Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 103066607
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: 103066607
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 238 characters in sequence are not A, C, G, or T
File 155 of 345
Found at i:42736374 original size:28 final size:29
Alignment explanation
Indices: 42736342--42736412 Score: 110
Period size: 29 Copynumber: 2.5 Consensus size: 29
42736332 ACAGTAAGTC
42736342 CGCACACTTAGTGCT-T-AATATTCAAACT
1 CGCACACTTAGTGCTATGAA-ATTCAAACT
*
42736370 CGCACACTTAGTGCTATGCAATTCAAACT
1 CGCACACTTAGTGCTATGAAATTCAAACT
42736399 CGCACACTTAGTGC
1 CGCACACTTAGTGC
42736413 CAATCTCATT
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
28 15 0.38
29 24 0.60
30 1 0.03
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCTATGAAATTCAAACT
Found at i:42744117 original size:28 final size:29
Alignment explanation
Indices: 42744085--42744155 Score: 119
Period size: 29 Copynumber: 2.5 Consensus size: 29
42744075 ACAGTAAGTC
42744085 CGCACACTTAGTGCT-TA-ATATTCAAACT
1 CGCACACTTAGTGCTATACA-ATTCAAACT
42744113 CGCACACTTAGTGCTATACAATTCAAACT
1 CGCACACTTAGTGCTATACAATTCAAACT
42744142 CGCACACTTAGTGC
1 CGCACACTTAGTGC
42744156 CAATCTCATT
Statistics
Matches: 41, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
28 15 0.37
29 25 0.61
30 1 0.02
ACGTcount: A:0.31, C:0.28, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCTATACAATTCAAACT
Found at i:42745279 original size:17 final size:18
Alignment explanation
Indices: 42745243--42745280 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
42745233 CACTTTTTTT
42745243 TTCCTTTGTTTTCATCTTA
1 TTCCTTTGTTTTCA-CTTA
*
42745262 TTCCTTTTTTTTCA-TTA
1 TTCCTTTGTTTTCACTTA
42745279 TT
1 TT
42745281 TTATTCTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
19 13 0.72
ACGTcount: A:0.11, C:0.18, G:0.03, T:0.68
Consensus pattern (18 bp):
TTCCTTTGTTTTCACTTA
Found at i:42760489 original size:40 final size:40
Alignment explanation
Indices: 42760330--42760475 Score: 211
Period size: 40 Copynumber: 3.6 Consensus size: 40
42760320 ACTTTATATC
* * * * * *
42760330 TCGCACCCTAAGTGTCATACATAGCCGAAGTTATCTCAAA
1 TCGCACACTAAGTGCCATATATAGCCGAAGCTATGTCGAA
42760370 TCGCACACTAAGTGCCATATATAGCCGAAGCTATGTCGAA
1 TCGCACACTAAGTGCCATATATAGCCGAAGCTATGTCGAA
* * *
42760410 TCACACATTAAGTGCCATATATGGCCGAAGCTATGTCGAA
1 TCGCACACTAAGTGCCATATATAGCCGAAGCTATGTCGAA
42760450 TCGCACACTAAGTGCCATATATAGCC
1 TCGCACACTAAGTGCCATATATAGCC
42760476 AATTTGTCGT
Statistics
Matches: 94, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 94 1.00
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (40 bp):
TCGCACACTAAGTGCCATATATAGCCGAAGCTATGTCGAA
Found at i:42764832 original size:40 final size:39
Alignment explanation
Indices: 42764773--42764904 Score: 149
Period size: 40 Copynumber: 3.3 Consensus size: 39
42764763 CAATTGAATG
* *
42764773 ATATCCGGGCTAAGCCCCGAAGGCATTTATGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTG-TT
* * *
42764813 ATATCCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGTT
* * * *
42764853 ATAGCCGGGCTAAGACCCGAAGGCAATTGCGCTTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGT-GTT
42764893 ATATCC-GGCTAA
1 ATATCCGGGCTAA
42764905 ATTCCGAAGA
Statistics
Matches: 77, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
39 7 0.09
40 68 0.88
41 2 0.03
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGTT
Found at i:42769666 original size:39 final size:39
Alignment explanation
Indices: 42769557--42769698 Score: 131
Period size: 39 Copynumber: 3.6 Consensus size: 39
42769547 GTTTGCATGG
* * * ***
42769557 GGAGCTTTGCTAATACACAGCTTATCCATAAGCTCACTTG
1 GGAGCTTTGCTGATACACAACTTATCC-TTAGCTCACAAA
* ** * * * * *
42769597 GGGGCTTCACTAATACACAAATTATTCTTAGCTTACAAG
1 GGAGCTTTGCTGATACACAACTTATCCTTAGCTCACAAA
* *
42769636 GGAGCTTTGCTGGTACACATCTTATCCTTAGCTCACAAA
1 GGAGCTTTGCTGATACACAACTTATCCTTAGCTCACAAA
42769675 GGAGCTTTGCTGATACACAACTTA
1 GGAGCTTTGCTGATACACAACTTA
42769699 CCCATAAGCT
Statistics
Matches: 80, Mismatches: 22, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
39 59 0.74
40 21 0.26
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (39 bp):
GGAGCTTTGCTGATACACAACTTATCCTTAGCTCACAAA
Found at i:42779342 original size:17 final size:18
Alignment explanation
Indices: 42779320--42779353 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
42779310 TCACATTGAA
42779320 GTGTTTT-AGTGAAAACC
1 GTGTTTTCAGTGAAAACC
*
42779337 GTGTTTTCATTGAAAAC
1 GTGTTTTCAGTGAAAAC
42779354 TCTTCTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.29, C:0.12, G:0.21, T:0.38
Consensus pattern (18 bp):
GTGTTTTCAGTGAAAACC
Found at i:42780470 original size:29 final size:30
Alignment explanation
Indices: 42780432--42780521 Score: 114
Period size: 29 Copynumber: 3.1 Consensus size: 30
42780422 GCCCAAACTC
*
42780432 ATTTATATGGCCCATCTA-GCCCAGTTCAT
1 ATTTATATGGCCCATCTAGGCCCAATTCAT
* *
42780461 ATTTTTATGGCCCA-CTAGGCCCAATTCAC
1 ATTTATATGGCCCATCTAGGCCCAATTCAT
* *
42780490 ATTCATATGGCCCAT-TAGGCCCAAATCAT
1 ATTTATATGGCCCATCTAGGCCCAATTCAT
42780519 ATT
1 ATT
42780522 ATACTCATGC
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
28 3 0.06
29 49 0.94
ACGTcount: A:0.27, C:0.28, G:0.13, T:0.32
Consensus pattern (30 bp):
ATTTATATGGCCCATCTAGGCCCAATTCAT
Found at i:42780483 original size:57 final size:58
Alignment explanation
Indices: 42780409--42780521 Score: 140
Period size: 58 Copynumber: 2.0 Consensus size: 58
42780399 CATACATGCA
* * * **
42780409 TATGACCCACTGGGCCCAA-ACTCATTTATATGGCCCATCTA-GCCCAGTTCATATTTT
1 TATGACCCACTAGGCCCAATACACATTCATATGGCCCAT-TAGGCCCAAATCATATTTT
* *
42780466 TATGGCCCACTAGGCCCAATTCACATTCATATGGCCCATTAGGCCCAAATCATATT
1 TATGACCCACTAGGCCCAATACACATTCATATGGCCCATTAGGCCCAAATCATATT
42780522 ATACTCATGC
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
57 19 0.40
58 28 0.60
ACGTcount: A:0.27, C:0.30, G:0.14, T:0.29
Consensus pattern (58 bp):
TATGACCCACTAGGCCCAATACACATTCATATGGCCCATTAGGCCCAAATCATATTTT
Found at i:42780628 original size:19 final size:19
Alignment explanation
Indices: 42780604--42780640 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
42780594 AGCCCATCAG
*
42780604 GCCCATTTAGCCCATTCTA
1 GCCCATTTAGCCAATTCTA
*
42780623 GCCCATTTGGCCAATTCT
1 GCCCATTTAGCCAATTCT
42780641 CAACCCAAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.19, C:0.35, G:0.14, T:0.32
Consensus pattern (19 bp):
GCCCATTTAGCCAATTCTA
Found at i:42784172 original size:93 final size:93
Alignment explanation
Indices: 42784060--42784230 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
42784050 GCCCATAAGT
* *
42784060 GAACTCGGACTCAACTCAACGAGCTT-GGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAG-TTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
42784124 ACGAGCTCAGATGCCTAGTTACATCTCTC
65 ACGAGCTCAGATGCCTAGTTACATCTCTC
42784153 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
* *
42784218 CGAGTTCGGATGC
66 CGAGCTCAGATGC
42784231 TCAACCATCC
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
92 2 0.03
93 71 0.97
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCAGATGCCTAGTTACATCTCTC
Found at i:42784222 original size:46 final size:46
Alignment explanation
Indices: 42784052--42784227 Score: 198
Period size: 46 Copynumber: 3.8 Consensus size: 46
42784042 TGTAACCCGC
* *
42784052 CCATAAGTGAACTCGGACTCAACTCAACGAGCTT-GGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAG-TTCGGACATTCGCAT
* * *
42784098 CCATAAGTGAACTCGGACTCAACTCAACGAGCTC--AGATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGC-A--T
* ***
42784144 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
42784191 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
42784228 TGCTCAACCA
Statistics
Matches: 106, Mismatches: 16, Indels: 16
0.77 0.12 0.12
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 65 0.61
47 30 0.28
49 5 0.05
50 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:42787989 original size:7 final size:7
Alignment explanation
Indices: 42787977--42788002 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
42787967 TTTTATGAAA
42787977 CCCAAAG
1 CCCAAAG
42787984 CCCAAAG
1 CCCAAAG
42787991 CCCAAAG
1 CCCAAAG
42787998 CCCAA
1 CCCAA
42788003 TTCATCTAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.46, G:0.12, T:0.00
Consensus pattern (7 bp):
CCCAAAG
Found at i:42795315 original size:42 final size:42
Alignment explanation
Indices: 42795269--42795348 Score: 110
Period size: 42 Copynumber: 1.9 Consensus size: 42
42795259 ATGTTATAGT
*
42795269 ATATCGATGCCAATAG-CCCA-ACTATGGTCTTATACGAATCTC
1 ATATCGATGCCAAT-GTCCCAGAC-ATGGTCTTACACGAATCTC
*
42795311 ATATCGATGCTAATGTCCCAGACATGGTCTTACACGAA
1 ATATCGATGCCAATGTCCCAGACATGGTCTTACACGAA
42795349 ATCACATCCT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
41 1 0.03
42 31 0.91
43 2 0.06
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (42 bp):
ATATCGATGCCAATGTCCCAGACATGGTCTTACACGAATCTC
Found at i:42797987 original size:40 final size:40
Alignment explanation
Indices: 42797943--42798025 Score: 114
Period size: 40 Copynumber: 2.1 Consensus size: 40
42797933 ATAAATTAGA
* * *
42797943 TATATGTGGCACTTAGTGTGTGATTCGATG-TAGCTTCGGC
1 TATATATGGCACTTAGTGTGCGATTC-AAGATAGCTTCGGC
*
42797983 TATATATGGCACTTAGTGTGCGATTCAAGATAGCTTTGGC
1 TATATATGGCACTTAGTGTGCGATTCAAGATAGCTTCGGC
42798023 TAT
1 TAT
42798026 GTACAGAACT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
39 2 0.05
40 36 0.95
ACGTcount: A:0.22, C:0.14, G:0.27, T:0.37
Consensus pattern (40 bp):
TATATATGGCACTTAGTGTGCGATTCAAGATAGCTTCGGC
Found at i:42798037 original size:40 final size:40
Alignment explanation
Indices: 42797953--42798042 Score: 101
Period size: 40 Copynumber: 2.2 Consensus size: 40
42797943 TATATGTGGC
* * ** *
42797953 ACTTAGTGTGTGATTCGATGTAGCTTCGGCTATATATGGC
1 ACTTAGTGTGCGATTCGAAGTAGCTTCGGCTATATACAGA
