Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 98600468
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: 98600468
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 273 characters in sequence are not A, C, G, or T
File 105 of 325
Found at i:30977033 original size:17 final size:19
Alignment explanation
Indices: 30976991--30977034 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
30976981 ATGAAATTTT
*
30976991 AATTAGTATTATGAGATAA
1 AATTATTATTATGAGATAA
*
30977010 AATTATTATTATTAGA-AA
1 AATTATTATTATGAGATAA
30977028 AA-TATTA
1 AATTATTA
30977035 CTGTATGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 5 0.22
18 4 0.17
19 14 0.61
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (19 bp):
AATTATTATTATGAGATAA
Found at i:30981265 original size:17 final size:19
Alignment explanation
Indices: 30981223--30981266 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
30981213 ATGAAATTTT
*
30981223 AATTAGTATTATGAGATAA
1 AATTATTATTATGAGATAA
*
30981242 AATTATTATTATTAGA-AA
1 AATTATTATTATGAGATAA
30981260 AA-TATTA
1 AATTATTA
30981267 CTGTATGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 5 0.22
18 4 0.17
19 14 0.61
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (19 bp):
AATTATTATTATGAGATAA
Found at i:30986287 original size:37 final size:37
Alignment explanation
Indices: 30986228--30986336 Score: 191
Period size: 37 Copynumber: 2.9 Consensus size: 37
30986218 AGCTCAGACG
* *
30986228 AAATCTCCACACGAAGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
30986265 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
30986302 TAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
30986337 ATACATTTCC
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 69 1.00
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.23
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:30986452 original size:48 final size:48
Alignment explanation
Indices: 30986381--30986814 Score: 697
Period size: 48 Copynumber: 9.0 Consensus size: 48
30986371 TGTTACAACA
* *
30986381 TTCACATTAGCCATTTGGCTTTACCACATATACATATCTCATACATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATAT
* * * *
30986429 TTCACATTCGTCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATAT
*
30986477 TTCACATTCGCCATTCGGCTTTACCACATATACATATCTCATATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATAT
* *
30986525 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATAT
*
30986573 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATAT
* * *
30986621 TTCACATTCGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATAT
*
30986669 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATAT
* * * *
30986717 TTCACATTCGCCATTTGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATAT
*
30986765 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATGTAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATAT
30986813 TT
1 TT
30986815 ATCTTGTACA
Statistics
Matches: 353, Mismatches: 33, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 353 1.00
ACGTcount: A:0.31, C:0.27, G:0.06, T:0.36
Consensus pattern (48 bp):
TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATAT
Found at i:30986814 original size:96 final size:96
Alignment explanation
Indices: 30986381--30986807 Score: 800
Period size: 96 Copynumber: 4.4 Consensus size: 96
30986371 TGTTACAACA
* *
30986381 TTCACATTAGCCATTTGGCTTTACCACATATACATATCTCATACATATTTCACATTCGTCATTCG
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTCGCCATTCG
30986446 GCTTTACCACATATACATATCACACATATAT
66 GCTTTACCACATATACATATCACACATATAT
* * *
30986477 TTCACATTCGCCATTCGGCTTTACCACATATACATATCTCATATATATTTCACATTAGCCATTCG
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTCGCCATTCG
30986542 GCTTTACCACATATACATATCACACATATAT
66 GCTTTACCACATATACATATCACACATATAT
30986573 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTCGCCATTCG
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTCGCCATTCG
30986638 GCTTTACCACATATACATATCACACATATAT
66 GCTTTACCACATATACATATCACACATATAT
*
30986669 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTCGCCATTTG
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTCGCCATTCG
30986734 GCTTTACCACATATACATATCACACATATAT
66 GCTTTACCACATATACATATCACACATATAT
30986765 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATA
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATA
30986808 TGTATTTATC
Statistics
Matches: 322, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
96 322 1.00
ACGTcount: A:0.31, C:0.27, G:0.06, T:0.35
Consensus pattern (96 bp):
TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATTTCACATTCGCCATTCG
GCTTTACCACATATACATATCACACATATAT
Found at i:30991008 original size:38 final size:38
Alignment explanation
Indices: 30990957--30991087 Score: 127
Period size: 38 Copynumber: 3.2 Consensus size: 38
30990947 TTTCAAATTA
* * *
30990957 ACATGTATAACCGTGGCATATCTATTTAGCACCATGTT
1 ACATGTATAACCGTGGCATATCCACTTAGCACCACGTT
* *
30990995 ACATGTTTAACCGTGGTATATCCACTTAGCACCACGTTAAT
1 ACATGTATAACCGTGGCATATCCACTTAGCACCACG-T--T
*
30991036 GAATCGATATATGTAACCGTGGCATATCCACTTAGCACCACGTT
1 --A-C-ATGTA--TAACCGTGGCATATCCACTTAGCACCACGTT
30991080 ACATGTAT
1 ACATGTAT
30991088 CAATATGTGT
Statistics
Matches: 75, Mismatches: 9, Indels: 18
0.74 0.09 0.18
Matches are distributed among these distances:
38 32 0.43
39 1 0.01
40 4 0.05
41 2 0.03
42 1 0.01
43 1 0.01
44 2 0.03
45 3 0.04
46 1 0.01
47 28 0.37
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (38 bp):
ACATGTATAACCGTGGCATATCCACTTAGCACCACGTT
Found at i:30991056 original size:47 final size:48
Alignment explanation
Indices: 30991002--30991127 Score: 200
Period size: 48 Copynumber: 2.6 Consensus size: 48
30990992 GTTACATGTT
*
30991002 TAACCGTGGTATATCCACTTAGCACCACGTTA-ATGAATCGATATATG
1 TAACCGTGGTATATCCACTTAGCACCACGTTACATGAATCAATATATG
* * *
30991049 TAACCGTGGCATATCCACTTAGCACCACGTTACATGTATCAATATGTG
1 TAACCGTGGTATATCCACTTAGCACCACGTTACATGAATCAATATATG
*
30991097 TAATCGTGGTATATCCACTTAGCACCACGTT
1 TAACCGTGGTATATCCACTTAGCACCACGTT
30991128 TTTCCATTCT
Statistics
Matches: 72, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
47 31 0.43
48 41 0.57
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (48 bp):
TAACCGTGGTATATCCACTTAGCACCACGTTACATGAATCAATATATG
Found at i:30995316 original size:39 final size:39
Alignment explanation
Indices: 30995244--30995418 Score: 236
Period size: 39 Copynumber: 4.6 Consensus size: 39
30995234 TACTCACTCG
*
30995244 AATGCC-TCGGGACATAGCCC-GATATAGTAACTCG-ACAA
1 AATGCCTTC-GGACTTAGCCCGGATATAGTAACTCGCAC-A
30995282 AATGCCTTCGGACTTAGCCCGGATATAGTAACTCGCACA
1 AATGCCTTCGGACTTAGCCCGGATATAGTAACTCGCACA
*
30995321 AATGCCTTCGGACTTAGCCTGGATATA--AACTCGCACA
1 AATGCCTTCGGACTTAGCCCGGATATAGTAACTCGCACA
* * *
30995358 AATGCCTTCGGACTTAGCCCGGA-ACTAGTCACTAGCGCA
1 AATGCCTTCGGACTTAGCCCGGATA-TAGTAACTCGCACA
30995397 AATGCCTTCGGACTTAGCCCGG
1 AATGCCTTCGGACTTAGCCCGG
30995419 TATCATCCAA
Statistics
Matches: 125, Mismatches: 6, Indels: 11
0.88 0.04 0.08
Matches are distributed among these distances:
36 1 0.01
37 34 0.27
38 16 0.13
39 72 0.58
40 2 0.02
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.22
Consensus pattern (39 bp):
AATGCCTTCGGACTTAGCCCGGATATAGTAACTCGCACA
Found at i:30995377 original size:76 final size:76
Alignment explanation
Indices: 30995272--30995415 Score: 229
Period size: 76 Copynumber: 1.9 Consensus size: 76
30995262 CCGATATAGT
*
30995272 AACTCGACAAAATGCCTTCGGACTTAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGACTT
1 AACTCGACAAAATGCCTTCGGACTTAGCCCGGA-ACTAGTAACTAGCACAAATGCCTTCGGACTT
30995336 AGCCTGGATATA
65 AGCCTGGATATA
* *
30995348 AACTCG-CACAAATGCCTTCGGACTTAGCCCGGAACTAGTCACTAGCGCAAATGCCTTCGGACTT
1 AACTCGACA-AAATGCCTTCGGACTTAGCCCGGAACTAGTAACTAGCACAAATGCCTTCGGACTT
30995412 AGCC
65 AGCC
30995416 CGGTATCATC
Statistics
Matches: 63, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
75 3 0.05
76 60 0.95
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.22
Consensus pattern (76 bp):
AACTCGACAAAATGCCTTCGGACTTAGCCCGGAACTAGTAACTAGCACAAATGCCTTCGGACTTA
GCCTGGATATA
Found at i:31005021 original size:29 final size:29
Alignment explanation
Indices: 31004997--31005090 Score: 170
Period size: 29 Copynumber: 3.2 Consensus size: 29
31004987 TCGCACACCC
*
31004997 AGTGCCGTATATTTCCAGCATGCACACTT
1 AGTGCCATATATTTCCAGCATGCACACTT
31005026 AGTGCCATATATTTCCAGCATGCACACTT
1 AGTGCCATATATTTCCAGCATGCACACTT
*
31005055 AGTGCCATATATTTCCAGCACGCACACTT
1 AGTGCCATATATTTCCAGCATGCACACTT
31005084 AGTGCCA
1 AGTGCCA
31005091 ATCTCGTCAC
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 63 1.00
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.29
Consensus pattern (29 bp):
AGTGCCATATATTTCCAGCATGCACACTT
Found at i:31005022 original size:58 final size:58
Alignment explanation
Indices: 31004959--31005090 Score: 167
Period size: 58 Copynumber: 2.3 Consensus size: 58
31004949 GATTTAAGCC
* * * *
31004959 CGCACACATAGTGCCATACCCTTCGAGC-TCGCACACCCAGTGCCGTATATTTCCAGCA
1 CGCACACTTAGTGCCATACACTTCCAGCAT-GCACACCCAGTGCCATATATTTCCAGCA
* * * **
31005017 TGCACACTTAGTGCCATATATTTCCAGCATGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATACACTTCCAGCATGCACACCCAGTGCCATATATTTCCAGCA
31005075 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
31005091 ATCTCGTCAC
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
58 62 0.98
59 1 0.02
ACGTcount: A:0.26, C:0.33, G:0.16, T:0.25
Consensus pattern (58 bp):
CGCACACTTAGTGCCATACACTTCCAGCATGCACACCCAGTGCCATATATTTCCAGCA
Found at i:31012645 original size:40 final size:40
Alignment explanation
Indices: 31012599--31012781 Score: 296
Period size: 40 Copynumber: 4.6 Consensus size: 40
31012589 TACTCACTCG
* *
31012599 AATGCCTTCGGGACATAGCCCGGATATAGTAGCTCGCACA
1 AATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACA
*
31012639 ATTGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACA
1 AATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACA
31012679 AATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACA
1 AATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACA
* * *
31012719 AATGCCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGCA
1 AATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACA
31012759 AATGCCTTCGGGACTTAGCCCGG
1 AATGCCTTCGGGACTTAGCCCGG
31012782 TTATCATCCA
Statistics
Matches: 135, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
39 1 0.01
40 134 0.99
ACGTcount: A:0.25, C:0.28, G:0.25, T:0.22
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACA
