Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3769
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: 50668
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31
Found at i:462 original size:39 final size:40
Alignment explanation
Indices: 326--492 Score: 191
Period size: 40 Copynumber: 4.2 Consensus size: 40
316 CGGATGATAA
*
326 CCGGACTAAGATCCCGAAGGCATTTGTGCGAGTTGCTATAT
1 CCGGGCTAAGA-CCCGAAGGCATTTGTGCGAGTTGCTATAT
* * * * * *
367 CCGGTCTATGTCCCGAAGGCATTTATTGCTAG-TGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTT-GTGCGAGTTG-CTATAT
*
408 CCGCGCTAAGA-CCGAAGGCATTTGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
*
447 -CGGGCTAAGACCCGAAGGCATTTGTG-GAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
485 CC-GGCTAA
1 CCGGGCTAA
493 TTTCCGAAGT
Statistics
Matches: 106, Mismatches: 15, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
38 26 0.25
39 26 0.25
40 29 0.27
41 25 0.24
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
Found at i:6903 original size:46 final size:47
Alignment explanation
Indices: 6725--7238 Score: 674
Period size: 47 Copynumber: 11.1 Consensus size: 47
6715 GAAATGATAG
* * *
6725 TAAGGCCAAATGGTCGATGTGATGAATGTGAAAGTG--TATGTGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
6770 TAAGGCCATAAT-GCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCC-TAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
6817 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
* * *
6864 TAAGGCCAAAT-GGCGATATGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
6910 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
*
6957 TAAGGCCTAAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCT-AATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
7005 T-A-GCCTAATAGCCGATGTGATG-ATGTGAAAGTGTATATAG-GTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATAT-GTGTGA
* * *
7049 TAAGGCCTAATAGCCGATGTGATTGAATGTGAAAGGGTATATATGTAA
1 TAAGGCCTAATAGCCGATGTGA-TGAATGTGAAAGTGTATATGTGTGA
* *
7097 TAAGGCCTAA-GGCCGATGTGATGAATGTGAAAGTGTA-ATATGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
* *
7142 TAAGGCCTAATGGCCGATGTG-TGAA-GTGGAAAGTGTATATATGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGT-GAAAGTGTATATGTGTGA
* * * * * * * * * **
7188 CAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGCATAAATGTGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
7235 TAAG
1 TAAG
7239 TCCCGAGGGC
Statistics
Matches: 425, Mismatches: 27, Indels: 32
0.88 0.06 0.07
Matches are distributed among these distances:
44 23 0.05
45 77 0.18
46 120 0.28
47 136 0.32
48 69 0.16
ACGTcount: A:0.33, C:0.09, G:0.31, T:0.28
Consensus pattern (47 bp):
TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
Found at i:6913 original size:93 final size:93
Alignment explanation
Indices: 6725--7238 Score: 670
Period size: 93 Copynumber: 5.5 Consensus size: 93
6715 GAAATGATAG
* * *
6725 TAAGGCCAAATGGTCGATGTGATGAATGTGAAAGTG--TATGTGTGATAAGGCCATAATGCCGAT
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCA-AATGCCGAT
*
6788 GTGATGAATGTGAAAGTGTATATGTGTGA
65 GTGATGAATGTGAAAGTGTATATATGTGA