* *
42797993 ACTTAGTGTGCGATTC-AAGATAGCTTTGGCTATGTACAGA
1 ACTTAGTGTGCGATTCGAAG-TAGCTTCGGCTATATACAGA
42798033 ACTTAGTGTG
1 ACTTAGTGTG
42798043 TGAGATATCG
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
39 2 0.05
40 40 0.95
ACGTcount: A:0.23, C:0.14, G:0.27, T:0.36
Consensus pattern (40 bp):
ACTTAGTGTGCGATTCGAAGTAGCTTCGGCTATATACAGA
Found at i:42802949 original size:17 final size:17
Alignment explanation
Indices: 42802927--42802959 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
42802917 TAGAATATGT
42802927 GTACCAAGAAATTTTGC
1 GTACCAAGAAATTTTGC
42802944 GTACCAAGAAATTTTG
1 GTACCAAGAAATTTTG
42802960 AACTCATTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.30
Consensus pattern (17 bp):
GTACCAAGAAATTTTGC
Found at i:42804046 original size:2 final size:2
Alignment explanation
Indices: 42804039--42804079 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
42804029 ATCTATTCGG
42804039 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
42804080 CTTAAGCACA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:42805175 original size:12 final size:12
Alignment explanation
Indices: 42805160--42805184 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42805150 TAAATCAAGC
42805160 TATAAATATTTT
1 TATAAATATTTT
42805172 TATAAATATTTT
1 TATAAATATTTT
42805184 T
1 T
42805185 GGAATGTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TATAAATATTTT
Found at i:42806931 original size:31 final size:31
Alignment explanation
Indices: 42806896--42807028 Score: 194
Period size: 31 Copynumber: 4.3 Consensus size: 31
42806886 TGATAAGTAA
*
42806896 TAGCTTCGGCTACCTGATCAGTGAAAAGTGG
1 TAGCTTCGGCTACCTGATCAGTGAAAAATGG
*
42806927 TAGCTTCTGCTACCTGATCAGTGAAAAATGG
1 TAGCTTCGGCTACCTGATCAGTGAAAAATGG
* *
42806958 TAGCTCCGACTACCTGATCAGTGAAAAATGG
1 TAGCTTCGGCTACCTGATCAGTGAAAAATGG
* * *
42806989 TAGCTCCGGCTACCTGATCAGTGAATAGTGG
1 TAGCTTCGGCTACCTGATCAGTGAAAAATGG
*
42807020 TAACTTCGG
1 TAGCTTCGG
42807029 TTACAAGTGA
Statistics
Matches: 92, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 92 1.00
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (31 bp):
TAGCTTCGGCTACCTGATCAGTGAAAAATGG
Found at i:42807168 original size:46 final size:49
Alignment explanation
Indices: 42807101--42807226 Score: 159
Period size: 49 Copynumber: 2.6 Consensus size: 49
42807091 TGCTACTGTA
* * *
42807101 TAAGACCATATCTGGGATATGGCATC-A-GTGAGATATGTGATT-CATG
1 TAAGACCATAGCTGGGCTATGGCATCGATATGAGATATGTGATTACATG
* * *
42807147 TAAGACTATAGCTGGGCTATGGCATCGATATGTGATATGTGATTACGTG
1 TAAGACCATAGCTGGGCTATGGCATCGATATGAGATATGTGATTACATG
* *
42807196 TAAGACCATAGCTTGGCTATGACATCGATAT
1 TAAGACCATAGCTGGGCTATGGCATCGATAT
42807227 ATGAAGATGT
Statistics
Matches: 68, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
46 23 0.34
47 1 0.01
48 13 0.19
49 31 0.46
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.31
Consensus pattern (49 bp):
TAAGACCATAGCTGGGCTATGGCATCGATATGAGATATGTGATTACATG
Found at i:42807208 original size:49 final size:48
Alignment explanation
Indices: 42807054--42807223 Score: 159
Period size: 47 Copynumber: 3.6 Consensus size: 48
42807044 GATTTCCGTA
* * * * * *
42807054 TAAGACCATATCTGGGATATGGCATTG-GTGTGATATATG-CTACTGTA
1 TAAGACCATAGCTGGGATATGGCATCGAATGTGATATGTGATTAC-GTG
* * * *
42807101 TAAGACCATATCTGGGATATGGCATC-AGTGAGATATGTGATT-CATG
1 TAAGACCATAGCTGGGATATGGCATCGAATGTGATATGTGATTACGTG
* *
42807147 TAAGACTATAGCTGGGCTATGGCATCGATATGTGATATGTGATTACGTG
1 TAAGACCATAGCTGGGATATGGCATCGA-ATGTGATATGTGATTACGTG
* * *
42807196 TAAGACCATAGCTTGGCTATGACATCGA
1 TAAGACCATAGCTGGGATATGGCATCGA
42807224 TATATGAAGA
Statistics
Matches: 103, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
46 24 0.23
47 37 0.36
48 14 0.14
49 28 0.27
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (48 bp):
TAAGACCATAGCTGGGATATGGCATCGAATGTGATATGTGATTACGTG
Found at i:42815303 original size:19 final size:19
Alignment explanation
Indices: 42815279--42815317 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
42815269 AACTAATCCA
42815279 ATATATATATA-AACAATAT
1 ATATATATATAGAAC-ATAT
42815298 ATATATATATAGAACATAT
1 ATATATATATAGAACATAT
42815317 A
1 A
42815318 ACAAAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 16 0.84
20 3 0.16
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.36
Consensus pattern (19 bp):
ATATATATATAGAACATAT
Found at i:42815316 original size:17 final size:17
Alignment explanation
Indices: 42815279--42815317 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
42815269 AACTAATCCA
*
42815279 ATATATATATAAACAAT
1 ATATATATATAAACAAC
* *
42815296 ATATATATATATAGAAC
1 ATATATATATAAACAAC
42815313 ATATA
1 ATATA
42815318 ACAAAATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.36
Consensus pattern (17 bp):
ATATATATATAAACAAC
Found at i:42817918 original size:46 final size:46
Alignment explanation
Indices: 42817868--42818040 Score: 199
Period size: 46 Copynumber: 3.7 Consensus size: 46
42817858 TGGTTGAGCA
*
42817868 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * * *
42817914 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GTTGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* *
42817961 TCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
42818007 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
42818041 GGGGCGGGTT
Statistics
Matches: 105, Mismatches: 15, Indels: 14
0.78 0.11 0.10
Matches are distributed among these distances:
43 5 0.05
45 3 0.03
46 61 0.58
47 29 0.28
48 3 0.03
50 4 0.04
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:42818024 original size:93 final size:93
Alignment explanation
Indices: 42817865--42818035 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
42817855 GGATGGTTGA
* *
42817865 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
42817930 TGAGTCCGAGTTCGTGAGTTGTAACTAG
66 TGAGTCCGAGTTCGTGAGTTGTAACTAG
* * *
42817958 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
42818023 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
42818036 ACTTAGGGGC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGTTGTAACTAG
Found at i:42818302 original size:19 final size:20
Alignment explanation
Indices: 42818265--42818302 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
42818255 ATAAGGTGGT
42818265 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
42818285 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
42818303 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:42818811 original size:45 final size:45
Alignment explanation
Indices: 42818762--42818852 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
42818752 TAAATATAAA
42818762 TAAATGATGAGTAAGTTATGAAATTGAAGCTTAATGAGTCTATTT
1 TAAATGATGAGTAAGTTATGAAATTGAAGCTTAATGAGTCTATTT
42818807 TAAATGATGAGTAAGTTATGAAATTGAAGCTTAATGAGTCTATTT
1 TAAATGATGAGTAAGTTATGAAATTGAAGCTTAATGAGTCTATTT
42818852 T
1 T
42818853 CATATGGATT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.37, C:0.04, G:0.20, T:0.38
Consensus pattern (45 bp):
TAAATGATGAGTAAGTTATGAAATTGAAGCTTAATGAGTCTATTT
Found at i:42826500 original size:40 final size:39
Alignment explanation
Indices: 42826406--42826607 Score: 210
Period size: 40 Copynumber: 5.2 Consensus size: 39
42826396 ATGATACCCG
* * * *
42826406 GGCTAAGTCCCGAAGGCATTTATGTTAGCGATTATATCC
1 GGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATATCC
* *
42826445 GGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATATCC
1 GGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATATCC
* *
42826484 GGGCTAAGACCCGAAGGCATTCGTGCGAGTTG-TTATATCC
1 -GGCTAAGACCCGAAGGCATTTGTGCTAG-TGATTATATCC
* * ** *
42826524 GGGCTAAGACCCGAAGGCATTTGTGCAAGTTACCAAATCC
1 -GGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATATCC
* * * *
42826564 GGTTAAGA-CCGAAGGCAATTGTGCTTGTGGTTATATCC
1 GGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATATCC
42826602 GGCTAA
1 GGCTAA
42826608 ATTCCGAAGA
Statistics
Matches: 138, Mismatches: 22, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
38 27 0.20
39 45 0.33
40 64 0.46
41 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.27
Consensus pattern (39 bp):
GGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATATCC
Found at i:42834709 original size:40 final size:40
Alignment explanation
Indices: 42834592--42834797 Score: 213
Period size: 39 Copynumber: 5.2 Consensus size: 40
42834582 TGAATGATAC
* *
42834592 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGCGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTATAT
*
42834632 CCGGGCTAAG-TCCGAAGGCATTTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTATAT
** *
42834671 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG-TTATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCTAG-TGATTATAT
* * * ** *
42834711 CCGGGCTAA-ACCCGAAGGCATTTGTGCAAGTTACCAAAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTATAT
* * * * * *
42834750 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTACAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTATAT
42834790 CC-GGCTAA
1 CCGGGCTAA
42834798 ATTCCGAAGA
Statistics
Matches: 140, Mismatches: 22, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
38 1 0.01
39 72 0.51
40 65 0.46
41 2 0.01
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTATAT
Found at i:42834805 original size:79 final size:79
Alignment explanation
Indices: 42834592--42834806 Score: 236
Period size: 79 Copynumber: 2.7 Consensus size: 79
42834582 TGAATGATAC
* * * * * *
42834592 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGCGATTATATCCGGGCTAAGTCCGAAGGCATTTAT
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGGTTATATCCGGGCTAAATCCGAAGGCATTTAT
* ** *
42834657 GCTAGTGATTATAT
66 GCAAGTGACCAAAT
* * * *
42834671 CCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTGTTATATCCGGGCTAAACCCGAAGGCATTTG
1 CCGGGCTAAGACCCGAAGGCAATT-GTGCTAGTGGTTATATCCGGGCTAAATCCGAAGGCATTTA