Found at i:31014697 original size:29 final size:28
Alignment explanation
Indices: 31014665--31014767 Score: 116
Period size: 29 Copynumber: 3.6 Consensus size: 28
31014655 GTAACGAGAT
* *
31014665 TGGCACTGAGTGTGCGAGCTTGTAATGTA
1 TGGCACTAAGTGTGCGAGCTTG-AATATA
* *
31014694 TGGCACTAAGTGTGCGAGTTTGGACTATA
1 TGGCACTAAGTGTGCGAGCTT-GAATATA
* * *
31014723 TGGCACTATGTGTGCGGGCTTGAATCACA
1 TGGCACTAAGTGTGCGAGCTTGAAT-ATA
31014752 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
31014768 TGATTGAGTA
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
28 3 0.05
29 58 0.94
30 1 0.02
ACGTcount: A:0.21, C:0.17, G:0.33, T:0.29
Consensus pattern (28 bp):
TGGCACTAAGTGTGCGAGCTTGAATATA
Found at i:31020400 original size:48 final size:47
Alignment explanation
Indices: 31020339--31020506 Score: 183
Period size: 48 Copynumber: 3.7 Consensus size: 47
31020329 ACATGTAACT
*
31020339 GTGGCATATCCACTTAGCACCACGTTACATGTATCAATATGTTGAATC
1 GTGGTATATCCACTTAGCACCACGTTACATGTATCAATATG-TGAATC
* ** * *
31020387 ATGGTATATCCACTTAGCACTGCGTTAC----A-C-GTA--T-AACC
1 GTGGTATATCCACTTAGCACCACGTTACATGTATCAATATGTGAATC
31020425 GTGGTATATCCACTTAGCACCACGTTACATGTATCAATATGTGTAATC
1 GTGGTATATCCACTTAGCACCACGTTACATGTATCAATATGTG-AATC
* *
31020473 GTGGTATATCCACTTAACACCACGTTACACGTAT
1 GTGGTATATCCACTTAGCACCACGTTACATGTAT
31020507 AACCGTGGTA
Statistics
Matches: 97, Mismatches: 13, Indels: 20
0.75 0.10 0.15
Matches are distributed among these distances:
38 28 0.29
39 1 0.01
42 3 0.03
43 2 0.02
44 3 0.03
46 1 0.01
48 59 0.61
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (47 bp):
GTGGTATATCCACTTAGCACCACGTTACATGTATCAATATGTGAATC
Found at i:31020439 original size:38 final size:38
Alignment explanation
Indices: 31020388--31020532 Score: 155
Period size: 38 Copynumber: 3.6 Consensus size: 38
31020378 TGTTGAATCA
**
31020388 TGGTATATCCACTTAGCACTGCGTTACACGTATAACCG
1 TGGTATATCCACTTAGCACCACGTTACACGTATAACCG
* *
31020426 TGGTATATCCACTTAGCACCACGTTACATGTATCAATATGTGTAATCG
1 TGGTATATCCACTTAGCACCACGTTAC----A-C-----GTATAACCG
*
31020474 TGGTATATCCACTTAACACCACGTTACACGTATAACCG
1 TGGTATATCCACTTAGCACCACGTTACACGTATAACCG
31020512 TGGTATATCCACTTAGCACCA
1 TGGTATATCCACTTAGCACCA
31020533 TGTTTTTCCA
Statistics
Matches: 89, Mismatches: 8, Indels: 20
0.76 0.07 0.17
Matches are distributed among these distances:
38 52 0.58
42 1 0.01
43 2 0.02
44 1 0.01
48 33 0.37
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.30
Consensus pattern (38 bp):
TGGTATATCCACTTAGCACCACGTTACACGTATAACCG
Found at i:31020499 original size:86 final size:86
Alignment explanation
Indices: 31020334--31020532 Score: 328
Period size: 86 Copynumber: 2.3 Consensus size: 86
31020324 TCGATACATG
* *
31020334 TAACTGTGGCATATCCACTTAGCACCACGTTACATGTATCAATATGTTGAATCATGGTATATCCA
1 TAACCGTGGTATATCCACTTAGCACCACGTTACATGTATCAATATGTTGAATCATGGTATATCCA
* **
31020399 CTTAGCACTGCGTTACACGTA
66 CTTAACACCACGTTACACGTA
*
31020420 TAACCGTGGTATATCCACTTAGCACCACGTTACATGTATCAATATG-TGTAATCGTGGTATATCC
1 TAACCGTGGTATATCCACTTAGCACCACGTTACATGTATCAATATGTTG-AATCATGGTATATCC
31020484 ACTTAACACCACGTTACACGTA
65 ACTTAACACCACGTTACACGTA
31020506 TAACCGTGGTATATCCACTTAGCACCA
1 TAACCGTGGTATATCCACTTAGCACCA
31020533 TGTTTTTCCA
Statistics
Matches: 106, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
85 2 0.02
86 104 0.98
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.30
Consensus pattern (86 bp):
TAACCGTGGTATATCCACTTAGCACCACGTTACATGTATCAATATGTTGAATCATGGTATATCCA
CTTAACACCACGTTACACGTA
Found at i:31022315 original size:43 final size:43
Alignment explanation
Indices: 31022175--31022472 Score: 354
Period size: 43 Copynumber: 7.0 Consensus size: 43
31022165 ATATCGTACA
* * * *
31022175 ATGCCAACGTCCTAGACGTGGTCATACATGTAATCACATATCG
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAATCACATATCG
* * *
31022218 ATGCC-ACTGTCCCAAACAGGGTCTTACACG-AATCAAATAT-G
1 ATGCCAAC-GTCCCAGACATGGTCTTACACGTAATCACATATCG
* *
31022259 ATGCCGATGTCCCAGACATGGTCTTACACGTAATCACATATCG
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAATCACATATCG
* * *
31022302 ATGCCAACATCCCAGACGA-GGTATTACACGTAATCACATATAG
1 ATGCCAACGTCCCAGAC-ATGGTCTTACACGTAATCACATATCG
* * *
31022345 ATTCCAACGTCCCAGACAAGGTCTTACACGTAATCACATATCA
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAATCACATATCG
*
31022388 ATGCCAACGTCCTAGACGA-GGTCTTACACGTAATCACATATCG
1 ATGCCAACGTCCCAGAC-ATGGTCTTACACGTAATCACATATCG
* ** *
31022431 ATGCCAACGTCCTAGATGTGGTCTTACACATAATCACATATC
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAATCACATATC
31022473 AGAATCACAT
Statistics
Matches: 220, Mismatches: 27, Indels: 16
0.84 0.10 0.06
Matches are distributed among these distances:
41 26 0.12
42 22 0.10
43 170 0.77
44 2 0.01
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.24
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACATGGTCTTACACGTAATCACATATCG
Found at i:31022480 original size:13 final size:13
Alignment explanation
Indices: 31022462--31022486 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31022452 TCTTACACAT
31022462 AATCACATATCAG
1 AATCACATATCAG
31022475 AATCACATATCA
1 AATCACATATCA
31022487 AATAGTCAAC
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:0.48, C:0.24, G:0.04, T:0.24
Consensus pattern (13 bp):
AATCACATATCAG
Found at i:31023327 original size:15 final size:14
Alignment explanation
Indices: 31023302--31023331 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
31023292 ATCGATATTC
31023302 AAACAGAAAAATTA
1 AAACAGAAAAATTA
31023316 AAACACGAAAAATTA
1 AAACA-GAAAAATTA
31023331 A
1 A
31023332 CACATATAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.70, C:0.10, G:0.07, T:0.13
Consensus pattern (14 bp):
AAACAGAAAAATTA
Found at i:31030934 original size:40 final size:40
Alignment explanation
Indices: 31030879--31030999 Score: 163
Period size: 40 Copynumber: 3.0 Consensus size: 40
31030869 ATTTGATGTG
31030879 TATCCGGGCTTAAAGACCCGCAGGCTATATGTTGGAATTA
1 TATCCGGGCTTAAAGACCCGCAGGCTATATGTTGGAATTA
* *
31030919 TATCCGGGCTTAAAGACCCGCAAGCTATATGCTGGAATTA
1 TATCCGGGCTTAAAGACCCGCAGGCTATATGTTGGAATTA
* * ** * *
31030959 TACCCGGACTT-AAGGTCCACAGGCTATGTGTTGGAATTA
1 TATCCGGGCTTAAAGACCCGCAGGCTATATGTTGGAATTA
31030998 TA
1 TA
31031000 ACTGGACTTA
Statistics
Matches: 71, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
39 24 0.34
40 47 0.66
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (40 bp):
TATCCGGGCTTAAAGACCCGCAGGCTATATGTTGGAATTA
Found at i:31030996 original size:39 final size:39
Alignment explanation
Indices: 31030896--31031023 Score: 157
Period size: 39 Copynumber: 3.3 Consensus size: 39
31030886 GCTTAAAGAC
* * **
31030896 CCGCAGGCTATATGTTGGAATTATATCCGGGCTTAAAGAC
1 CCGCAGGCTATATGTTGGAATTATAACCGGACTT-AAGGT
* * *
31030936 CCGCAAGCTATATGCTGGAATTATACCCGGACTTAAGGT
1 CCGCAGGCTATATGTTGGAATTATAACCGGACTTAAGGT
* * *
31030975 CCACAGGCTATGTGTTGGAATTATAACTGGACTTAAGGT
1 CCGCAGGCTATATGTTGGAATTATAACCGGACTTAAGGT
31031014 CCGCAGGCTA
1 CCGCAGGCTA
31031024 CGTACTGGAA
Statistics
Matches: 75, Mismatches: 13, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
39 45 0.60
40 30 0.40
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.27
Consensus pattern (39 bp):
CCGCAGGCTATATGTTGGAATTATAACCGGACTTAAGGT
Found at i:31031033 original size:39 final size:39
Alignment explanation
Indices: 31030950--31031033 Score: 114
Period size: 39 Copynumber: 2.2 Consensus size: 39
31030940 AAGCTATATG
* * *
31030950 CTGGAATTATACCCGGACTTAAGGTCCACAGGCTATGTG
1 CTGGAATTATAACCGGACTTAAGGTCCACAGGCTACGTA
* * *
31030989 TTGGAATTATAACTGGACTTAAGGTCCGCAGGCTACGTA
1 CTGGAATTATAACCGGACTTAAGGTCCACAGGCTACGTA
31031028 CTGGAA
1 CTGGAA
31031034 ATATGTCCGG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.26
Consensus pattern (39 bp):
CTGGAATTATAACCGGACTTAAGGTCCACAGGCTACGTA
Found at i:31033469 original size:28 final size:28
Alignment explanation
Indices: 31033437--31033499 Score: 117
Period size: 28 Copynumber: 2.2 Consensus size: 28
31033427 ATGTACAAGA
31033437 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATTACCATT
*
31033465 ATACCCCTATGTATGCAAAATTACCGTT
1 ATACCCCTATGTATGCAAAATTACCATT
31033493 ATACCCC
1 ATACCCC
31033500 GAGGGTAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.33, C:0.29, G:0.08, T:0.30
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATTACCATT
Found at i:31033647 original size:28 final size:27
Alignment explanation
Indices: 31033606--31033687 Score: 103
Period size: 27 Copynumber: 3.0 Consensus size: 27
31033596 AGGAAGCGTC
31033606 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAA-TATCTGTT
* **
31033634 CTGGTGGCCCTGCCACGTATATCTGTT
1 CTGGTGGCACTGCCACAAATATCTGTT
31033661 CTGGTGGCACTGCCACAAAATATCTGT
1 CTGGTGGCACTGCCAC-AAATATCTGT
31033688 ATCTAGTGAC
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
27 23 0.50
28 23 0.50
ACGTcount: A:0.20, C:0.26, G:0.23, T:0.32
Consensus pattern (27 bp):
CTGGTGGCACTGCCACAAATATCTGTT
Found at i:31033714 original size:55 final size:56
Alignment explanation
Indices: 31033606--31033721 Score: 130
Period size: 55 Copynumber: 2.1 Consensus size: 56
31033596 AGGAAGCGTC
* * * *
31033606 CTGGTGGCTATGCCACAAATTATCTGTTCTGGTGGCCCTGCCACGTATATCTGT-T
1 CTGGTGGCTATGCCACAAAATATCTGTTCTAGTGACCCTGCCACATATATCTGTAT
* * *
31033661 CTGGTGGC-ACTGCCACAAAATATCTGTATCTAGTGACTCTGTCACAT-TTTCTGTAT
1 CTGGTGGCTA-TGCCACAAAATATCTGT-TCTAGTGACCCTGCCACATATATCTGTAT
31033717 CTGGT
1 CTGGT
31033722 AGCCATGCTG
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
54 1 0.02
55 30 0.59
56 20 0.39
ACGTcount: A:0.19, C:0.24, G:0.22, T:0.35
Consensus pattern (56 bp):
CTGGTGGCTATGCCACAAAATATCTGTTCTAGTGACCCTGCCACATATATCTGTAT
Found at i:31034175 original size:19 final size:19
Alignment explanation
Indices: 31034151--31034189 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
31034141 AAGGCAATTT
* *
31034151 TTTTATGGTTTTGTTTTAC
1 TTTTATGATTTTATTTTAC
*
31034170 TTTTATTATTTTATTTTAC
1 TTTTATGATTTTATTTTAC
31034189 T
1 T
31034190 ATGGAAAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.15, C:0.05, G:0.08, T:0.72
Consensus pattern (19 bp):
TTTTATGATTTTATTTTAC
Found at i:31034800 original size:11 final size:10
Alignment explanation
Indices: 31034772--31034805 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
31034762 AGCCTGTAAG
31034772 TATTCTGAAT
1 TATTCTGAAT
*
31034782 TTTTCTGAAT
1 TATTCTGAAT
31034792 ATATTCTGAAT
1 -TATTCTGAAT
31034803 TAT
1 TAT
31034806 CTGTCTGTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.29, C:0.09, G:0.09, T:0.53
Consensus pattern (10 bp):
TATTCTGAAT
Found at i:31039196 original size:93 final size:93