* *
6817 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCAAATGGCGATA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCAAATGCCGATG
*
6882 TGATGAATGTGAAAGTGTATATGTGTGA
66 TGATGAATGTGAAAGTGTATATATGTGA
6910 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAAATAGCCGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCC-AAAT-GCCGA
6975 TGTGATGAATGTGAAAGTGTATATATGTGA
64 TGTGATGAATGTGAAAGTGTATATATGTGA
*
7005 T-A-GCCTAATAGCCGATGTGATG-ATGTGAAAGTGTATATAG-GTGATAAGGCCTAATAGCCGA
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATAT-GTGTGATAAGGCCAAAT-GCCGA
* *
7066 TGTGATTGAATGTGAAAGGGTATATATGTAA
64 TGTGA-TGAATGTGAAAGTGTATATATGTGA
* * *
7097 TAAGGCCTAA-GGCCGATGTGATGAATGTGAAAGTGTA-ATATGTGATAAGGCCTAATGGCCGAT
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCAAAT-GCCGAT
7160 GTG-TGAA-GTGGAAAGTGTATATATGTGA
65 GTGATGAATGT-GAAAGTGTATATATGTGA
* * * * * * * * * **
7188 CAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGCATAAATGTGATAAG
1 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGATAAG
7239 TCCCGAGGGC
Statistics
Matches: 384, Mismatches: 25, Indels: 25
0.88 0.06 0.06
Matches are distributed among these distances:
90 2 0.01
91 40 0.10
92 107 0.28
93 161 0.42
94 41 0.11
95 33 0.09
ACGTcount: A:0.33, C:0.09, G:0.31, T:0.28
Consensus pattern (93 bp):
TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCAAATGCCGATG
TGATGAATGTGAAAGTGTATATATGTGA
Found at i:7210 original size:139 final size:141
Alignment explanation
Indices: 6725--7238 Score: 674
Period size: 139 Copynumber: 3.7 Consensus size: 141
6715 GAAATGATAG
* * *
6725 TAAGGCCAAATGGTCGATGTGATGAA-TGTGAAAGTG--TATGTGTGATAAGGCCATAAT-GCCG
1 TAAGGCCTAATGGCCGATGTGATGAAGTG-GAAAGTGTATATATGTGATAAGGCC-TAATAGCCG
6786 ATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAG
64 ATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAG
*
6851 TGTATATGTGTGA
129 TGTATATATGTGA
* * *
6864 TAAGGCCAAATGG-CGATATGATGAA-TGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGA
1 TAAGGCCTAATGGCCGATGTGATGAAGTG-GAAAGTGTATATATGTGATAAGGCCTAATAGCCGA
6927 TGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAAATAGCCGATGTGATGAATGTGAAAG
65 TGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCT-AATAGCCGATGTGATGAATGTGAAAG
6992 TGTATATATGTGA
129 TGTATATATGTGA
* * *
7005 T-A-GCCTAATAGCCGATGTGATGATGT-GAAAGTGTATATAGGTGATAAGGCCTAATAGCCGAT
1 TAAGGCCTAATGGCCGATGTGATGAAGTGGAAAGTGTATATATGTGATAAGGCCTAATAGCCGAT
* * * *
7067 GTGATTGAATGTGAAAGGGTATATATGTAATAAGGCCTAA-GGCCGATGTGATGAATGTGAAAGT
66 GTGA-TGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGT
7131 GTA-ATATGTGA
130 GTATATATGTGA
* * * * * * *
7142 TAAGGCCTAATGGCCGATGTG-TGAAGTGGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAAC
1 TAAGGCCTAATGGCCGATGTGATGAAGTGGAAAGTGTATATATGTGATAAGGCCTAATAGCCGAT
* * **
7206 GTGATGGATGTGAAAGTGCATAAATGTGATAAG
66 GTGATGAATGTGAAAGTGTATATGTGTGATAAG
7239 TCCCGAGGGC
Statistics
Matches: 338, Mismatches: 27, Indels: 21
0.88 0.07 0.05
Matches are distributed among these distances:
137 9 0.03
138 77 0.23
139 112 0.33
140 100 0.30
141 40 0.12