*
42834735 TGCAAGTTACCAAAT
65 TGCAAGTGACCAAAT
* * *
42834750 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTACATCC-GGCTAAATTCCGAAG
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGGTTATATCCGGGCTAAA-TCCGAAG
42834807 AGACTCGGTT
Statistics
Matches: 112, Mismatches: 21, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
78 9 0.08
79 100 0.89
80 3 0.03
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (79 bp):
CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGGTTATATCCGGGCTAAATCCGAAGGCATTTAT
GCAAGTGACCAAAT
Found at i:42836211 original size:19 final size:20
Alignment explanation
Indices: 42836174--42836211 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
42836164 ATAAGGTGGT
42836174 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
42836194 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
42836212 TGGTGGTACG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:42837969 original size:43 final size:43
Alignment explanation
Indices: 42837903--42837993 Score: 116
Period size: 43 Copynumber: 2.1 Consensus size: 43
42837893 AAATCGTACA
* *
42837903 ATGCCAACGTCCCAGACGTGGTCTTACAT-GTAGTCACATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTAC-TCGGAATCACATATCG
42837946 ATGCC-ACTGTCCCAGACAG-GGTCTTACTCGGAATCACATATCG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACTCGGAATCACATATCG
42837989 ATGCC
1 ATGCC
42837994 TTGGTATTAC
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
42 3 0.07
43 39 0.91
44 1 0.02
ACGTcount: A:0.25, C:0.30, G:0.21, T:0.24
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACTCGGAATCACATATCG
Found at i:42841789 original size:19 final size:20
Alignment explanation
Indices: 42841765--42841802 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
42841755 CGTACCACCA
42841765 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
42841784 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
42841803 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:42842098 original size:46 final size:45
Alignment explanation
Indices: 42842031--42842198 Score: 180
Period size: 46 Copynumber: 3.6 Consensus size: 45
42842021 CGCCCCTAAG
*
42842031 TGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAA
1 TGAACTCGGACTCAACTCAACGAGTTCGGGCGTT-GCATCCATAAA
* *
42842077 TGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-T-CA
1 TGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTGCATCCATAAA
* * * * *
42842124 CGAACTCGGACTCAACTCAACGAGTTCAGACATTTGCATCCATAAG
1 TGAACTCGGACTCAACTCAACGAGTTCGGGC-GTTGCATCCATAAA
42842170 TGAACTCGGACTCAACTCAACGAGTTCGG
1 TGAACTCGGACTCAACTCAACGAGTTCGG
42842199 ATGCTCAACC
Statistics
Matches: 102, Mismatches: 12, Indels: 16
0.78 0.09 0.12
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 1 0.01
46 55 0.54
47 28 0.27
48 2 0.02
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (45 bp):
TGAACTCGGACTCAACTCAACGAGTTCGGGCGTTGCATCCATAAA
Found at i:42842142 original size:93 final size:93
Alignment explanation
Indices: 42842032--42842202 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
42842022 GCCCCTAAGT
* * *
42842032 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAATGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
42842097 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* * *
42842125 GAACTCGGACTCAACTCAACGAGTTCAGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
42842190 CGAGTTCGGATGC
66 CGAGTTCGGATGC
42842203 TCAACCATCC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:42842655 original size:29 final size:29
Alignment explanation
Indices: 42842622--42842680 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
42842612 ATTTAATACG
42842622 AACTTTAAAAAAATTACACTTTTGCCCCT
1 AACTTTAAAAAAATTACACTTTTGCCCCT
*** *
42842651 AACTTTTGCATAATTACACTTTTGCCCCT
1 AACTTTAAAAAAATTACACTTTTGCCCCT
42842680 A
1 A
42842681 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.32, C:0.25, G:0.05, T:0.37
Consensus pattern (29 bp):
AACTTTAAAAAAATTACACTTTTGCCCCT
Found at i:42863058 original size:28 final size:27
Alignment explanation
Indices: 42862995--42863064 Score: 104
Period size: 27 Copynumber: 2.6 Consensus size: 27
42862985 ATAGTGAGTC
*
42862995 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
*
42863022 CGCACACTTAGTGCTATATGATCAAACT
1 CGCACACTTAGTGCTATATAATC-AACT
*
42863050 TGCACACTTAGTGCT
1 CGCACACTTAGTGCT
42863065 GTACAAGTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
27 21 0.54
28 18 0.46
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:42865024 original size:19 final size:19
Alignment explanation
Indices: 42865000--42865037 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
42864990 TTGCAATTTA
42865000 AATTTTT-ATTTTATTTTCT
1 AATTTTTCA-TTTATTTTCT
42865019 AATTTTTCATTTATTTTCT
1 AATTTTTCATTTATTTTCT
42865038 TCTGACAGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 17 0.94
20 1 0.06
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.71
Consensus pattern (19 bp):
AATTTTTCATTTATTTTCT
Found at i:42874504 original size:2 final size:2
Alignment explanation
Indices: 42874497--42874522 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
42874487 CGGCTCTTGC
42874497 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
42874523 GTTTGCACAT
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42875438 original size:40 final size:40
Alignment explanation
Indices: 42875276--42875475 Score: 217
Period size: 40 Copynumber: 5.0 Consensus size: 40
42875266 TGAATGATAC
* * *
42875276 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGAATATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
* * *
42875316 CCGGGCTAAGTCCTGAAGGCATTTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
* *
42875356 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG-TTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATTATAT
* ** *
42875396 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGAT-ACCAAAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATTATAT
* * * *
42875436 CCGGGTTAAGACCCG-AGGCAATTGTGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
42875475 C
1 C
42875476 TGGCTAAATT
Statistics
Matches: 136, Mismatches: 21, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
38 1 0.01
39 16 0.12
40 117 0.86
41 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
Found at i:42889044 original size:26 final size:26
Alignment explanation
Indices: 42888948--42889121 Score: 264
Period size: 26 Copynumber: 6.8 Consensus size: 26
42888938 CCTCTTTAAT
**
42888948 AACTGGGGCA-AAGCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCAATA
*
42888973 AACTAGGGCA-AAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCAATA
42888998 AACTGGGGCA-AAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCAATA
**
42889023 AACTGGGGCATAAGCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCAATA
42889049 AACTGGGGCATAAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCAATA
**
42889075 AACTGGGGCATAAGCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCAATA
42889101 AACTGGGGCATAAGCCCTTTT
1 AACTGGGGCATAAGCCCTTTT
42889122 GCACTTCCTC
Statistics
Matches: 138, Mismatches: 10, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
25 56 0.41
26 82 0.59
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.26
Consensus pattern (26 bp):
AACTGGGGCATAAGCCCTTTTCAATA
Found at i:42892029 original size:39 final size:39
Alignment explanation
Indices: 42891975--42892053 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
42891965 TTGATGTGGA
*
42891975 ATTGTATCTGGGCTTAAAGACCCGCAGGCTTCGTGCTGG
1 ATTGTATCCGGGCTTAAAGACCCGCAGGCTTCGTGCTGG
*
42892014 ATTGTATCCGGGCTTAAAGACCCGTAGGCTTCGTGCTGG
1 ATTGTATCCGGGCTTAAAGACCCGCAGGCTTCGTGCTGG
42892053 A
1 A
42892054 ATGATTAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.19, C:0.23, G:0.30, T:0.28
Consensus pattern (39 bp):
ATTGTATCCGGGCTTAAAGACCCGCAGGCTTCGTGCTGG
Found at i:42896020 original size:40 final size:39
Alignment explanation
Indices: 42895829--42896020 Score: 172
Period size: 40 Copynumber: 4.8 Consensus size: 39
42895819 GGATATAACG
* ** *
42895829 ACTCGCTCAAATGCCTTCGGGACAAAGCCCGGTTATAGTA
1 ACTCGCACAAA-GCCTTCGGGACTTAGCCCGGATATAGTA
* * * *
42895869 ACTCGCACGAATGCCTTCGGGACTTAACCCGGGTTTAGTA
1 ACTCGCAC-AAAGCCTTCGGGACTTAGCCCGGATATAGTA
* * * *
42895909 ACTCGCACAAATGCCTTCGGG-CTTGGCCTGGATTTATTA
1 ACTCGCACAAA-GCCTTCGGGACTTAGCCCGGATATAGTA
* * *
42895948 ACTCGCACGAACGCCTTC-GGATCTTAGTCCGGATATAGTC
1 ACTCGCAC-AAAGCCTTCGGGA-CTTAGCCCGGATATAGTA
*
42895988 ACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
1 AC-TCGCACAAAGCCTTCGGGACTTAGCCCGGA
42896021 CATCATTCAA
Statistics
Matches: 122, Mismatches: 23, Indels: 14
0.77 0.14 0.09
Matches are distributed among these distances:
38 2 0.02
39 29 0.24
40 81 0.66
41 10 0.08
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.24
Consensus pattern (39 bp):
ACTCGCACAAAGCCTTCGGGACTTAGCCCGGATATAGTA
Found at i:42903327 original size:40 final size:40
Alignment explanation
Indices: 42903269--42903381 Score: 158
Period size: 40 Copynumber: 2.9 Consensus size: 40
42903259 TTATTTGATG
**
42903269 TGGAATTGTATCTAGGCTTAAAGACCCGCAGGCTTCGTGC
1 TGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTTCGTGC
42903309 TGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTTCGTGC
1 TGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTTCGTGC
* * *
42903349 TGGAA-TGACATCCGGG-TTAAAAACCTGCAGGCT
1 TGGAATTG-TATCCGGGCTTAAAGACCCGCAGGCT
42903382 GTGCTAATAT
Statistics
Matches: 67, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
39 17 0.25
40 50 0.75
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
TGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTTCGTGC
Found at i:42903567 original size:2 final size:2
Alignment explanation
