Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D13
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 64892201
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 60 of 221
Found at i:17324166 original size:19 final size:18
Alignment explanation
Indices: 17324121--17324166 Score: 58
Period size: 17 Copynumber: 2.5 Consensus size: 18
17324111 TAGTTCACTC
*
17324121 TTACTTTATTTTTTTAGTT
1 TTACTTT-TATTTTTAGTT
17324140 TTAC-TTTATTTTTAGTTT
1 TTACTTTTATTTTTAG-TT
17324158 TTACTTTTA
1 TTACTTTTA
17324167 CAATTTATAG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 8 0.33
18 8 0.33
19 8 0.33
ACGTcount: A:0.17, C:0.07, G:0.04, T:0.72
Consensus pattern (18 bp):
TTACTTTTATTTTTAGTT
Found at i:17337164 original size:19 final size:19
Alignment explanation
Indices: 17337140--17337193 Score: 81
Period size: 19 Copynumber: 2.8 Consensus size: 19
17337130 AATCATATCT
*
17337140 TCTAAGATTGTATATCATA
1 TCTAAGATTGCATATCATA
*
17337159 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
*
17337178 TTTAAGATTGCATATC
1 TCTAAGATTGCATATC
17337194 CTTGAAGATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.41
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:17340667 original size:3 final size:3
Alignment explanation
Indices: 17340659--17340704 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
17340649 ATTTGTATTT
17340659 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
17340705 AGTAAACAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:17341084 original size:6 final size:6
Alignment explanation
Indices: 17341073--17341097 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
17341063 AAAACTACAC
17341073 AGATGA AGATGA AGATGA AGATGA A
1 AGATGA AGATGA AGATGA AGATGA A
17341098 CAAAACCGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.32, T:0.16
Consensus pattern (6 bp):
AGATGA
Found at i:17343883 original size:16 final size:15
Alignment explanation
Indices: 17343862--17343891 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
17343852 TATTATATAT
17343862 TTTACTTTATTTATTA
1 TTTACTTT-TTTATTA
17343878 TTTACTTTTTTATT
1 TTTACTTTTTTATT
17343892 TACTTTACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTACTTTTTTATTA
Found at i:17343888 original size:24 final size:24
Alignment explanation
Indices: 17343848--17343898 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 24
17343838 GATTTGATTA
17343848 TTATTATTATATATTTTACTTTA-T
1 TTATTATTATATATTTTA-TTTACT
*
17343872 TTATTATT-TACTTTTTTATTTACT
1 TTATTATTATA-TATTTTATTTACT
17343896 TTA
1 TTA
17343899 CCACTCTTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 6 0.25
24 18 0.75
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (24 bp):
TTATTATTATATATTTTATTTACT
Found at i:17345973 original size:14 final size:15
Alignment explanation
Indices: 17345943--17345975 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
17345933 ACCACTTTTT
*
17345943 TTTTCTTTTTACTTA
1 TTTTCTTTTTACCTA
17345958 TTTTCTTTTT-CCTA
1 TTTTCTTTTTACCTA
17345972 TTTT
1 TTTT
17345976 TTCCCTGCAT
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:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTCTTTTTACCTA
Found at i:17350723 original size:9 final size:9
Alignment explanation
Indices: 17350709--17350742 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
17350699 AGACAGTGGC
17350709 GCAGCAACA
1 GCAGCAACA
17350718 GCAGCAACA
1 GCAGCAACA
*
17350727 GCAGCAGCA
1 GCAGCAACA
*
17350736 GCCGCAA
1 GCAGCAA
17350743 TGGGGGCAGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.38, C:0.35, G:0.26, T:0.00
Consensus pattern (9 bp):
GCAGCAACA
Found at i:17354882 original size:42 final size:39
Alignment explanation
Indices: 17354834--17354964 Score: 118
Period size: 40 Copynumber: 3.2 Consensus size: 39
17354824 ATTTTCAATG
17354834 GGCATGCTTAACATGTGAATCAAATTCATAATCAATACAGT
1 GGCATGCTTAACATGTGAATCAAATT--TAATCAATACAGT
* * * * *
17354875 CGGCATGCTAAACAGGTGAACCGAATTTAATCAGTACAGT
1 -GGCATGCTTAACATGTGAATCAAATTTAATCAATACAGT
* * *
17354915 GAGCATGCTTAACATGCGAATCATATCTTAATTACCATAACAGT
1 G-GCATGCTTAACATGTGAATCAAAT-TTAA-T-CAAT-ACAGT
17354959 GGCATG
1 GGCATG
17354965 ATTTATATAT
Statistics
Matches: 71, Mismatches: 13, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
39 1 0.01
40 30 0.42
41 4 0.06
42 23 0.32
43 7 0.10
44 6 0.08
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.27
Consensus pattern (39 bp):
GGCATGCTTAACATGTGAATCAAATTTAATCAATACAGT
Found at i:17356931 original size:18 final size:19
Alignment explanation
Indices: 17356904--17356940 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
17356894 CTTGAAAAGT
*
17356904 ATATTGTGTGA-TGTGATG
1 ATATTATGTGATTGTGATG
17356922 ATATTATGTGATTGTGATG
1 ATATTATGTGATTGTGATG
17356941 TTTGTACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.24, C:0.00, G:0.30, T:0.46
Consensus pattern (19 bp):
ATATTATGTGATTGTGATG
Found at i:17357159 original size:22 final size:22
Alignment explanation
Indices: 17357131--17357181 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
17357121 AGAAGAAAGA
*
17357131 TATGTGGCAGTTTATCTACAAT
1 TATGTGGCAGTTTATCGACAAT
* *
17357153 TGTGTGGCCGTTTATCGACAAT
1 TATGTGGCAGTTTATCGACAAT
17357175 TATGTGG
1 TATGTGG
17357182 TGGCTTGTCC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.22, C:0.14, G:0.25, T:0.39
Consensus pattern (22 bp):
TATGTGGCAGTTTATCGACAAT
Found at i:17365833 original size:40 final size:40
Alignment explanation
Indices: 17365739--17365852 Score: 126
Period size: 40 Copynumber: 2.9 Consensus size: 40
17365729 TCTGGCATGA
* *
17365739 TTCGGGTGGATCAGCTCTTATGAGCTTCTA-TTGGCGTGT
1 TTCGAGTGGATCAACTCTTATGAGCTTCTATTTGGCGTGT
* *
17365778 TTCGAGTGGACCAACTCTTATAAGCTTCTATTTGGCGCAT-T
1 TTCGAGTGGATCAACTCTTATGAGCTTCTATTTGGCG--TGT
* * *
17365819 TTTG-TTGGATCAACTCTTATGAGCTTCTGTTTGG
1 TTCGAGTGGATCAACTCTTATGAGCTTCTATTTGG
17365853 TGTGCTCGGT
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
39 26 0.41
40 32 0.51
41 4 0.06
42 1 0.02
ACGTcount: A:0.17, C:0.18, G:0.25, T:0.40
Consensus pattern (40 bp):
TTCGAGTGGATCAACTCTTATGAGCTTCTATTTGGCGTGT
Found at i:17366361 original size:15 final size:17
Alignment explanation
Indices: 17366333--17366364 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
17366323 TTCATTATTG
17366333 AAAGGTGATATGATGAA
1 AAAGGTGATATGATGAA
17366350 AAAGG-GAT-TGATGAA
1 AAAGGTGATATGATGAA
17366365 TTGAATGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 3 0.20
17 5 0.33
ACGTcount: A:0.47, C:0.00, G:0.31, T:0.22
Consensus pattern (17 bp):
AAAGGTGATATGATGAA
Found at i:17374201 original size:37 final size:37
Alignment explanation
Indices: 17374140--17374278 Score: 215
Period size: 37 Copynumber: 3.8 Consensus size: 37
17374130 AACTCAGACG
* *
17374140 AAATCTCCACACGAAGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
17374177 AAATCTCCACACGTAGTCACCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
* *
17374214 TAATCTCCACACGTATTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
* *
17374251 TAATCTCCACATGTAGTCATCGGGTCTT
1 AAATCTCCACACGTAGTCATCGGGTCTT
17374279 TAGAGCTCGG
Statistics
Matches: 94, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 94 1.00
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.25
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:17374475 original size:47 final size:47
Alignment explanation
Indices: 17374397--17374669 Score: 350
Period size: 47 Copynumber: 5.6 Consensus size: 47
17374387 CCCTTCGGGA
* * * * * * *
17374397 CTTATCACATTTATACAGTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
17374444 CCTGTCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
17374491 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
17374538 CTTATCACATATATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC------ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
17374591 CTTATCACATATATATACACTTTCACATTCATCACATTC-GCCATTCGGT
1 CTTATCAC--ATATATACACTTTCACATTCATCACA-TCGGCCATTAGGC
17374640 CTTATCACATATATACACTTTCACATTCAT
1 CTTATCACATATATACACTTTCACATTCAT
17374670 TCAAATATAC
Statistics
Matches: 204, Mismatches: 15, Indels: 14
0.88 0.06 0.06
Matches are distributed among these distances:
47 111 0.54
49 44 0.22
50 2 0.01
53 47 0.23
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.34
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:17374594 original size:100 final size:101
Alignment explanation
Indices: 17374452--17374654 Score: 347
Period size: 102 Copynumber: 2.0 Consensus size: 101
17374442 GCCCTGTCAC
*
17374452 ATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCAC-ATATATACACTTTCACA
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAATATATACACTTTCACA
17374516 TTCATCACA-TCGGCCATTAGGCCTTATCACATATAT
66 TTCATCACATTC-GCCATTAGGCCTTATCACATATAT
17374552 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCAC
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACA-ATATATACACTTTCAC
* *
17374617 ATTCATCACATTCGCCATTCGGTCTTATCACATATAT
65 ATTCATCACATTCGCCATTAGGCCTTATCACATATAT
17374654 A
1 A
17374655 CACTTTCACA
Statistics
Matches: 97, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
100 46 0.47
102 49 0.51
103 2 0.02
ACGTcount: A:0.31, C:0.27, G:0.07, T:0.34
Consensus pattern (101 bp):
ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAATATATACACTTTCACA
TTCATCACATTCGCCATTAGGCCTTATCACATATAT
Found at i:17374671 original size:100 final size:100
Alignment explanation
Indices: 17374397--17374672 Score: 329
Period size: 102 Copynumber: 2.8 Consensus size: 100
17374387 CCCTTCGGGA
* * * * * * *
17374397 CTTATCACAT-T-TATACAGTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATTCGCCATTCGGCCTTATCACATATATAC
*
17374460 ACTTT--CA--CATTCATCACATCGGCTATTAGGC
66 ACTTTCACATTCATTCATCACATCGGCCATTAGGC
*
17374491 CTTATCAC--ATATATACACTTTCACATTCATCACA-TCGGCCATTAGGCCTTATCACATATATA
1 CTTATCACATATATATACACTTTCACATTCATCACATTC-GCCATTCGGCCTTATCACATATATA
* * *
17374553 TA-TATACACTTTCACATTCATCACATCGGCCATTAGGC
65 CACT-TTCACATT--CATTCATCACATCGGCCATTAGGC
*
17374591 CTTATCACATATATATACACTTTCACATTCATCACATTCGCCATTCGGTCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATTCGCCATTCGGCCTTATCACATATATAC
17374656 ACTTTCACATTCATTCA
66 ACTTTCACATTCATTCA
17374673 AATATACTTC
Statistics
Matches: 151, Mismatches: 17, Indels: 22
0.79 0.09 0.12
Matches are distributed among these distances:
93 3 0.02
94 51 0.34
96 1 0.01
100 37 0.25
102 56 0.37
103 3 0.02
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.34
Consensus pattern (100 bp):
CTTATCACATATATATACACTTTCACATTCATCACATTCGCCATTCGGCCTTATCACATATATAC
ACTTTCACATTCATTCATCACATCGGCCATTAGGC
Found at i:17376987 original size:84 final size:85
Alignment explanation
Indices: 17376856--17377033 Score: 331
Period size: 84 Copynumber: 2.1 Consensus size: 85
17376846 TATTTTATTG
*
17376856 CCCATGCCCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATG-TTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
17376920 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
*
17376940 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCTCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
17377005 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
17377025 CCCATGCTC
1 CCCATGCTC
17377034 ATGGCCGGCC
Statistics
Matches: 91, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
84 59 0.65
85 32 0.35
ACGTcount: A:0.26, C:0.28, G:0.08, T:0.38
Consensus pattern (85 bp):
CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
TAGCCATAACATCTTGTCCA