ACGTcount: A:0.33, C:0.09, G:0.31, T:0.28
Consensus pattern (141 bp):
TAAGGCCTAATGGCCGATGTGATGAAGTGGAAAGTGTATATATGTGATAAGGCCTAATAGCCGAT
GTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTG
TATATATGTGA
Found at i:9310 original size:43 final size:43
Alignment explanation
Indices: 9262--9364 Score: 206
Period size: 43 Copynumber: 2.4 Consensus size: 43
9252 GTGGTTTTCA
9262 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
9305 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
9348 GCACTAAGTGTGCGGGC
1 GCACTAAGTGTGCGGGC
9365 TTGAAATGCA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 60 1.00
ACGTcount: A:0.22, C:0.16, G:0.36, T:0.26
Consensus pattern (43 bp):
GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
Found at i:9381 original size:29 final size:30
Alignment explanation
Indices: 9346--9419 Score: 98
Period size: 29 Copynumber: 2.5 Consensus size: 30
9336 GTTGTGAGAT
* *
9346 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAGCTTGAAAGTACA
* *
9375 TGGCACTAAGTGT-CGAGTTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGCTTGAAAGTACA
9404 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
9420 TGGTTGATTA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
28 8 0.21
29 29 0.74
30 2 0.05
ACGTcount: A:0.26, C:0.16, G:0.31, T:0.27
Consensus pattern (30 bp):
TGGCACTAAGTGTGCGAGCTTGAAAGTACA
Found at i:13304 original size:44 final size:47
Alignment explanation
Indices: 13198--13642 Score: 495
Period size: 44 Copynumber: 9.7 Consensus size: 47
13188 AGCAAATGGT
*
13198 GATGTGATGAA--TGAAAGTG--TATGTGTGATAAGG-C-AAT-GGC
1 GATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCC
*
13238 GATGTGATG-ATGTG-AAGTGTATATGTGTGATAAGGCCTCATAGCC
1 GATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCC
* *
13283 GA-GTGATG-ATGTGAAAG-GTATATGTGTGATAAGG-CAAATGGCC
1 GATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCC
* *
13326 GATATGCTGAATGT-AACAGTGTATATGTGTGATAA-GCGCTAATAGCCC
1 GATGTGATGAATGTGAA-AGTGTATATGTGTGATAAGGC-CTAATAG-CC
13374 GATGTGAATGAATGTGATAAAGTGTATATGTGTGATCAAGGCCTAATAGCC
1 GATGTG-ATGAATGTG--AAAGTGTATATGTGTGAT-AAGGCCTAATAGCC
* *
13425 G-TGTGATGAATGTGAAAATGTAATCATATGTGATAATGGCCTAATAGCC
1 GATGTGATGAATGTGAAAGTGT-AT-ATGTGTGATAA-GGCCTAATAGCC
13474 GATGTGATGAATGTGAAAGTAGTATATAG-GTGATAAGGCCTAATAGCC
1 GATGTGATGAATGTGAAAGT-GTATAT-GTGTGATAAGGCCTAATAGCC
* * *
13522 GAT-TGATGAATGTGAAAG-GGATAT-TAGTAATAAGGCCTAATGGCC
1 GATGTGATGAATGTGAAAGTGTATATGT-GTGATAAGGCCTAATAGCC
*
13567 GATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAAT-G-C
1 GATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCC
*
13612 GATGTG-TGAATGTGAAAGTGTATATATGTGA
1 GATGTGATGAATGTGAAAGTGTATATGTGTGA
13643 CAGGCGCGGA
Statistics
Matches: 353, Mismatches: 20, Indels: 60
0.82 0.05 0.14
Matches are distributed among these distances:
39 1 0.00
40 14 0.04
41 2 0.01
42 14 0.04
43 9 0.03
44 61 0.17
45 46 0.13
46 31 0.09
47 45 0.13
48 27 0.08
49 46 0.13
50 23 0.07
51 21 0.06
52 11 0.03
53 2 0.01
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (47 bp):
GATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCC
Found at i:13359 original size:90 final size:94
Alignment explanation
Indices: 13198--13642 Score: 495
Period size: 97 Copynumber: 4.8 Consensus size: 94
13188 AGCAAATGGT
*
13198 GATGTGATGAA--TGAAAGTG--TATGTGTGATAAGG-C-AAT-GGCGATGTGATG-ATGTG-AA
1 GATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAA
* *
13254 GTGTATATGTGTGATAAGGCCTCATAGCC
66 GTGTATATATGTGATAAGGCCTAATAGCC
* * * *
13283 GA-GTGATG-ATGTGAAAG-GTATATGTGTGATAAGG-CAAATGGCCGATATGCTGAATGT-AAC
1 GATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA-
*
13343 AGTGTATATGTGTGATAA-GCGCTAATAGCCC
65 AGTGTATATATGTGATAAGGC-CTAATAG-CC
13374 GATGTGAATGAATGTGATAAAGTGTATATGTGTGATCAAGGCCTAATAGCCG-TGTGATGAATGT
1 GATGTG-ATGAATGTG--AAAGTGTATATGTGTGAT-AAGGCCTAATAGCCGATGTGATGAATGT
*
13438 GAAAATGTAATCATATGTGATAATGGCCTAATAGCC
62 GAAAGTGT-AT-ATATGTGATAA-GGCCTAATAGCC
13474 GATGTGATGAATGTGAAAGTAGTATATAG-GTGATAAGGCCTAATAGCCGAT-TGATGAATGTGA
1 GATGTGATGAATGTGAAAGT-GTATAT-GTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGA
* * *
13537 AAG-GGATAT-TAGTAATAAGGCCTAATGGCC
64 AAGTGTATATAT-GTGATAAGGCCTAATAGCC
*
13567 GATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAAT-G-CGATGTG-TGAATGTGAAA
1 GATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAA
13629 GTGTATATATGTGA
66 GTGTATATATGTGA
13643 CAGGCGCGGA
Statistics
Matches: 311, Mismatches: 17, Indels: 58
0.81 0.04 0.15
Matches are distributed among these distances:
83 1 0.00
84 7 0.02
85 8 0.03
86 15 0.05
87 3 0.01
88 9 0.03
89 7 0.02
90 40 0.13
91 15 0.05
92 25 0.08
93 35 0.11
94 13 0.04
95 2 0.01
96 5 0.02
97 47 0.15
98 30 0.10
99 22 0.07
100 18 0.06
101 7 0.02
102 2 0.01
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (94 bp):
GATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAA
GTGTATATATGTGATAAGGCCTAATAGCC
Found at i:14475 original size:97 final size:93
Alignment explanation
Indices: 14340--14784 Score: 348
Period size: 95 Copynumber: 4.7 Consensus size: 93
14330 CCTGTCACAA
* *
14340 ATATAATACCACTTTCACGATTCA-CACA-C-GCCATTAGGCCTTTATCACATATAGCACCTTTC
1 ATATAGTA-CACTTTCAC-ATTCATCACATCGGCTATTAGGCC-TTATCACATATA-CA-CTTTC
*
14402 ACATTCCATCACATCGGCCATTTAGCCTTATTAC
61 ACATT-CATCACATCGGCCATTTAGGCTTATTAC
* *
14436 ATATA-TACCCTTTTCCCATTCATCACATCGGCTATTAGGCCTTATCACCTTATATTA-ACTTTT
1 ATATAGTACAC-TTTCACATTCATCACATCGGCTATTAGGCCTTATCA-C--ATA-TACAC-TTT
* *
14499 CACATTCATGCACATCGAG-C-TATAGGCTTATCAC
60 CACATTCAT-CACATCG-GCCATTTAGGCTTATTAC
14533 ATATAGTA-ACTTTCACATTCATCACATCGGCTATTTAGGGCCTTATTCACACATATACACTTTC
1 ATATAGTACACTTTCACATTCATCACATCGGCTA-TTA-GGCCTTA-T--CACATATACACTTTC
*
14597 ACATTCAT-ACAATCGGCTA-TTAGGCTTA-TAC
61 ACATTCATCAC-ATCGGCCATTTAGGCTTATTAC
* * * * *
14628 ACATATTACAC-TTCACATTCATCATATCGGCCATTTGGCC-TATCACACATATACACTTTCACA
1 ATATAGTACACTTTCACATTCATCACATCGGCTATTAGGCCTTAT--CACATATACACTTTCACA
* *
14691 TTCATCACATCGGCTA-TTAGGACCTTATCAC
64 TTCATCACATCGGCCATTTAGG--CTTATTAC
* * * *
14722 ACAT--TACA-TTTCACATTCATCAACATCAGGCCATTTGGCCCTTATCACAACATACACTTTCA
1 ATATAGTACACTTTCACATTCATC-ACATC-GGCTATTAGG-CCTTATCAC-ATATACACTTTCA
14784 C
62 C
14785 CCATTCTCAC
Statistics