Indices: 42903560--42903584 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
42903550 CAAAGAATGG
42903560 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 T
42903585 GTGACAGCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:42905970 original size:39 final size:39
Alignment explanation
Indices: 42905920--42906031 Score: 145
Period size: 39 Copynumber: 2.8 Consensus size: 39
42905910 ATATCACGAT
42905920 TTGCACAAATGCCTTCGGGTCTTAGCCCGGATTTA-AAAC
1 TTGCAC-AATGCCTTCGGGTCTTAGCCCGGATTTAGAAAC
* **
42905959 TTGCACGAATGCCTTCGGGTCTTAGCCCGGATATAGCTAC
1 TTGCAC-AATGCCTTCGGGTCTTAGCCCGGATTTAGAAAC
* *
42905999 TAGCACAATTGCCTTCGGGTCTTAACCCGGATT
1 TTGCACAA-TGCCTTCGGGTCTTAGCCCGGATT
42906032 AATTTCAGCA
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
39 35 0.55
40 29 0.45
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.29
Consensus pattern (39 bp):
TTGCACAATGCCTTCGGGTCTTAGCCCGGATTTAGAAAC
Found at i:42906066 original size:38 final size:40
Alignment explanation
Indices: 42905890--42906070 Score: 163
Period size: 40 Copynumber: 4.6 Consensus size: 40
42905880 CCGCACCAAG
* * * * * * * *
42905890 GCCTACGGGACTTAACCCGGATATCACGATTTGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAACTACTAGCACAATT
* * *
42905930 GCCTTCGGGTCTTAGCCCGGATTTAA-AACTTGCACGAA-T
1 GCCTTCGGGTCTTAGCCCGGATATAACTACTAGCAC-AATT
*
42905969 GCCTTCGGGTCTTAGCCCGGATATAGCTACTAGCACAATT
1 GCCTTCGGGTCTTAGCCCGGATATAACTACTAGCACAATT
* * * *
42906009 GCCTTCGGGTCTTAACCCGGAT-TAATTTC-AGCATAATT
1 GCCTTCGGGTCTTAGCCCGGATATAACTACTAGCACAATT
* *
42906047 GTCTTCGGGGCTTAGCCCGGATAT
1 GCCTTCGGGTCTTAGCCCGGATAT
42906071 CATTCAATTT
Statistics
Matches: 118, Mismatches: 19, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
38 27 0.23
39 39 0.33
40 52 0.44
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.28
Consensus pattern (40 bp):
GCCTTCGGGTCTTAGCCCGGATATAACTACTAGCACAATT
Found at i:42914059 original size:79 final size:79
Alignment explanation
Indices: 42913945--42914123 Score: 182
Period size: 79 Copynumber: 2.3 Consensus size: 79
42913935 TCGTTCAATC
* * *
42913945 GCCTTCGGGACATAGCCCGGATATGGTAACCCGCACCAAGGCCTACGGGACTTAACCCGGATAT-
1 GCCTTCGGGTCTTAGCCCGGATATGATAACCCGCACCAAGGCCTACGGGACTTAACCCGGATATA
*
42914009 CACAATTGCACAAAT
66 C-CAATAGCACAAAT
* * * * * * *
42914024 GCCTTCGGGTCTTAGCCCGGATA-GAATGACTCGCACGAATGCCTTCGGGTCTTAGCCCGGATAT
1 GCCTTCGGGTCTTAGCCCGGATATG-ATAACCCGCACCAAGGCCTACGGGACTTAACCCGGATAT
* * *
42914088 AGCCACTAGCACCATT
65 A-CCAATAGCACAAAT
*
42914104 GCCTTCGGGTCTTAACCCGG
1 GCCTTCGGGTCTTAGCCCGG
42914124 TTATAATTTC
Statistics
Matches: 82, Mismatches: 15, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
78 1 0.01
79 52 0.63
80 28 0.34
81 1 0.01
ACGTcount: A:0.23, C:0.31, G:0.25, T:0.21
Consensus pattern (79 bp):
GCCTTCGGGTCTTAGCCCGGATATGATAACCCGCACCAAGGCCTACGGGACTTAACCCGGATATA
CCAATAGCACAAAT
Found at i:42914068 original size:40 final size:40
Alignment explanation
Indices: 42914016--42914123 Score: 135
Period size: 40 Copynumber: 2.7 Consensus size: 40
42914006 TATCACAATT
** *
42914016 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAACCACTA
* * *
42914056 GCACGAATGCCTTCGGGTCTTAGCCCGGATATAGCCACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAACCACTA
* * *
42914096 GCACCATTGCCTTCGGGTCTTAACCCGG
1 GCACAAATGCCTTCGGGTCTTAGCCCGG
42914124 TTATAATTTC
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 59 1.00
ACGTcount: A:0.21, C:0.31, G:0.25, T:0.23
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAACCACTA
Found at i:42916186 original size:75 final size:75
Alignment explanation
Indices: 42916062--42916212 Score: 257
Period size: 75 Copynumber: 2.0 Consensus size: 75
42916052 CCATCTTGAC
* * *
42916062 AAGACTATCTACAATTGTATTTTCTTCATAGGGAATATGTTGAATCTTCCACTGCTTTACCATCA
1 AAGACTATCTACAATTGTATTTTCTTCACAGGGAATATGTTCAAACTTCCACTGCTTTACCATCA
42916127 ACAAAGTTTG
66 ACAAAGTTTG
* *
42916137 AAGACTATCTACAATTGTATTTTCTTCCCAGGGAATATGTTCAAACTTCCACTGCTTTACCATCG
1 AAGACTATCTACAATTGTATTTTCTTCACAGGGAATATGTTCAAACTTCCACTGCTTTACCATCA
42916202 ACAAAGTTTG
66 ACAAAGTTTG
42916212 A
1 A
42916213 TGAATTCTTC
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 71 1.00
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (75 bp):
AAGACTATCTACAATTGTATTTTCTTCACAGGGAATATGTTCAAACTTCCACTGCTTTACCATCA
ACAAAGTTTG
Found at i:42927339 original size:18 final size:17
Alignment explanation
Indices: 42927316--42927349 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
42927306 TAGCTGTGCC
42927316 GTTTTCTCTTCTGTATTA
1 GTTTTCTCTTCT-TATTA
42927334 GTTTTCTCTTCTTATT
1 GTTTTCTCTTCTTATT
42927350 TTCTTCCCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.09, C:0.18, G:0.09, T:0.65
Consensus pattern (17 bp):
GTTTTCTCTTCTTATTA
Found at i:42928585 original size:20 final size:20
Alignment explanation
Indices: 42928562--42928620 Score: 82
Period size: 20 Copynumber: 3.0 Consensus size: 20
42928552 TAAACATGGT
*
42928562 ATGTATTATATGCACATGAC
1 ATGTATGATATGCACATGAC
*
42928582 ATGTATGATATGCACATGAT
1 ATGTATGATATGCACATGAC
* *
42928602 ATGAATGACATGCACATGA
1 ATGTATGATATGCACATGA
42928621 TGTATTTATG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.31
Consensus pattern (20 bp):
ATGTATGATATGCACATGAC
Found at i:42928602 original size:11 final size:11
Alignment explanation
Indices: 42928569--42928621 Score: 51
Period size: 11 Copynumber: 5.2 Consensus size: 11
42928559 GGTATGTATT
42928569 ATATGCACATG
1 ATATGCACATG
* *
42928580 ACATG--TATG
1 ATATGCACATG
42928589 ATATGCACATG
1 ATATGCACATG
42928600 ATATG-A-ATG
1 ATATGCACATG
*
42928609 ACATGCACATG
1 ATATGCACATG
42928620 AT
1 AT
42928622 GTATTTATGA
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
9 14 0.44
10 2 0.06
11 16 0.50
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (11 bp):
ATATGCACATG
Found at i:42928749 original size:23 final size:24
Alignment explanation
Indices: 42928670--42928813 Score: 213
Period size: 24 Copynumber: 6.0 Consensus size: 24
42928660 GAGGAAGTGC
42928670 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
42928694 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
42928718 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
42928742 -AAAGGGCTTCTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
42928765 AAAAAAGGGCTT-TGCCCCAGTTATT
1 --AAAAGGGCTTATGCCCCAGTTATT
*
42928790 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
42928814 ATGATAAAGC
Statistics
Matches: 112, Mismatches: 2, Indels: 11
0.90 0.02 0.09
Matches are distributed among these distances:
23 28 0.25
24 54 0.48
25 21 0.19
26 9 0.08
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.28
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:42929931 original size:24 final size:24
Alignment explanation
Indices: 42929903--42929949 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
42929893 CTGATAGGAG
**
42929903 AGGATTTAGGAGTTGATAAGGGAT
1 AGGATTTAGGAGCAGATAAGGGAT
42929927 AGGATTTAGGAGCAGATAAGGGA
1 AGGATTTAGGAGCAGATAAGGGA
42929950 GGAAATCTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.36, C:0.02, G:0.38, T:0.23
Consensus pattern (24 bp):
AGGATTTAGGAGCAGATAAGGGAT
Found at i:42931405 original size:27 final size:26
Alignment explanation
Indices: 42931365--42931476 Score: 118
Period size: 27 Copynumber: 4.2 Consensus size: 26
42931355 AGGAAGCGTC
*
42931365 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
42931392 CTGGTGGCTCTGCCACATATATCT-ATT
1 CTGGTGGCTCTGCCACAT-TATCTGA-T
* *
42931419 CTAGTAGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCAC-ATTATCTG-AT
* * *
42931447 CTGGTGACTCTGTCACATTATCTGTT
1 CTGGTGGCTCTGCCACATTATCTGAT
42931473 CTGG
1 CTGG
42931477 CAGCCATGCT
Statistics
Matches: 72, Mismatches: 8, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
26 8 0.11
27 48 0.67
28 15 0.21
29 1 0.01
ACGTcount: A:0.19, C:0.24, G:0.21, T:0.37
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGAT
Found at i:42934911 original size:25 final size:25
Alignment explanation
Indices: 42934883--42934945 Score: 99
Period size: 25 Copynumber: 2.5 Consensus size: 25
42934873 ACTCTTTATG
42934883 AGCGTCCTGATATAAGCTCTTCTTA
1 AGCGTCCTGATATAAGCTCTTCTTA
* *
42934908 AGCGTCCTAATATAAGCTCTTCTTG
1 AGCGTCCTGATATAAGCTCTTCTTA
*
42934933 AGCTTCCTGATAT
1 AGCGTCCTGATAT
42934946 GGCTCACTTG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.37
Consensus pattern (25 bp):
AGCGTCCTGATATAAGCTCTTCTTA
Found at i:42942502 original size:11 final size:11
Alignment explanation
Indices: 42942486--42942510 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
42942476 TTATATATAC
42942486 TAATAAAATAA
1 TAATAAAATAA
42942497 TAATAAAATAA
1 TAATAAAATAA
42942508 TAA
1 TAA
42942511 AATATCATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
TAATAAAATAA
Found at i:42945656 original size:40 final size:40
Alignment explanation
Indices: 42945526--42945690 Score: 161
Period size: 40 Copynumber: 4.1 Consensus size: 40
42945516 CGGGATTCAA
* * * * *
42945526 CCGGACATAACCACAAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* ** * * *
42945566 CCGGATTTGGTGACTTGCACAATTGCCTTCGGGTCTTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTC-TTAGC
* *
42945607 CCGGATATAA-CAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATC-ACTAGCACAAATGCCTTCGGGTCTTAGC
* * *
42945647 CTGGATATAATCACTAGCATAAATGCCTTCGGGACTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
42945687 CCGG
1 CCGG
42945691 GTATCATTCA
Statistics
Matches: 100, Mismatches: 22, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
40 68 0.68
41 32 0.32
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:42947679 original size:2 final size:2
Alignment explanation
Indices: 42947674--42947722 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
42947664 TATATATATA
42947674 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