Alignment explanation
Indices: 31039089--31039260 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
31039079 CGCCCATAAG
* *
31039089 CGAACTCGAACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGAACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
31039154 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
* *
31039182 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGAACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
31039247 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
31039261 TCAACCATCC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (93 bp):
CGAACTCGAACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:31039257 original size:46 final size:46
Alignment explanation
Indices: 31039082--31039257 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
31039072 TGTAACCCGC
* * * *
31039082 CCATAAGCGAACTCGAACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
31039128 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
31039178 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
31039221 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
31039258 TGCTCAACCA
Statistics
Matches: 110, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 62 0.56
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:31039276 original size:46 final size:46
Alignment explanation
Indices: 31039131--31039269 Score: 144
Period size: 47 Copynumber: 3.0 Consensus size: 46
31039121 TTCGCATCCA
31039131 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CTAGTTA-CATC
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC-A---ACCATC
* * * * *
31039179 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA--
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGCTCAACCATC
31039224 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATC
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATC
31039270 CTAGTGACAT
Statistics
Matches: 75, Mismatches: 9, Indels: 16
0.75 0.09 0.16
Matches are distributed among these distances:
44 8 0.11
45 2 0.03
46 28 0.37
47 30 0.40
48 2 0.03
49 4 0.05
50 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATC
Found at i:31044105 original size:28 final size:28
Alignment explanation
Indices: 31044073--31044137 Score: 121
Period size: 28 Copynumber: 2.3 Consensus size: 28
31044063 ATGTACAAGA
31044073 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATTACCATT
*
31044101 ATACCCCTATGTATGCAAAATTACCGTT
1 ATACCCCTATGTATGCAAAATTACCATT
31044129 ATACCCCTA
1 ATACCCCTA
31044138 GGGTTAATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.34, C:0.28, G:0.08, T:0.31
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATTACCATT
Found at i:31044304 original size:27 final size:28
Alignment explanation
Indices: 31044245--31044332 Score: 99
Period size: 27 Copynumber: 3.1 Consensus size: 28
31044235 GAAGCGTCCC
*
31044245 GGTGGCTA-TGCCACAAATTATCTGTTCT
1 GGTGGC-ACTGCCACAAAATATCTGTTCT
* * **
31044273 TGTGGCCCTGCCAC-GTATATCTGTTCT
1 GGTGGCACTGCCACAAAATATCTGTTCT
31044300 GGTGGCACTGCCACAAAATATCTGTATCT
1 GGTGGCACTGCCACAAAATATCTGT-TCT
31044329 GGTG
1 GGTG
31044333 ACTCTGTCAC
Statistics
Matches: 48, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
27 22 0.46
28 19 0.40
29 7 0.15
ACGTcount: A:0.19, C:0.24, G:0.24, T:0.33
Consensus pattern (28 bp):
GGTGGCACTGCCACAAAATATCTGTTCT
Found at i:31044343 original size:29 final size:28
Alignment explanation
Indices: 31044253--31044343 Score: 85
Period size: 27 Copynumber: 3.2 Consensus size: 28
31044243 CCGGTGGCTA
* * * *
31044253 TGCCACAAATTATCTGTTCTTGTGGCCC
1 TGCCACAAAATATCTGTTCTGGTGACAC
** *
31044281 TGCCAC-GTATATCTGTTCTGGTGGCAC
1 TGCCACAAAATATCTGTTCTGGTGACAC
*
31044308 TGCCACAAAATATCTGTATCTGGTGACTC
1 TGCCACAAAATATCTGT-TCTGGTGACAC
*
31044337 TGTCACA
1 TGCCACA
31044344 TTTTCTGTAT
Statistics
Matches: 51, Mismatches: 10, Indels: 3
0.80 0.16 0.05
Matches are distributed among these distances:
27 22 0.43
28 14 0.27
29 15 0.29
ACGTcount: A:0.21, C:0.26, G:0.20, T:0.33
Consensus pattern (28 bp):
TGCCACAAAATATCTGTTCTGGTGACAC
Found at i:31044820 original size:19 final size:19
Alignment explanation
Indices: 31044796--31044834 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
31044786 TTTTAATTAT
* *
31044796 TTTTATGGTTTTGTTTTAC
1 TTTTATGATTTTATTTTAC
*
31044815 TTTTATTATTTTATTTTAC
1 TTTTATGATTTTATTTTAC
31044834 T
1 T
31044835 ATGGTGAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.15, C:0.05, G:0.08, T:0.72
Consensus pattern (19 bp):
TTTTATGATTTTATTTTAC
Found at i:31051263 original size:40 final size:40
Alignment explanation
Indices: 31051208--31051289 Score: 137
Period size: 40 Copynumber: 2.0 Consensus size: 40
31051198 ATTTGATGTG
* *
31051208 TATCCGGGCTTAAAGACCCGCAGGCTATATGCTAGAATTA
1 TATCCAGGCTTAAAGACCCACAGGCTATATGCTAGAATTA
*
31051248 TATCCAGGCTTAAAGACCCACAGGCTATATGCTGGAATTA
1 TATCCAGGCTTAAAGACCCACAGGCTATATGCTAGAATTA
31051288 TA
1 TA
31051290 CCCGGACTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.26
Consensus pattern (40 bp):
TATCCAGGCTTAAAGACCCACAGGCTATATGCTAGAATTA
Found at i:31051300 original size:40 final size:40
Alignment explanation
Indices: 31051208--31051300 Score: 134
Period size: 40 Copynumber: 2.3 Consensus size: 40
31051198 ATTTGATGTG
* *
31051208 TATCCGGGCTTAAAGACCCGCAGGCTATATGCTAGAATTA
1 TATCCCGGCTTAAAGACCCACAGGCTATATGCTAGAATTA
* *
31051248 TATCCAGGCTTAAAGACCCACAGGCTATATGCTGGAATTA
1 TATCCCGGCTTAAAGACCCACAGGCTATATGCTAGAATTA
31051288 TA-CCCGGACTTAA
1 TATCCCGG-CTTAA
31051301 GGTTCGCAGG
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
39 4 0.08
40 44 0.92
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (40 bp):
TATCCCGGCTTAAAGACCCACAGGCTATATGCTAGAATTA
Found at i:31051322 original size:39 final size:39
Alignment explanation
Indices: 31051268--31051362 Score: 129
Period size: 39 Copynumber: 2.4 Consensus size: 39
31051258 TAAAGACCCA
* * * *
31051268 CAGGCTATATGCTGGAATTATACCCGGACTTAAGGTTCG
1 CAGGCTCTGTGCTGGAATTATAACCGGACTTAAGGTCCG
*
31051307 CAGGCTCTGTGCTGGAATTATAACTGGACTTAAGGTCCG
1 CAGGCTCTGTGCTGGAATTATAACCGGACTTAAGGTCCG
31051346 CAGGCTAC-GTGCTGGAA
1 CAGGCT-CTGTGCTGGAA
31051363 ATATGTCCGG
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
39 49 0.98
40 1 0.02
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
CAGGCTCTGTGCTGGAATTATAACCGGACTTAAGGTCCG
Found at i:31055813 original size:39 final size:39
Alignment explanation
Indices: 31055767--31055864 Score: 160
Period size: 39 Copynumber: 2.5 Consensus size: 39
31055757 GCTTAAAGAC
* *
31055767 CCGCAGGCTATATGCTGGAATTATACCCGGACTTAAGGT
1 CCGCAGGCTATGTGCTGGAATTATAACCGGACTTAAGGT
31055806 CCGCAGGCTATGTGCTGGAATTATAACCGGACTTAAGGT
1 CCGCAGGCTATGTGCTGGAATTATAACCGGACTTAAGGT
* *
31055845 TCGCAGGCTACGTGCTGGAA
1 CCGCAGGCTATGTGCTGGAA
31055865 ATACGTCCGG
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 55 1.00
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.24
Consensus pattern (39 bp):
CCGCAGGCTATGTGCTGGAATTATAACCGGACTTAAGGT
Found at i:31060291 original size:26 final size:26
Alignment explanation
Indices: 31060238--31060302 Score: 80
Period size: 26 Copynumber: 2.5 Consensus size: 26
31060228 GCGTACTTCT
31060238 AACAATCATTTTACCTCATAGGGCAA
1 AACAATCATTTTACCTCATAGGGCAA
*
31060264 AACATTCATTTTACCAT-ATAAGGG-AA
1 AACAATCATTTTACC-TCAT-AGGGCAA
*
31060290 AATAATCATTTTA
1 AACAATCATTTTA
31060303 TCGATTAGGG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
26 29 0.85
27 5 0.15
ACGTcount: A:0.42, C:0.17, G:0.09, T:0.32
Consensus pattern (26 bp):
AACAATCATTTTACCTCATAGGGCAA
Found at i:31062651 original size:27 final size:27
Alignment explanation
Indices: 31062591--31062673 Score: 103
Period size: 27 Copynumber: 3.0 Consensus size: 27
31062581 TGGCTGCCAG
* * *
31062591 AACAGATATTGTGACAGAGTCACCAGA
1 AACAGATATTGTGGCAGAGCCACTAGA
* *
31062618 TACAGATATTGTGGCAAAGCCACTAGA
1 AACAGATATTGTGGCAGAGCCACTAGA
*
31062645 AATAGATATTTGTGGCAGAGCCACTAGA
1 AACAGATA-TTGTGGCAGAGCCACTAGA
31062673 A
1 A
31062674 CGCTTCCTCC
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
27 28 0.60
28 19 0.40
ACGTcount: A:0.39, C:0.17, G:0.23, T:0.22
Consensus pattern (27 bp):
AACAGATATTGTGGCAGAGCCACTAGA
Found at i:31064670 original size:27 final size:27
Alignment explanation
Indices: 31064542--31064810 Score: 204
Period size: 27 Copynumber: 10.0 Consensus size: 27
31064532 GTTAATTCTG
**** *
31064542 TAAATCGAGGGTAAAACAGTAATTCTA
1 TAAATCGAGGGTAATTTGGTAATTTTA
** *
31064569 TAAATCGAGGGTAAAATGGTAATTCTA
1 TAAATCGAGGGTAATTTGGTAATTTTA
** *
31064596 TAAATCGAGGGTAAAATGGTAATTCTA
1 TAAATCGAGGGTAATTTGGTAATTTTA
*** *
31064623 TAAATCGAGGGTAAAACGGTAATTTTG
1 TAAATCGAGGGTAATTTGGTAATTTTA
*
31064650 TAAATCGAGGGTACTTTGGTAATTTTA
1 TAAATCGAGGGTAATTTGGTAATTTTA
* * *
31064677 CAAATTGAGGG-AATTTCAGTAATTTTA
1 TAAATCGAGGGTAATTT-GGTAATTTTA
* *
31064704 T-AATCGATGGTATTTTGGTAATTTTA
1 TAAATCGAGGGTAATTTGGTAATTTTA
* * **
31064730 TAAACCGGGGGTGCTTTGGTAATTTTA
1 TAAATCGAGGGTAATTTGGTAATTTTA
* * * *
31064757 CAAGTCGAAGGT-ATTTCAGTAATTTTA
1 TAAATCGAGGGTAATTT-GGTAATTTTA
* *
31064784 CAAATCGAGGGT-ATTTCAGTAATTTTA
1 TAAATCGAGGGTAATTT-GGTAATTTTA
31064811 CAAACTATAG
Statistics
Matches: 205, Mismatches: 33, Indels: 8
0.83 0.13 0.03
Matches are distributed among these distances:
26 24 0.12
27 181 0.88
ACGTcount: A:0.35, C:0.09, G:0.22, T:0.35
Consensus pattern (27 bp):
TAAATCGAGGGTAATTTGGTAATTTTA
Found at i:31064699 original size:81 final size:81
Alignment explanation
Indices: 31064534--31064796 Score: 260
Period size: 81 Copynumber: 3.3 Consensus size: 81
31064524 TTGTCGCAGT
* * * *** * *
31064534 TAATTCTGTAAATCGAGGGTAAAACAGTAATTCTATAAATCGAGGGTAAAATGGTAATTCTATAA
1 TAATTCTATAAATCGAGGGTAAAACGGTAATTTTATAAATCGAGGGTACTTTGGTAATTTTACAA
** *
31064599 ATCGAGGGTAAAAT-GG
66 ATCGAGGG-AATTTCAG
*
31064615 TAATTCTATAAATCGAGGGTAAAACGGTAATTTTGTAAATCGAGGGTACTTTGGTAATTTTACAA
1 TAATTCTATAAATCGAGGGTAAAACGGTAATTTTATAAATCGAGGGTACTTTGGTAATTTTACAA
*
31064680 ATTGAGGGAATTTCAG
66 ATCGAGGGAATTTCAG
* * **** * * *
31064696 TAATTTTAT-AATCGATGGTATTTTGGTAATTTTATAAACCGGGGGTGCTTTGGTAATTTTACAA
1 TAATTCTATAAATCGAGGGTAAAACGGTAATTTTATAAATCGAGGGTACTTTGGTAATTTTACAA
* * *
31064760 GTCGAAGGTATTTCAG
66 ATCGAGGGAATTTCAG
* *
31064776 TAATTTTACAAATCGAGGGTA
1 TAATTCTATAAATCGAGGGTA
31064797 TTTCAGTAAT
Statistics
Matches: 151, Mismatches: 29, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
80 69 0.46
81 82 0.54
ACGTcount: A:0.35, C:0.09, G:0.22, T:0.35
Consensus pattern (81 bp):
TAATTCTATAAATCGAGGGTAAAACGGTAATTTTATAAATCGAGGGTACTTTGGTAATTTTACAA