Matches: 298, Mismatches: 19, Indels: 65
0.78 0.05 0.17
Matches are distributed among these distances:
91 39 0.13
92 20 0.07
93 12 0.04
94 28 0.09
95 57 0.19
96 51 0.17
97 49 0.16
98 32 0.11
99 5 0.02
100 3 0.01
101 2 0.01
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (93 bp):
ATATAGTACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATACACTTTCACATT
CATCACATCGGCCATTTAGGCTTATTAC
Found at i:14677 original size:46 final size:47
Alignment explanation
Indices: 14349--14784 Score: 415
Period size: 46 Copynumber: 9.2 Consensus size: 47
14339 AATATAATAC
*
14349 CACTTTCACGATTCA-CACA-C-GCCATTAGGCCTT-T-ATCACATATA
1 CACTTTCAC-ATTCATCACATCGGCTATTAGGCCTTATCA-CACATATA
* * *
14393 GCACCTTTCACATTCCATCACATCGGCCATTTA-GCCTTATTACATATATA
1 -CA-CTTTCACATT-CATCACATCGGCTA-TTAGGCCTTATCACACATATA
* *
14443 CCCTTTTCCCATTCATCACATCGGCTATTAGGCCTTATCAC-CTTATATTA
1 CAC-TTTCACATTCATCACATCGGCTATTAGGCCTTATCACAC--ATA-TA
*
14493 -ACTTTTCACATTCATGCACATCGAGCTA-TAGG-CTTATCACATATAGTA
1 CAC-TTTCACATTCAT-CACATCG-GCTATTAGGCCTTATCACACATA-TA
14541 -ACTTTCACATTCATCACATCGGCTATTTAGGGCCTTATTCACACATATA
1 CACTTTCACATTCATCACATCGGCTA-TTA-GGCCTTA-TCACACATATA
14590 CACTTTCACATTCAT-ACAATCGGCTATTAGG-CTTAT-ACACATATTA
1 CACTTTCACATTCATCAC-ATCGGCTATTAGGCCTTATCACACATA-TA
* * *
14636 CAC-TTCACATTCATCATATCGGCCATTTGGCC-TATCACACATATA
1 CACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACACATATA
14681 CACTTTCACATTCATCACATCGGCTATTAGGACCTTATCACACAT-TA
1 CACTTTCACATTCATCACATCGGCTATTAGG-CCTTATCACACATATA
* * *
14728 CA-TTTCACATTCATCAACATCAGGCCATTTGGCCCTTATCACA-ACATA
1 CACTTTCACATTCATC-ACATC-GGCTATTAGG-CCTTATCACACATATA
14776 CACTTTCAC
1 CACTTTCAC
14785 CCATTCTCAC
Statistics
Matches: 336, Mismatches: 21, Indels: 64
0.80 0.05 0.15
Matches are distributed among these distances:
45 46 0.14
46 68 0.20
47 37 0.11
48 67 0.20
49 59 0.18
50 54 0.16
51 5 0.01
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (47 bp):
CACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACACATATA
Found at i:14784 original size:141 final size:139
Alignment explanation
Indices: 14385--14784 Score: 397
Period size: 141 Copynumber: 2.8 Consensus size: 139
14375 AGGCCTTTAT
* * * *
14385 CACATATAGCACCTTTCACATTCCATCACATCGGCCATTTA-GCCTTATTACATATATACCCTTT
1 CACATATA-CA-CTTTCACATT-CATCACATCGGCTATTTAGGCCTTATCACACATATA--CATT
* *
14449 TCCCATTCATCACATCGGCTATTAGGCCTTATCACCTTATATTA-ACTTTTCACATTCATGCACA
61 TCACATTCATCACATCGGCTATTAGGCCTTATCA-C--A-AATACAC-TTTCACATTCATGCACA
* *
14513 TCGAGCTATAGGCTTATCA
121 TCGAGCCATAGGCCTATCA
*
14532 CATATAGTA-ACTTTCACATTCATCACATCGGCTATTTAGGGCCTTATTCACACATATACACTTT
1 CACATA-TACACTTTCACATTCATCACATCGGCTATTTA-GGCCTTA-TCACACATATACA-TTT
* *
14596 CACATTCAT-ACAATCGGCTATTAGG-CTTATACACATATTACAC-TTCACATTCAT-CATATCG
62 CACATTCATCAC-ATCGGCTATTAGGCCTTAT-CACA-AATACACTTTCACATTCATGCACATCG
*
14657 -GCCATTTGGCCTATCA
124 AGCCA-TAGGCCTATCA
14673 CACATATACACTTTCACATTCATCACATCGGCTA-TTAGGACCTTATCACACAT-TACATTTCAC
1 CACATATACACTTTCACATTCATCACATCGGCTATTTAGG-CCTTATCACACATATACATTTCAC
* *
14736 ATTCATCAACATCAGGCCATTTGGCCCTTATCACAACATACACTTTCAC
65 ATTCATC-ACATC-GGCTATTAGG-CCTTATCACAA-ATACACTTTCAC