42947716 TG TG TG T
1 TG TG TG T
42947723 ATACATGGTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:42948524 original size:40 final size:40
Alignment explanation
Indices: 42948475--42948616 Score: 207
Period size: 40 Copynumber: 3.5 Consensus size: 40
42948465 TGAGGAATGT
*
42948475 TATCTGGGCTTAAAGACCCGCAGGCTTCGTGCTGGAATTG
1 TATCCGGGCTTAAAGACCCGCAGGCTTCGTGCTGGAATTG
* *
42948515 TATCCGGGCTTAAAGACCCACAGGCTAT-ATGCTGGAA-TG
1 TATCCGGGCTTAAAGACCCGCAGGCT-TCGTGCTGGAATTG
*
42948554 TTATCCGGGCTTAAAGACCCGTAGGCTTCGTGCTGGAATTG
1 -TATCCGGGCTTAAAGACCCGCAGGCTTCGTGCTGGAATTG
*
42948595 TATCCAGGCTTAAAGACCCGCA
1 TATCCGGGCTTAAAGACCCGCA
42948617 AGCTACGAGC
Statistics
Matches: 90, Mismatches: 8, Indels: 8
0.85 0.08 0.08
Matches are distributed among these distances:
39 3 0.03
40 84 0.93
41 3 0.03
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25
Consensus pattern (40 bp):
TATCCGGGCTTAAAGACCCGCAGGCTTCGTGCTGGAATTG
Found at i:42953037 original size:20 final size:20
Alignment explanation
Indices: 42953012--42953070 Score: 109
Period size: 20 Copynumber: 3.0 Consensus size: 20
42953002 TAAATATGGT
42953012 ATGTATGATATGCACATGAA
1 ATGTATGATATGCACATGAA
*
42953032 ATGTATGATATGCACATGAT
1 ATGTATGATATGCACATGAA
42953052 ATGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
42953071 GGTAATCATA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.32
Consensus pattern (20 bp):
ATGTATGATATGCACATGAA
Found at i:42953052 original size:11 final size:11
Alignment explanation
Indices: 42953016--42953070 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
42953006 TATGGTATGT
42953016 ATGATATGCAC
1 ATGATATGCAC
* *
42953027 ATGAAATG--T
1 ATGATATGCAC
42953036 ATGATATGCAC
1 ATGATATGCAC
*
42953047 ATGATATG--T
1 ATGATATGCAC
42953056 ATGATATGCAC
1 ATGATATGCAC
42953067 ATGA
1 ATGA
42953071 GGTAATCATA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:42953148 original size:24 final size:24
Alignment explanation
Indices: 42953121--42953239 Score: 170
Period size: 24 Copynumber: 5.0 Consensus size: 24
42953111 GAGGAAGTGA
*
42953121 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATT
42953145 AAAAGGGCTTATGCCCCAGTTA-T
1 AAAAGGGCTTATGCCCCAGTTATT
42953168 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
* *
42953192 GAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
42953216 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
42953240 ATGATAAAGC
Statistics
Matches: 86, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
23 22 0.26
24 53 0.62
25 11 0.13
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:42953190 original size:47 final size:48
Alignment explanation
Indices: 42953121--42953239 Score: 170
Period size: 47 Copynumber: 2.5 Consensus size: 48
42953111 GAGGAAGTGA
42953121 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTA-T
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
** *
42953168 AAAAGGGCTTATGCCCCAGTTATTGAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
*
42953216 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
42953240 ATGATAAAGC
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
47 43 0.66
48 11 0.17
49 11 0.17
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.27
Consensus pattern (48 bp):
AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
Found at i:42953518 original size:30 final size:31
Alignment explanation
Indices: 42953431--42953524 Score: 154
Period size: 31 Copynumber: 3.1 Consensus size: 31
42953421 CGTTTACAGT
*
42953431 AAAGGCTTCGGCCCAGTAATGTGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
*
42953462 AAAGGCTTCGGCCCAGTAATAAGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
*
42953493 AAAGGCTTCGG-CCAGTATTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
42953523 AA
1 AA
42953525 TATGAAAAGG
Statistics
Matches: 59, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
30 19 0.32
31 40 0.68
ACGTcount: A:0.39, C:0.15, G:0.23, T:0.22
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:42954688 original size:33 final size:33
Alignment explanation
Indices: 42954651--42954716 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
42954641 TGTGAAAAAG
42954651 AAAGACGAAACCATGAGAATGTGCATTGACTAT
1 AAAGACGAAACCATGAGAATGTGCATTGACTAT
*
42954684 AAAGACGGAACCATGAGAATGTGCATTGACTAT
1 AAAGACGAAACCATGAGAATGTGCATTGACTAT
42954717 CGTCAATTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.41, C:0.15, G:0.23, T:0.21
Consensus pattern (33 bp):
AAAGACGAAACCATGAGAATGTGCATTGACTAT
Found at i:42959572 original size:2 final size:2
Alignment explanation
Indices: 42959567--42959594 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
42959557 TCAAAAAACG
42959567 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42959595 GTGTGGATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42973023 original size:49 final size:49
Alignment explanation
Indices: 42972968--42973776 Score: 1103
Period size: 49 Copynumber: 16.4 Consensus size: 49
42972958 ATCAAGATTC
*
42972968 GTGAAAATGTATATATATGTGATGAGGCCTAATGGCCGATGTGATGAAT
1 GTGAAAATGTATATATATGTGATGAGGCCTAATGGCCGATGCGATGAAT
* * *
42973017 GTGAAAATGTATGTATATGTGATAAGGCCAAATGGCCGATGCGATGAAT
1 GTGAAAATGTATATATATGTGATGAGGCCTAATGGCCGATGCGATGAAT
42973066 GTGAAAATGTATATATATGTGATGAGGCCTAATGGCCGATGCGATGAAT
1 GTGAAAATGTATATATATGTGATGAGGCCTAATGGCCGATGCGATGAAT
* * **** *
42973115 GCGAAAATGTATGTATATGTGATGTATATATATGTGATGAGGCCTAATGGCCGATGTGATGAAT
1 GTGAAAATGTATATATATGTGATG-AGGCCTA----AT--GGCC-GAT-G-CGA-----TGAAT
* * *
42973179 GTGAAAATGTATGTATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
1 GTGAAAATGTATATATATGTGATGAGGCCTAATGGCCGATGCGATGAAT
42973228 GTGAAAATGTATATATATGTGATGAGGCCTAATGGCCGATGCGATGAAT
1 GTGAAAATGTATATATATGTGATGAGGCCTAATGGCCGATGCGATGAAT
*
42973277 GTGAAAATGTATGTATATGTGATGAGGCCTAATGGCCGATGCGATGAAT
1 GTGAAAATGTATATATATGTGATGAGGCCTAATGGCCGATGCGATGAAT
42973326 GTGAAAATGTATATATATGTGATGAGGCCTAATGGCCGATGCGATGAA-
1 GTGAAAATGTATATATATGTGATGAGGCCTAATGGCCGATGCGATGAAT
42973374 -TG----TG--TATATATGTGATGAGGCCTAATGGCCGATGCGATGAAT
1 GTGAAAATGTATATATATGTGATGAGGCCTAATGGCCGATGCGATGAAT
* *
42973416 GTGAAAATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
1 GTGAAAATGTATATATATGTGATGAGGCCTAATGGCCGATGCGATGAAT
*
42973465 GTGAAAATGTATATATATGTGATGAGGCCTAATGGCCGATGTGATGAAT
1 GTGAAAATGTATATATATGTGATGAGGCCTAATGGCCGATGCGATGAAT
42973514 GTGAAAATGTATATATATGTGATGAGGCCTAATGGCCGATGCGATGAAT
1 GTGAAAATGTATATATATGTGATGAGGCCTAATGGCCGATGCGATGAAT
* *
42973563 GCGAAAATGTATGTATATGTGATGAGGCCTAATGGCCGATGCGATGAAT
1 GTGAAAATGTATATATATGTGATGAGGCCTAATGGCCGATGCGATGAAT
* * * * *
42973612 GCGAAAATGTATGTATATGTGATAAGGCCTAATGGCCGATGTGGTGAAT
1 GTGAAAATGTATATATATGTGATGAGGCCTAATGGCCGATGCGATGAAT
* * * * * *
42973661 GTGAAAGTATATGTATATGTGATAAGGCCTAATGGCCGATGTGGTGAAT
1 GTGAAAATGTATATATATGTGATGAGGCCTAATGGCCGATGCGATGAAT
* * * *
42973710 GTGAAAGTGTATGTATATGTGATAAGGCCTAATGGCCGATGTGATGAAT
1 GTGAAAATGTATATATATGTGATGAGGCCTAATGGCCGATGCGATGAAT
*
42973759 GTGAAAGTGTATATATAT
1 GTGAAAATGTATATATAT
42973777 ATGTGGTAAA
Statistics
Matches: 695, Mismatches: 42, Indels: 46
0.89 0.05 0.06
Matches are distributed among these distances:
41 37 0.05
43 4 0.01
47 4 0.01
49 594 0.85
50 3 0.00
54 4 0.01
55 1 0.00
56 6 0.01
57 6 0.01
58 1 0.00
59 5 0.01
63 3 0.00
64 27 0.04
ACGTcount: A:0.32, C:0.09, G:0.29, T:0.30
Consensus pattern (49 bp):
GTGAAAATGTATATATATGTGATGAGGCCTAATGGCCGATGCGATGAAT
Found at i:42973141 original size:15 final size:15
Alignment explanation
Indices: 42973121--42973153 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
42973111 GAATGCGAAA
*
42973121 ATGTATGTATATGTG
1 ATGTATATATATGTG
42973136 ATGTATATATATGTG
1 ATGTATATATATGTG
42973151 ATG
1 ATG
42973154 AGGCCTAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.24, T:0.45
Consensus pattern (15 bp):
ATGTATATATATGTG
Found at i:42973147 original size:64 final size:64
Alignment explanation
Indices: 42973072--42973201 Score: 242
Period size: 64 Copynumber: 2.0 Consensus size: 64
42973062 GAATGTGAAA
42973072 ATGTATATATATGTGATGAGGCCTAATGGCCGATGCGATGAATGCGAAAATGTATGTATATGTG
1 ATGTATATATATGTGATGAGGCCTAATGGCCGATGCGATGAATGCGAAAATGTATGTATATGTG
* *
42973136 ATGTATATATATGTGATGAGGCCTAATGGCCGATGTGATGAATGTGAAAATGTATGTATATGTG
1 ATGTATATATATGTGATGAGGCCTAATGGCCGATGCGATGAATGCGAAAATGTATGTATATGTG
42973200 AT
1 AT
42973202 AAGGCCTAAT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 64 1.00
ACGTcount: A:0.32, C:0.08, G:0.28, T:0.33
Consensus pattern (64 bp):
ATGTATATATATGTGATGAGGCCTAATGGCCGATGCGATGAATGCGAAAATGTATGTATATGTG
Found at i:42973225 original size:113 final size:113
Alignment explanation
Indices: 42973023--42973251 Score: 377
Period size: 113 Copynumber: 2.0 Consensus size: 113
42973013 GAATGTGAAA
*
42973023 ATGTATGTATATGTGATAAGGCCAAATGGCCGATGCGATGAATGTGAAAATGTATATATATGTGA
1 ATGTATATATATGTGATAAGGCCAAATGGCCGATGCGATGAATGTGAAAATGTATATATATGTGA
* *
42973088 TGAGGCCTAATGGCCGATGCGATGAATGCGAAAATGTATGTATATGTG
66 TAAGGCCTAATGGCCGATGCGATGAATGCGAAAATGTATATATATGTG
* * * *
42973136 ATGTATATATATGTGATGAGGCCTAATGGCCGATGTGATGAATGTGAAAATGTATGTATATGTGA
1 ATGTATATATATGTGATAAGGCCAAATGGCCGATGCGATGAATGTGAAAATGTATATATATGTGA
* *
42973201 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAATGTATATATATGTG
66 TAAGGCCTAATGGCCGATGCGATGAATGCGAAAATGTATATATATGTG
42973249 ATG
1 ATG
42973252 AGGCCTAATG
Statistics
Matches: 107, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
113 107 1.00
ACGTcount: A:0.33, C:0.08, G:0.28, T:0.31
Consensus pattern (113 bp):
ATGTATATATATGTGATAAGGCCAAATGGCCGATGCGATGAATGTGAAAATGTATATATATGTGA
TAAGGCCTAATGGCCGATGCGATGAATGCGAAAATGTATATATATGTG
Found at i:42978998 original size:23 final size:23
Alignment explanation
Indices: 42978972--42979021 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
42978962 AAATGTCAAC
* * *