Found at i:17378725 original size:40 final size:40
Alignment explanation
Indices: 17378699--17379004 Score: 468
Period size: 40 Copynumber: 7.7 Consensus size: 40
17378689 TGATTACTCT
* * * *
17378699 TCGGGACCTAGCCCGGATATAACACCAGCACGAATGCTCT
1 TCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCC
* ** * *
17378739 TTGGGGTTTAGCACGGATATATCACTAGCACGAATGCTCT
1 TCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCC
* *
17378779 TCGGAACTTAGCCCGGATACATCACTAGCACGAATGCTCC
1 TCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCC
17378819 TCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCC
1 TCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCC
*
17378859 TCGGGACTTAGCCCGGATATATTACTAGCACGAATGCTCC
1 TCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCC
* *
17378899 TCGGGACTTAGCCCGAATATATCACTAGCACAAATGCTCC
1 TCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCC
*
17378939 TCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCT
1 TCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCC
*
17378979 TCGAGACTTAGCCCGGATATATCACT
1 TCGGGACTTAGCCCGGATATATCACT
17379005 CTCAATTCTT
Statistics
Matches: 242, Mismatches: 24, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 242 1.00
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
TCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCC
Found at i:17380332 original size:37 final size:37
Alignment explanation
Indices: 17380273--17380411 Score: 224
Period size: 37 Copynumber: 3.8 Consensus size: 37
17380263 AACTCAGACG
* *
17380273 AAATCTCCACACGAAGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
17380310 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
17380347 TAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
* * *
17380384 TAATCTCCAGACGTAGTCATTGGGTCTT
1 AAATCTCCACACGTAGTCATCGGGTCTT
17380412 TAGAGCTCGG
Statistics
Matches: 97, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 97 1.00
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.25
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:17380845 original size:49 final size:47
Alignment explanation
Indices: 17380530--17381233 Score: 1048
Period size: 47 Copynumber: 14.6 Consensus size: 47
17380520 CCCTTCGGGA
* * * * * * *
17380530 CTTATCACATTTATACAGTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
17380577 CTTGTCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
17380624 CTTATCACATATATACACTTTCACATTCATCACATCGACCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
17380671 CTTATCACATATATACACTTTCACATTTATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
17380718 CTTATCACATATATACACTTTCACATTTATCACATCAGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
17380765 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
17380812 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
17380861 CTTATCACATATATACACTTTCACATTCATCATATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
17380908 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
17380957 CTTATCACATATACACACTTTCACATTCATCACATCGACCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
17381004 CTTATCACATATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC----ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
17381055 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
17381104 CTTATCACATATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC----ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
17381155 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
17381204 CTTATCACATATATACACTTTCACATTCAT
1 CTTATCACATATATACACTTTCACATTCAT
17381234 TCAAATATAC
Statistics
Matches: 612, Mismatches: 35, Indels: 20
0.92 0.05 0.03
Matches are distributed among these distances:
47 333 0.54
49 185 0.30
51 94 0.15
ACGTcount: A:0.30, C:0.28, G:0.08, T:0.34
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:17380863 original size:96 final size:96
Alignment explanation
Indices: 17380530--17381233 Score: 1073
Period size: 96 Copynumber: 7.3 Consensus size: 96
17380520 CCCTTCGGGA
* * * * * * *
17380530 CTTATCACAT-T-TATACAGTTTCACATCCATCACGTTGGCCACTCGGCCTTGTCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
*
17380593 ACTTTCACATTCATCACATCGGCTATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
*
17380624 CTTATCAC--ATATATACACTTTCACATTCATCACATCGACCATTAGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
* *
17380687 ACTTTCACATTTATCACATCGGCTATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
* * *
17380718 CTTATCAC--ATATATACACTTTCACATTTATCACATCAGCTATTAGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
17380781 ACTTTCACATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
* *
17380812 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
*
17380877 ACTTTCACATTCATCATATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
* * *
17380908 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATACAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
*
17380973 ACTTTCACATTCATCACATCGACCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
17381004 CTTATCACATATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATAT
1 CTTATCAC--ATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATAT
17381069 ATACACTTTCACATTCATCACATCGGCCATTAGGC
62 ATACACTTTCACATTCATCACATCGGCCATTAGGC
17381104 CTTATCACATATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATAT
1 CTTATCAC--ATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATAT
* *
17381169 ATACACTTTCACATTCATCACATTGGCCATTCGGC
62 ATACACTTTCACATTCATCACATCGGCCATTAGGC
17381204 CTTATCAC--ATATATACACTTTCACATTCAT
1 CTTATCACATATATATACACTTTCACATTCAT
17381234 TCAAATATAC
Statistics
Matches: 572, Mismatches: 30, Indels: 14
0.93 0.05 0.02
Matches are distributed among these distances:
93 1 0.00
94 178 0.31
96 203 0.35
98 47 0.08
100 143 0.25
ACGTcount: A:0.30, C:0.28, G:0.08, T:0.34
Consensus pattern (96 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
ACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:17384210 original size:95 final size:94
Alignment explanation
Indices: 17384003--17384709 Score: 796
Period size: 95 Copynumber: 7.6 Consensus size: 94
17383993 TTGTTAATGG
* * *
17384003 TTAGGGTTTTTAATTAAATTAAGTTAGGGTTTAGGGTTTTTAATTAAATTATGTT---G-TTAGG
1 TTAGGGTTTTTAATTAAATTAGGTTAAGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGG
17384064 GTTTTTAATTAAATTA----AGTTAGGGT
66 GTTTTTAATTAAATTAGGTTAGTTAGGGT
17384089 TTAGGGTTTTTAATTAAATTAGGTTAAGG-TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGG
1 TTAGGGTTTTTAATTAAATTAGGTTAAGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGG
17384153 GTTTTTAATTAAATTAGGTTAGGGTTAGGGT
66 GTTTTTAATTAAATTAGGTTA--GTTAGGGT
* *
17384184 TTAGGGTTTTTAATTAAATTAAGTTAAGG-TTAGTGTTTTTAATTAAATTAGGTTAGGGTTAGGG
1 TTAGGGTTTTTAATTAAATTAGGTTAAGGTTTAGGGTTTTTAATT-AA--A--TTA-GGTTAGGG
*
17384248 TTTAAGGTTTTTAATTAAATTA----AGTTAGGGT
60 TTTAGGGTTTTTAATTAAATTAGGTTAGTTAGGGT
* *
17384279 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGGGTCTTTAATTAAATTAGGTTAGGGTTTAGG
1 TTAGGGTTTTTAATTAAATTAGGTTAAGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGG
*
17384344 GTCTTTAATTAAATTAGGTTAGGGTTAGGGT
66 GTTTTTAATTAAATTAGGTTA--GTTAGGGT
17384375 TTAGGGTTTTTAATTAAATTAGGTT-AGGATTT-GGGTTTTTAATTAAATTAGGTTAGGG-TTAG
1 TTAGGGTTTTTAATTAAATTAGGTTAAGG-TTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAG
*
17384437 TGTTTTTAATTAAATTA-G---GTTAGGG-
65 GGTTTTTAATTAAATTAGGTTAGTTAGGGT
17384462 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGG
1 TTAGGGTTTTTAATTAAATTAGGTTA-----A-GGTTTAGGGTTTTTAATT-AA--A--TTA-GG
*
17384527 TTAGGGTTTAGGGTTTTTAATTAAATTA----AGTTAGAG-
54 TTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGTTAGGGT
*
17384563 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAAGG
1 TTAGGGTTTTTAATTAAATTAGGTTAAGGTTTAGGGTTTTTAATTAAATTAGGTTA--G----GG
17384628 TTTAGGGTTTTTAATTAAATTAGGTT-G---GGG-
60 TTTAGGGTTTTTAATTAAATTAGGTTAGTTAGGGT
*
17384658 TTAGGGTGTTTAATTAAATTAGGTT-AGTGTTTAGGGTTTTTAATTAAATTAG
1 TTAGGGTTTTTAATTAAATTAGGTTAAG-GTTTAGGGTTTTTAATTAAATTAG
17384710 AATTTTTATT
Statistics
Matches: 548, Mismatches: 22, Indels: 93
0.83 0.03 0.14
Matches are distributed among these distances:
85 24 0.04
86 27 0.05
87 25 0.05
88 8 0.01
89 26 0.05
90 31 0.06
91 4 0.01
92 1 0.00
93 7 0.01
94 37 0.07
95 208 0.38
96 51 0.09
97 2 0.00
98 2 0.00
99 3 0.01
100 11 0.02
101 81 0.15
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.46
Consensus pattern (94 bp):
TTAGGGTTTTTAATTAAATTAGGTTAAGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGG
GTTTTTAATTAAATTAGGTTAGTTAGGGT
Found at i:17384709 original size:30 final size:30
Alignment explanation
Indices: 17384003--17384709 Score: 851
Period size: 30 Copynumber: 22.7 Consensus size: 30
17383993 TTGTTAATGG
*
17384003 TTAGGGTTTTTAATTAAATTAAGTTAGGGT
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGT
*
17384033 TTAGGGTTTTTAATTAAATTATGTT---G-
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGT
*
17384059 TTAGGGTTTTTAATTAAATTAAGTTAGGGT
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGT
*
17384089 TTAGGGTTTTTAATTAAATTAGGTTAAGG-
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGT
17384118 TTAGGGTTTTTAATTAAATTAGGTTAGGGT
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGT
17384148 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGT
1 TTAGGGTTTTTAATT-AA--A--TTA-GGTTAGGGT
* *
17384184 TTAGGGTTTTTAATTAAATTAAGTTAAGG-
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGT
*
17384213 TTAGTGTTTTTAATTAAATTAGGTTAGGGTTAGGGT
1 TTAGGGTTTTTAATT-AA--A--TTA-GGTTAGGGT
* *
17384249 TTAAGGTTTTTAATTAAATTAAGTTAGGGT
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGT
17384279 TTAGGGTTTTTAATTAAATTAGGTTAGGGT
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGT
*
17384309 TTAGGGTCTTTAATTAAATTAGGTTAGGGT
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGT
*
17384339 TTAGGGTCTTTAATTAAATTAGGTTAGGGTTAGGGT
1 TTAGGGTTTTTAATT-AA--A--TTA-GGTTAGGGT
*
17384375 TTAGGGTTTTTAATTAAATTAGGTTAGGAT
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGT
17384405 TT-GGGTTTTTAATTAAATTAGGTTAGGG-
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGT
*
17384433 TTAGTGTTTTTAATTAAATTAGGTTAGGG-
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGT
17384462 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGT
1 TTAGGGTTTTTAATT-AA--A--TTA-GGTTAGGGT
17384498 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGT
1 TTAGGGTTTTTAATT-AA--A--TTA-GGTTAGGGT
* *
17384534 TTAGGGTTTTTAATTAAATTAAGTTAGAG-
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGT
17384563 TTAGGGTTTTTAATTAAATTAGGTTAGGGT
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGT
17384593 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTAAGGT
1 TTAGGGTTTTTAATTAAATTAGGTTA--G----GGT
*
17384629 TTAGGGTTTTTAATTAAATTAGGTT-GGGG
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGT
* *
17384658 TTAGGGTGTTTAATTAAATTAGGTTAGTGT
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGT
17384688 TTAGGGTTTTTAATTAAATTAG
1 TTAGGGTTTTTAATTAAATTAG
17384710 AATTTTTATT
Statistics
Matches: 607, Mismatches: 30, Indels: 80
0.85 0.04 0.11
Matches are distributed among these distances:
26 24 0.04
27 1 0.00
28 2 0.00
29 160 0.26
30 221 0.36
31 16 0.03
32 3 0.00
33 7 0.01
34 6 0.01
35 28 0.05
36 139 0.23
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.46
Consensus pattern (30 bp):
TTAGGGTTTTTAATTAAATTAGGTTAGGGT
Found at i:17386455 original size:38 final size:38