ATCGAGGGAATTTCAG
Found at i:31064751 original size:80 final size:81
Alignment explanation
Indices: 31064614--31064815 Score: 235
Period size: 80 Copynumber: 2.5 Consensus size: 81
31064604 GGGTAAAATG
* * *** * *
31064614 GTAATTCTATAAATCGAGGGTAAAACGGTAATTTTGTAAATCGAGGGTACTTTGGTAATTTTACA
1 GTAATTTTACAAATCGAGGGTATTTCGGTAATTTTATAAACCGAGGGTACTTTGGTAATTTTACA
* *
31064679 AATTGAGGGAATTTCA
66 AATCGAAGGAATTTCA
* * * * *
31064695 GTAATTTTA-TAATCGATGGTATTTTGGTAATTTTATAAACCGGGGGTGCTTTGGTAATTTTACA
1 GTAATTTTACAAATCGAGGGTATTTCGGTAATTTTATAAACCGAGGGTACTTTGGTAATTTTACA
* *
31064759 AGTCGAAGGTATTTCA
66 AATCGAAGGAATTTCA
* *
31064775 GTAATTTTACAAATCGAGGGTATTTCAGTAATTTTACAAAC
1 GTAATTTTACAAATCGAGGGTATTTCGGTAATTTTATAAAC
31064816 TATAGGTATT
Statistics
Matches: 100, Mismatches: 20, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
80 66 0.66
81 34 0.34
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.38
Consensus pattern (81 bp):
GTAATTTTACAAATCGAGGGTATTTCGGTAATTTTATAAACCGAGGGTACTTTGGTAATTTTACA
AATCGAAGGAATTTCA
Found at i:31064782 original size:54 final size:53
Alignment explanation
Indices: 31064652--31064843 Score: 181
Period size: 54 Copynumber: 3.6 Consensus size: 53
31064642 TAATTTTGTA
* * ** * *
31064652 AATCGAGGGTACTTT-GGTAATTTTACAAATTGAGGGAATTTCAGTAATTTTAT
1 AATCGAAGGTA-TTTCGGTAATTTTATAAACCGAGGGTATTTCAGTAATTTTAC
* * * * *
31064705 AATCGATGGTATTTTGGTAATTTTATAAACCGGGGGTGCTTT-GGTAATTTTAC
1 AATCGAAGGTATTTCGGTAATTTTATAAACCGAGGGT-ATTTCAGTAATTTTAC
* * *
31064758 AAGTCGAAGGTATTTCAGTAATTTTACAAATCGAGGGTATTTCAGTAATTTTAC
1 AA-TCGAAGGTATTTCGGTAATTTTATAAACCGAGGGTATTTCAGTAATTTTAC
* *
31064812 AAACTATAGGTATTTCGGTAATTTTAGTAAAC
1 AATCGA-AGGTATTTCGGTAATTTTA-TAAAC
31064844 TAAAGTATTC
Statistics
Matches: 111, Mismatches: 22, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
52 3 0.03
53 43 0.39
54 62 0.56
55 3 0.03
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.39
Consensus pattern (53 bp):
AATCGAAGGTATTTCGGTAATTTTATAAACCGAGGGTATTTCAGTAATTTTAC
Found at i:31064851 original size:27 final size:27
Alignment explanation
Indices: 31064767--31064852 Score: 86
Period size: 27 Copynumber: 3.2 Consensus size: 27
31064757 CAAGTCGAAG
* **
31064767 GTATTTCAGTAATTTTACAAATCGA-GG
1 GTATTTCAGTAATTTTACAAA-CTATAA
*
31064794 GTATTTCAGTAATTTTACAAACTATAG
1 GTATTTCAGTAATTTTACAAACTATAA
* *
31064821 GTATTTCGGTAATTTTAGTAAACTA-AA
1 GTATTTCAGTAATTTTA-CAAACTATAA
31064848 GTATT
1 GTATT
31064853 CTAAACAGGG
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
26 2 0.04
27 44 0.85
28 6 0.12
ACGTcount: A:0.35, C:0.09, G:0.15, T:0.41
Consensus pattern (27 bp):
GTATTTCAGTAATTTTACAAACTATAA
Found at i:31069492 original size:28 final size:27
Alignment explanation
Indices: 31069419--31069498 Score: 97
Period size: 27 Copynumber: 2.9 Consensus size: 27
31069409 CTGCCAGAAC
* * * *
31069419 AGATATTGTGACAGAGTCACTAGATAT
1 AGATATTGTGGCAGAGCCACCAGAAAT
*
31069446 AGATATTGTGGTAGAGCCACCAGAAAT
1 AGATATTGTGGCAGAGCCACCAGAAAT
*
31069473 AGATATTTGTGGCAGGGCCACCAGAA
1 AGATA-TTGTGGCAGAGCCACCAGAA
31069499 CGCTTCCTCC
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
27 27 0.60
28 18 0.40
ACGTcount: A:0.35, C:0.15, G:0.26, T:0.24
Consensus pattern (27 bp):
AGATATTGTGGCAGAGCCACCAGAAAT
Found at i:31069664 original size:27 final size:27
Alignment explanation
Indices: 31069603--31069664 Score: 65
Period size: 26 Copynumber: 2.3 Consensus size: 27
31069593 AAATTAACCC
* * *
31069603 TAGGGGTATAATGGTAATTTTGCACCT
1 TAGGAGTATAATGGTAAATTTGCAACT
31069630 T-GGAGTATAATGGTAAATTT-CATACT
1 TAGGAGTATAATGGTAAATTTGCA-ACT
*
31069656 TAGGCGTAT
1 TAGGAGTAT
31069665 TTTAGTAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
25 2 0.07
26 20 0.69
27 7 0.24
ACGTcount: A:0.29, C:0.10, G:0.24, T:0.37
Consensus pattern (27 bp):
TAGGAGTATAATGGTAAATTTGCAACT
Found at i:31069935 original size:16 final size:15
Alignment explanation
Indices: 31069914--31069943 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
31069904 CAAAATGCCG
31069914 GCTTTTCGGCATTTTA
1 GCTTTTCGGC-TTTTA
31069930 GCTTTTCGGCTTTT
1 GCTTTTCGGCTTTT
31069944 GCCGATCTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.07, C:0.20, G:0.20, T:0.53
Consensus pattern (15 bp):
GCTTTTCGGCTTTTA
Found at i:31074455 original size:40 final size:39
Alignment explanation
Indices: 31074287--31074457 Score: 159
Period size: 40 Copynumber: 4.3 Consensus size: 39
31074277 AGAAATTGAA
* *
31074287 TGATATCCGGGCTAAGCCCCGAAGACAATTATGCTG-AAAT-
1 TGATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATG
* * * * *
31074327 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAG
1 TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAAT-G
* *
31074367 CT-ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTG
1 -TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAA-ATG
* *
31074407 TTAAATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG
1 TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAAT-G
31074447 TGATATCCGGG
1 TGATATCCGGG
31074458 TAAAGTCCCG
Statistics
Matches: 107, Mismatches: 17, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
37 2 0.02
38 4 0.04
39 4 0.04
40 95 0.89
41 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24
Consensus pattern (39 bp):
TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATG
Found at i:31082369 original size:39 final size:40
Alignment explanation
Indices: 31082311--31082411 Score: 132
Period size: 39 Copynumber: 2.5 Consensus size: 40
31082301 AAATTGAATG
* *
31082311 ATATCCGGGCTAAGCCCCGAAGACAATTATGCT-GAAATT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * * *
31082350 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAGCT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
31082390 ATATCCGGGCTAAGACCCGAAG
1 ATATCCGGGCTAAGACCCGAAG
31082412 GCATTCGTGC
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
39 29 0.55
40 24 0.45
ACGTcount: A:0.31, C:0.23, G:0.25, T:0.22
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
Found at i:31082404 original size:40 final size:40
Alignment explanation
Indices: 31082311--31082492 Score: 181
Period size: 40 Copynumber: 4.6 Consensus size: 40
31082301 AAATTGAATG
* * * * *
31082311 ATATCCGGGCTAAGCCCCGAAGACAATTATGCT-GAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* *
31082350 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* *
31082390 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTAGTAGTT
* * * * * *
31082430 AAATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGTG
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* *
31082470 ATATCCGGG-TAAGTCCCGTAGGC
1 ATATCCGGGCTAAGACCCGAAGGC
31082493 CTTGGTGCGG
Statistics
Matches: 121, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
39 44 0.36
40 75 0.62
41 2 0.02
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
Found at i:31086572 original size:40 final size:40
Alignment explanation
Indices: 31086513--31086681 Score: 173
Period size: 40 Copynumber: 4.2 Consensus size: 40
31086503 CGGGACTTTA
* * *
31086513 CCCGGATATCACGATTTGCACAAATGCCTTCGGGTCTTAG
1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
* *
31086553 CCCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAG
1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
* * * * *
31086593 CCCGGATATAGCTACTAGCACAATTGCCTTCGGGTCTTAA
1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
* * *
31086633 CCCGGATAT-A-AA-TTTCAGCATAATTGTCTTCGGGGCTTAG
1 CCCGGATATAACAACTTGCA-CA-AA-TGCCTTCGGGTCTTAG
31086673 CCCGGATAT
1 CCCGGATAT
31086682 CATTCAATTT
Statistics
Matches: 106, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
37 3 0.03
38 3 0.03
39 1 0.01
40 99 0.93
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.28
Consensus pattern (40 bp):
CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
Found at i:31094590 original size:40 final size:40
Alignment explanation
Indices: 31094531--31094699 Score: 173
Period size: 40 Copynumber: 4.2 Consensus size: 40
31094521 CGGGACTTTA
* * *
31094531 CCCGGATATCACGATTTGCACAAATGCCTTCGGGTCTTAG
1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
* *
31094571 CCCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAG
1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
* * * * *
31094611 CCCGGATATAGCTACTAGCACAATTGCCTTCGGGTCTTAA
1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
* * *
31094651 CCCGGATAT-A-AA-TTTCAGCATAATTGTCTTCGGGGCTTAG
1 CCCGGATATAACAACTTGCA-CA-AA-TGCCTTCGGGTCTTAG
31094691 CCCGGATAT
1 CCCGGATAT
31094700 CATTCAATTT
Statistics
Matches: 106, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
37 3 0.03
38 3 0.03
39 1 0.01
40 99 0.93
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.28
Consensus pattern (40 bp):
CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
Found at i:31100074 original size:20 final size:20
Alignment explanation
Indices: 31100041--31100093 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
31100031 GGAAGAATAA
31100041 AGAAATGAAAAAAAA-AAAG
1 AGAAATGAAAAAAAACAAAG
*
31100060 AGAATATGAAGAAAAACAAAG
1 AGAA-ATGAAAAAAAACAAAG
31100081 A-AAA-GAAAAAAAA
1 AGAAATGAAAAAAAA
31100094 AGTGTTCATT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
18 8 0.27
19 5 0.17
20 12 0.40
21 5 0.17
ACGTcount: A:0.77, C:0.02, G:0.15, T:0.06
Consensus pattern (20 bp):
AGAAATGAAAAAAAACAAAG
Found at i:31101288 original size:29 final size:29
Alignment explanation
Indices: 31101255--31101337 Score: 157
Period size: 29 Copynumber: 2.9 Consensus size: 29
31101245 GTGACGAGAT
*
31101255 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
31101284 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
31101313 TGGCACTAAGTGTGCATGCTGGAAA
1 TGGCACTAAGTGTGCATGCTGGAAA
31101338 AAAATACGGC
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 53 1.00
ACGTcount: A:0.29, C:0.14, G:0.30, T:0.27
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAATATA
Found at i:31101358 original size:31 final size:29
Alignment explanation
Indices: 31101256--31101350 Score: 127
Period size: 29 Copynumber: 3.2 Consensus size: 29
31101246 TGACGAGATT
* * *
31101256 GGCACTAAGTGTGCGTGCTGGAAATATAT
1 GGCACTAAGTGTGCATGCTGGAAAAATAC
* *
31101285 GGCACTAAGTGTGCATGCTGGAAATATAT
1 GGCACTAAGTGTGCATGCTGGAAAAATAC
31101314 GGCACTAAGTGTGCATGCTGGAAAAAAATAC
1 GGCACTAAGTGTGCATGCTGG--AAAAATAC
31101345 GGCACT
1 GGCACT
31101351 GGGTGTGCGA
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
29 49 0.80
31 12 0.20
ACGTcount: A:0.32, C:0.16, G:0.28, T:0.24
