TTTTGGAAAGTTTAGGGGTAAAAATGT-AA
* * *
13896671 TTTTGG-AAG-TTCGAGGGCAAAAATGTGA
1 TTTTGGAAAGTTTAG-GGGTAAAAATGTAA
* * * *
13896699 TTTTGAAAAGTTTGGGGGTCAAAATATAA
1 TTTTGGAAAGTTTAGGGGTAAAAATGTAA
* * *
13896728 TTTTGGAAAATTTAAGGGTCAAAATGTAA
1 TTTTGGAAAGTTTAGGGGTAAAAATGTAA
* * *
13896757 TTTTGGAAAGTTTAAGGGTCAGAATATG-AT
1 TTTTGGAAAGTTTAGGGGT-A-AAAATGTAA
*
13896787 TTTTGGACAGTTTAGGG
1 TTTTGGAAAGTTTAGGG
13896804 ACCTTTTGGG
Statistics
Matches: 168, Mismatches: 43, Indels: 20
0.73 0.19 0.09
Matches are distributed among these distances:
28 18 0.11
29 100 0.60
30 45 0.27
31 5 0.03
ACGTcount: A:0.33, C:0.04, G:0.27, T:0.36
Consensus pattern (29 bp):
TTTTGGAAAGTTTAGGGGTAAAAATGTAA
Found at i:13896710 original size:58 final size:58
Alignment explanation
Indices: 13896573--13896768 Score: 162
Period size: 58 Copynumber: 3.4 Consensus size: 58
13896563 GTTTGGGGTT
* * ** *
13896573 AAAATATAATTTTGGAAAGTTTTAGGGGTAAAAATGTGATTTTTTAAAGCTCGAGGGCA
1 AAAATGTAATTTTTGAAAG-TTCGGGGGTAAAAATGTGATTTTTGAAAGCTCGAGGGCA
* * * * *
13896632 AAATTTTAATTTTTGGAAGTTCGGGGGTAAAAATGTGATTTTTGGAAGTTCGAGGGCA
1 AAAATGTAATTTTTGAAAGTTCGGGGGTAAAAATGTGATTTTTGAAAGCTCGAGGGCA
* * * * * * ** **
13896690 AAAATGTGA-TTTTGAAAAGTTTGGGGGTCAAAATATAATTTTGGAAAATTTAAGGGTC-
1 AAAATGTAATTTTTG-AAAGTTCGGGGGTAAAAATGTGATTTTTGAAAGCTCGAGGG-CA
*
13896748 AAAATGTAATTTTGGAAAGTT
1 AAAATGTAATTTTTGAAAGTT
13896769 TAAGGGTCAG
Statistics
Matches: 110, Mismatches: 24, Indels: 7
0.78 0.17 0.05
Matches are distributed among these distances:
57 5 0.05
58 85 0.77
59 20 0.18
ACGTcount: A:0.36, C:0.04, G:0.25, T:0.35
Consensus pattern (58 bp):
AAAATGTAATTTTTGAAAGTTCGGGGGTAAAAATGTGATTTTTGAAAGCTCGAGGGCA
Found at i:13896768 original size:87 final size:88
Alignment explanation
Indices: 13896568--13896768 Score: 194
Period size: 87 Copynumber: 2.3 Consensus size: 88
13896558 GGAGAGTTTG
* * ** * **
13896568 GGGTTAAAATATAATTTTGGAAAGTTTTAGGGGTAAAAATGTGATTTTTTAAAGCTCGAGGGCAA
1 GGGTAAAAATGTAATTTTGGAAAGTTCGAGGGGCAAAAATGTGATTTTGAAAAGCTCGAGGGCAA
* * **
13896633 AATTTTAATTTTTGGAAGTTCGG
66 AATTATAATTTTTGGAAATTCAA
* * * *
13896656 GGGTAAAAATGTGATTTTTGG-AAGTTCGA-GGGCAAAAATGTGATTTTGAAAAGTTTGGGGGTC
1 GGGTAAAAATGT-AATTTTGGAAAGTTCGAGGGGCAAAAATGTGATTTTGAAAAGCTCGAGGG-C
*
13896719 AAAA-TATAA-TTTTGGAAAATTTAA
64 AAAATTATAATTTTTGG-AAATTCAA
*
13896743 GGGTCAAAATGTAATTTTGGAAAGTT
1 GGGTAAAAATGTAATTTTGGAAAGTT
13896769 TAAGGGTCAG
Statistics
Matches: 91, Mismatches: 18, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
86 13 0.14
87 50 0.55
88 21 0.23
89 7 0.08
ACGTcount: A:0.35, C:0.04, G:0.26, T:0.35
Consensus pattern (88 bp):
GGGTAAAAATGTAATTTTGGAAAGTTCGAGGGGCAAAAATGTGATTTTGAAAAGCTCGAGGGCAA
AATTATAATTTTTGGAAATTCAA
Found at i:13898118 original size:23 final size:24
Alignment explanation
Indices: 13898092--13898138 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
13898082 TGTACTCTGT
13898092 TTGTT-TGTGTATTGATTTC-AAAA
1 TTGTTCTGTGT-TTGATTTCTAAAA
13898115 TTGTTCTGTGTTTGATTTCTAAAA
1 TTGTTCTGTGTTTGATTTCTAAAA
13898139 AGTCTGTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 13 0.59
24 9 0.41
ACGTcount: A:0.23, C:0.06, G:0.17, T:0.53
Consensus pattern (24 bp):
TTGTTCTGTGTTTGATTTCTAAAA