Alignment explanation
Indices: 17386413--17386486 Score: 139
Period size: 38 Copynumber: 1.9 Consensus size: 38
17386403 ATTTGAAGAA
17386413 TGTATGATCGAGCATATCGGATTCTTTCAATTTCGGAG
1 TGTATGATCGAGCATATCGGATTCTTTCAATTTCGGAG
*
17386451 TGTATGATCGAGCATATTGGATTCTTTCAATTTCGG
1 TGTATGATCGAGCATATCGGATTCTTTCAATTTCGG
17386487 TTGAATTTGC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.39
Consensus pattern (38 bp):
TGTATGATCGAGCATATCGGATTCTTTCAATTTCGGAG
Found at i:17386935 original size:14 final size:15
Alignment explanation
Indices: 17386918--17386951 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
17386908 AATAATTATC
17386918 TAAAAATA-CATAAA
1 TAAAAATATCATAAA
*
17386932 TAAAAATATCTTAAA
1 TAAAAATATCATAAA
17386947 TAAAA
1 TAAAA
17386952 TTTAAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAAAATATCATAAA
Found at i:17386946 original size:25 final size:25
Alignment explanation
Indices: 17386896--17386942 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
17386886 CTTTTATAAC
*
17386896 AAATAATAAATTAATAATTATCTAA
1 AAATAATAAATTAATAAATATCTAA
17386921 AAATACATAAA-TAA-AAATATCT
1 AAATA-ATAAATTAATAAATATCT
17386943 TAAATAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 7 0.35
25 8 0.40
26 5 0.25
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (25 bp):
AAATAATAAATTAATAAATATCTAA
Found at i:17387084 original size:29 final size:28
Alignment explanation
Indices: 17387042--17387105 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 28
17387032 GCCATTGATG
*
17387042 AAAATATAAAAAAAATTAAAATTATTTTA
1 AAAAAATAAAAAAAATTAAAATTA-TTTA
* *
17387071 AAAAAATATAAAAATTTAAAATTATTTA
1 AAAAAATAAAAAAAATTAAAATTATTTA
17387099 AAAAAAT
1 AAAAAAT
17387106 GAAATTGAGG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
28 11 0.34
29 21 0.66
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (28 bp):
AAAAAATAAAAAAAATTAAAATTATTTA
Found at i:17387087 original size:19 final size:18
Alignment explanation
Indices: 17387050--17387091 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 18
17387040 TGAAAATATA
17387050 AAAAAAATTAAAATTATTTT
1 AAAAAAATTAAAA-TA-TTT
17387070 AAAAAAATATAAAA-ATTT
1 AAAAAAAT-TAAAATATTT
17387088 AAAA
1 AAAA
17387092 TTATTTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
18 7 0.33
19 1 0.05
20 8 0.38
21 5 0.24
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
AAAAAAATTAAAATATTT
Found at i:17387174 original size:30 final size:30
Alignment explanation
Indices: 17387138--17387197 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
17387128 TTAATATGAA
17387138 TTTGAGA-AATTTTTGGAAGGAAATTGAGAG
1 TTTGAGAGAA-TTTTGGAAGGAAATTGAGAG
*
17387168 TTTGAGAGGATTTTGGAAGGAAATTGAGAG
1 TTTGAGAGAATTTTGGAAGGAAATTGAGAG
17387198 GATTTTGGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
30 27 0.96
31 1 0.04
ACGTcount: A:0.35, C:0.00, G:0.33, T:0.32
Consensus pattern (30 bp):
TTTGAGAGAATTTTGGAAGGAAATTGAGAG
Found at i:17387194 original size:22 final size:22
Alignment explanation
Indices: 17387169--17387218 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
17387159 AATTGAGAGT
17387169 TTGAGAGGATTTTGGAAGGAAA
1 TTGAGAGGATTTTGGAAGGAAA
17387191 TTGAGAGGATTTTGGAAGGAAA
1 TTGAGAGGATTTTGGAAGGAAA
17387213 TTGAGA
1 TTGAGA
17387219 TAGGATTTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.36, C:0.00, G:0.36, T:0.28
Consensus pattern (22 bp):
TTGAGAGGATTTTGGAAGGAAA
Found at i:17391723 original size:2 final size:2
Alignment explanation
Indices: 17391716--17391741 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
17391706 CAAAAGTAAC
17391716 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
17391742 GGAGCTAAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:17392223 original size:19 final size:19
Alignment explanation
Indices: 17392171--17392224 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
17392161 TTATCACCTT
17392171 AAAATATTTAAAAATTACAA
1 AAAATATTTAAAAA-TACAA
** *
17392191 AAAATATAAAAAAATGCAA
1 AAAATATTTAAAAATACAA
*
17392210 AAAATATTTTAAAAT
1 AAAATATTTAAAAAT
17392225 TTTAAAATTA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.28
Consensus pattern (19 bp):
AAAATATTTAAAAATACAA
Found at i:17393018 original size:19 final size:20
Alignment explanation
Indices: 17392996--17393040 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
17392986 ACTTTTCCTA
17392996 TTTTTTAATAATTTAAAT-T
1 TTTTTTAATAATTTAAATAT
**
17393015 TTTTTTAATTTTTTAAATAT
1 TTTTTTAATAATTTAAATAT
17393035 TTTTTT
1 TTTTTT
17393041 TGTAATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTTTTAATAATTTAAATAT
Found at i:17393098 original size:13 final size:13
Alignment explanation
Indices: 17393080--17393104 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17393070 AATTTTTAAA
17393080 TAATTTTTGTATT
1 TAATTTTTGTATT
17393093 TAATTTTTGTAT
1 TAATTTTTGTAT
17393105 ATATTTTTTT
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:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (13 bp):
TAATTTTTGTATT
Found at i:17393112 original size:13 final size:13
Alignment explanation
Indices: 17393067--17393124 Score: 61
Period size: 12 Copynumber: 4.8 Consensus size: 13
17393057 CTTGTATATT
17393067 TATAA-TTTT-TA
1 TATAATTTTTGTA
*
17393078 AATAATTTTTGTA
1 TATAATTTTTGTA
*
17393091 TTTAATTTTTGTA
1 TATAATTTTTGTA
*
17393104 TAT-ATTTTTTTA
1 TATAATTTTTGTA
17393116 -ATAATTTTT
1 TATAATTTTT
17393125 AAAGATTTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
11 6 0.15
12 18 0.46
13 15 0.38
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (13 bp):
TATAATTTTTGTA
Found at i:17393112 original size:26 final size:24
Alignment explanation
Indices: 17393013--17393133 Score: 83
Period size: 23 Copynumber: 5.1 Consensus size: 24
17393003 ATAATTTAAA
17393013 TTTTT-TTTAATTTTTTAAATATT
1 TTTTTATTTAATTTTTTAAATATT
*
17393036 TTTTT-TGTAA-TTTTTATAAT-TCT
1 TTTTTATTTAATTTTTTA-AATAT-T
* * *
17393059 TGTATATTTATAATTTTTAAATAATT
1 TTTTTATTTA-ATTTTTTAAAT-ATT
* *
17393085 TTTGTATTTAATTTTTGTATATATT
1 TTTTTATTTAATTTTT-TAAATATT
* *
17393110 TTTTTA-ATAA-TTTTTAAAGATT
1 TTTTTATTTAATTTTTTAAATATT
17393132 TT
1 TT
17393134 AAGGTTTTTT
Statistics
Matches: 78, Mismatches: 12, Indels: 17
0.73 0.11 0.16
Matches are distributed among these distances:
22 15 0.19
23 20 0.26
24 6 0.08
25 17 0.22
26 19 0.24
27 1 0.01
ACGTcount: A:0.29, C:0.01, G:0.04, T:0.66
Consensus pattern (24 bp):
TTTTTATTTAATTTTTTAAATATT
Found at i:17398863 original size:19 final size:19
Alignment explanation
Indices: 17398841--17398901 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 19
17398831 ATTAAAGTAG
17398841 GAAAGAAAGAGATATGGGA
1 GAAAGAAAGAGATATGGGA
*
17398860 GAAAGATAGAG--A-GGCGA
1 GAAAGAAAGAGATATGG-GA
* *
17398877 GAGAGAAAGAGATATGAGA
1 GAAAGAAAGAGATATGGGA
17398896 GAAAGA
1 GAAAGA
17398902 TAGAAAGACG
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
16 2 0.06
17 12 0.36
19 18 0.55
20 1 0.03
ACGTcount: A:0.52, C:0.02, G:0.38, T:0.08
Consensus pattern (19 bp):
GAAAGAAAGAGATATGGGA
Found at i:17398884 original size:36 final size:36
Alignment explanation
Indices: 17398844--17398917 Score: 121
Period size: 36 Copynumber: 2.1 Consensus size: 36
17398834 AAAGTAGGAA
* * *
17398844 AGAAAGAGATATGGGAGAAAGATAGAGAGGCGAGAG
1 AGAAAGAGATATGAGAGAAAGATAGAAAGACGAGAG
17398880 AGAAAGAGATATGAGAGAAAGATAGAAAGACGAGAG
1 AGAAAGAGATATGAGAGAAAGATAGAAAGACGAGAG
17398916 AG
1 AG
17398918 GGAAAGGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.51, C:0.03, G:0.38, T:0.08
Consensus pattern (36 bp):
AGAAAGAGATATGAGAGAAAGATAGAAAGACGAGAG
Found at i:17400689 original size:50 final size:50
Alignment explanation
Indices: 17400634--17400818 Score: 178
Period size: 50 Copynumber: 3.7 Consensus size: 50
17400624 CATTGAGGTT
* *
17400634 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAG
1 ATGAGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAA
** * * *
17400684 ATGAGAGATCCCCCGTAAGACCATGTCTGGGAGATGGCATGGGCACCGAT
1 ATGAGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAA
* * * * **
17400734 ATGAGA-ACTCCCATGTAAAACTATATCTAGGTTATGGCATTGGCA--GTAA
1 ATGAGAGA-TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AA
* * * *
17400783 AAGAAACATCCCATGTAAGGCCATGTCTGGGACATG
1 ATGAGAGATCCCATGTAAGACCATGTCTGGGACATG
17400819 ACTTTCGCAT
Statistics
Matches: 107, Mismatches: 25, Indels: 7
0.77 0.18 0.05
Matches are distributed among these distances:
48 1 0.01
49 27 0.25
50 79 0.74
ACGTcount: A:0.30, C:0.21, G:0.28, T:0.22
Consensus pattern (50 bp):
ATGAGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAA
Found at i:17405116 original size:10 final size:11
Alignment explanation
Indices: 17405101--17405129 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
17405091 GCAATTTGAT
17405101 AAATAAAAT-A
1 AAATAAAATAA
17405111 AAATAAAATAA
1 AAATAAAATAA
17405122 AAATAAAA
1 AAATAAAA
17405130 GCTATCATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.50
11 9 0.50
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (11 bp):
AAATAAAATAA
Found at i:17415467 original size:38 final size:38
Alignment explanation
Indices: 17415425--17415498 Score: 139
Period size: 38 Copynumber: 1.9 Consensus size: 38
17415415 TTCAGTTCAA
17415425 GCTAATAAGCTCCTGAATCAAGGTTGTGAAGCTTTCGT
1 GCTAATAAGCTCCTGAATCAAGGTTGTGAAGCTTTCGT
*
17415463 GCTAATAAGTTCCTGAATCAAGGTTGTGAAGCTTTC
1 GCTAATAAGCTCCTGAATCAAGGTTGTGAAGCTTTC
17415499 CTAGCCTACG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (38 bp):
GCTAATAAGCTCCTGAATCAAGGTTGTGAAGCTTTCGT
Found at i:17417819 original size:50 final size:50
Alignment explanation
Indices: 17417635--17417821 Score: 160
Period size: 49 Copynumber: 3.6 Consensus size: 50
17417625 GGGAATGAGA
* * * * **
17417635 TCCCATGTAAGACCATGTCTAGGACATGGCATTGGCATCATTGAGATTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGATATGGCATGGGCACCA---AG---ATGAGAAC
* * * * **
17417691 TCTCATGTAAGACCATGTCTGGGATATGACGTTGGCACCAAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGATATGGCATGGGCACCAAGATGAGAAC
* * * *
17417741 TCCC-CGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGATATGGCATGGGCACCAAGATGAGAAC
*
17417790 TCCCATGTAAGACCATATCTGGGATATGGCAT
1 TCCCATGTAAGACCATGTCTGGGATATGGCAT
17417822 TGGTAGTATA
Statistics
Matches: 111, Mismatches: 19, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
49 40 0.36
50 35 0.32
53 2 0.02
56 34 0.31
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.24
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGATATGGCATGGGCACCAAGATGAGAAC
Found at i:17417860 original size:49 final size:49
Alignment explanation
Indices: 17417746--17417865 Score: 145
Period size: 50 Copynumber: 2.4 Consensus size: 49
17417736 AGAGGTCCCC
*
17417746 GTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAACTCCCAT
1 GTAAGACCATGTCTGGGACATGGCATGGGCA-CGATATGAAAACTCCCAT
* * * *
17417796 GTAAGACCATATCTGGGATATGGCATTGGTA-G-TATAGAAAACATCCCAT
1 GTAAGACCATGTCTGGGACATGGCATGGGCACGATAT-GAAAAC-TCCCAT
*
17417845 GTAAGACTATGTCTGGGACAT
1 GTAAGACCATGTCTGGGACAT
17417866 AGCTTTGGCA
Statistics
Matches: 60, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
47 3 0.05
48 6 0.10
49 24 0.40
50 27 0.45
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.24
Consensus pattern (49 bp):
GTAAGACCATGTCTGGGACATGGCATGGGCACGATATGAAAACTCCCAT
Found at i:17418092 original size:12 final size:12
Alignment explanation
Indices: 17418075--17418113 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
17418065 ATGAGTTATT
17418075 TAAGTAAGCAAG
1 TAAGTAAGCAAG
*
17418087 TAAGTAAACAAG