Consensus pattern (29 bp):
GGCACTAAGTGTGCATGCTGGAAAAATAC
Found at i:31101378 original size:60 final size:58
Alignment explanation
Indices: 31101251--31101387 Score: 143
Period size: 60 Copynumber: 2.3 Consensus size: 58
31101241 TACGGTGACG
* * * *
31101251 AGAT-TGGCACTAAGTGTGCGTGCTGGAAATATATGGCACTAAGTGTGCATGCTGGAA
1 AGATATGGCACTAAGTGTGCATGCTGGAAAAATACGGCACTAAGTGTGCATGCTCGAA
* **
31101308 ATATATGGCACTAAGTGTGCATGCTGGAAAAAAATACGGCACTGGGTGTGCGA-GCTCGAA
1 AGATATGGCACTAAGTGTGCATGCTGG--AAAAATACGGCACTAAGTGTGC-ATGCTCGAA
* * *
31101368 GGGTATGGCACTATGTGTGC
1 AGATATGGCACTAAGTGTGC
31101388 GGGCTTAAAT
Statistics
Matches: 65, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
57 3 0.05
58 21 0.32
60 40 0.62
61 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.32, T:0.25
Consensus pattern (58 bp):
AGATATGGCACTAAGTGTGCATGCTGGAAAAATACGGCACTAAGTGTGCATGCTCGAA
Found at i:31110706 original size:18 final size:18
Alignment explanation
Indices: 31110683--31110718 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
31110673 ACCTCAAAAT
31110683 AGAATGAATGGTAAGTTA
1 AGAATGAATGGTAAGTTA
31110701 AGAATGAATGGTAAGTTA
1 AGAATGAATGGTAAGTTA
31110719 CGTACCATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.28, T:0.28
Consensus pattern (18 bp):
AGAATGAATGGTAAGTTA
Found at i:31112253 original size:21 final size:20
Alignment explanation
Indices: 31112224--31112262 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
31112214 GAGCAAAACT
31112224 GCCCTCGATGTCGCGATACG
1 GCCCTCGATGTCGCGATACG
*
31112244 GCCCTTCGATGTCTCGATA
1 GCCC-TCGATGTCGCGATA
31112263 TCGGACTCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.15, C:0.33, G:0.26, T:0.26
Consensus pattern (20 bp):
GCCCTCGATGTCGCGATACG
Found at i:31113606 original size:15 final size:15
Alignment explanation
Indices: 31113586--31113615 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
31113576 AGAAAGAATT
*
31113586 AAGAAATGAAAAAAA
1 AAGAAAAGAAAAAAA
31113601 AAGAAAAGAAAAAAA
1 AAGAAAAGAAAAAAA
31113616 TGAGCATGGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.03
Consensus pattern (15 bp):
AAGAAAAGAAAAAAA
Found at i:31114074 original size:12 final size:12
Alignment explanation
Indices: 31114059--31114087 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
31114049 TGTAGCAATC
31114059 TTGAGTAAGACA
1 TTGAGTAAGACA
31114071 TTGAGTAAGACA
1 TTGAGTAAGACA
31114083 TTGAG
1 TTGAG
31114088 CATGATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.38, C:0.07, G:0.28, T:0.28
Consensus pattern (12 bp):
TTGAGTAAGACA
Found at i:31114866 original size:39 final size:39
Alignment explanation
Indices: 31114812--31114974 Score: 263
Period size: 39 Copynumber: 4.2 Consensus size: 39
31114802 TGTGAATGAA
31114812 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
31114851 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
** *
31114890 TGTGCGAGCTATGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
* * *
31114929 TGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGCATT
1 TGTGCGAATTGTGATATCCGGGCTAAG-CCCGAAGGCAAT
31114969 TGTGCG
1 TGTGCG
31114975 GGTTACCATA
Statistics
Matches: 116, Mismatches: 7, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
39 99 0.85
40 17 0.15
ACGTcount: A:0.23, C:0.20, G:0.32, T:0.25
Consensus pattern (39 bp):
TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
Found at i:31114990 original size:40 final size:39
Alignment explanation
Indices: 31114812--31115004 Score: 251
Period size: 39 Copynumber: 4.9 Consensus size: 39
31114802 TGTGAATGAA
* *
31114812 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAAT
* *
31114851 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAAT
*
31114890 TGTGCGAGCTATGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAAT
* * *
31114929 TGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGCATT
1 TGTGCGAGTTATGATATCCGGGCTAAG-CCCGAAGGCAAT
* ** * *
31114969 TGTGCGGGTTACCATAACCGGGCTATGTCCCGAAGG
1 TGTGCGAGTTATGATATCCGGGCTAAG-CCCGAAGG
31115005 TGTTTTGAAC
Statistics
Matches: 139, Mismatches: 14, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
39 99 0.71
40 40 0.29
ACGTcount: A:0.23, C:0.21, G:0.32, T:0.24
Consensus pattern (39 bp):
TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAAT
Found at i:31119791 original size:46 final size:46
Alignment explanation
Indices: 31119738--31119913 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
31119728 TATTTGGGCA
31119738 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* * * *
31119784 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---CGA-GCG
*
31119831 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* *
31119877 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
31119914 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 4 0.04
45 2 0.02
46 67 0.60
47 33 0.29
48 2 0.02
50 4 0.04
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
Found at i:31119893 original size:93 final size:93
Alignment explanation
Indices: 31119734--31119905 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
31119724 GGGATATTTG
* *
31119734 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
31119799 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
*
31119827 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
31119892 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
31119906 ACTTATGGGC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:31122904 original size:15 final size:15
Alignment explanation
Indices: 31122865--31122944 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
31122855 GTATCTTGGG
*
31122865 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
*
31122880 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
* *
31122895 TTTCTTTATTCCGGG
1 TTTCTTTATTCTGGA
*
31122910 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
*
31122925 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
31122939 TTTCTT
1 TTTCTT
31122945 GTTATCTTTG
Statistics
Matches: 53, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
14 10 0.19
15 41 0.77
16 2 0.04
ACGTcount: A:0.10, C:0.19, G:0.14, T:0.57
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:31122934 original size:30 final size:30
Alignment explanation
Indices: 31122856--31122943 Score: 92
Period size: 30 Copynumber: 3.0 Consensus size: 30
31122846 CATAGTATCG
* * *
31122856 TATCTTGGGTTTCTTTA-TCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCC-GGATTTCTC
*
31122886 TAT-TCTGGATTTCTTTATTCCGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCCGGATTTCTC
*
31122916 TATCTTGGATTTCTTTATT-CGGTTTTCT
1 TATCTTGGATTTCTTTATTCCGGATTTCT
31122944 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
29 9 0.18
30 37 0.74
31 4 0.08
ACGTcount: A:0.10, C:0.18, G:0.16, T:0.56
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCCGGATTTCTC
Found at i:31124912 original size:46 final size:46
Alignment explanation
Indices: 31124859--31125034 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
31124849 TATTTGGGCA
31124859 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* * * *
31124905 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---CGA-GCG
*
31124952 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* *
31124998 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
31125035 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 4 0.04
45 2 0.02
46 67 0.60
47 33 0.29
48 2 0.02
50 4 0.04
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
Found at i:31125014 original size:93 final size:93
Alignment explanation
Indices: 31124855--31125026 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
31124845 GGGATATTTG
* *
31124855 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
31124920 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
*
31124948 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
31125013 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
31125027 ACTTATGGGC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:31127584 original size:28 final size:27
Alignment explanation
Indices: 31127544--31127606 Score: 108
Period size: 28 Copynumber: 2.3 Consensus size: 27
31127534 TGTACTAGAG
*
31127544 TACCCCTATGTATGCAAAATTACCATTA
1 TACCCCTATGTATGCAAAATGACC-TTA
31127572 TACCCCTATGTATGCAAAATGACCTTA
1 TACCCCTATGTATGCAAAATGACCTTA
31127599 TACCCCTA
1 TACCCCTA
31127607 GGGTTAATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 11 0.32
28 23 0.68
ACGTcount: A:0.33, C:0.29, G:0.08, T:0.30
Consensus pattern (27 bp):
TACCCCTATGTATGCAAAATGACCTTA
Found at i:31127770 original size:27 final size:28
Alignment explanation
Indices: 31127712--31127801 Score: 112
Period size: 27 Copynumber: 3.2 Consensus size: 28
31127702 AGGAAGCGTC
*
31127712 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAAATATCTGTT
* **
31127740 CTGGTGGCCCTGCCAC-GTATATCTGTT
1 CTGGTGGCACTGCCACAAAATATCTGTT
31127767 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCACAAAATATCTGT-T
31127796 CTGGTG
1 CTGGTG
31127802 ACTCTGTCTC
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
27 23 0.44
28 22 0.42
29 7 0.13
ACGTcount: A:0.19, C:0.24, G:0.24, T:0.32
Consensus pattern (28 bp):
CTGGTGGCACTGCCACAAAATATCTGTT
Found at i:31127820 original size:55 final size:56
Alignment explanation
Indices: 31127712--31127826 Score: 128
Period size: 55 Copynumber: 2.1 Consensus size: 56
31127702 AGGAAGCGTC
* * *
31127712 CTGGTGGCTATGCCACAAATTATCTGTTCTGGTGGCCCTGCCACGTATATCTGT-T
1 CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTAT
* * * *
31127767 CTGGTGGC-ACTGCCACAAAATATCTGTATCTGGTGACTCTGTCTCAT-TTTCTGTAT
1 CTGGTGGCTA-TGCCACAAAATATCTGT-TCTGGTGACCCTGCCACATATATCTGTAT
31127823 CTGG
1 CTGG
31127827 CAGCCATGCT
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
54 1 0.02
55 30 0.60
56 19 0.38
ACGTcount: A:0.17, C:0.24, G:0.23, T:0.36
Consensus pattern (56 bp):
CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTAT
Found at i:31128285 original size:19 final size:19
Alignment explanation
Indices: 31128261--31128299 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
31128251 TTTTAATTAT
* *
31128261 TTTTATGGTTTTGTTTTAC
1 TTTTATGATTTTATTTTAC
*
31128280 TTTTATTATTTTATTTTAC
1 TTTTATGATTTTATTTTAC
31128299 T
1 T
31128300 ATGATGAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.15, C:0.05, G:0.08, T:0.72
Consensus pattern (19 bp):
TTTTATGATTTTATTTTAC
Found at i:31135451 original size:28 final size:28
Alignment explanation
Indices: 31135404--31135467 Score: 85
Period size: 28 Copynumber: 2.3 Consensus size: 28