42978972 AAAACAACAGTGAAATAACACCA
1 AAAACAACAATAAAATAACACAA
* *
42978995 AAAATAGCAATAAAATAACACAA
1 AAAACAACAATAAAATAACACAA
42979018 AAAA
1 AAAA
42979022 TAACCTGCAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.68, C:0.16, G:0.06, T:0.10
Consensus pattern (23 bp):
AAAACAACAATAAAATAACACAA
Found at i:42979021 original size:12 final size:12
Alignment explanation
Indices: 42978984--42979025 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
42978974 AACAACAGTG
*
42978984 AAATAACACCAA
1 AAATAACACAAA
* *
42978996 AAATAGCA-ATA
1 AAATAACACAAA
42979007 AAATAACACAAA
1 AAATAACACAAA
42979019 AAATAAC
1 AAATAAC
42979026 CTGCAAAATG
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
11 8 0.33
12 16 0.67
ACGTcount: A:0.69, C:0.17, G:0.02, T:0.12
Consensus pattern (12 bp):
AAATAACACAAA
Found at i:42990141 original size:28 final size:28
Alignment explanation
Indices: 42990101--42990155 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
42990091 ATACTAAGAA
42990101 TAATAAAAATAGCTTCCATGCAAAATTT
1 TAATAAAAATAGCTTCCATGCAAAATTT
*
42990129 TAATAAAAATAGCTTCTATGCAAAATT
1 TAATAAAAATAGCTTCCATGCAAAATT
42990156 CATTTAAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.47, C:0.13, G:0.07, T:0.33
Consensus pattern (28 bp):
TAATAAAAATAGCTTCCATGCAAAATTT
Found at i:43000443 original size:13 final size:13
Alignment explanation
Indices: 43000425--43000449 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43000415 AAGTAATCGC
43000425 ACACGGGCGTGTT
1 ACACGGGCGTGTT
43000438 ACACGGGCGTGT
1 ACACGGGCGTGT
43000450 CCTTACCGAG
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:0.16, C:0.24, G:0.40, T:0.20
Consensus pattern (13 bp):
ACACGGGCGTGTT
Found at i:43006324 original size:55 final size:55
Alignment explanation
Indices: 43006264--43006382 Score: 141
Period size: 55 Copynumber: 2.2 Consensus size: 55
43006254 TGAGTTATTG
* * *
43006264 TTGTACACGGGCAGGCCACACAGGCGTGTG-CGATGGCCGTGTATTAAAGTCAGTA
1 TTGTACACGGGCAAGCCACACAGGCATGCGTC-ATGGCCGTGTATTAAAGTCAGTA
* * * * *
43006319 TTGTACACAGGCAAGCCACACTGGCATGCGTCATGGTCGTGTTTTAAAGTCAGTG
1 TTGTACACGGGCAAGCCACACAGGCATGCGTCATGGCCGTGTATTAAAGTCAGTA
*
43006374 TTGCACACG
1 TTGTACACG
43006383 AGCTAAGGAC
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
55 52 0.98
56 1 0.02
ACGTcount: A:0.24, C:0.23, G:0.29, T:0.24
Consensus pattern (55 bp):
TTGTACACGGGCAAGCCACACAGGCATGCGTCATGGCCGTGTATTAAAGTCAGTA
Found at i:43015836 original size:20 final size:21
Alignment explanation
Indices: 43015808--43015846 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
43015798 GTTACATCTC
43015808 ACGAACTCGG-ACTCAAATCA
1 ACGAACTCGGAACTCAAATCA
*
43015828 ACGAGCTCGGAACTCAAAT
1 ACGAACTCGGAACTCAAAT
43015847 ATCCTAGTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.38, C:0.28, G:0.18, T:0.15
Consensus pattern (21 bp):
ACGAACTCGGAACTCAAATCA
Found at i:43033235 original size:28 final size:28
Alignment explanation
Indices: 43033191--43033258 Score: 113
Period size: 28 Copynumber: 2.5 Consensus size: 28
43033181 TTTAAAACCC
43033191 TAGGGGT-A-TTCGGTAATTTTACTCTT
1 TAGGGGTAATTTCGGTAATTTTACTCTT
*
43033217 TAGGGGTAATTTCGGTAATTTTGCTCTT
1 TAGGGGTAATTTCGGTAATTTTACTCTT
43033245 TAGGGGTAATTTCG
1 TAGGGGTAATTTCG
43033259 TGATCTACGC
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
26 7 0.18
27 1 0.03
28 31 0.79
ACGTcount: A:0.19, C:0.10, G:0.26, T:0.44
Consensus pattern (28 bp):
TAGGGGTAATTTCGGTAATTTTACTCTT
Found at i:43035085 original size:19 final size:18
Alignment explanation
Indices: 43035048--43035091 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
43035038 ATACATACAG
43035048 TAAT-ATTTTTCTAATAA
1 TAATAATTTTTCTAATAA
*
43035065 TAATAATTTTATCTCATAA
1 TAATAATTTT-TCTAATAA
*
43035084 TACTAATT
1 TAATAATT
43035092 AAAATTTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 5 0.22
19 14 0.61
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATAATTTTTCTAATAA
Found at i:43036609 original size:19 final size:18
Alignment explanation
Indices: 43036572--43036615 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
43036562 ATACATACAG
43036572 TAAT-ATTTTTCTAATAA
1 TAATAATTTTTCTAATAA
*
43036589 TAATAATTTTATCTCATAA
1 TAATAATTTT-TCTAATAA
*
43036608 TACTAATT
1 TAATAATT
43036616 AAAATTTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 5 0.22
19 14 0.61
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATAATTTTTCTAATAA
Found at i:43039051 original size:28 final size:28
Alignment explanation
Indices: 43039007--43039074 Score: 113
Period size: 28 Copynumber: 2.5 Consensus size: 28
43038997 TTTAAAACCC
43039007 TAGGGGT-A-TTCGGTAATTTTACTCTT
1 TAGGGGTAATTTCGGTAATTTTACTCTT
*
43039033 TAGGGGTAATTTCGGTAATTTTGCTCTT
1 TAGGGGTAATTTCGGTAATTTTACTCTT
43039061 TAGGGGTAATTTCG
1 TAGGGGTAATTTCG
43039075 TGATCTACGC
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
26 7 0.18
27 1 0.03
28 31 0.79
ACGTcount: A:0.19, C:0.10, G:0.26, T:0.44
Consensus pattern (28 bp):
TAGGGGTAATTTCGGTAATTTTACTCTT
Found at i:43040898 original size:19 final size:18
Alignment explanation
Indices: 43040861--43040904 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
43040851 ATACATACAG
43040861 TAAT-ATTTTTCTAATAA
1 TAATAATTTTTCTAATAA
*
43040878 TAATAATTTTATCTCATAA
1 TAATAATTTT-TCTAATAA
*
43040897 TACTAATT
1 TAATAATT
43040905 AAAATTTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 5 0.22
19 14 0.61
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATAATTTTTCTAATAA
Found at i:43054682 original size:26 final size:26
Alignment explanation
Indices: 43054643--43054703 Score: 95
Period size: 26 Copynumber: 2.3 Consensus size: 26
43054633 CATATTGCTT
*
43054643 TTATGTTGTATTAGGAGATTCAGTGA
1 TTATGTTGTATTAGGAAATTCAGTGA
* *
43054669 TTATGTTGTCTTAGGAAATTTAGTGA
1 TTATGTTGTATTAGGAAATTCAGTGA
43054695 TTATGTTGT
1 TTATGTTGT
43054704 GTAAGTAGTC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.25, C:0.03, G:0.25, T:0.48
Consensus pattern (26 bp):
TTATGTTGTATTAGGAAATTCAGTGA
Found at i:43072527 original size:14 final size:14
Alignment explanation
Indices: 43072508--43072547 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
43072498 AGAAAGGCAA
43072508 AAAAAAAAAAAAAG
1 AAAAAAAAAAAAAG
*
43072522 AAAAAAAAGAAAAG
1 AAAAAAAAAAAAAG
43072536 AAAAGAAAAAAA
1 AAAA-AAAAAAA
43072548 TTCTAAAGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 17 0.74
15 6 0.26
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAAAG
Found at i:43072528 original size:19 final size:19
Alignment explanation
Indices: 43072506--43072547 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
43072496 GTAGAAAGGC
43072506 AAAAAAAAAAAAAAAGAAA
1 AAAAAAAAAAAAAAAGAAA
* *
43072525 AAAAAGAAAAGAAAAGAAA
1 AAAAAAAAAAAAAAAGAAA
43072544 AAAA
1 AAAA
43072548 TTCTAAAGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAAAAAAAGAAA
Found at i:43079546 original size:9 final size:9
Alignment explanation
Indices: 43079534--43079584 Score: 57
Period size: 9 Copynumber: 5.4 Consensus size: 9
43079524 CACATCATTA
43079534 TCTCAACTC
1 TCTCAACTC
*
43079543 TCTCAATTC
1 TCTCAACTC
*
43079552 TCTCAAATTC
1 TCTC-AACTC
*
43079562 TCTCAAACAC
1 TCTC-AACTC
43079572 TCTCAACTC
1 TCTCAACTC
43079581 TCTC
1 TCTC
43079585 GTTTTTAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
9 20 0.54
10 17 0.46
ACGTcount: A:0.25, C:0.39, G:0.00, T:0.35
Consensus pattern (9 bp):
TCTCAACTC
Found at i:43082121 original size:6 final size:6
Alignment explanation
Indices: 43082081--43082120 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
43082071 TAGTAAGCAA
* *
43082081 CAAAAA CAAAAG CAAAAG CAAAAG CAAAAG AAAAAG -AAAA
1 CAAAAG CAAAAG CAAAAG CAAAAG CAAAAG CAAAAG CAAAA
43082121 AATGAAATGA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
5 4 0.12
6 28 0.88
ACGTcount: A:0.75, C:0.12, G:0.12, T:0.00
Consensus pattern (6 bp):
CAAAAG
Found at i:43088400 original size:31 final size:30
Alignment explanation
Indices: 43088358--43088434 Score: 136
Period size: 31 Copynumber: 2.5 Consensus size: 30
43088348 TGGTAAAACG
43088358 ACCATTTTGCCCCTAGACTTTAACAAAATA
1 ACCATTTTGCCCCTAGACTTTAACAAAATA
43088388 ACCATTTTTGCCCCTAGACTTTAACAAAATA
1 ACCA-TTTTGCCCCTAGACTTTAACAAAATA
*
43088419 ACCATTTTCCCCCTAG
1 ACCATTTTGCCCCTAG
43088435 GCTCAAAAAT
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
30 15 0.33
31 30 0.67
ACGTcount: A:0.32, C:0.30, G:0.06, T:0.31
Consensus pattern (30 bp):
ACCATTTTGCCCCTAGACTTTAACAAAATA
Found at i:43095575 original size:18 final size:18
Alignment explanation
Indices: 43095549--43095587 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
43095539 AATCAAAATT
43095549 TAAAAATCAAAATTAAAC
1 TAAAAATCAAAATTAAAC
* *
43095567 TAAAGATCAAATTTAAAC
1 TAAAAATCAAAATTAAAC
43095585 TAA
1 TAA
43095588 TTACAAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.62, C:0.10, G:0.03, T:0.26
Consensus pattern (18 bp):
TAAAAATCAAAATTAAAC
Found at i:43095606 original size:17 final size:18
Alignment explanation
Indices: 43095575--43095612 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
43095565 ACTAAAGATC
43095575 AAATTTAAACTAATTACA
1 AAATTTAAACTAATTACA
* *
43095593 AAATTTTAAC-AATTTCA
1 AAATTTAAACTAATTACA
43095610 AAA
1 AAA
43095613 ATAATTTGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (18 bp):
AAATTTAAACTAATTACA
Found at i:43095659 original size:29 final size:29
Alignment explanation
Indices: 43095621--43095683 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
43095611 AAATAATTTG
* * * *
43095621 ATCTTTATCTAATCAATTTCAAATCTTTA
1 ATCTTTATCTAACCAAGTTCAAATATTCA
*
43095650 ATCTTTATCTAGCCAAGTTCAAATATTCA
1 ATCTTTATCTAACCAAGTTCAAATATTCA
43095679 ATCTT
1 ATCTT
43095684 GCAATTTTGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.33, C:0.19, G:0.03, T:0.44
Consensus pattern (29 bp):
ATCTTTATCTAACCAAGTTCAAATATTCA