14785 CCATTCTCAC
Statistics
Matches: 221, Mismatches: 14, Indels: 42
0.80 0.05 0.15
Matches are distributed among these distances:
137 12 0.05
138 7 0.03
139 21 0.10
140 22 0.10
141 55 0.25
142 11 0.05
143 6 0.03
144 19 0.09
145 19 0.09
146 33 0.15
147 14 0.06
148 2 0.01
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (139 bp):
CACATATACACTTTCACATTCATCACATCGGCTATTTAGGCCTTATCACACATATACATTTCACA
TTCATCACATCGGCTATTAGGCCTTATCACAAATACACTTTCACATTCATGCACATCGAGCCATA
GGCCTATCA
Found at i:18689 original size:29 final size:29
Alignment explanation
Indices: 18650--18728 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
18640 CTTAATAATC
*
18650 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
18680 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
18709 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
18729 ATCTCACAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 38 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:18771 original size:43 final size:43
Alignment explanation
Indices: 18710--18812 Score: 206
Period size: 43 Copynumber: 2.4 Consensus size: 43
18700 TGCATTTCAA
18710 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
18753 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
18796 GCCCGCACACTTAGTGC
1 GCCCGCACACTTAGTGC
18813 TGAAAACCAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 60 1.00
ACGTcount: A:0.26, C:0.36, G:0.16, T:0.22
Consensus pattern (43 bp):
GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
Found at i:20700 original size:37 final size:37
Alignment explanation
Indices: 20650--20728 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
20640 TTATTACGAA
* * *
20650 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
20687 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
20724 GTCTT
1 GTCTT
20729 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:20997 original size:47 final size:47
Alignment explanation
Indices: 20847--21361 Score: 754
Period size: 47 Copynumber: 11.1 Consensus size: 47
20837 CCCTTCGGGA
* * * * * * *
20847 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
20894 CCTGTCACATATATACACTTTCACATTCA-CACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
20940 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
20987 CTTATTACATATATACCCTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
21034 CTTATCACCTATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
21081 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
21128 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
21175 CTTATCACACATATACACTTTCACATTCAT--CA-CGGCCATTTGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
21219 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
21266 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTTGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
21313 CTTATCAC--ACATACACTTTCACATTCATCACATCGACCATTTGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
21358 CTTA
1 CTTA
21362 CTATCATTTC
Statistics
Matches: 437, Mismatches: 27, Indels: 10
0.92 0.06 0.02