1 TAAGTAAGCAAG
* *
17418099 TAAGTGAGTAAG
1 TAAGTAAGCAAG
17418111 TAA
1 TAA
17418114 ACAAGCGAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.51, C:0.05, G:0.23, T:0.21
Consensus pattern (12 bp):
TAAGTAAGCAAG
Found at i:17418101 original size:20 final size:20
Alignment explanation
Indices: 17418076--17418118 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
17418066 TGAGTTATTT
17418076 AAGTAAGCAAGTAAGTAAAC
1 AAGTAAGCAAGTAAGTAAAC
**
17418096 AAGTAAGTGAGTAAGTAAAC
1 AAGTAAGCAAGTAAGTAAAC
17418116 AAG
1 AAG
17418119 CGAGTAAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.53, C:0.07, G:0.23, T:0.16
Consensus pattern (20 bp):
AAGTAAGCAAGTAAGTAAAC
Found at i:17424267 original size:50 final size:50
Alignment explanation
Indices: 17424149--17424548 Score: 514
Period size: 50 Copynumber: 7.8 Consensus size: 50
17424139 GATCATAACA
* ** *
17424149 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTC-GG
* ***
17424201 TGTCC-ATGCCATGTCCCAGACATGGTCTTATGGGGGACCTCTCATCTCGG
1 TG-CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* **
17424251 TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATCTTAG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * *
17424301 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTTTCACCTCGA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
17424351 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGAACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
17424401 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
17424451 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATGATATCAAGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC--GG
* * * *
17424506 ATTCCAATGTCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
17424549 TTACCCAAAT
Statistics
Matches: 306, Mismatches: 34, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
49 2 0.01
50 221 0.72
51 8 0.03
52 30 0.10
53 6 0.02
55 2 0.01
56 37 0.12
ACGTcount: A:0.22, C:0.30, G:0.21, T:0.26
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:17430209 original size:8 final size:9
Alignment explanation
Indices: 17430181--17430228 Score: 55
Period size: 9 Copynumber: 5.4 Consensus size: 9
17430171 CATTTTTAAT
17430181 AAATATTAAA
1 AAATA-TAAA
17430191 AAATATAAA
1 AAATATAAA
17430200 AAATATAAA
1 AAATATAAA
*
17430209 AAA-AGAAA
1 AAATATAAA
*
17430217 AAA-AGAAA
1 AAATATAAA
17430225 AAAT
1 AAAT
17430229 TATTTTAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
8 15 0.42
9 16 0.44
10 5 0.14
ACGTcount: A:0.79, C:0.00, G:0.04, T:0.17
Consensus pattern (9 bp):
AAATATAAA
Found at i:17430219 original size:19 final size:19
Alignment explanation
Indices: 17430181--17430220 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
17430171 CATTTTTAAT
* * *
17430181 AAATATTAAAAAATATAAA
1 AAATATAAAAAAAGAAAAA
17430200 AAATATAAAAAAAGAAAAA
1 AAATATAAAAAAAGAAAAA
17430219 AA
1 AA
17430221 GAAAAAATTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (19 bp):
AAATATAAAAAAAGAAAAA
Found at i:17430238 original size:11 final size:11
Alignment explanation
Indices: 17430224--17430251 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
17430214 AAAAAAAGAA
17430224 AAAATTATTTT
1 AAAATTATTTT
17430235 AAAATTATTTT
1 AAAATTATTTT
17430246 AAAATT
1 AAAATT
17430252 TAAAAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
AAAATTATTTT
Found at i:17431728 original size:3 final size:3
Alignment explanation
Indices: 17431720--17431762 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
17431710 TGAAAAAGTA
17431720 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
17431763 GGATTTCATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:17434473 original size:15 final size:15
Alignment explanation
Indices: 17434453--17434483 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
17434443 AATAAAGAAA
17434453 TCTAGGTGCAAATGT
1 TCTAGGTGCAAATGT
17434468 TCTAGGTGCAAATGT
1 TCTAGGTGCAAATGT
17434483 T
1 T
17434484 ATGAGTACGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.13, G:0.26, T:0.35
Consensus pattern (15 bp):
TCTAGGTGCAAATGT
Found at i:17437324 original size:49 final size:50
Alignment explanation
Indices: 17437270--17437439 Score: 158
Period size: 49 Copynumber: 3.5 Consensus size: 50
17437260 AGGTCCCATA
** *
17437270 TAAGACCATGTCTGGGACATGGCATTG-GCACCGAGATGAGGGTCTCTC-G
1 TAAGACCATGTCTGGGACATGGCATTGTGCACCGAGATGA-GAACTCCCAG
*
17437319 TAAGACCATGTCTGGGACATGGCA-TGTGCACCGATATGAGAACTCCCATG
1 TAAGACCATGTCTGGGACATGGCATTGTGCACCGAGATGAGAACTCCCA-G
* * * * *
17437369 TAAGACCAT-TCTGGGATATGGCATT-AGCA--GTACAAGA-AACATCCAATG
1 TAAGACCATGTCTGGGACATGGCATTGTGCACCG-AGATGAGAAC-TCCCA-G
17437417 TAAGACCATGTCTGGGACATGGC
1 TAAGACCATGTCTGGGACATGGC
17437440 TTTGGCATGT
Statistics
Matches: 104, Mismatches: 10, Indels: 14
0.81 0.08 0.11
Matches are distributed among these distances:
47 4 0.04
48 26 0.25
49 63 0.61
50 11 0.11
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.22
Consensus pattern (50 bp):
TAAGACCATGTCTGGGACATGGCATTGTGCACCGAGATGAGAACTCCCAG
Found at i:17443105 original size:26 final size:26
Alignment explanation
Indices: 17443069--17443121 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
17443059 CTTTGCCAAC
17443069 TGAGTTAGAGAAGATTCATAATGTAT
1 TGAGTTAGAGAAGATTCATAATGTAT
17443095 TGAGTTAGAGAAGATTCATAATGTAT
1 TGAGTTAGAGAAGATTCATAATGTAT
17443121 T
1 T
17443122 CTATGTGTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.38, C:0.04, G:0.23, T:0.36
Consensus pattern (26 bp):
TGAGTTAGAGAAGATTCATAATGTAT
Found at i:17444697 original size:56 final size:50
Alignment explanation
Indices: 17444611--17444857 Score: 216
Period size: 50 Copynumber: 4.8 Consensus size: 50
17444601 ATTTGGGTAA
*
17444611 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAAGTTATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CG-AG--ATG
**
17444667 AGAGATCCCATGTAAGACCATGTCTGGGACATGGTGTTGGCACCGAGATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * *
17444717 AGAGGTCCCCCT-TAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGAT-CCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * * *
17444767 AGA-ACTCCCATGTAAGACCATATTTGGGATATGGTATTGGCA--GTACAAT-
1 AGAGA-TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-A-GATG
* * * * *
17444816 AAACATCCTATGTAATACCATGTCTGGGACATGGCTTTGGCA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
17444858 TGTTATTATC
Statistics
Matches: 160, Mismatches: 25, Indels: 19
0.78 0.12 0.09
Matches are distributed among these distances:
48 1 0.01
49 37 0.23
50 74 0.46
51 4 0.03
52 2 0.01
53 1 0.01
55 1 0.01
56 40 0.25
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25
Consensus pattern (50 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:17444807 original size:100 final size:104
Alignment explanation
Indices: 17444623--17444808 Score: 256
Period size: 100 Copynumber: 1.8 Consensus size: 104
17444613 AGATCCCATG
* *
17444623 TAAGACCATGTCTGGGACATGGCATTGGCATCATTGAAGTTATGAGAGATCCCATGTAAGACCAT
1 TAAGACCATGTCTGGGACATGGCATGGGCATCA-CGAAG-TATGAGAGATCCCATGTAAGACCAT
* *
17444688 GTCTGGGACATGGTGTTGGCACCGAGATGAGAGGTCCCCCT
64 ATCTGGGACATGGTATTGGCACCGAGATGAGAGGTCCCCCT
17444729 TAAGACCATGTCTGGGACATGGCATGGGCA-C-CG-A-TATGAGA-ACTCCCATGTAAGACCATA
1 TAAGACCATGTCTGGGACATGGCATGGGCATCACGAAGTATGAGAGA-TCCCATGTAAGACCATA
* *
17444789 TTTGGGATATGGTATTGGCA
65 TCTGGGACATGGTATTGGCA
17444809 GTACAATAAA
Statistics
Matches: 73, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
99 1 0.01
100 40 0.55
102 1 0.01
103 1 0.01
105 1 0.01
106 29 0.40
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.25
Consensus pattern (104 bp):
TAAGACCATGTCTGGGACATGGCATGGGCATCACGAAGTATGAGAGATCCCATGTAAGACCATAT
CTGGGACATGGTATTGGCACCGAGATGAGAGGTCCCCCT
Found at i:17451507 original size:13 final size:13
Alignment explanation
Indices: 17451489--17451517 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
17451479 AGACCTCAAG
17451489 ATAATATCCCATA
1 ATAATATCCCATA
17451502 ATAATATCCCATA
1 ATAATATCCCATA
17451515 ATA
1 ATA
17451518 TCCTATTAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.48, C:0.21, G:0.00, T:0.31
Consensus pattern (13 bp):
ATAATATCCCATA
Found at i:17454652 original size:41 final size:44
Alignment explanation
Indices: 17454570--17454665 Score: 119
Period size: 46 Copynumber: 2.2 Consensus size: 44
17454560 AATTTTAATT
*
17454570 CAAAAATCTATATTTAAATTAAAATATTAATAAATAAAAATGTTA
1 CAAAAATCTATATTTAAATTAAAATATTAATAAAT-AAAATGTAA
* *
17454615 CAAAAAGTTTATATTTAAATTCAAA-A-T-ATAAAT-AAATGTAA
1 CAAAAA-TCTATATTTAAATTAAAATATTAATAAATAAAATGTAA
17454656 CAAAAATCTA
1 CAAAAATCTA
17454666 ATCTGTGTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
40 3 0.07
41 13 0.28
43 6 0.13
44 1 0.02
45 7 0.15
46 16 0.35
ACGTcount: A:0.57, C:0.06, G:0.03, T:0.33
Consensus pattern (44 bp):
CAAAAATCTATATTTAAATTAAAATATTAATAAATAAAATGTAA
Found at i:17463068 original size:6 final size:6
Alignment explanation
Indices: 17463052--17463113 Score: 106
Period size: 6 Copynumber: 10.0 Consensus size: 6
17463042 CAGACCATAA
17463052 AAAATAT AAAAAT AAAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
1 AAAA-AT AAAAAT -AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
17463102 AAAAAT AAAAAT
1 AAAAAT AAAAAT
17463114 CCAAACTAAA
Statistics
Matches: 54, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
6 44 0.81
7 10 0.19
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (6 bp):
AAAAAT
Found at i:17467516 original size:29 final size:29
Alignment explanation
Indices: 17467474--17467540 Score: 125
Period size: 29 Copynumber: 2.3 Consensus size: 29
17467464 TATTTAATTA
*
17467474 ATGTTAAATGATTTTATTGAGTTGTTTTG
1 ATGTTAAATAATTTTATTGAGTTGTTTTG
17467503 ATGTTAAATAATTTTATTGAGTTGTTTTG
1 ATGTTAAATAATTTTATTGAGTTGTTTTG
17467532 ATGTTAAAT
1 ATGTTAAAT
17467541 GTTACACCCA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.28, C:0.00, G:0.18, T:0.54
Consensus pattern (29 bp):
ATGTTAAATAATTTTATTGAGTTGTTTTG
Found at i:17474947 original size:12 final size:12
Alignment explanation
Indices: 17474930--17474960 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
17474920 AGTGGATGGA
*
17474930 TCCTATTTGAAG
1 TCCTATTGGAAG
17474942 TCCTATTGGAAG
1 TCCTATTGGAAG
17474954 TCCTATT
1 TCCTATT
17474961 CTACCATGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.23, C:0.19, G:0.16, T:0.42
Consensus pattern (12 bp):
TCCTATTGGAAG
Found at i:17482199 original size:24 final size:24
Alignment explanation
Indices: 17482154--17482199 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
17482144 GCTCTTCAGT
* *
17482154 AGCAGTTAGATTGGGCTCCTCGAA
1 AGCAGTTAGAGTGGCCTCCTCGAA
* *
17482178 AGCAGTTTGAGTGGCCTTCTCG
1 AGCAGTTAGAGTGGCCTCCTCG
17482200 GCAGCATAAG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (24 bp):
AGCAGTTAGAGTGGCCTCCTCGAA
Found at i:17488248 original size:27 final size:27
Alignment explanation
Indices: 17488204--17488567 Score: 332
Period size: 27 Copynumber: 13.5 Consensus size: 27
17488194 CTTTCGATTT
17488204 GAAGGGTAAAATGATCGAAATACCCTC
1 GAAGGGTAAAATGATCGAAATACCCTC
* * *
17488231 GAAAGCTAAAATAATCGAAATACCC-C
1 GAAGGGTAAAATGATCGAAATACCCTC
*
17488257 TGAAGGGTAAAATGATTGAAATACCCTC
1 -GAAGGGTAAAATGATCGAAATACCCTC
* * *
17488285 AAAGGGTAAAATAACCGAAATACCCTC
1 GAAGGGTAAAATGATCGAAATACCCTC
* *
17488312 AAAGAGTAAAATGA-CAGAAATACCCTC
1 GAAGGGTAAAATGATC-GAAATACCCTC
* * *
17488339 AAAGGGTAAAATGA-CTAAAATACCCAC
1 GAAGGGTAAAATGATC-GAAATACCCTC
17488366 GAAGGGTAAAATGATCGAAATACCCAT-