Found at i:13898556 original size:17 final size:17
Alignment explanation
Indices: 13898536--13898619 Score: 80
Period size: 17 Copynumber: 4.9 Consensus size: 17
13898526 ATTTTTAATT
13898536 AAATTTAAATTTAAAAC
1 AAATTTAAATTTAAAAC
* *
13898553 AAATTTAAATTTAGAAT
1 AAATTTAAATTTAAAAC
* * *
13898570 GAATTTAAATTCAAAAT
1 AAATTTAAATTTAAAAC
* *
13898587 AAATTTAGATTT-ATAC
1 AAATTTAAATTTAAAAC
*
13898603 TAAATTTAAACTTAAAA
1 -AAATTTAAATTTAAAA
13898620 ATAAATTAAA
Statistics
Matches: 52, Mismatches: 13, Indels: 3
0.76 0.19 0.04
Matches are distributed among these distances:
16 2 0.04
17 48 0.92
18 2 0.04
ACGTcount: A:0.54, C:0.05, G:0.04, T:0.38
Consensus pattern (17 bp):
AAATTTAAATTTAAAAC
Found at i:13898560 original size:34 final size:34
Alignment explanation
Indices: 13898522--13898619 Score: 92
Period size: 34 Copynumber: 2.9 Consensus size: 34
13898512 TGGACTCTCT
*
13898522 TTTAATTTTTAATTAAATTTAAATTTAAAACAAA
1 TTTAATTTTTAAATAAATTTAAATTTAAAACAAA
* * * *
13898556 TTTAA-ATTTAGAATGAATTTAAATTCAAAATAAA
1 TTTAATTTTTA-AATAAATTTAAATTTAAAACAAA
* * *
13898590 TTTAGATTTAT-ACTAAATTTAAACTTAAAA
1 TTTA-ATTTTTAAATAAATTTAAATTTAAAA
13898620 ATAAATTAAA
Statistics
Matches: 50, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
33 4 0.08
34 43 0.86
35 1 0.02
36 2 0.04
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.43
Consensus pattern (34 bp):
TTTAATTTTTAAATAAATTTAAATTTAAAACAAA
Found at i:13905569 original size:32 final size:30
Alignment explanation
Indices: 13905529--13905624 Score: 165
Period size: 30 Copynumber: 3.1 Consensus size: 30
13905519 AAAAGGAATT
*
13905529 TTGATTTTTTTTTAAAACACATTCAAAGAA
1 TTGATTTTTTTTAAAAACACATTCAAAGAA
13905559 TTGATTTTTTTTAAAAACACATTCAAAGAA
1 TTGATTTTTTTTAAAAACACATTCAAAGAA
13905589 TTGATTTTTTTTAAAAAAACACATTCAAAGAA
1 TTGATTTTTTTT--AAAAACACATTCAAAGAA
13905621 TTGA
1 TTGA
13905625 CAATAAATGT
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
30 41 0.65
32 22 0.35
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.41
Consensus pattern (30 bp):
TTGATTTTTTTTAAAAACACATTCAAAGAA
Found at i:13906435 original size:83 final size:83
Alignment explanation
Indices: 13906296--13906464 Score: 338
Period size: 83 Copynumber: 2.0 Consensus size: 83
13906286 AGACAACTTT
13906296 CAAGCAATATGCATTCTTCAAGACATGGATGCCTATCATTTGTGTCTACATTGGAGTAATAGCAC
1 CAAGCAATATGCATTCTTCAAGACATGGATGCCTATCATTTGTGTCTACATTGGAGTAATAGCAC
13906361 CCTGACAGGTTGAAATGA
66 CCTGACAGGTTGAAATGA
13906379 CAAGCAATATGCATTCTTCAAGACATGGATGCCTATCATTTGTGTCTACATTGGAGTAATAGCAC
1 CAAGCAATATGCATTCTTCAAGACATGGATGCCTATCATTTGTGTCTACATTGGAGTAATAGCAC
13906444 CCTGACAGGTTGAAATGA
66 CCTGACAGGTTGAAATGA
13906462 CAA
1 CAA
13906465 TTTGGGTCCA
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 86 1.00
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (83 bp):
CAAGCAATATGCATTCTTCAAGACATGGATGCCTATCATTTGTGTCTACATTGGAGTAATAGCAC
CCTGACAGGTTGAAATGA
Found at i:13917045 original size:2 final size:2
Alignment explanation
Indices: 13917040--13917085 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
13917030 TAAATTCATT
13917040 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
13917082 CA CA
1 CA CA
13917086 TATATATATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Done.