Matches are distributed among these distances:
44 40 0.09
45 41 0.09
46 42 0.10
47 314 0.72
ACGTcount: A:0.28, C:0.31, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:21343 original size:23 final size:23
Alignment explanation
Indices: 21273--21344 Score: 58
Period size: 23 Copynumber: 3.2 Consensus size: 23
21263 GGCCTTATCA
*
21273 CACATATACACTTTCACATTCAT
1 CACACATACACTTTCACATTCAT
*** ** *
21296 CACATCGGCCA-TTTGGCCTT-AT
1 CACA-CATACACTTTCACATTCAT
21318 CACACATACACTTTCACATTCAT
1 CACACATACACTTTCACATTCAT
21341 CACA
1 CACA
21345 TCGACCATTT
Statistics
Matches: 33, Mismatches: 13, Indels: 6
0.63 0.25 0.12
Matches are distributed among these distances:
21 3 0.09
22 12 0.36
23 16 0.48
24 2 0.06
ACGTcount: A:0.31, C:0.33, G:0.06, T:0.31
Consensus pattern (23 bp):
CACACATACACTTTCACATTCAT
Found at i:27723 original size:40 final size:40
Alignment explanation
Indices: 27665--27832 Score: 214
Period size: 40 Copynumber: 4.2 Consensus size: 40
27655 TCTTCGGAAA
*
27665 TTAG-CCGGATATAACAACTCGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGGTC
*
27704 TTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGAGTC
1 TTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGGTC
* * * * *
27744 TTAGCGCGGATATAATC-ACTAGCATAAATGCCTTCGGGAC
1 TTAGCCCGGATAT-AGCAACTCGCACAAATGCCTTCGGGTC
* * *
27784 ATAGACCGGATATAGCAACTCGCACAAATGCCTTCGGATC
1 TTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGGTC
*
27824 TTAGTCCGG
1 TTAGCCCGG
27833 TTATCATCCG
Statistics
Matches: 108, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
39 6 0.06
40 100 0.93
41 2 0.02
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (40 bp):
TTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGGTC
Found at i:27793 original size:80 final size:79
Alignment explanation
Indices: 27656--27832 Score: 241
Period size: 80 Copynumber: 2.2 Consensus size: 79
27646 ACCCAAGTAT
** * * * *
27656 CTTCGGAAATTAGCCGGATATAACAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCA
1 CTTCGGATCTTAGCCGGATATAACAACTAGCACAAATGCCTTCGGGACATAGACCGGATATAGCA
27721 ACTCGCACAAATGC
66 ACTCGCACAAATGC
*
27735 CTTC-GAGTCTTAGCGCGGATATAATC-ACTAGCATAAATGCCTTCGGGACATAGACCGGATATA
1 CTTCGGA-TCTTAGC-CGGATATAA-CAACTAGCACAAATGCCTTCGGGACATAGACCGGATATA
27798 GCAACTCGCACAAATGC
63 GCAACTCGCACAAATGC
27815 CTTCGGATCTTAGTCCGG
1 CTTCGGATCTTAG-CCGG
27833 TTATCATCCG
Statistics
Matches: 86, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
78 2 0.02
79 9 0.10
80 71 0.83
81 4 0.05
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (79 bp):
CTTCGGATCTTAGCCGGATATAACAACTAGCACAAATGCCTTCGGGACATAGACCGGATATAGCA
ACTCGCACAAATGC
Found at i:33628 original size:590 final size:590
Alignment explanation
Indices: 32510--33691 Score: 2292
Period size: 590 Copynumber: 2.0 Consensus size: 590
32500 GGGAATGCTG
*
32510 GAAGCGTACGGGGGCTTGTCTTCGTTGTGGGTCAAAGGAACATAGGATCAGGGATTGTCCTAGGA
1 GAAGCGTACGGGGGCTTGTCTTCATTGTGGGTCAAAGGAACATAGGATCAGGGATTGTCCTAGGA
32575 GGCCAACTTAGACTCAAGTGGTTGAACAGGGGGCTGTTCAACCTGTGCAACCAGCACGAGGTGGA
66 GGCCAACTTAGACTCAAGTGGTTGAACAGGGGGCTGTTCAACCTGTGCAACCAGCACGAGGTGGA