1 GAAGGGTAAAATGATCGAAATACCC-TC
* *
17488393 GAAGGGTAAAATGA-CAAAAATACCCTT
1 GAAGGGTAAAATGATC-GAAATACCCTC
* * * * *
17488420 GAAGGGTAAAATCACCAAAACACCCCC
1 GAAGGGTAAAATGATCGAAATACCCTC
* * *
17488447 GAAGGGAAAAATGATCAAAACACCCTC
1 GAAGGGTAAAATGATCGAAATACCCTC
*
17488474 GAAGGGTAAAATAATCGAAATACCC-C
1 GAAGGGTAAAATGATCGAAATACCCTC
* * * *
17488500 TAAAGGGTAAACTGACCAAAATACCC-C
1 -GAAGGGTAAAATGATCGAAATACCCTC
* *
17488527 GCAGGGTAAAATGA-CTGAAATACCTTC
1 GAAGGGTAAAATGATC-GAAATACCCTC
17488554 -ATAGGGTAAAATGA
1 GA-AGGGTAAAATGA
17488568 CCATTATACC
Statistics
Matches: 281, Mismatches: 44, Indels: 24
0.81 0.13 0.07
Matches are distributed among these distances:
25 1 0.00
26 23 0.08
27 254 0.90
28 3 0.01
ACGTcount: A:0.46, C:0.20, G:0.18, T:0.16
Consensus pattern (27 bp):
GAAGGGTAAAATGATCGAAATACCCTC
Found at i:17488344 original size:81 final size:79
Alignment explanation
Indices: 17488204--17488568 Score: 369
Period size: 81 Copynumber: 4.5 Consensus size: 79
17488194 CTTTCGATTT
* * *
17488204 GAAGGGTAAAATGATCGAAATACCCTCGAAA-GCTAAAATAATCGAAATACCCCTGAAGGGTAAA
1 GAAGGGTAAAATGATCGAAATACCCTC-AAAGGGTAAAATGA-CGAAATACCCCTAAAGGGTAAA
***
17488268 ATGATTGAAATACCCTC
64 ATGACCAAAATACCC-C
* * * *
17488285 AAAGGGTAAAATAACCGAAATACCCTCAAAGAGTAAAATGACAGAAATA-CCCTCAAAGGGTAAA
1 GAAGGGTAAAATGATCGAAATACCCTCAAAGGGTAAAATGAC-GAAATACCCCT-AAAGGGTAAA
*
17488349 ATGACTAAAATACCCAC
64 ATGACCAAAATACCC-C
* * * *
17488366 GAAGGGTAAAATGATCGAAATACCCAT-GAAGGGTAAAATGACAAAAATACCCTTGAAGGGTAAA
1 GAAGGGTAAAATGATCGAAATACCC-TCAAAGGGTAAAATGAC-GAAATACCCCTAAAGGGTAAA
* *
17488430 ATCACCAAAACACCCCC
64 ATGACCAAAATA-CCCC
* * * * * *
17488447 GAAGGGAAAAATGATCAAAACACCCTCGAAGGGTAAAATAATCGAAATACCCCTAAAGGGTAAAC
1 GAAGGGTAAAATGATCGAAATACCCTCAAAGGGTAAAATGA-CGAAATACCCCTAAAGGGTAAAA
17488512 TGACCAAAATACCCC
65 TGACCAAAATACCCC
* * *
17488527 GCAGGGTAAAATGA-CTGAAATACCTTCATAGGGTAAAATGAC
1 GAAGGGTAAAATGATC-GAAATACCCTCAAAGGGTAAAATGAC
17488569 CATTATACCC
Statistics
Matches: 236, Mismatches: 39, Indels: 20
0.80 0.13 0.07
Matches are distributed among these distances:
79 2 0.01
80 44 0.19
81 182 0.77
82 8 0.03
ACGTcount: A:0.46, C:0.20, G:0.18, T:0.16
Consensus pattern (79 bp):
GAAGGGTAAAATGATCGAAATACCCTCAAAGGGTAAAATGACGAAATACCCCTAAAGGGTAAAAT
GACCAAAATACCCC
Found at i:17495881 original size:27 final size:27
Alignment explanation
Indices: 17495850--17496268 Score: 388
Period size: 27 Copynumber: 15.5 Consensus size: 27
17495840 TTTTGATTCG
*
17495850 AAGGGTAAAATGATCGAAATATCCTCA
1 AAGGGTAAAATGATCGAAATACCCTCA
17495877 AAGGGTAAAATGATCGAAATACCC-CGA
1 AAGGGTAAAATGATCGAAATACCCTC-A
*
17495904 AAGGGTAAAATGATCGAAATACCCTCG
1 AAGGGTAAAATGATCGAAATACCCTCA
*
17495931 AAGGGTAAAATAATCGAAATATCCCT-A
1 AAGGGTAAAATGATCGAAATA-CCCTCA
* * *
17495958 AAGGTTAAAACGATCGAAATACCCTTA
1 AAGGGTAAAATGATCGAAATACCCTCA
* * *
17495985 AAGGGTAAAAT-AGCTAAAATACCCTCG
1 AAGGGTAAAATGATC-GAAATACCCTCA
*
17496012 AAGGGTAAAATGACCGAAATACCCT-A
1 AAGGGTAAAATGATCGAAATACCCTCA
* * *
17496038 GAATGGTAAAATGACCGAAATACCCCCGA
1 -AAGGGTAAAATGATCGAAATACCCTC-A
* * * *
17496067 AA-GGTAAAATGACCGGAATAACCAT-G
1 AAGGGTAAAATGATCGAAAT-ACCCTCA
* * *
17496093 AAGGGTAAAATAATTGAAATACCCTCG
1 AAGGGTAAAATGATCGAAATACCCTCA
*
17496120 AAGGGTAAAATGATCGAAATACTCTCA
1 AAGGGTAAAATGATCGAAATACCCTCA
* * *
17496147 AAGGGTAAAATGA-CTGAAACACCACCCG
1 AAGGGTAAAATGATC-GAAATACC-CTCA
* *
17496175 GAGGGTAAAATGA-CTAATATACCCTCGA
1 AAGGGTAAAATGATCGAA-ATACCCTC-A
* * *
17496203 AA-GGTAAAATGACCAAAATACCCCCA
1 AAGGGTAAAATGATCGAAATACCCTCA
* * *
17496229 CAGGGTAAAATGATCGAAATACCTTTA
1 AAGGGTAAAATGATCGAAATACCCTCA
*
17496256 TAGGGTAAAATGA
1 AAGGGTAAAATGA
17496269 CCATTATACC
Statistics
Matches: 324, Mismatches: 50, Indels: 36
0.79 0.12 0.09
Matches are distributed among these distances:
26 16 0.05
27 272 0.84
28 35 0.11
29 1 0.00
ACGTcount: A:0.44, C:0.18, G:0.19, T:0.19
Consensus pattern (27 bp):
AAGGGTAAAATGATCGAAATACCCTCA
Found at i:17496631 original size:28 final size:28
Alignment explanation
Indices: 17496590--17496681 Score: 107
Period size: 28 Copynumber: 3.3 Consensus size: 28
17496580 GTTGCATTAT
*
17496590 CACACTGTTACTGTAATAGGCTAAGGCC
1 CACACTGTTTCTGTAATAGGCTAAGGCC
* *
17496618 CACACTGTTTCTGTATTGGGCTAAGGCC
1 CACACTGTTTCTGTAATAGGCTAAGGCC
* *
17496646 CACATTG-TTAT-TATATCAGGCTAAGGCC
1 CACACTGTTTCTGTA-AT-AGGCTAAGGCC
17496674 CACACTGT
1 CACACTGT
17496682 ACTATTATTG
Statistics
Matches: 53, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
26 2 0.04
27 4 0.08
28 47 0.89
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (28 bp):
CACACTGTTTCTGTAATAGGCTAAGGCC
Found at i:17508200 original size:16 final size:16
Alignment explanation
Indices: 17508179--17508250 Score: 92
Period size: 16 Copynumber: 4.5 Consensus size: 16
17508169 CAAGAATACT
17508179 ATTACAGTTCTATTCC
1 ATTACAGTTCTATTCC
*
17508195 ATTACAGCTT-TATTCT
1 ATTACAG-TTCTATTCC
* *
17508211 ATTACAGCTCTATTCA
1 ATTACAGTTCTATTCC
*
17508227 ATTACAGCTCTATTCC
1 ATTACAGTTCTATTCC
17508243 ATTACAGT
1 ATTACAGT
17508251 GAACCAAACG
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
15 1 0.02
16 46 0.94
17 2 0.04
ACGTcount: A:0.28, C:0.24, G:0.07, T:0.42
Consensus pattern (16 bp):
ATTACAGTTCTATTCC
Found at i:17508223 original size:32 final size:32
Alignment explanation
Indices: 17508177--17508249 Score: 110
Period size: 32 Copynumber: 2.3 Consensus size: 32
17508167 CACAAGAATA
* * *
17508177 CTATTACAGTTCTATTCCATTACAGCTTTATT
1 CTATTACAGCTCTATTCAATTACAGCTCTATT
17508209 CTATTACAGCTCTATTCAATTACAGCTCTATT
1 CTATTACAGCTCTATTCAATTACAGCTCTATT
*
17508241 CCATTACAG
1 CTATTACAG
17508250 TGAACCAAAC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.27, C:0.25, G:0.07, T:0.41
Consensus pattern (32 bp):
CTATTACAGCTCTATTCAATTACAGCTCTATT
Found at i:17508335 original size:16 final size:16
Alignment explanation
Indices: 17508313--17508381 Score: 111
Period size: 16 Copynumber: 4.2 Consensus size: 16
17508303 TTTGGTTCGC
17508313 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* *
17508329 CGTATTGAATTAGAGG
1 TGTATTGGATTAGAGG
17508345 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
17508362 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
17508378 TGTA
1 TGTA
17508382 ATAGCTAATC
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
16 33 0.69
17 15 0.31
ACGTcount: A:0.26, C:0.01, G:0.36, T:0.36
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:17508359 original size:33 final size:32
Alignment explanation
Indices: 17508313--17508381 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 32
17508303 TTTGGTTCGC
17508313 TGTATTGGATTAGAGGCGTATTGAATTAGAGG
1 TGTATTGGATTAGAGGCGTATTGAATTAGAGG
* *
17508345 TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATT-GGATTAGAGGCGTATTGAATTAGAGG
17508378 TGTA
1 TGTA
17508382 ATAGCTAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
32 6 0.18
33 28 0.82
ACGTcount: A:0.26, C:0.01, G:0.36, T:0.36
Consensus pattern (32 bp):
TGTATTGGATTAGAGGCGTATTGAATTAGAGG
Found at i:17508446 original size:44 final size:45
Alignment explanation
Indices: 17508362--17508452 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
17508352 GGATTAGAGG
* * *
17508362 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
17508407 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
17508451 TG
1 TG
17508453 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:17509330 original size:120 final size:120
Alignment explanation
Indices: 17508600--17509705 Score: 1943
Period size: 121 Copynumber: 9.2 Consensus size: 120
17508590 ATCATATTTA
*
17508600 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAAT-AAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATGAAATTCTTAATAATTAA
*
17508664 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
* *
17508719 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATGAAATTCTTAATTGGA-T
1 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATGAAATTCTTAA-T-AATT
*
17508783 AATATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
64 AATATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
* *
17508840 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATGAAATTCTTAATTGGA-T
1 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATGAAATTCTTAA-T-AATT
*
17508904 AATATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
64 AATATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
*
17508961 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATGAAATTCTTAATTGGA-T
1 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATGAAATTCTTAA-T-AATT
*
17509025 AATATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
64 AATATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
**
17509082 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAAATTCTTAATAATTA
1 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTT-AATGAAATTCTTAATAATTA
17509147 ATATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
65 ATATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
17509203 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATGAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATGAAATTCTTAATAATTAA
17509268 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
17509323 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATGAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATGAAATTCTTAATAATTAA
17509388 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
*
17509443 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTTAA-AAAATTCTTAATAATTA
1 AACATAATTATTATTAAATATATTTTAATTAAACTATATAA-TTTAATGAAATTCTTAATAATTA
*
17509507 ATGTTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
65 ATATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
* **
17509563 AACATAATTATTATTAAATGTATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATGAAATTCTTAATAATTAA
*
17509628 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAGATATAAATT
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
17509683 AACATAATTATTATTAAATATAT
1 AACATAATTATTATTAAATATAT
17509706 AACTTGAAAA
Statistics
Matches: 966, Mismatches: 14, Indels: 13
0.97 0.01 0.01
Matches are distributed among these distances:
119 52 0.05
120 450 0.47
121 451 0.47
122 13 0.01
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATGAAATTCTTAATAATTAA
TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:17509473 original size:240 final size:241
Alignment explanation
Indices: 17508600--17509705 Score: 1947
Period size: 240 Copynumber: 4.6 Consensus size: 241
17508590 ATCATATTTA
*
17508600 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAAT-AAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
*
17508664 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATTAACATAATTA
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATTAACATAATTA
* *
17508729 TTATTAAATATATTTTAATTAAAATATATAATTTAATGAAATTCTTAATTGGATAATATTCTTAT
131 TTATTAAATATATTTTAATTAAACTATATAATTTAATGAAATTCTTAATTGAATAATATTCTTAT
*
17508794 ATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
196 ATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
* * *
17508840 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATGAAATTCTTAATTGGA-T
1 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATAAAATTCTTAA-T-AATT
*
17508904 AATATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATTAACATAAT
64 AATATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATTAACATAAT
*
17508969 TATTATTAAATATATTTTAATTAAACTATATAATTTAATGAAATTCTTAATTGGATAATATTCTT
129 TATTATTAAATATATTTTAATTAAACTATATAATTTAATGAAATTCTTAATTGAATAATATTCTT