31135394 TGTACTAGAG
*
31135404 TACCCCTATGTATGCAAAATTACCAT-TA
1 TACCCCTATGTATGCAAAATGACC-TCTA
* *
31135432 TACCCCTATGTGTGCCAAATGACCTCTA
1 TACCCCTATGTATGCAAAATGACCTCTA
31135460 TACCCCTA
1 TACCCCTA
31135468 GGGTTAATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
27 1 0.03
28 31 0.97
ACGTcount: A:0.30, C:0.31, G:0.09, T:0.30
Consensus pattern (28 bp):
TACCCCTATGTATGCAAAATGACCTCTA
Found at i:31135614 original size:28 final size:29
Alignment explanation
Indices: 31135573--31135635 Score: 92
Period size: 28 Copynumber: 2.2 Consensus size: 29
31135563 AGGAAGCGTC
* *
31135573 CTGGTGGCTATGCCACAAATTATCTGT-T
1 CTGGTGGCCATGCCACAAAATATCTGTAT
*
31135601 CTGGTGGCCCTGCCACAAAATATCTGTAT
1 CTGGTGGCCATGCCACAAAATATCTGTAT
31135630 CTGGTG
1 CTGGTG
31135636 ACTCTGTCAC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
28 24 0.77
29 7 0.23
ACGTcount: A:0.21, C:0.24, G:0.24, T:0.32
Consensus pattern (29 bp):
CTGGTGGCCATGCCACAAAATATCTGTAT
Found at i:31135646 original size:29 final size:28
Alignment explanation
Indices: 31135583--31135646 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
31135573 CTGGTGGCTA
* *
31135583 TGCCACAAATTATCTGTTCTGGTGGCCC
1 TGCCACAAAATATCTGTTCTGGTGACCC
*
31135611 TGCCACAAAATATCTGTATCTGGTGACTC
1 TGCCACAAAATATCTGT-TCTGGTGACCC
*
31135640 TGTCACA
1 TGCCACA
31135647 TTTTCTATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 16 0.52
29 15 0.48
ACGTcount: A:0.23, C:0.27, G:0.19, T:0.31
Consensus pattern (28 bp):
TGCCACAAAATATCTGTTCTGGTGACCC
Found at i:31136123 original size:19 final size:19
Alignment explanation
Indices: 31136099--31136137 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
31136089 TTTTAATTAT
* *
31136099 TTTTATGGTTTTGTTTTAC
1 TTTTATGATTTTATTTTAC
*
31136118 TTTTATTATTTTATTTTAC
1 TTTTATGATTTTATTTTAC
31136137 T
1 T
31136138 ATGAAAAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.15, C:0.05, G:0.08, T:0.72
Consensus pattern (19 bp):
TTTTATGATTTTATTTTAC
Found at i:31139013 original size:98 final size:96
Alignment explanation
Indices: 31138717--31139128 Score: 292
Period size: 96 Copynumber: 4.4 Consensus size: 96
31138707 TTATTTGTGT
* * * ** * *
31138717 GCTAGTGTAAGA-CATGTCTGGGACAT-GCTTCAGCCACATTAT-GGGAGCCAGTGTAAGATCAT
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACAATATAGATAGTCAGTGTAAGACCAT
* * *
31138779 GTCTAGGACATGGCATCGGCATTGA-GACGA-GA
66 ATCTGGGACATGGCATCGACA-TGATG--GATGA
* *
31138811 GCTAGTGTAAGA-CATGTCTGGGATAT-G-ATCGGCCTCACA-AT-G-TAAG-CTAGTGTAAGA-
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACA-ATATAGAT-AGTC-AGTGTAAGAC
* * *
31138868 CATGTCCGGGACAT-GCATC-AGC-T-ATGAGATGT
63 CATATCTGGGACATGGCATCGA-CATGATG-GATGA
* * * *
31138900 GTTAGTGTAAGACCATGTCTGGGACATGGCATCGG-CAC-ATATAGAGGT-GTTAGTGTAATATC
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACAATATAGA--TAGTCAGTGTAAGACC
31138962 ATATCTGGGACATGGCATCGGCACGGAT-ATGTGA-GA
64 ATATCTGGGACATGGCATC-G-AC--ATGATG-GATGA
** * * *
31138998 GCTAGTGTAAGACCATGTCTGGGACATGGTGTCGGCCTCAATTTCGATAGTCAGTGTAAGACCAT
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACAATATAGATAGTCAGTGTAAGACCAT
* *
31139063 GTCTGGGACATGGCATCGACTTGATGGATGA
66 ATCTGGGACATGGCATCGACATGATGGATGA
*
31139094 GCTAGTGTAAGACCATGTCTGGGACATGACATCGG
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGG
31139129 TATCATACCC
Statistics
Matches: 256, Mismatches: 34, Indels: 54
0.74 0.10 0.16
Matches are distributed among these distances:
88 3 0.01
89 15 0.06
90 15 0.06
91 10 0.04
92 27 0.11
93 33 0.13
94 32 0.12
95 3 0.01
96 38 0.15
97 3 0.01
98 35 0.14
99 37 0.14
100 5 0.02
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (96 bp):
GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACAATATAGATAGTCAGTGTAAGACCAT
ATCTGGGACATGGCATCGACATGATGGATGA
Found at i:31141076 original size:30 final size:30
Alignment explanation
Indices: 31141020--31141076 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
31141010 ATCCCGAGCC
*
31141020 TAGGGGCAAAAATGTAAATATGCAAAAGTT
1 TAGGGGCAAAAATGTAAATATCCAAAAGTT
* * *
31141050 TAGGGGCAAAATTGTAATTTTCCAAAA
1 TAGGGGCAAAAATGTAAATATCCAAAA
31141077 TTTGAGTTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.44, C:0.09, G:0.21, T:0.26
Consensus pattern (30 bp):
TAGGGGCAAAAATGTAAATATCCAAAAGTT
Found at i:31141547 original size:46 final size:45
Alignment explanation
Indices: 31141497--31141670 Score: 194
Period size: 46 Copynumber: 3.8 Consensus size: 45
31141487 TGGTTGAGCA
31141497 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* * * *
31141543 TCCGAACT-GTTGAGTTGAGTCCGAGTTC-GTGAATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACT-TATG-GA-T-GCGAAG
31141588 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* * * *
31141634 CCCGAGCTTGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
31141671 GCGGGTTACA
Statistics
Matches: 107, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
43 1 0.01
44 4 0.04
45 32 0.30
46 65 0.61
47 4 0.04
48 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.30
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:31149072 original size:46 final size:46
Alignment explanation
Indices: 31149022--31149197 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
31149012 TGGTTGAGCA
31149022 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
31149068 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
31149113 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
31149161 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
31149198 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:31149178 original size:93 final size:93
Alignment explanation
Indices: 31149019--31149190 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
31149009 GGATGGTTGA
* *
31149019 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
31149084 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
31149112 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
31149177 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
31149191 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:31150111 original size:40 final size:40
Alignment explanation
Indices: 31150066--31150232 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
31150056 CGGAATATAA
31150066 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
31150106 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
31150146 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
31150186 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
31150225 CCGGATAT
1 CCGGATAT
31150233 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 14 0.13
40 93 0.87
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:31158111 original size:40 final size:40
Alignment explanation
Indices: 31158066--31158232 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
31158056 CGGAATATAA
31158066 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
31158106 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
31158146 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
31158186 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
31158225 CCGGATAT
1 CCGGATAT
31158233 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 14 0.13
40 93 0.87
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:31176241 original size:16 final size:16
Alignment explanation
Indices: 31176220--31176254 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
31176210 TGAACTCCGT
*
31176220 ATACCAGGCATTCATC
1 ATACCAGGAATTCATC
31176236 ATACCAGGAATTCATC
1 ATACCAGGAATTCATC
31176252 ATA
1 ATA
31176255 TAGAGGAAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.37, C:0.26, G:0.11, T:0.26
Consensus pattern (16 bp):
ATACCAGGAATTCATC
Found at i:31181333 original size:29 final size:29
Alignment explanation
Indices: 31181300--31181431 Score: 122
Period size: 29 Copynumber: 4.6 Consensus size: 29
31181290 GTGACGAGAT
31181300 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
*
31181329 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* ** * * ***
31181358 CGGCACTGGGTGTGCGAGCTCGAAGGGTA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* * * **
31181387 TGGCACTATGTGTGCGGGCT-TAAATCGCA
1 TGGCACTAAGTGTGCGTGCTGGAAAT-ATA
31181416 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
31181432 AAATCGAGTA
Statistics
Matches: 83, Mismatches: 19, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
28 2 0.02
29 81 0.98
ACGTcount: A:0.23, C:0.17, G:0.34, T:0.25
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAATATA
Found at i:31181467 original size:2 final size:2
Alignment explanation
Indices: 31181462--31181500 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
31181452 GTGTGCGTAC
31181462 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
31181501 CTCCGATCGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:31189254 original size:29 final size:29
Alignment explanation
Indices: 31189221--31189352 Score: 122
Period size: 29 Copynumber: 4.6 Consensus size: 29
31189211 GTGACGAGAT
31189221 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
*
31189250 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* ** * * ***
31189279 CGGCACTGGGTGTGCGAGCTCGAAGGGTA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* * * **
31189308 TGGCACTATGTGTGCGGGCT-TAAATCGCA
1 TGGCACTAAGTGTGCGTGCTGGAAAT-ATA
31189337 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
31189353 AAATCGAGTA
Statistics
Matches: 83, Mismatches: 19, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
28 2 0.02
29 81 0.98
ACGTcount: A:0.23, C:0.17, G:0.34, T:0.25
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAATATA
Found at i:31189388 original size:2 final size:2
Alignment explanation
Indices: 31189383--31189411 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
31189373 GTGTGCGTAC
31189383 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
31189412 CTCCGATCGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31197145 original size:47 final size:47
Alignment explanation
Indices: 31197074--31197299 Score: 212
Period size: 47 Copynumber: 4.8 Consensus size: 47
31197064 TGGGTAAGGT
31197074 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCATATCTC-AA
1 GCCGATG-CATGTCCCAGACATGGTCTTACACTAGCTCATATCTCGAA
* * * * *
31197121 GTCGATGCCATGTCCCAAACATGGTCTAAAACT-GACT-ATCATCTCGTA
1 GCCGATG-CATGTCCCAGACATGGTCTTACACTAG-CTCAT-ATCTCGAA
* * * * *
31197169 GCCGATGCATGTCCCAGACA-AGTCTTGCACTAGCTTATGTCTCGAG
1 GCCGATGCATGTCCCAGACATGGTCTTACACTAGCTCATATCTCGAA
* * * *
31197215 GCCGATGCATGTCCTAAACAT-GTCTTACACTAGCTCTTGTCTC-AA