Found at i:43098917 original size:18 final size:17
Alignment explanation
Indices: 43098890--43098925 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
43098880 AAGATGGGTG
*
43098890 AAGAAGAAGAAGAGGGAA
1 AAGAAAAAGAA-AGGGAA
43098908 AAGAAAAAGAAAGGGAA
1 AAGAAAAAGAAAGGGAA
43098925 A
1 A
43098926 GGTGTATGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (17 bp):
AAGAAAAAGAAAGGGAA
Found at i:43101093 original size:40 final size:40
Alignment explanation
Indices: 43101048--43101232 Score: 180
Period size: 40 Copynumber: 4.6 Consensus size: 40
43101038 TACACATTCA
* *
43101048 AATGCCTTCGGGACATAGCCCGG-TTACAGTAACTCGCACG
1 AATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCACG
* * *
43101088 AATGCCTTCGGGACTTAACCCGGATTTAGTAGCTCGCTCG
1 AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACG
* *
43101128 AAAGCCTTC-GGATCTTAGTCCGGATTTAGTAACTCGCACG
1 AATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCGCACG
* * ** * *
43101168 TATGCCGTC-GGATCTTATTCCGGATTTAGTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCACG
*
43101208 AAAGCCTTCGGGACTTAGCCCGGAT
1 AATGCCTTCGGGACTTAGCCCGGAT
43101233 ATCATTCGAA
Statistics
Matches: 120, Mismatches: 21, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
39 3 0.03
40 107 0.89
41 10 0.08
ACGTcount: A:0.23, C:0.27, G:0.24, T:0.26
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACG
Found at i:43101212 original size:80 final size:80
Alignment explanation
Indices: 43101051--43101232 Score: 203
Period size: 80 Copynumber: 2.3 Consensus size: 80
43101041 ACATTCAAAT
* * *
43101051 GCCTTCGGGACATAGCCCGG-TTACAGTAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTT
1 GCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCACGAATGCCGTCGGGACTTAACCCGGATTT
* *
43101115 AGTAGCTCGCTCGAAA
65 AGTAGCTAGCACGAAA
* * **
43101131 GCCTTC-GGATCTTAGTCCGGATTTAGTAACTCGCACGTATGCCGTC-GGATCTTATTCCGGATT
1 GCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCGCACGAATGCCGTCGGGA-CTTAACCCGGATT
43101194 TAGTCA-CTTAGCAC-AAA
64 TAGT-AGC-TAGCACGAAA
43101211 GCCTTCGGGACTTAGCCCGGAT
1 GCCTTCGGGACTTAGCCCGGAT
43101233 ATCATTCGAA
Statistics
Matches: 86, Mismatches: 10, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
79 6 0.07
80 70 0.81
81 10 0.12
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.26
Consensus pattern (80 bp):
GCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACGAATGCCGTCGGGACTTAACCCGGATTTA
GTAGCTAGCACGAAA
Found at i:43109061 original size:40 final size:40
Alignment explanation
Indices: 43109016--43109200 Score: 180
Period size: 40 Copynumber: 4.6 Consensus size: 40
43109006 TACACATTCA
* *
43109016 AATGCCTTCGGGACATAGCCCGG-TTACAGTAACTCGCACG
1 AATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCACG
* * *
43109056 AATGCCTTCGGGACTTAACCCGGATTTAGTAGCTCGCTCG
1 AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACG
* *
43109096 AAAGCCTTC-GGATCTTAGTCCGGATTTAGTAACTCGCACG
1 AATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCGCACG
* * ** * *
43109136 TATGCCGTC-GGATCTTATTCCGGATTTAGTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCACG
*
43109176 AAAGCCTTCGGGACTTAGCCCGGAT
1 AATGCCTTCGGGACTTAGCCCGGAT
43109201 ATCATTCGAA
Statistics
Matches: 120, Mismatches: 21, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
39 3 0.03
40 107 0.89
41 10 0.08
ACGTcount: A:0.23, C:0.27, G:0.24, T:0.26
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACG
Found at i:43109180 original size:80 final size:80
Alignment explanation
Indices: 43109019--43109200 Score: 203
Period size: 80 Copynumber: 2.3 Consensus size: 80
43109009 ACATTCAAAT
* * *
43109019 GCCTTCGGGACATAGCCCGG-TTACAGTAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTT
1 GCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCACGAATGCCGTCGGGACTTAACCCGGATTT
* *
43109083 AGTAGCTCGCTCGAAA
65 AGTAGCTAGCACGAAA
* * **
43109099 GCCTTC-GGATCTTAGTCCGGATTTAGTAACTCGCACGTATGCCGTC-GGATCTTATTCCGGATT
1 GCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCGCACGAATGCCGTCGGGA-CTTAACCCGGATT
43109162 TAGTCA-CTTAGCAC-AAA
64 TAGT-AGC-TAGCACGAAA
43109179 GCCTTCGGGACTTAGCCCGGAT
1 GCCTTCGGGACTTAGCCCGGAT
43109201 ATCATTCGAA
Statistics
Matches: 86, Mismatches: 10, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
79 6 0.07
80 70 0.81
81 10 0.12
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.26
Consensus pattern (80 bp):
GCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACGAATGCCGTCGGGACTTAACCCGGATTTA
GTAGCTAGCACGAAA
Found at i:43112871 original size:38 final size:38
Alignment explanation
Indices: 43112815--43112892 Score: 147
Period size: 38 Copynumber: 2.1 Consensus size: 38
43112805 TGGCTTTCTT
*
43112815 TATGTGAATATTACATATTTTGCAGGATATAGAAAACA
1 TATGCGAATATTACATATTTTGCAGGATATAGAAAACA
43112853 TATGCGAATATTACATATTTTGCAGGATATAGAAAACA
1 TATGCGAATATTACATATTTTGCAGGATATAGAAAACA
43112891 TA
1 TA
43112893 CATTGGTCGT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.33
Consensus pattern (38 bp):
TATGCGAATATTACATATTTTGCAGGATATAGAAAACA
Found at i:43121319 original size:17 final size:19
Alignment explanation
Indices: 43121297--43121334 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
43121287 AAGGGAGAAT
43121297 AAAG-AAATG-GAAAAAAA
1 AAAGAAAATGAGAAAAAAA
43121314 AAAGAAAATGATGAAAAAAA
1 AAAGAAAATGA-GAAAAAAA
43121334 A
1 A
43121335 TGTGTGTGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.22
18 5 0.28
20 9 0.50
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (19 bp):
AAAGAAAATGAGAAAAAAA
Found at i:43122675 original size:29 final size:29
Alignment explanation
Indices: 43122643--43122745 Score: 118
Period size: 29 Copynumber: 3.6 Consensus size: 29
43122633 GTGACGAGAT
* *
43122643 TGGCACTGAGTGTGCGAGCTTGAAATGTA
1 TGGCACTAAGTGTGCGAGCTTGAAATATA
* * *
43122672 TGGCACTAAGTGTGCGAGTTTGGACTATA
1 TGGCACTAAGTGTGCGAGCTTGAAATATA
* * *
43122701 TGGCACTATGTGTGCGGGCTT-AAATCACA
1 TGGCACTAAGTGTGCGAGCTTGAAAT-ATA
43122730 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
43122746 TGATCGAGTA
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
28 2 0.03
29 59 0.97
ACGTcount: A:0.23, C:0.17, G:0.32, T:0.28
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGCTTGAAATATA
Found at i:43128224 original size:17 final size:19
Alignment explanation
Indices: 43128202--43128239 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
43128192 AAGGGAGAAT
43128202 AAAG-AAATG-GAAAAAAA
1 AAAGAAAATGAGAAAAAAA
43128219 AAAGAAAATGATGAAAAAAA
1 AAAGAAAATGA-GAAAAAAA
43128239 A
1 A
43128240 TGTGTGTGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.22
18 5 0.28
20 9 0.50
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (19 bp):
AAAGAAAATGAGAAAAAAA
Found at i:43129580 original size:29 final size:29
Alignment explanation
Indices: 43129548--43129650 Score: 118
Period size: 29 Copynumber: 3.6 Consensus size: 29
43129538 GTGACGAGAT
* *
43129548 TGGCACTGAGTGTGCGAGCTTGAAATGTA
1 TGGCACTAAGTGTGCGAGCTTGAAATATA
* * *
43129577 TGGCACTAAGTGTGCGAGTTTGGACTATA
1 TGGCACTAAGTGTGCGAGCTTGAAATATA
* * *
43129606 TGGCACTATGTGTGCGGGCTT-AAATCACA
1 TGGCACTAAGTGTGCGAGCTTGAAAT-ATA
43129635 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
43129651 TGATCGAGTA
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
28 2 0.03
29 59 0.97
ACGTcount: A:0.23, C:0.17, G:0.32, T:0.28
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGCTTGAAATATA
Found at i:43135772 original size:68 final size:68
Alignment explanation
Indices: 43135622--43135779 Score: 169
Period size: 68 Copynumber: 2.3 Consensus size: 68
43135612 CTAGCCAATT
* * *
43135622 TATCTCGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACACATGCGACCTAGCTACA
1 TATCTCGTAGCTCTCTTGTCTACATGGTGTACATCAC-TCGAATCACACATGCGACCTAGCTACA
**
43135687 TTTA
65 CATA
* * *
43135691 TCTCTCCCGTAGCTCTCTTGTCTACATGG-GATACATC-C-CGTATCACACATGTGACCTAGCTA
1 TATCT--CGTAGCTCTCTTGTCTACATGGTG-TACATCACTCGAATCACACATGCGACCTAGCTA
43135753 CTACATA
63 C-ACATA
43135760 GTATCTCGTAGCTCTCTTGT
1 -TATCTCGTAGCTCTCTTGT
43135780 ACACATGATG
Statistics
Matches: 75, Mismatches: 9, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
68 36 0.48
69 7 0.09
70 6 0.08
71 26 0.35
ACGTcount: A:0.21, C:0.29, G:0.16, T:0.34
Consensus pattern (68 bp):
TATCTCGTAGCTCTCTTGTCTACATGGTGTACATCACTCGAATCACACATGCGACCTAGCTACAC
ATA
Found at i:43142954 original size:68 final size:66
Alignment explanation
Indices: 43142809--43142968 Score: 182
Period size: 68 Copynumber: 2.4 Consensus size: 66
43142799 ACTATTTTCG
* * *
43142809 GAATCACACATGGTGTCCTAGCTACATTTATCTTGTAGCTCTCTTGTCTACATGGTGTCCTTCAC
1 GAATCACACAT-GTGACCTAGCTACATTTATCTTGTAGCTCTCTTGTCTACATGGTGTACATCAC
*
43142874 TTG
65 -TC
*
43142877 GAATCACACATGCGACCTAGCTACATTTATCTCTCCCGTAGCTCTCTTGTCTACATGG-GATACA
1 GAATCACACATGTGACCTAGCTACATTTATCT-T---GTAGCTCTCTTGTCTACATGGTG-TACA
43142941 TC-C-C
61 TCACTC
*
43142945 GTATCACACATGTGACCTAGCTAC
1 GAATCACACATGTGACCTAGCTAC
43142969 TGCATAGTAT
Statistics
Matches: 80, Mismatches: 7, Indels: 10
0.82 0.07 0.10
Matches are distributed among these distances:
67 19 0.24
68 34 0.43
70 2 0.03
71 25 0.31
ACGTcount: A:0.23, C:0.29, G:0.16, T:0.33
Consensus pattern (66 bp):
GAATCACACATGTGACCTAGCTACATTTATCTTGTAGCTCTCTTGTCTACATGGTGTACATCACT
C
Found at i:43146122 original size:12 final size:12
Alignment explanation
Indices: 43146105--43146130 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
43146095 TCCCCAACAT
43146105 ATTCCTTTTGAA
1 ATTCCTTTTGAA
43146117 ATTCCTTTTGAA
1 ATTCCTTTTGAA
43146129 AT
1 AT
43146131 AGGTCACATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.15, G:0.08, T:0.50
Consensus pattern (12 bp):
ATTCCTTTTGAA
Found at i:43147855 original size:41 final size:39
Alignment explanation
Indices: 43147749--43147856 Score: 103
Period size: 38 Copynumber: 2.8 Consensus size: 39
43147739 CGGATAGTTT