*
17509034 ATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
194 ATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
*
17509082 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAAAAAAAATTCTTAATAATTA
1 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTT-AATAAAATTCTTAATAATTA
17509147 ATATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATTAACATAATT
65 ATATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATTAACATAATT
17509212 ATTATTAAATATATTTTAATTAAACTATATAATTTAATGAAATTCTTAA-T-AATTAATATTCTT
130 ATTATTAAATATATTTTAATTAAACTATATAATTTAATGAAATTCTTAATTGAA-TAATATTCTT
17509275 ATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
194 ATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
*
17509323 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATGAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
17509388 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATTAACATAATTA
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATTAACATAATTA
* *
17509453 TTATTAAATATATTTTAATTAAACTATATAATTTTAA-AAAATTCTTAA-T-AATTAATGTTCTT
131 TTATTAAATATATTTTAATTAAACTATATAA-TTTAATGAAATTCTTAATTGAA-TAATATTCTT
17509515 ATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
194 ATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
* *
17509563 AACATAATTATTATTAAATGTATTTTAATTAAACTATATAATTTAAAAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
*
17509628 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAGATATAAATTAACATAATTA
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATTAACATAATTA
17509693 TTATTAAATATAT
131 TTATTAAATATAT
17509706 AACTTGAAAA
Statistics
Matches: 842, Mismatches: 17, Indels: 14
0.96 0.02 0.02
Matches are distributed among these distances:
240 373 0.44
241 118 0.14
242 338 0.40
243 13 0.02
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (241 bp):
AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATTAACATAATTA
TTATTAAATATATTTTAATTAAACTATATAATTTAATGAAATTCTTAATTGAATAATATTCTTAT
ATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:17512761 original size:33 final size:33
Alignment explanation
Indices: 17512722--17512831 Score: 127
Period size: 33 Copynumber: 3.3 Consensus size: 33
17512712 ATTATAAAGC
17512722 ATGTATAATTGACCTAAAATTAATTGTTGGTGT
1 ATGTATAATTGACCTAAAATTAATTGTTGGTGT
* *
17512755 ATGTATAATTGACCTAAAATTACTTGTTGGTTT
1 ATGTATAATTGACCTAAAATTAATTGTTGGTGT
* * *
17512788 AATGT-T-ATTGTCCCTAAAA-AACATTGCTGGTGT
1 -ATGTATAATTG-ACCTAAAATTA-ATTGTTGGTGT
17512821 ATGTATAATTG
1 ATGTATAATTG
17512832 TTGGTTTAAT
Statistics
Matches: 65, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
32 9 0.14
33 48 0.74
34 8 0.12
ACGTcount: A:0.32, C:0.09, G:0.17, T:0.42
Consensus pattern (33 bp):
ATGTATAATTGACCTAAAATTAATTGTTGGTGT
Found at i:17512838 original size:51 final size:51
Alignment explanation
Indices: 17512778--17513034 Score: 462
Period size: 51 Copynumber: 5.0 Consensus size: 51
17512768 CTAAAATTAC
*
17512778 TTGTTGGTTTAATGTTATTGT-CCCTAAAAAACATTGCTGGTGTATGTATAA
1 TTGTTGGTTTAATGTTATT-TACCCTAAAAAACATTGTTGGTGTATGTATAA
*
17512829 TTGTTGGTTTAATGTTATTTACCCTAAAAAACATTGCTGGTGTATGTATAA
1 TTGTTGGTTTAATGTTATTTACCCTAAAAAACATTGTTGGTGTATGTATAA
*
17512880 TTGTTGGTTTAATGTTATTTACCCTAAAATCACATTGTTGGTGTATGTATAA
1 TTGTTGGTTTAATGTTATTTACCCTAAAA-AACATTGTTGGTGTATGTATAA
17512932 TTGTTGGTTTAATGTTATTTACCCTAAAAAACATTGTTGGTGTATGTATAA
1 TTGTTGGTTTAATGTTATTTACCCTAAAAAACATTGTTGGTGTATGTATAA
17512983 TTGTTGGTTTAATGTTATTTACCCTAAAAAACATTGTTGGTGTATGTATAA
1 TTGTTGGTTTAATGTTATTTACCCTAAAAAACATTGTTGGTGTATGTATAA
17513034 T
1 T
17513035 CTTTTAATTT
Statistics
Matches: 201, Mismatches: 3, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
50 1 0.00
51 151 0.75
52 49 0.24
ACGTcount: A:0.28, C:0.09, G:0.18, T:0.45
Consensus pattern (51 bp):
TTGTTGGTTTAATGTTATTTACCCTAAAAAACATTGTTGGTGTATGTATAA
Found at i:17512956 original size:103 final size:102
Alignment explanation
Indices: 17512778--17513034 Score: 462
Period size: 103 Copynumber: 2.5 Consensus size: 102
17512768 CTAAAATTAC
*
17512778 TTGTTGGTTTAATGTTATTGT-CCCTAAAAAACATTGCTGGTGTATGTATAATTGTTGGTTTAAT
1 TTGTTGGTTTAATGTTATT-TACCCTAAAAAACATTGTTGGTGTATGTATAATTGTTGGTTTAAT
17512842 GTTATTTACCCTAAAAAACATTGCTGGTGTATGTATAA
65 GTTATTTACCCTAAAAAACATTGCTGGTGTATGTATAA
*
17512880 TTGTTGGTTTAATGTTATTTACCCTAAAATCACATTGTTGGTGTATGTATAATTGTTGGTTTAAT
1 TTGTTGGTTTAATGTTATTTACCCTAAAA-AACATTGTTGGTGTATGTATAATTGTTGGTTTAAT
*
17512945 GTTATTTACCCTAAAAAACATTGTTGGTGTATGTATAA
65 GTTATTTACCCTAAAAAACATTGCTGGTGTATGTATAA
17512983 TTGTTGGTTTAATGTTATTTACCCTAAAAAACATTGTTGGTGTATGTATAAT
1 TTGTTGGTTTAATGTTATTTACCCTAAAAAACATTGTTGGTGTATGTATAAT
17513035 CTTTTAATTT
Statistics
Matches: 149, Mismatches: 4, Indels: 4
0.95 0.03 0.03
Matches are distributed among these distances:
101 1 0.01
102 49 0.33
103 99 0.66
ACGTcount: A:0.28, C:0.09, G:0.18, T:0.45
Consensus pattern (102 bp):
TTGTTGGTTTAATGTTATTTACCCTAAAAAACATTGTTGGTGTATGTATAATTGTTGGTTTAATG
TTATTTACCCTAAAAAACATTGCTGGTGTATGTATAA
Found at i:17519645 original size:23 final size:20
Alignment explanation
Indices: 17519608--17519648 Score: 55
Period size: 23 Copynumber: 1.9 Consensus size: 20
17519598 TAAAAGAAAT
17519608 AATTATTATTTTTTTAAGTA
1 AATTATTATTTTTTTAAGTA
17519628 AATTGATTAATTTATTTTAAG
1 AATT-ATT-ATTT-TTTTAAG
17519649 AGGGACTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 3 0.17
22 4 0.22
23 7 0.39
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (20 bp):
AATTATTATTTTTTTAAGTA
Found at i:17521677 original size:17 final size:18
Alignment explanation
Indices: 17521655--17521688 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
17521645 TTATTTATAA
17521655 TTTAAA-AAATTAATTAT
1 TTTAAATAAATTAATTAT
*
17521672 TTTAAATAATTTAATTA
1 TTTAAATAAATTAATTA
17521689 AATTAAGTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTAAATAAATTAATTAT
Found at i:17524773 original size:16 final size:15
Alignment explanation
Indices: 17524752--17524781 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
17524742 CATTTTTTTT
17524752 AAGAAAAAGAAAAGAA
1 AAGAAAAA-AAAAGAA
17524768 AAGAAAAAAAAAGA
1 AAGAAAAAAAAAGA
17524782 TGCATTCAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (15 bp):
AAGAAAAAAAAAGAA
Found at i:17535695 original size:9 final size:9
Alignment explanation
Indices: 17535681--17535762 Score: 51
Period size: 9 Copynumber: 9.1 Consensus size: 9
17535671 TTCTAGTTTA
17535681 TTTTATTAT
1 TTTTATTAT
17535690 TTTTATTA-
1 TTTTATTAT
* *
17535698 TTATATTAG
1 TTTTATTAT
17535707 TTTTATTAT
1 TTTTATTAT
**
17535716 TACTATTA-
1 TTTTATTAT
* *
17535724 TTATATTGT
1 TTTTATTAT
17535733 TTTTAGATTAT
1 TTTT--ATTAT
* *
17535744 TTATCTTAT
1 TTTTATTAT
*
17535753 TTTCATTAT
1 TTTTATTAT
17535762 T
1 T
17535763 AGGATTAGTT
Statistics
Matches: 54, Mismatches: 15, Indels: 8
0.70 0.19 0.10
Matches are distributed among these distances:
8 12 0.22
9 35 0.65
11 7 0.13
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.67
Consensus pattern (9 bp):
TTTTATTAT
Found at i:17535698 original size:3 final size:3
Alignment explanation
Indices: 17535678--17535727 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
17535668 TCCTTCTAGT
* *
17535678 TTA TT- TTA TTA TTT TTA TTA TTA -TA TTA GTT- TTA TTA TTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
17535721 TTA TTA T
1 TTA TTA T
17535728 ATTGTTTTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
2 6 0.15
3 31 0.79
4 2 0.05
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:17535704 original size:17 final size:17
Alignment explanation
Indices: 17535678--17535725 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
17535668 TCCTTCTAGT
*
17535678 TTATTTTATTATTTTTA
1 TTATTATATTATTTTTA
*
17535695 TTATTATATTAGTTTTA
1 TTATTATATTATTTTTA
17535712 TTATTACTATTATT
1 TTATTA-TATTATT
17535726 ATATTGTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 21 0.78
18 6 0.22
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (17 bp):
TTATTATATTATTTTTA
Found at i:17535737 original size:26 final size:26
Alignment explanation
Indices: 17535681--17535735 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
17535671 TTCTAGTTTA
**
17535681 TTTTATTATTTTTATTATTATATTAG
1 TTTTATTATTACTATTATTATATTAG
17535707 TTTTATTATTACTATTATTATATT-G
1 TTTTATTATTACTATTATTATATTAG
17535732 TTTT
1 TTTT
17535736 TAGATTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 5 0.19
26 22 0.81
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.69
Consensus pattern (26 bp):
TTTTATTATTACTATTATTATATTAG
Found at i:17535824 original size:27 final size:28
Alignment explanation
Indices: 17535761--17535834 Score: 91
Period size: 27 Copynumber: 2.7 Consensus size: 28
17535751 ATTTTCATTA
* *
17535761 TTAGGATTAGTTTTATTTTTATTATTGC
1 TTAGTATTAGTTTTATTTTTATTACTGC
*
17535789 -TA-TAGTTAGTTCTATTTTTATT-CTGC
1 TTAGTA-TTAGTTTTATTTTTATTACTGC
17535815 TTAGTATTAGTTTTATTTTT
1 TTAGTATTAGTTTTATTTTT
17535835 TGTATTAGGA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
26 4 0.10
27 33 0.85
28 2 0.05
ACGTcount: A:0.20, C:0.05, G:0.12, T:0.62
Consensus pattern (28 bp):
TTAGTATTAGTTTTATTTTTATTACTGC
Found at i:17537484 original size:23 final size:22
Alignment explanation
Indices: 17537458--17537500 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
17537448 TTTTCTAGTT
17537458 TTTTTATCTATTTATCTTATTCA
1 TTTTTATCTATTT-TCTTATTCA
*
17537481 TTTTTGTCTATTTTCTTATT
1 TTTTTATCTATTTTCTTATT
17537501 AGTTTGCTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.16, C:0.12, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTTTATCTATTTTCTTATTCA
Found at i:17538216 original size:35 final size:35
Alignment explanation
Indices: 17538170--17538239 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
17538160 GTTGTATTAA
17538170 CCCCTAGTAAACATTGCTAATCCTAACACATTTTT
1 CCCCTAGTAAACATTGCTAATCCTAACACATTTTT
* *
17538205 CCCCTAGTAAACATTGTTGATCCTAACACATTTTT
1 CCCCTAGTAAACATTGCTAATCCTAACACATTTTT
17538240 TTTTCTCTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.30, C:0.27, G:0.07, T:0.36
Consensus pattern (35 bp):
CCCCTAGTAAACATTGCTAATCCTAACACATTTTT
Found at i:17544472 original size:18 final size:18
Alignment explanation
Indices: 17544445--17544530 Score: 75
Period size: 18 Copynumber: 4.6 Consensus size: 18
17544435 CACATTTTTC
17544445 TTCATTTCATATTTTTCAT
1 TTCA-TTCATATTTTTCAT
* **
17544464 TTCAGTCATATATCCTCAT
1 TTCATTCATAT-TTTTCAT
* **
17544483 TCCAATTCCCATTTTTC-T
1 TTC-ATTCATATTTTTCAT
17544501 TTCATTTCATATTTTTCAT
1 TTCA-TTCATATTTTTCAT
17544520 TTCATTCATAT
1 TTCATTCATAT
17544531 ATCCTTATTC
Statistics
Matches: 51, Mismatches: 12, Indels: 9
0.71 0.17 0.12
Matches are distributed among these distances:
17 1 0.02
18 26 0.51
19 19 0.37
20 5 0.10
ACGTcount: A:0.22, C:0.22, G:0.01, T:0.55
Consensus pattern (18 bp):
TTCATTCATATTTTTCAT
Found at i:17544517 original size:56 final size:55
Alignment explanation
Indices: 17544437--17544554 Score: 200
Period size: 56 Copynumber: 2.1 Consensus size: 55
17544427 TTCCATGTCA
17544437 CATTTTTCTTCATTTCATATTTTTCATTTCAGTCATATATCCTCATTCCAATTCC
1 CATTTTTCTTCATTTCATATTTTTCATTTCAGTCATATATCCTCATTCCAATTCC
* * *
17544492 CATTTTTCTTTCATTTCATATTTTTCATTTCATTCATATATCCTTATTCCAATTCT
1 CATTTTTC-TTCATTTCATATTTTTCATTTCAGTCATATATCCTCATTCCAATTCC
17544548 CATTTTT
1 CATTTTT
17544555 ATTTGCCTAT
Statistics
Matches: 59, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
55 8 0.14
56 51 0.86
ACGTcount: A:0.21, C:0.23, G:0.01, T:0.55
Consensus pattern (55 bp):