1 GCCGATGCATGTCCCAGACATGGTCTTACACTAGCTCATATCTCGAA
* *
31197260 TGCCGATATCATGTCCCAGACATGGTCTTACACTGGCTCA
1 -GCCGAT-GCATGTCCCAGACATGGTCTTACACTAGCTCA
31197300 CAAACAAATG
Statistics
Matches: 145, Mismatches: 25, Indels: 17
0.78 0.13 0.09
Matches are distributed among these distances:
45 1 0.01
46 60 0.41
47 63 0.43
48 21 0.14
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (47 bp):
GCCGATGCATGTCCCAGACATGGTCTTACACTAGCTCATATCTCGAA
Found at i:31212161 original size:28 final size:28
Alignment explanation
Indices: 31212119--31212190 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
31212109 ATCTTCGATG
*
31212119 TCTCGCACACTAAGTTTCATACTCAATA
1 TCTCGCACACTAAGTGTCATACTCAATA
* * *
31212147 TCTCACACACCAAGTGTCATTCTCAATA
1 TCTCGCACACTAAGTGTCATACTCAATA
*
31212175 TTTCGCACACTAAGTG
1 TCTCGCACACTAAGTG
31212191 CCACATATAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.31, C:0.29, G:0.10, T:0.31
Consensus pattern (28 bp):
TCTCGCACACTAAGTGTCATACTCAATA
Found at i:31212290 original size:40 final size:40
Alignment explanation
Indices: 31212199--31212278 Score: 115
Period size: 40 Copynumber: 2.0 Consensus size: 40
31212189 TGCCACATAT
* **
31212199 ACATATAGCCGAAGCTATCTCAAATTGCACACGAAGTGCC
1 ACATTTAGCCGAAGCTATCTCAAACCGCACACGAAGTGCC
* *
31212239 ACATTTAGCCGAAGCTATTTCAAACCGCACACTAAGTGCC
1 ACATTTAGCCGAAGCTATCTCAAACCGCACACGAAGTGCC
31212279 GTTCTTAGCC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.34, C:0.29, G:0.16, T:0.21
Consensus pattern (40 bp):
ACATTTAGCCGAAGCTATCTCAAACCGCACACGAAGTGCC
Found at i:31215694 original size:40 final size:41
Alignment explanation
Indices: 31215660--31215907 Score: 294
Period size: 40 Copynumber: 6.2 Consensus size: 41
31215650 GGGCATGTAA
* * *
31215660 GTGCATTCAGGGGTA-TAGAAGTACAAACATGGGCACAAAT
1 GTGCAATCAGGGGTACTAGAAGTACAAACAGGGGCACATAT
*
31215700 GTGCAATCAGGGGTACCA-AAGTAC-AACAGGGGCACATAT
1 GTGCAATCAGGGGTACTAGAAGTACAAACAGGGGCACATAT
* * *
31215739 GTGCAATTAGGGGTAC-CGAAGTACAAACAGGGGAACATAT
1 GTGCAATCAGGGGTACTAGAAGTACAAACAGGGGCACATAT
* * * *
31215779 GTGAAATCAGGGGTACT-GAAGTACAAATAAGGGCACGTAT
1 GTGCAATCAGGGGTACTAGAAGTACAAACAGGGGCACATAT
*
31215819 GTGCAATCAGGGGTACTA-AAGCACAAACAGGGGCACATAT
1 GTGCAATCAGGGGTACTAGAAGTACAAACAGGGGCACATAT
* * * *
31215859 GTGCAATCAGAGGTA-TCGAAGTACAAACAAGGGCACGTAT
1 GTGCAATCAGGGGTACTAGAAGTACAAACAGGGGCACATAT
*
31215899 ATGCAATCA
1 GTGCAATCA
31215908 TCGATAAATA
Statistics
Matches: 178, Mismatches: 24, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
39 35 0.20
40 142 0.80
41 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.28, T:0.18
Consensus pattern (41 bp):
GTGCAATCAGGGGTACTAGAAGTACAAACAGGGGCACATAT
Found at i:31215770 original size:20 final size:20
Alignment explanation
Indices: 31215678--31215771 Score: 59
Period size: 20 Copynumber: 4.8 Consensus size: 20
31215668 AGGGGTATAG
* *
31215678 AAGTACAAACATGGGCA-CA
1 AAGTACAAACAGGGGTACCA
* *
31215697 AATGTGCAATCAGGGGTACCA
1 AA-GTACAAACAGGGGTACCA
*
31215718 AAGTAC-AACAGGGGCA-CA
1 AAGTACAAACAGGGGTACCA
* * ** *
31215736 TATGTGCAATTAGGGGTACCG
1 -AAGTACAAACAGGGGTACCA
31215757 AAGTACAAACAGGGG
1 AAGTACAAACAGGGG
31215772 AACATATGTG
Statistics
Matches: 53, Mismatches: 17, Indels: 9
0.67 0.22 0.11
Matches are distributed among these distances:
18 2 0.04
19 14 0.26
20 32 0.60
21 5 0.09
ACGTcount: A:0.38, C:0.18, G:0.29, T:0.15
Consensus pattern (20 bp):
AAGTACAAACAGGGGTACCA
Found at i:31224769 original size:46 final size:46
Alignment explanation
Indices: 31224556--31224918 Score: 240
Period size: 46 Copynumber: 7.7 Consensus size: 46
31224546 TTTGTGTGCT
* * *
31224556 AGTGTAAGA-CATGTCTAGGACAT-GCATCGGCTAC-ATTATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCT-CGA-GATG-TAGCC
* * * * * *
31224602 AGTGTAAAACCAAGTTTGGGACATGGCATCGGCATTGAGATGAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGC-TCGAGATG-TAGCC
* *
31224650 AGTGTAAGA-CTTGTCTAGGACAT-GCATCGGCCTCGAGATGTGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGG-CTCGAGATGT-AGCC
* * *
31224696 AATATAAGA-CATGTCTGGGACAT-GCATCGGCTACGAGATGT-GTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCT-CGAGATGTAGCC
* * * *
31224740 AGTGTAAGACCATGTCTGAGACATGGCATCGGCATAGATATGTGAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGC-TCGAGATGT---AGCC
* * * * ** *
31224790 AGTGTAAGACCATATTTGGGACATGGCGTCGGCCTCAATTTTGATAGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGG-CTCGA-GATG-TAGCC
* * * *
31224839 AATGTAAGACCATGCCTGGGACATGGCATCGACTTGATGGATG-AGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCTCGA--GATGTAGCC
*
31224886 AGTGTAAGACCATGCCTGGGACATGGCATCGGC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGC
31224919 ATTATACCCT
Statistics
Matches: 249, Mismatches: 50, Indels: 35
0.75 0.15 0.10
Matches are distributed among these distances:
44 9 0.04
45 15 0.06
46 73 0.29
47 57 0.23
48 27 0.11
49 32 0.13
50 31 0.12
51 4 0.02
52 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (46 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCTCGAGATGTAGCC
Found at i:31224859 original size:49 final size:48
Alignment explanation
Indices: 31224667--31224918 Score: 157
Period size: 47 Copynumber: 5.3 Consensus size: 48
31224657 GACTTGTCTA
* *
31224667 GGACAT-GCATCGGCCTCGAGAT-G-TGAGCCAATATAAGA-CATGTCTG
1 GGACATGGCATCGGCCTC-A-ATGGATGAGCCAATGTAAGACCATGCCTG
* * * * *
31224713 GGACAT-GCATCGG-CT--ACGAGATGTGTCAGTGTAAGACCATGTCTG
1 GGACATGGCATCGGCCTCAATG-GATGAGCCAATGTAAGACCATGCCTG
* * * * * ***
31224758 AGACATGGCATCGGCATAGATATGTGA-GAGCTAGTGTAAGACCATATTTG
1 GGACATGGCATCGGCCT-CA-ATG-GATGAGCCAATGTAAGACCATGCCTG
* * *
31224808 GGACATGGCGTCGGCCTCAATTTTGAT-AGTCAATGTAAGACCATGCCTG
1 GGACATGGCATCGGCCTCAA--TGGATGAGCCAATGTAAGACCATGCCTG
* ** *
31224857 GGACATGGCATC-GACTTGATGGATGAGCCAGTGTAAGACCATGCCTG
1 GGACATGGCATCGGCCTCAATGGATGAGCCAATGTAAGACCATGCCTG
31224904 GGACATGGCATCGGC
1 GGACATGGCATCGGC
31224919 ATTATACCCT
Statistics
Matches: 158, Mismatches: 33, Indels: 28
0.72 0.15 0.13
Matches are distributed among these distances:
41 1 0.01
43 1 0.01
44 11 0.07
45 15 0.09
46 24 0.15
47 33 0.21
48 6 0.04
49 30 0.19
50 33 0.21
51 4 0.03
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.23
Consensus pattern (48 bp):
GGACATGGCATCGGCCTCAATGGATGAGCCAATGTAAGACCATGCCTG
Found at i:31224907 original size:96 final size:98
Alignment explanation
Indices: 31224737--31224918 Score: 235
Period size: 96 Copynumber: 1.9 Consensus size: 98
31224727 TACGAGATGT
* * * *
31224737 GTCAGTGTAAGACCATGTCTGAGACATGGCATCGGCATAGATATGTGAGAGCTAGTGTAAGACCA
1 GTCAATGTAAGACCATGCCTGAGACATGGCATCGACATAGA-ATGTGAGAGCCAGTGTAAGACCA
** *
31224802 TATTTGGGACATGGCGTCGGCCTCAATTTTGATA
65 TACCTGGGACATGGCATCGGCCTCAATTTTGATA
* *
31224836 GTCAATGTAAGACCATGCCTGGGACATGGCATCGAC-TTG-ATG-GATGAGCCAGTGTAAGACCA
1 GTCAATGTAAGACCATGCCTGAGACATGGCATCGACATAGAATGTGA-GAGCCAGTGTAAGACCA
*
31224898 TGCCTGGGACATGGCATCGGC
65 TACCTGGGACATGGCATCGGC
31224919 ATTATACCCT
Statistics
Matches: 72, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
95 2 0.03
96 36 0.50
98 2 0.03
99 32 0.44
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (98 bp):
GTCAATGTAAGACCATGCCTGAGACATGGCATCGACATAGAATGTGAGAGCCAGTGTAAGACCAT
ACCTGGGACATGGCATCGGCCTCAATTTTGATA
Found at i:31230747 original size:41 final size:41
Alignment explanation
Indices: 31230702--31230799 Score: 142
Period size: 41 Copynumber: 2.4 Consensus size: 41
31230692 TGCGATTACT
* *
31230702 TGACAGCTTGTATGAGCAGCACTGCATAGCTACGTCTCGAC
1 TGACAGCTTGTGTGAGCAGCACCGCATAGCTACGTCTCGAC
** *
31230743 TGACAGCTTGTGTGAGCAGCACCGTGTAGCTACGTCTCGAT
1 TGACAGCTTGTGTGAGCAGCACCGCATAGCTACGTCTCGAC
*
31230784 TGACAGTTTGTGTGAG
1 TGACAGCTTGTGTGAG
31230800 TAGGCCCGTT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (41 bp):
TGACAGCTTGTGTGAGCAGCACCGCATAGCTACGTCTCGAC
Found at i:31231434 original size:2 final size:2
Alignment explanation
Indices: 31231427--31231467 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
31231417 GTTGTAAGCC
31231427 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
31231468 GCATGCAGGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:31236141 original size:40 final size:40
Alignment explanation
Indices: 31236084--31236308 Score: 249
Period size: 40 Copynumber: 5.7 Consensus size: 40
31236074 CTAACGGGGT
* * * ** *
31236084 TAAGTCCCGAAGACATTTGTGCTAGTGATTAATTTCGGGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACAAATTCCGGGC
31236124 TAAGTCCCGAAGGCATTTGTGCGAGTTACAAATTCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACAAATTCCGGGC
*
31236164 TAAGTCCCGAAGGCTTTTGTGCGAGTTACAAATTCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACAAATTCCGGGC
* * **
31236204 TAAGCCCCGAAGGCATTTGTGCAAGTTA-TTATATCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACAAAT-TCCGGGC
* * * * *
31236244 TAAGTCCCGAAGGCATCTGTGCTAGTGAC-CATATCCGGAC
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACAAAT-TCCGGGC
* *
31236284 TAAGACCCGAAGGC-CTTGTGCGAGT
1 TAAGTCCCGAAGGCATTTGTGCGAGT
31236309 GGTTATATCT
Statistics
Matches: 161, Mismatches: 22, Indels: 5
0.86 0.12 0.03
Matches are distributed among these distances:
39 10 0.06
40 151 0.94
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (40 bp):
TAAGTCCCGAAGGCATTTGTGCGAGTTACAAATTCCGGGC
Found at i:31243657 original size:18 final size:18
Alignment explanation
Indices: 31243634--31243668 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
31243624 ACAATAATAT
* *
31243634 ATTAATATAATATTAAAA
1 ATTAATAAAATAATAAAA
31243652 ATTAATAAAATAATAAA
1 ATTAATAAAATAATAAA
31243669 TTTAGAAACA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
ATTAATAAAATAATAAAA
Found at i:31244718 original size:16 final size:17
Alignment explanation
Indices: 31244699--31244734 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
31244689 TTTATTTTTA
*
31244699 TTTTTTCAATTATAA-T
1 TTTTTTAAATTATAACT
31244715 TTTTTTAAATTATAACT
1 TTTTTTAAATTATAACT
31244732 TTT
1 TTT
31244735 GCAACAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTTTTAAATTATAACT
Found at i:31244794 original size:3 final size:3
Alignment explanation
Indices: 31244782--31244831 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
31244772 TTTTTAATTG
31244782 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
31244829 ATA
1 ATA
31244832 TAACAAAACA
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 44 0.96
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:31247653 original size:17 final size:16
Alignment explanation
Indices: 31247626--31247667 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