* * **
43147749 GAAGCAATAGTTGACACCCAGTGTTTCATCGGTCTAGCC
1 GAAGTAATAGTTGACACCCAGTGTCTCATCAATCTAGCC
** ** *
43147788 GAAGTAA-AG-TGGTACCCAGTACCTCATCAAATCTATCC
1 GAAGTAATAGTTGACACCCAGTGTCTCATC-AATCTAGCC
43147826 GAAGTAATAGTATGACACCCAGTGTCTCATC
1 GAAGTAATAGT-TGACACCCAGTGTCTCATC
43147857 GACTCGAGGT
Statistics
Matches: 52, Mismatches: 13, Indels: 6
0.73 0.18 0.08
Matches are distributed among these distances:
37 14 0.27
38 15 0.29
39 8 0.15
41 15 0.29
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (39 bp):
GAAGTAATAGTTGACACCCAGTGTCTCATCAATCTAGCC
Found at i:43148909 original size:12 final size:12
Alignment explanation
Indices: 43148894--43148924 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
43148884 TTCTCTTTTA
43148894 TTTTTCTTTCCC
1 TTTTTCTTTCCC
*
43148906 TTTTTCTTTCTC
1 TTTTTCTTTCCC
43148918 TTTTTCT
1 TTTTTCT
43148925 CCTTTCTTCC
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:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTTCTTTCCC
Found at i:43149750 original size:19 final size:19
Alignment explanation
Indices: 43149726--43149764 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
43149716 TTAAACACAC
43149726 TACTAGACTTATAATTATT
1 TACTAGACTTATAATTATT
43149745 TACTAGACTTATAATTATT
1 TACTAGACTTATAATTATT
43149764 T
1 T
43149765 CTAATAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.36, C:0.10, G:0.05, T:0.49
Consensus pattern (19 bp):
TACTAGACTTATAATTATT
Found at i:43151617 original size:31 final size:31
Alignment explanation
Indices: 43151579--43151644 Score: 123
Period size: 31 Copynumber: 2.1 Consensus size: 31
43151569 TATACGAGTA
*
43151579 AATTTAACTCAATTTAATAAAATTCACAGTT
1 AATTTAACTCAATTTAATAAAATTCACAGTC
43151610 AATTTAACTCAATTTAATAAAATTCACAGTC
1 AATTTAACTCAATTTAATAAAATTCACAGTC
43151641 AATT
1 AATT
43151645 CCATCCAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.45, C:0.14, G:0.03, T:0.38
Consensus pattern (31 bp):
AATTTAACTCAATTTAATAAAATTCACAGTC
Found at i:43154730 original size:55 final size:52
Alignment explanation
Indices: 43154654--43154881 Score: 216
Period size: 55 Copynumber: 4.3 Consensus size: 52
43154644 AGGATACCGG
* * * *
43154654 GTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAATCAT
1 GTAAGACCATGTCAAGACATGGC-ATTGGTAA-GTTTCTAAGGCAAGG-TACCAT
* * *
43154709 GTAAGACCATGTCAAGACATGGCATTGATAAGTTACTATAAGGCAAAGGTCCCAT
1 GTAAGACCATGTCAAGACATGGCATTGGTAAGTT--TCTAAGGC-AAGGTACCAT
* *
43154764 GTAAGACCATG-CGAAGGCATGGCATTGGTGAG-TTCATAAGGCAAGGCTACCAT
1 GTAAGACCATGTC-AAGACATGGCATTGGTAAGTTTC-TAAGGCAAGG-TACCAT
* *
43154817 GTAAGACCATGTCAAGACATGGCAATGGTAAGTTTC-AA---AAGGATACCAC
1 GTAAGACCATGTCAAGACATGGCATTGGTAAGTTTCTAAGGCAAGG-TACCAT
*
43154866 GTAAGACCATGACAAG
1 GTAAGACCATGTCAAG
43154882 TCATAGAAAT
Statistics
Matches: 147, Mismatches: 18, Indels: 22
0.79 0.10 0.12
Matches are distributed among these distances:
49 24 0.16
52 7 0.05
53 41 0.28
54 13 0.09
55 58 0.39
56 4 0.03
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.21
Consensus pattern (52 bp):
GTAAGACCATGTCAAGACATGGCATTGGTAAGTTTCTAAGGCAAGGTACCAT
Found at i:43154826 original size:53 final size:52
Alignment explanation
Indices: 43154654--43154850 Score: 218
Period size: 55 Copynumber: 3.7 Consensus size: 52
43154644 AGGATACCGG
* * * *
43154654 GTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTC-TAAGGCAAGGAAATCAT
1 GTAAGACCATGTCAAGACATGGC-ATTGGTAA-G-TTCATAAGGCAAGG-TACCAT
* *
43154709 GTAAGACCATGTCAAGACATGGCATTGATAAGTTACTATAAGGCAAAGGTCCCAT
1 GTAAGACCATGTCAAGACATGGCATTGGTAAGTT-C-ATAAGGC-AAGGTACCAT
* *
43154764 GTAAGACCATG-CGAAGGCATGGCATTGGTGAGTTCATAAGGCAAGGCTACCAT
1 GTAAGACCATGTC-AAGACATGGCATTGGTAAGTTCATAAGGCAAGG-TACCAT
*
43154817 GTAAGACCATGTCAAGACATGGCAATGGTAAGTT
1 GTAAGACCATGTCAAGACATGGCATTGGTAAGTT
43154851 TCAAAAGGAT
Statistics
Matches: 122, Mismatches: 13, Indels: 16
0.81 0.09 0.11
Matches are distributed among these distances:
52 6 0.05
53 43 0.35
54 10 0.08
55 59 0.48
56 4 0.03
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.22
Consensus pattern (52 bp):
GTAAGACCATGTCAAGACATGGCATTGGTAAGTTCATAAGGCAAGGTACCAT
Found at i:43154849 original size:108 final size:110
Alignment explanation
Indices: 43154654--43154850 Score: 301
Period size: 108 Copynumber: 1.8 Consensus size: 110
43154644 AGGATACCGG
*
43154654 GTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAATCATGTAAGACCAT
1 GTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGACCAT
*
43154719 GTCAAGACATGGCATTGATAAGTTACTATAAGGCAAAGGTCCCAT
66 GTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTCCCAT
* * **
43154764 GTAAGACCATGCGAAGGCATGGC-ATTGGTGA-G-TTCATAAGGCAAGGCTACCATGTAAGACCA
1 GTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTC-TAAGGCAAGGAAACCATGTAAGACCA
*
43154826 TGTCAAGACATGGCAATGGTAAGTT
65 TGTCAAGACATGGCAATGATAAGTT
43154851 TCAAAAGGAT
Statistics
Matches: 79, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
107 3 0.04
108 47 0.59
109 7 0.09
110 22 0.28
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.22
Consensus pattern (110 bp):
GTAAGACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGACCAT
GTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTCCCAT
Found at i:43155110 original size:16 final size:16
Alignment explanation
Indices: 43155089--43155119 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
43155079 ATAAATTTGA
43155089 TTAAGTAAGTAAGTAT
1 TTAAGTAAGTAAGTAT
*
43155105 TTAAGTAAGTGAGTA
1 TTAAGTAAGTAAGTA
43155120 AGTGAAGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (16 bp):
TTAAGTAAGTAAGTAT
Found at i:43157032 original size:25 final size:21
Alignment explanation
Indices: 43157006--43157047 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
43156996 TTCGTGACAA
43157006 GTAAGTTTTACATATTTATAT
1 GTAAGTTTTACATATTTATAT
43157027 GTAAGTTTTACATATTTATAT
1 GTAAGTTTTACATATTTATAT
43157048 TTAATCGTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.05, G:0.10, T:0.52
Consensus pattern (21 bp):
GTAAGTTTTACATATTTATAT
Found at i:43162383 original size:46 final size:46
Alignment explanation
Indices: 43162318--43162605 Score: 301
Period size: 46 Copynumber: 6.0 Consensus size: 46
43162308 TTATCTTTGA
* * * * * *
43162318 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGT
1 CATGCTGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATAT
* *** *
43162364 CATGTTGCCATGGTATCTTTCAACCATGGTCTTGTTCATTTCATGT
1 CATGCTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
*
43162410 CACGCTGCCATGGTATCTTT-AGACCATGGTCTTACACATTTCATAT
1 CATGCTGCCATGGTATCTTTCA-ACCATGGTCTTACACATTTCATAT
*
43162456 CAAGCTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGCTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
* *
43162502 CAGGTTGCCATGGTATCTTTCAACCATGGCCTTACATGGTCTTACACATTTCATAT
1 CATGCTGCCATGGTATCTTTC-A--A----C---CATGGTCTTACACATTTCATAT
* *
43162558 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGCTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
43162604 CA
1 CA
43162606 GAGAGTACAT
Statistics
Matches: 214, Mismatches: 15, Indels: 26
0.84 0.06 0.10
Matches are distributed among these distances:
45 5 0.02
46 159 0.74
47 2 0.01
49 2 0.01
53 2 0.01
55 1 0.00
56 43 0.20
ACGTcount: A:0.23, C:0.24, G:0.15, T:0.38
Consensus pattern (46 bp):
CATGCTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
Found at i:43162515 original size:30 final size:30
Alignment explanation
Indices: 43162479--43162571 Score: 83
Period size: 30 Copynumber: 3.2 Consensus size: 30
43162469 TATCTTTCAA
43162479 CCATGGTCTTACACATTTCATATCAGGTTG
1 CCATGGTCTTACACATTTCATATCAGGTTG
* *
43162509 CCATGG---TA-TC-TTTCA-ACCATGGCCTT-
1 CCATGGTCTTACACATTTCATATCA-GG--TTG
*
43162535 ACATGGTCTTACACATTTCATATCAGGTTG
1 CCATGGTCTTACACATTTCATATCAGGTTG
43162565 CCATGGT
1 CCATGGT
43162572 ATCTTTCAAC
Statistics
Matches: 47, Mismatches: 6, Indels: 20
0.64 0.08 0.27
Matches are distributed among these distances:
24 3 0.06
25 7 0.15
26 6 0.13
27 4 0.09
29 4 0.09
30 13 0.28
31 7 0.15
32 3 0.06
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.35
Consensus pattern (30 bp):
CCATGGTCTTACACATTTCATATCAGGTTG
Found at i:43162566 original size:56 final size:56
Alignment explanation
Indices: 43162480--43162593 Score: 219
Period size: 56 Copynumber: 2.0 Consensus size: 56
43162470 ATCTTTCAAC
43162480 CATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGCCTTA
1 CATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGCCTTA
*
43162536 CATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTA
1 CATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGCCTTA
43162592 CA
1 CA
43162594 CATTTCATAT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.24, C:0.25, G:0.16, T:0.36
Consensus pattern (56 bp):
CATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGCCTTA
Found at i:43164798 original size:30 final size:33
Alignment explanation
Indices: 43164758--43164821 Score: 82
Period size: 31 Copynumber: 2.0 Consensus size: 33
43164748 TGTCATTATT
43164758 TAATATATTT-ATCATATAAA-ATCT-TATAATA
1 TAATATATTTAATCA-ATAAATATCTATATAATA
*
43164789 TAAT-TATTTAATTAATAAATATCTATATAATA
1 TAATATATTTAATCAATAAATATCTATATAATA
43164821 T
1 T
43164822 CTAATACATG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
30 10 0.34
31 11 0.38
32 8 0.28
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.47
Consensus pattern (33 bp):
TAATATATTTAATCAATAAATATCTATATAATA
Found at i:43174130 original size:20 final size:20
Alignment explanation
Indices: 43174102--43174139 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
43174092 AATCGATAAA
* *
43174102 TTAGGAAATTTTTGAAAAAC
1 TTAGAAAATTTTTCAAAAAC
43174122 TTAGAAAATTTTTCAAAA
1 TTAGAAAATTTTTCAAAA
43174140 TACAGGGGAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.05, G:0.11, T:0.37
Consensus pattern (20 bp):
TTAGAAAATTTTTCAAAAAC
Done.