CATTTTTCTTCATTTCATATTTTTCATTTCAGTCATATATCCTCATTCCAATTCC
Found at i:17557691 original size:12 final size:14
Alignment explanation
Indices: 17557674--17557706 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
17557664 GATAGGTCAC
17557674 ATGTGTA-G-TACT
1 ATGTGTAGGCTACT
17557686 ATGTGTAGGCTACT
1 ATGTGTAGGCTACT
17557700 ATGTGTA
1 ATGTGTA
17557707 CTGGATAGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
13 1 0.05
14 11 0.58
ACGTcount: A:0.24, C:0.09, G:0.27, T:0.39
Consensus pattern (14 bp):
ATGTGTAGGCTACT
Found at i:17557740 original size:51 final size:49
Alignment explanation
Indices: 17557620--17557806 Score: 207
Period size: 51 Copynumber: 3.7 Consensus size: 49
17557610 AAAGTGATGG
* * * ** * *
17557620 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTATACCAGA-ATGATAGG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACTGGATA-G-TTGA
*
17557670 TCACATGTGTAGTACTATGTGTAGGCTACTATGTGTACTGGATAGCTTCGA
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACTGGATAG-TT-GA
* *
17557721 TCACGTGTGTAGTACTATGTGCAGGCTACCATGTGTA-TCGGATAGTGATGA
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACT-GGATAGT--TGA
17557772 TCACATGTGTAGTACTATGTGCAGGCTACTATGTG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGTG
17557807 AACCGATATC
Statistics
Matches: 118, Mismatches: 14, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
50 40 0.34
51 77 0.65
52 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.32
Consensus pattern (49 bp):
TCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACTGGATAGTTGA
Found at i:17557756 original size:26 final size:26
Alignment explanation
Indices: 17557726--17557806 Score: 71
Period size: 26 Copynumber: 3.2 Consensus size: 26
17557716 TTCGATCACG
17557726 TGTGTAGTACTATGTGCAGGCTACCA
1 TGTGTAGTACTATGTGCAGGCTACCA
* * *
17557752 TGTGTA-T-CGGATAGTG-ATGAT-CACA
1 TGTGTAGTAC-TAT-GTGCAGGCTAC-CA
*
17557777 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACCA
17557803 TGTG
1 TGTG
17557807 AACCGATATC
Statistics
Matches: 41, Mismatches: 7, Indels: 14
0.66 0.11 0.23
Matches are distributed among these distances:
24 2 0.05
25 17 0.41
26 20 0.49
27 2 0.05
ACGTcount: A:0.23, C:0.15, G:0.28, T:0.33
Consensus pattern (26 bp):
TGTGTAGTACTATGTGCAGGCTACCA
Found at i:17557882 original size:46 final size:44
Alignment explanation
Indices: 17557811--17557900 Score: 119
Period size: 46 Copynumber: 2.0 Consensus size: 44
17557801 TATGTGAACC
*
17557811 GATATCATTAATTATAAGGTGGTTGCTATGTGCTG-ATCCCACCG
1 GATATCATTAATTAAAAGGTGGTTGCTATGTGCTGAAT-CCACCG
* *
17557855 GATATCATTGATTACAAAGGGTGGTTGCTGTGTGCTGAATCCACCG
1 GATATCATTAATTA-AAA-GGTGGTTGCTATGTGCTGAATCCACCG
17557901 TGTATCAGTT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
44 13 0.32
45 2 0.05
46 23 0.57
47 2 0.05
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (44 bp):
GATATCATTAATTAAAAGGTGGTTGCTATGTGCTGAATCCACCG
Found at i:17570323 original size:29 final size:29
Alignment explanation
Indices: 17570290--17570348 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
17570280 AATGTTGTCA
17570290 TAAGATCATGATTCATTCCATTTGCATGC
1 TAAGATCATGATTCATTCCATTTGCATGC
17570319 TAAGATCATGATTCATTCCATTTGCATGC
1 TAAGATCATGATTCATTCCATTTGCATGC
17570348 T
1 T
17570349 TACCATTTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (29 bp):
TAAGATCATGATTCATTCCATTTGCATGC
Found at i:17580142 original size:36 final size:36
Alignment explanation
Indices: 17580095--17580171 Score: 127
Period size: 36 Copynumber: 2.1 Consensus size: 36
17580085 AACGGTGTCA
* *
17580095 TTTTGAGAGTTGGGTTCAGAGACCAAAACAGCGTCG
1 TTTTGAGAGTTGGGTTCAAAGACCAAAACAGCATCG
*
17580131 TTTTGAGAGTTGGGTTCAAAGACCAAAACGGCATCG
1 TTTTGAGAGTTGGGTTCAAAGACCAAAACAGCATCG
17580167 TTTTG
1 TTTTG
17580172 GCCTCTGACC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.29
Consensus pattern (36 bp):
TTTTGAGAGTTGGGTTCAAAGACCAAAACAGCATCG
Found at i:17582091 original size:23 final size:23
Alignment explanation
Indices: 17582061--17582113 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
17582051 ATGTACATCT
17582061 TTATTTTGATCATTTTAAGAAGA
1 TTATTTTGATCATTTTAAGAAGA
*
17582084 TTATTTTGATCATTTTAGGAAGA
1 TTATTTTGATCATTTTAAGAAGA
17582107 TTATTTT
1 TTATTTT
17582114 AAGAGACGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.30, C:0.04, G:0.13, T:0.53
Consensus pattern (23 bp):
TTATTTTGATCATTTTAAGAAGA
Found at i:17589258 original size:4 final size:4
Alignment explanation
Indices: 17589251--17589284 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
17589241 AATCAATCAA
* *
17589251 TCAT TCAT TCAT TCAT CCAT TCAT TCAC TCAT TC
1 TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TC
17589285 GATCATTAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.24, C:0.32, G:0.00, T:0.44
Consensus pattern (4 bp):
TCAT
Found at i:17597022 original size:16 final size:17
Alignment explanation
Indices: 17596980--17597023 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
17596970 TTGTTTAAAT
*
17596980 CAAGAAAAAAAACAAAA
1 CAAGAAAAAAACCAAAA
17596997 CAA-AAAAAAACCAAAA
1 CAAGAAAAAAACCAAAA
*
17597013 -AAGAAGAAAAC
1 CAAGAAAAAAAC
17597024 TTAGAGAGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 2 0.08
16 19 0.79
17 3 0.12
ACGTcount: A:0.80, C:0.14, G:0.07, T:0.00
Consensus pattern (17 bp):
CAAGAAAAAAACCAAAA
Found at i:17597488 original size:42 final size:42
Alignment explanation
Indices: 17597429--17597604 Score: 262
Period size: 42 Copynumber: 4.2 Consensus size: 42
17597419 GAGGAAAGCA
*
17597429 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
*
17597471 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACCT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * *
17597513 TTCATTGCATTTAGAGGCCCAGGGGTGGAAGACCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* ** *
17597555 TTCATTGCATTTAGAGGCTCAGGAATGGAGGTCCATTTATTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
17597597 TATCATTG
1 T-TCATTG
17597605 TATATGAAAG
Statistics
Matches: 121, Mismatches: 12, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
42 115 0.95
43 6 0.05
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.36
Consensus pattern (42 bp):
TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
Found at i:17597635 original size:84 final size:84
Alignment explanation
Indices: 17597429--17597636 Score: 231
Period size: 84 Copynumber: 2.5 Consensus size: 84
17597419 GAGGAAAGCA
* * *
17597429 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCAGG
1 TTCATTGCATTGAGAAGCATAGGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCAGG
**
17597494 TGTGGAGGTCCATTTACCT
66 AATGGAGGTCCATTTACCT
* * ** * * * *
17597513 TTCATTGCATTTAGAGGCCCAGGGGTGGAAGACCATTTACTTTTCATTGCATTTAGAGGCTCAGG
1 TTCATTGCATTGAGAAGCATAGGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCAGG
**
17597578 AATGGAGGTCCATTTATTT
66 AATGGAGGTCCATTTACCT
* *
17597597 TATCATTGTATATGA-AAGCATAGGTGT-GAGGTCTATTTAC
1 T-TCATTGCAT-TGAGAAGCATAGGTGTGGAGGTCCATTTAC
17597637 ATTTATTCTA
Statistics
Matches: 104, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
84 86 0.83
85 16 0.15
86 2 0.02
ACGTcount: A:0.23, C:0.16, G:0.25, T:0.36
Consensus pattern (84 bp):
TTCATTGCATTGAGAAGCATAGGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCAGG
AATGGAGGTCCATTTACCT
Found at i:17598058 original size:3 final size:3
Alignment explanation
Indices: 17598052--17598076 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
17598042 AATTATTATC
17598052 ACT ACT ACT ACT ACT ACT ACT ACT A
1 ACT ACT ACT ACT ACT ACT ACT ACT A
17598077 TTATCAAACA
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:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ACT
Found at i:17598797 original size:142 final size:142
Alignment explanation
Indices: 17598546--17598846 Score: 367
Period size: 142 Copynumber: 2.1 Consensus size: 142
17598536 GAAAAGTTTT
** * ** * **
17598546 ATTTTTTTTAAGAAAAGAGAGTTTAGATTTTTTTTAAATAAAATCTTTTTAGTCATTTAAATTAA
1 ATTTTTTAAAAGAAAAGAAAGTTTAGATTTTTTAAAAATAAAATCTTTTTAGTAATTTAAAGGAA
* *
17598611 AAGTTTAAATTTGTAAAACAAAGTTTAATCTTTTTCAACTATTTC-AAATAAAGCTTTAATTTTT
66 AAGTTTAAATTTGTAAAACAAAGTTTAATCTTTTTCAACAATTTCGAAATAAAACTTTAATTTTT
17598675 AAGAAAAATAGTG
131 AA-AAAAATAGTG
* *
17598688 ATTTTTTAAAAGAAATAGAAAGTTTAGA-TTTTTAAAAAT-AATTTTTTTTAGTAATTTTAAAGG
1 ATTTTTTAAAAGAAA-AGAAAGTTTAGATTTTTTAAAAATAAAATCTTTTTAGTAA-TTTAAAGG
* * * **
17598751 AAAAGTTTAAATTT-TAAAACAAAATTTTGATCTTTTTGAACAATTTCGAAATAAAACTTTGGTT
64 AAAAGTTTAAATTTGTAAAAC-AAAGTTTAATCTTTTTCAACAATTTCGAAATAAAACTTTAATT
*
17598815 TTTAAAAAAGTAGTG
128 TTTAAAAAAATAGTG
17598830 ATTTTTTTAAAAGAAAA
1 A-TTTTTTAAAAGAAAA
17598847 CTTTGATTTT
Statistics
Matches: 136, Mismatches: 18, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
141 18 0.13
142 75 0.55
143 43 0.32
ACGTcount: A:0.43, C:0.04, G:0.10, T:0.43
Consensus pattern (142 bp):
ATTTTTTAAAAGAAAAGAAAGTTTAGATTTTTTAAAAATAAAATCTTTTTAGTAATTTAAAGGAA
AAGTTTAAATTTGTAAAACAAAGTTTAATCTTTTTCAACAATTTCGAAATAAAACTTTAATTTTT
AAAAAAATAGTG
Found at i:17603245 original size:27 final size:27
Alignment explanation
Indices: 17603188--17603362 Score: 151
Period size: 27 Copynumber: 6.6 Consensus size: 27
17603178 TTATTGAGCC
* * *
17603188 CGCACACTCAGTGCTATAT-ATCAACT
1 CGCACACTTAGTGCTACATAATCAAAT
*
17603214 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
* * *
17603241 CGCACACTTAGTGC-ACATAGTCCACT
1 CGCACACTTAGTGCTACATAATCAAAT
** ** *
17603267 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAAAT
**
17603294 CGCACACTTAGTGC-ATCAT-ATCCATTT
1 CGCACACTTAGTGCTA-CATAAT-CAAAT
* * *
17603321 CGCACACTTAGTGCAACATAGTCGAAT
1 CGCACACTTAGTGCTACATAATCAAAT
17603348 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
17603363 GTACAATTTA
Statistics
Matches: 123, Mismatches: 20, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
26 39 0.32
27 82 0.67
28 2 0.02
ACGTcount: A:0.28, C:0.30, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAAAT
Found at i:17603268 original size:53 final size:52
Alignment explanation
Indices: 17603188--17603361 Score: 204
Period size: 53 Copynumber: 3.3 Consensus size: 52
17603178 TTATTGAGCC
* * * * * *
17603188 CGCACACTCAGTGCTATATATCAACTCGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGC-ACATATCCACTCGCACACTTAGTGCAACATAGTCAAAT
** * *
17603241 CGCACACTTAGTGCACATAGTCCACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCACATA-TCCACTCGCACACTTAGTGCAACATAGTCAAAT
* *
17603294 CGCACACTTAGTGCATCATATCCATTTCGCACACTTAGTGCAACATAGTCGAAT
1 CGCACACTTAGTGCA-CATATCCA-CTCGCACACTTAGTGCAACATAGTCAAAT
17603348 CGCACACTTAGTGC
1 CGCACACTTAGTGC
17603362 TGTACAATTT
Statistics
Matches: 103, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
52 4 0.04
53 58 0.56
54 41 0.40
ACGTcount: A:0.28, C:0.30, G:0.16, T:0.26
Consensus pattern (52 bp):
CGCACACTTAGTGCACATATCCACTCGCACACTTAGTGCAACATAGTCAAAT
Found at i:17603803 original size:1 final size:1
Alignment explanation
Indices: 17603799--17603870 Score: 144
Period size: 1 Copynumber: 72.0 Consensus size: 1
17603789 CATTCAAATC
17603799 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
17603864 AAAAAAA
1 AAAAAAA
17603871 CAAATTCAAC
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 71 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:17604069 original size:1 final size:1
Alignment explanation
Indices: 17604065--17604118 Score: 99
Period size: 1 Copynumber: 54.0 Consensus size: 1
17604055 AAAAACATTT
*
17604065 AAAAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