31247616 AAAATATGAT
* *
31247626 TAAA-TTATTTATTAT
1 TAAATTTATTTAATAA
31247641 TAAATTATATTTAATAA
1 TAAATT-TATTTAATAA
31247658 TAAATTTATT
1 TAAATTTATT
31247668 AAAAGTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 4 0.17
16 5 0.22
17 14 0.61
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TAAATTTATTTAATAA
Found at i:31249288 original size:35 final size:35
Alignment explanation
Indices: 31249242--31249312 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
31249232 GCCATGCCAC
* *
31249242 ACGCCCTTGTGCTAGGCCTTGTGGTTAATTTATTT
1 ACGCCCGTGTGCTAGGCCTTATGGTTAATTTATTT
31249277 ACGCCCGTGTGCTAGGCCTTATGGTTAATTTATTT
1 ACGCCCGTGTGCTAGGCCTTATGGTTAATTTATTT
31249312 A
1 A
31249313 ATTCGAATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.17, C:0.20, G:0.23, T:0.41
Consensus pattern (35 bp):
ACGCCCGTGTGCTAGGCCTTATGGTTAATTTATTT
Found at i:31249770 original size:2 final size:2
Alignment explanation
Indices: 31249763--31249797 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
31249753 ACACATGTGG
*
31249763 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
31249798 CCATAATAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:31256166 original size:39 final size:39
Alignment explanation
Indices: 31255964--31256164 Score: 296
Period size: 39 Copynumber: 5.2 Consensus size: 39
31255954 TATGGTAACC
* * *
31255964 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAATT
* **
31256004 CGCACAATTGCCTTC-GGCTTAGCCCGGATATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
*
31256042 CGTACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
*
31256081 CGCATAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
* *
31256120 CGCACATTTTCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
31256159 CGCACA
1 CGCACA
31256165 TTCATTCACA
Statistics
Matches: 147, Mismatches: 13, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
38 32 0.22
39 101 0.69
40 14 0.10
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
Found at i:31263407 original size:39 final size:39
Alignment explanation
Indices: 31263204--31263405 Score: 323
Period size: 39 Copynumber: 5.2 Consensus size: 39
31263194 TATGGTAACC
* * *
31263204 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAATT
* * *
31263244 CGCACAATTGCCTTCGGGTTTAGCCCGGATATCATAGTT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
31263283 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
*
31263322 CGCATAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
*
31263361 CGCACATTTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
31263400 CGCACA
1 CGCACA
31263406 TTCATTCACA
Statistics
Matches: 150, Mismatches: 12, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
39 133 0.89
40 17 0.11
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.26
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
Found at i:31283460 original size:23 final size:23
Alignment explanation
Indices: 31283434--31283486 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
31283424 TATATTAACA
31283434 ATATAACCGCTTTCATATGGCAC
1 ATATAACCGCTTTCATATGGCAC
*
31283457 ATATAACTGCTTTCATATGGCAC
1 ATATAACCGCTTTCATATGGCAC
*
31283480 GTATAAC
1 ATATAAC
31283487 ATGCCCACAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (23 bp):
ATATAACCGCTTTCATATGGCAC
Found at i:31285657 original size:28 final size:28
Alignment explanation
Indices: 31285622--31285685 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 28
31285612 TAGAACAGAT
*
31285622 TAGTCCTTAACAGGCATTCCACATAAGA
1 TAGTCCTTAACAGACATTCCACATAAGA
*** *
31285650 TAGTCCTTGGTAGATATTCCACATAAGA
1 TAGTCCTTAACAGACATTCCACATAAGA
31285678 TAGTCCTT
1 TAGTCCTT
31285686 GGAGGACTTC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (28 bp):
TAGTCCTTAACAGACATTCCACATAAGA
Found at i:31286783 original size:23 final size:23
Alignment explanation
Indices: 31286753--31286809 Score: 96
Period size: 23 Copynumber: 2.5 Consensus size: 23
31286743 AGACCCAAGT
31286753 TGAATTAATTCTGATTTCGTTAG
1 TGAATTAATTCTGATTTCGTTAG
* *
31286776 TGAATTAATTCTGATTTTGTTTG
1 TGAATTAATTCTGATTTCGTTAG
31286799 TGAATTAATTC
1 TGAATTAATTC
31286810 ACTTGTGACG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.26, C:0.07, G:0.16, T:0.51
Consensus pattern (23 bp):
TGAATTAATTCTGATTTCGTTAG
Found at i:31293303 original size:17 final size:18
Alignment explanation
Indices: 31293291--31293359 Score: 61
Period size: 17 Copynumber: 3.8 Consensus size: 18
31293281 ATTATTTTAA
31293291 TAAATTTAATA-TTAAAT
1 TAAATTTAATATTTAAAT
* *
31293308 TTAATTTAATATTTAAGT
1 TAAATTTAATATTTAAAT
* *
31293326 GATTATCTTAATATTT-AAT
1 TA-AAT-TTAATATTTAAAT
*
31293345 TTAATTTAATATTTA
1 TAAATTTAATATTTA
31293360 CCTTGTAGAT
Statistics
Matches: 39, Mismatches: 9, Indels: 7
0.71 0.16 0.13
Matches are distributed among these distances:
17 19 0.49
18 7 0.18
19 4 0.10
20 9 0.23
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (18 bp):
TAAATTTAATATTTAAAT
Found at i:31293308 original size:12 final size:12
Alignment explanation
Indices: 31293291--31293359 Score: 56
Period size: 12 Copynumber: 5.7 Consensus size: 12
31293281 ATTATTTTAA
31293291 TAAATTTAATAT
1 TAAATTTAATAT
31293303 TAAATTTAAT-T
1 TAAATTTAATAT
31293314 TAATATTTAAGTGAT
1 TAA-ATTTAA-T-AT
31293329 T--ATCTTAATAT
1 TAAAT-TTAATAT
*
31293340 TTAATTTAAT-T
1 TAAATTTAATAT
31293351 TAATATTTA
1 TAA-ATTTA
31293360 CCTTGTAGAT
Statistics
Matches: 48, Mismatches: 1, Indels: 16
0.74 0.02 0.25
Matches are distributed among these distances:
11 10 0.21
12 29 0.60
13 7 0.15
15 2 0.04
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (12 bp):
TAAATTTAATAT
Found at i:31293397 original size:61 final size:58
Alignment explanation
Indices: 31293332--31293445 Score: 156
Period size: 61 Copynumber: 1.9 Consensus size: 58
31293322 AAGTGATTAT
* * **
31293332 CTTAATATTTAATTTAATTTAATATTTACCTTGTAGATAAATATTCTATTAATTTAATAGA
1 CTTAATATTAAATTTAATCTAATATTTACC-T-TA-ATAAATATAATATTAATTTAATAGA
*
31293393 CTTAATATTAAATTTAATCTAATATTTATCTTAATAAATATAATATTAATTTA
1 CTTAATATTAAATTTAATCTAATATTTACCTTAATAAATATAATATTAATTTA
31293446 TTATTAAAGT
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
58 18 0.38
59 2 0.04
60 1 0.02
61 27 0.56
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.49
Consensus pattern (58 bp):
CTTAATATTAAATTTAATCTAATATTTACCTTAATAAATATAATATTAATTTAATAGA
Found at i:31297181 original size:45 final size:45
Alignment explanation
Indices: 31297085--31297188 Score: 120
Period size: 45 Copynumber: 2.3 Consensus size: 45
31297075 CACCTAGAGT
* * * *
31297085 GAGTAAGACCATAGCTGAAAGATGTTATGGCATCATGATGGAAAT
1 GAGTAAGACCATAGCTAAAAGATGCTATGGCATCATGATGAAAAA
* *
31297130 GAGTAAGACCATTGCTAAAAGATGCTATGGCATCATGGT-AAACAA
1 GAGTAAGACCATAGCTAAAAGATGCTATGGCATCATGATGAAA-AA
* *
31297175 GTGTAAGGCCATAG
1 GAGTAAGACCATAG
31297189 TTGGACTTTG
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
44 2 0.04
45 47 0.96
ACGTcount: A:0.38, C:0.13, G:0.26, T:0.23
Consensus pattern (45 bp):
GAGTAAGACCATAGCTAAAAGATGCTATGGCATCATGATGAAAAA
Found at i:31297446 original size:27 final size:27
Alignment explanation
Indices: 31297416--31297486 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
31297406 GTAGATAGCC
*
31297416 CGACGGGATGTTAAACACAAGATAGTT
1 CGACGGGACGTTAAACACAAGATAGTT
** **
31297443 CGACAAGACGTTAAACACGGGATAGTT
1 CGACGGGACGTTAAACACAAGATAGTT
* *
31297470 CGATGGAACGTTAAACA
1 CGACGGGACGTTAAACA
31297487 TGAGAGTACG
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.20
Consensus pattern (27 bp):
CGACGGGACGTTAAACACAAGATAGTT
Found at i:31298457 original size:17 final size:17
Alignment explanation
Indices: 31298435--31298526 Score: 50
Period size: 17 Copynumber: 5.4 Consensus size: 17
31298425 ACCTAAGGGC
31298435 TATTAAATTAAATTTAA
1 TATTAAATTAAATTTAA
* *
31298452 TATTAAGATAGTCACTTTAA
1 TATTAA-AT--TAAATTTAA
* * **
31298472 TATT-AAGTGAATAAAA
1 TATTAAATTAAATTTAA
31298488 TATT--ATTAAGA--TAA
1 TATTAAATTAA-ATTTAA
31298502 GTATTAAATTAAATTTAA
1 -TATTAAATTAAATTTAA
31298520 TATTAAA
1 TATTAAA
31298527 ATATTAAAAT
Statistics
Matches: 56, Mismatches: 10, Indels: 18
0.67 0.12 0.21
Matches are distributed among these distances:
14 2 0.04
15 7 0.12
16 11 0.20
17 18 0.32
18 6 0.11
19 1 0.02
20 11 0.20
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.41
Consensus pattern (17 bp):
TATTAAATTAAATTTAA
Found at i:31299885 original size:42 final size:42
Alignment explanation
Indices: 31299826--31299923 Score: 153
Period size: 42 Copynumber: 2.3 Consensus size: 42
31299816 ACCGAGACTA
31299826 TGTGTAAGACCATATCTGGGATACGGCATC-ATTATAAGATTT
1 TGTGTAAGACCATATCTGGGATACGGCATCGA-TATAAGATTT
* *
31299868 TGTGTAAGACCATATCTGGGATATGGCATCGATATGAGATTT
1 TGTGTAAGACCATATCTGGGATACGGCATCGATATAAGATTT
*
31299910 CGTGTAAGACCATA
1 TGTGTAAGACCATA
31299924 GTTGGGCTAT
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
42 51 0.98
43 1 0.02
ACGTcount: A:0.31, C:0.14, G:0.23, T:0.32
Consensus pattern (42 bp):
TGTGTAAGACCATATCTGGGATACGGCATCGATATAAGATTT
Found at i:31301235 original size:51 final size:51
Alignment explanation
Indices: 31301164--31301324 Score: 268
Period size: 51 Copynumber: 3.2 Consensus size: 51
31301154 CTGATCACAT
31301164 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
*
31301215 TTATCACTTGTCACTGATCAGATAAATGTAGCTAAAGCTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
* * * *
31301266 TTGTCACTTATCACTGATCAGATAAGTGTAGCTGAGGCTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
*
31301317 TTGTCACT
1 TTATCACT
31301325 GATCAGAAGT
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 104 1.00
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (51 bp):
TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
Found at i:31308447 original size:42 final size:42
Alignment explanation
Indices: 31308393--31308542 Score: 149
Period size: 42 Copynumber: 3.5 Consensus size: 42
31308383 GTCACCAAGA
*
31308393 TTGTGTAAGACCATATCTGGGATACGTCATC-ATTATGAGATT
1 TTGTGTAAGACCATATCTGGGATACGGCATCGA-TATGAGATT
* *
31308435 TTGTGTAAGACCATATCTAGGATATGGCATCGATATGAGATT
1 TTGTGTAAGACCATATCTGGGATACGGCATCGATATGAGATT
* * * * * * *
31308477 TCGTGTAAGACCATAGCTGGGCTATTGGCATCGAAACGAGATC
1 TTGTGTAAGACCATATCTGGGATA-CGGCATCGATATGAGATT
*** *
31308520 CCATATAAGACCATATCTGGGAT
1 TTGTGTAAGACCATATCTGGGAT
31308543 CTGACATTGG
Statistics
Matches: 91, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
42 57 0.63
43 34 0.37
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (42 bp):
TTGTGTAAGACCATATCTGGGATACGGCATCGATATGAGATT
Done.