17604119 CAATTATCAA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
1 51 1.00
ACGTcount: A:0.98, C:0.00, G:0.00, T:0.02
Consensus pattern (1 bp):
A
Found at i:17604171 original size:1 final size:1
Alignment explanation
Indices: 17604167--17604218 Score: 104
Period size: 1 Copynumber: 52.0 Consensus size: 1
17604157 GCAAATGAAG
17604167 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
17604219 TGAAAACCAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 51 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:17610585 original size:27 final size:27
Alignment explanation
Indices: 17610555--17610732 Score: 180
Period size: 27 Copynumber: 6.6 Consensus size: 27
17610545 ATATTGAGCC
* * *
17610555 CGCACACTCAGTGCTATATATTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
* * * *
17610582 CGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAACT
17610609 CGCACACTTAGTGCTACATAGTCAGACT
1 CGCACACTTAGTGCTACATAGTCA-ACT
** * *
17610637 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
* **
17610664 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAACT
*
17610691 CGCACACTTAGTGCAACATAGTCGAA-T
1 CGCACACTTAGTGCTACATAGTC-AACT
17610718 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
17610733 GTACAATTTA
Statistics
Matches: 126, Mismatches: 21, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
27 101 0.80
28 25 0.20
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:17610694 original size:82 final size:81
Alignment explanation
Indices: 17610576--17610731 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
17610566 TGCTATATAT
* * *
17610576 TCAACTCGCACACTTAGTGCCACGTAATCAAATCGCACACTTAGTGCTACATAGTCAGACTCGCA
1 TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTC-GAATCGCA
17610641 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
17610658 TCAATTCGCACACTTAGTG-CATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAATCGCA
1 TCAACTCGCACACTTAGTGCCA-CATAATCAAATCGCACACTTAGTGCAACATAGTCGAATCGCA
17610722 CACTTAGTGC
65 CACTTAGTGC
17610732 TGTACAATTT
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 19 0.29
82 47 0.71
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.26
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTCGAATCGCAC
ACTTAGTGCCGCATGG
Found at i:17624839 original size:42 final size:42
Alignment explanation
Indices: 17624780--17624955 Score: 262
Period size: 42 Copynumber: 4.2 Consensus size: 42
17624770 GAGGAAAGCA
*
17624780 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
*
17624822 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACCT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * *
17624864 TTCATTGCATTTAGAGGCCCAGGGGTGGAAGACCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* ** *
17624906 TTCATTGCATTTAGAGGCTCAGGAATGGAGGTCCATTTATTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
17624948 TATCATTG
1 T-TCATTG
17624956 TATATGAAAG
Statistics
Matches: 121, Mismatches: 12, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
42 115 0.95
43 6 0.05
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.36
Consensus pattern (42 bp):
TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
Found at i:17624986 original size:84 final size:84
Alignment explanation
Indices: 17624780--17624987 Score: 231
Period size: 84 Copynumber: 2.5 Consensus size: 84
17624770 GAGGAAAGCA
* * *
17624780 TTCATTGCATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCAGG
1 TTCATTGCATTGAGAAGCATAGGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCAGG
**
17624845 TGTGGAGGTCCATTTACCT
66 AATGGAGGTCCATTTACCT
* * ** * * * *
17624864 TTCATTGCATTTAGAGGCCCAGGGGTGGAAGACCATTTACTTTTCATTGCATTTAGAGGCTCAGG
1 TTCATTGCATTGAGAAGCATAGGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCAGG
**
17624929 AATGGAGGTCCATTTATTT
66 AATGGAGGTCCATTTACCT
* *
17624948 TATCATTGTATATGA-AAGCATAGGTGT-GAGGTCTATTTAC
1 T-TCATTGCAT-TGAGAAGCATAGGTGTGGAGGTCCATTTAC
17624988 ATTTATTCTA
Statistics
Matches: 104, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
84 86 0.83
85 16 0.15
86 2 0.02
ACGTcount: A:0.23, C:0.16, G:0.25, T:0.36
Consensus pattern (84 bp):
TTCATTGCATTGAGAAGCATAGGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCAGG
AATGGAGGTCCATTTACCT
Found at i:17625410 original size:3 final size:3
Alignment explanation
Indices: 17625404--17625428 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
17625394 AATTATTATC
17625404 ACT ACT ACT ACT ACT ACT ACT ACT A
1 ACT ACT ACT ACT ACT ACT ACT ACT A
17625429 TTATCAAACA
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:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ACT
Found at i:17626166 original size:145 final size:145
Alignment explanation
Indices: 17625955--17626215 Score: 366
Period size: 145 Copynumber: 1.8 Consensus size: 145
17625945 AATAAAAATC
* ** * *
17625955 TTTTTTAGTCATTTAAATTAAAAGTTTAAATTTGTAAAACAAAGTTTTAATCTTTTTCAACTATT
1 TTTTTTAGTAATTTAAAGGAAAAGTTTAAATTTGTAAAACAAAATTTTAATCTTTTTCAACAATT
*
17626020 TCAAAATAAAGCTTTAATTTTTAAGAAAA-ATAGTGA-TTTTTTAAAAGAAATAGAAAGTTTAGA
66 TCAAAATAAAACTTTAATTTTTAA-AAAAGATAGTGATTTTTTTAAAAGAAATAGAAAGTTTAGA
17626083 TTTTTAAAAATAATTT
130 TTTTTAAAAATAATTT
* *
17626099 TTTTTTAGTAATTTTAAAGGAAAAGTTTAAAATTT-TAAAACAAAATTTTGATCTTTTTGAACAA
1 TTTTTTAGTAA-TTTAAAGGAAAAGTTT-AAATTTGTAAAACAAAATTTTAATCTTTTTCAACAA
* ** *
17626163 TTTCGAAATAAAACTTTGGTTTTTAAAAAAGGTAGTGATTTTTTTAAAAGAAA
64 TTTCAAAATAAAACTTTAATTTTTAAAAAAGATAGTGATTTTTTTAAAAGAAA
17626216 CTTTGATTTT
Statistics
Matches: 101, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
144 14 0.14
145 67 0.66
146 20 0.20
ACGTcount: A:0.43, C:0.05, G:0.10, T:0.43
Consensus pattern (145 bp):
TTTTTTAGTAATTTAAAGGAAAAGTTTAAATTTGTAAAACAAAATTTTAATCTTTTTCAACAATT
TCAAAATAAAACTTTAATTTTTAAAAAAGATAGTGATTTTTTTAAAAGAAATAGAAAGTTTAGAT
TTTTAAAAATAATTT
Found at i:17630638 original size:27 final size:27
Alignment explanation
Indices: 17630608--17630785 Score: 155
Period size: 27 Copynumber: 6.6 Consensus size: 27
17630598 TTATTGAGCC
* *
17630608 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
17630635 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
* * *
17630662 CGCACACTTAGTGCCACATAGTCCATCT
1 CGCACACTTAGTGCTACATAAT-CAACT
** ** *
17630690 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
**
17630717 CGCACACTTAGTGC-ATCAT-ATCCATTT
1 CGCACACTTAGTGCTA-CATAAT-CAACT
* *
17630744 CGCACACTTAGTGCAACATAGTCGAA-T
1 CGCACACTTAGTGCTACATAATC-AACT
17630771 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
17630786 GTACAATTTA
Statistics
Matches: 126, Mismatches: 19, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
26 1 0.01
27 99 0.79
28 26 0.21
ACGTcount: A:0.28, C:0.30, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:17630774 original size:54 final size:53
Alignment explanation
Indices: 17630633--17630784 Score: 189
Period size: 54 Copynumber: 2.8 Consensus size: 53
17630623 ATATAATCAA
* * *
17630633 CTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCCACATAGTCCAT
1 CTCGCACACTTAGTGCAACATAGTC-AATCGCACACTTAGTG-CACATAGTCCAT
** *
17630688 CTCGCACACTTAGTGCCGCATGGTCAATTCGCACACTTAGTGCATCATA-TCCAT
1 CTCGCACACTTAGTGCAACATAGTCAA-TCGCACACTTAGTGCA-CATAGTCCAT
*
17630742 TTCGCACACTTAGTGCAACATAGTCGAATCGCACACTTAGTGC
1 CTCGCACACTTAGTGCAACATAGTC-AATCGCACACTTAGTGC
17630785 TGTACAATTT
Statistics
Matches: 85, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
54 45 0.53
55 40 0.47
ACGTcount: A:0.27, C:0.30, G:0.16, T:0.26
Consensus pattern (53 bp):
CTCGCACACTTAGTGCAACATAGTCAATCGCACACTTAGTGCACATAGTCCAT
Found at i:17637899 original size:27 final size:27
Alignment explanation
Indices: 17637869--17638046 Score: 155
Period size: 27 Copynumber: 6.6 Consensus size: 27
17637859 TTATTGAGCC
* *
17637869 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
17637896 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
* * *
17637923 CGCACACTTAGTGCCACATAGTCCATCT
1 CGCACACTTAGTGCTACATAAT-CAACT
** ** *
17637951 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
**
17637978 CGCACACTTAGTGC-ATCAT-ATCCATTT
1 CGCACACTTAGTGCTA-CATAAT-CAACT
* *
17638005 CGCACACTTAGTGCAACATAGTCGAA-T
1 CGCACACTTAGTGCTACATAATC-AACT
17638032 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
17638047 GTACAATTTA
Statistics
Matches: 126, Mismatches: 19, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
26 1 0.01
27 99 0.79
28 26 0.21
ACGTcount: A:0.28, C:0.30, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:17638035 original size:54 final size:53
Alignment explanation
Indices: 17637894--17638045 Score: 189
Period size: 54 Copynumber: 2.8 Consensus size: 53
17637884 ATATAATCAA
* * *
17637894 CTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCCACATAGTCCAT
1 CTCGCACACTTAGTGCAACATAGTC-AATCGCACACTTAGTG-CACATAGTCCAT
** *
17637949 CTCGCACACTTAGTGCCGCATGGTCAATTCGCACACTTAGTGCATCATA-TCCAT
1 CTCGCACACTTAGTGCAACATAGTCAA-TCGCACACTTAGTGCA-CATAGTCCAT
*
17638003 TTCGCACACTTAGTGCAACATAGTCGAATCGCACACTTAGTGC
1 CTCGCACACTTAGTGCAACATAGTC-AATCGCACACTTAGTGC
17638046 TGTACAATTT
Statistics
Matches: 85, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
54 45 0.53
55 40 0.47
ACGTcount: A:0.27, C:0.30, G:0.16, T:0.26
Consensus pattern (53 bp):
CTCGCACACTTAGTGCAACATAGTCAATCGCACACTTAGTGCACATAGTCCAT
Found at i:17642125 original size:30 final size:30
Alignment explanation
Indices: 17642089--17642176 Score: 122
Period size: 30 Copynumber: 2.9 Consensus size: 30
17642079 CTGGGCACTT
*
17642089 CCACACGAGCTGGCCACACACCCATGTGAG
1 CCACACGAGATGGCCACACACCCATGTGAG
* *
17642119 CCACACGAGATGGCCACATACCCCTGTGAG
1 CCACACGAGATGGCCACACACCCATGTGAG
* * *
17642149 CCATACGGGTTGGCCACACACCCATGTG
1 CCACACGAGATGGCCACACACCCATGTG
17642177 CCAGCCTGTG
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.25, C:0.38, G:0.24, T:0.14
Consensus pattern (30 bp):
CCACACGAGATGGCCACACACCCATGTGAG
Found at i:17645984 original size:33 final size:34
Alignment explanation
Indices: 17645941--17646007 Score: 93
Period size: 33 Copynumber: 2.0 Consensus size: 34
17645931 GCACAGTTGA
*
17645941 ACAGTCTTGGGCCTAAGCCC-TTTCAGTATCAGTG
1 ACAGTCTTGGGCCTAAGCCCATCTCAGTA-CAGTG
*
17645975 ACAGT-TTGGGCCTTAGCCCATCTCAGTACAGTG
1 ACAGTCTTGGGCCTAAGCCCATCTCAGTACAGTG
17646008 TCAAAAATGC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
33 18 0.60
34 12 0.40
ACGTcount: A:0.21, C:0.27, G:0.24, T:0.28
Consensus pattern (34 bp):
ACAGTCTTGGGCCTAAGCCCATCTCAGTACAGTG
Found at i:17649518 original size:6 final size:5
Alignment explanation
Indices: 17649512--17649584 Score: 51
Period size: 6 Copynumber: 13.6 Consensus size: 5
17649502 ATTGAGTTTA
*
17649512 TTATT ATTATT ATTATT TTCGTT TTATTT TTATT TTATT TTATT TT-TAT
1 TTATT -TTATT -TTATT TT-ATT TTA-TT TTATT TTATT TTATT TTAT-T
*
17649561 TTATCT TT-TT TTAATT TTGTT TTA
1 TTAT-T TTATT TT-ATT TTATT TTA
17649585 GTTGCTTTAT
Statistics
Matches: 56, Mismatches: 5, Indels: 13
0.76 0.07 0.18
Matches are distributed among these distances:
4 4 0.07
5 24 0.43
6 28 0.50
ACGTcount: A:0.19, C:0.03, G:0.03, T:0.75
Consensus pattern (5 bp):
TTATT
Found at i:17649563 original size:20 final size:21
Alignment explanation
Indices: 17649540--17649578 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
17649530 TCGTTTTATT
17649540 TTTATTTTATTTT-ATTTTTA
1 TTTATTTTATTTTAATTTTTA
17649560 TTTATCTTT-TTTTAATTTT
1 TTTAT-TTTATTTTAATTTT
17649579 GTTTTAGTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (21 bp):
TTTATTTTATTTTAATTTTTA
Done.