32640 CCACCGCCGCCGAGAGGTCGTGGACAAGGTCGCGGTGGCAATGGCCGTTGACGTGGGGCACCTGG
131 CCACCGCCGCCGAGAGGTCGTGGACAAGGTCGCGGTGGCAATGGCCGTTGACGTGGGGCACCTGG
32705 CAAGGGTGTTGTTAATGCTGAGGCTCGTCAGCCAGCTTTGTTATATGCTGCTCGTCGCCGCGAGA
196 CAAGGGTGTTGTTAATGCTGAGGCTCGTCAGCCAGCTTTGTTATATGCTGCTCGTCGCCGCGAGA
32770 AGGGTGACGCACCTGATGTCATAACAGGTACGTTTTTAATCTCTGGCGTACGTTATACTGCTCTG
261 AGGGTGACGCACCTGATGTCATAACAGGTACGTTTTTAATCTCTGGCGTACGTTATACTGCTCTG
32835 GTGTGGGGTTAACTCATTCGTATGTTGCATGTGACATTTTTGGGGCATTAGGTGTACACTTTGAG
326 GTGTGGGGTTAACTCATTCGTATGTTGCATGTGACATTTTTGGGGCATTAGGTGTACACTTTGAG
32900 GAGACTGTGTATGGGGTAACTGTGATAAGTCCTTTAGGTCACTCGGTTAAGGTAGAGAAACTCTT
391 GAGACTGTGTATGGGGTAACTGTGATAAGTCCTTTAGGTCACTCGGTTAAGGTAGAGAAACTCTT
32965 TAGGGAGGTGCCTTTAGAGACTCAAGGTAAGATTTTCTGTAGAGACTTGATGGAATTACCGTTCG
456 TAGGGAGGTGCCTTTAGAGACTCAAGGTAAGATTTTCTGTAGAGACTTGATGGAATTACCGTTCG
33030 GAGAATTCGATTTGATTCTAGAGATGGACTGGTTGACCAAGCAAAGGGCAACTCTGGATTGTGCA
521 GAGAATTCGATTTGATTCTAGAGATGGACTGGTTGACCAAGCAAAGGGCAACTCTGGATTGTGCA
33095 GCTAA
586 GCTAA
33100 GAAGCGTACGGGGGCTTGTCTTCATTGTGGGTCAAAGGAACATAGGATCAGGGATTGTCCTAGGA
1 GAAGCGTACGGGGGCTTGTCTTCATTGTGGGTCAAAGGAACATAGGATCAGGGATTGTCCTAGGA
33165 GGCCAACTTAGACTCAAGTGGTTGAACAGGGGGCTGTTCAACCTGTGCAACCAGCACGAGGTGGA
66 GGCCAACTTAGACTCAAGTGGTTGAACAGGGGGCTGTTCAACCTGTGCAACCAGCACGAGGTGGA
* *
33230 CCGCCGCCGTCGAGAGGTCGTGGACAAGGTCGCGGTGGCAATGGCCGTTGACGTGGGGCACCTGG
131 CCACCGCCGCCGAGAGGTCGTGGACAAGGTCGCGGTGGCAATGGCCGTTGACGTGGGGCACCTGG
* *
33295 CAAGGGTGTTGTTAATGCTGAGGCTCGTCATCCAGCTTTTTTATATGCTGCTCGTCGCCGCGAGA
196 CAAGGGTGTTGTTAATGCTGAGGCTCGTCAGCCAGCTTTGTTATATGCTGCTCGTCGCCGCGAGA
33360 AGGGTGACGCACCTGATGTCATAACAGGTACGTTTTTAATCTCTGGCGTACGTTATACTGCTCTG
261 AGGGTGACGCACCTGATGTCATAACAGGTACGTTTTTAATCTCTGGCGTACGTTATACTGCTCTG
33425 GTGTGGGGTTAACTCATTCGTATGTTGCATGTGACATTTTTGGGGCATTAGGTGTACACTTTGAG
326 GTGTGGGGTTAACTCATTCGTATGTTGCATGTGACATTTTTGGGGCATTAGGTGTACACTTTGAG
*
33490 GAGACTGTGTGTGGGGTAACTGTGATAAGTCCTTTAGGTCACTCGGTTAAGGTAGAGAAACTCTT
391 GAGACTGTGTATGGGGTAACTGTGATAAGTCCTTTAGGTCACTCGGTTAAGGTAGAGAAACTCTT
*
33555 TAGGGAGGTGCCTTTAGAGACTCAAGGTAAGATTTTCTGTAGAGACTTGATGGAGTTACCGTTCG
456 TAGGGAGGTGCCTTTAGAGACTCAAGGTAAGATTTTCTGTAGAGACTTGATGGAATTACCGTTCG
*
33620 GAGAATTCGATTTGATTCTAGGGATGGACTGGTTGACCAAGCAAAGGGCAACTCTGGATTGTGCA
521 GAGAATTCGATTTGATTCTAGAGATGGACTGGTTGACCAAGCAAAGGGCAACTCTGGATTGTGCA
33685 GCTAA
586 GCTAA
33690 GA
1 GA
33692 GGATGGTGTT
Statistics
Matches: 584, Mismatches: 8, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
590 584 1.00
ACGTcount: A:0.23, C:0.19, G:0.32, T:0.27
Consensus pattern (590 bp):
GAAGCGTACGGGGGCTTGTCTTCATTGTGGGTCAAAGGAACATAGGATCAGGGATTGTCCTAGGA
GGCCAACTTAGACTCAAGTGGTTGAACAGGGGGCTGTTCAACCTGTGCAACCAGCACGAGGTGGA
CCACCGCCGCCGAGAGGTCGTGGACAAGGTCGCGGTGGCAATGGCCGTTGACGTGGGGCACCTGG
CAAGGGTGTTGTTAATGCTGAGGCTCGTCAGCCAGCTTTGTTATATGCTGCTCGTCGCCGCGAGA
AGGGTGACGCACCTGATGTCATAACAGGTACGTTTTTAATCTCTGGCGTACGTTATACTGCTCTG
GTGTGGGGTTAACTCATTCGTATGTTGCATGTGACATTTTTGGGGCATTAGGTGTACACTTTGAG
GAGACTGTGTATGGGGTAACTGTGATAAGTCCTTTAGGTCACTCGGTTAAGGTAGAGAAACTCTT
TAGGGAGGTGCCTTTAGAGACTCAAGGTAAGATTTTCTGTAGAGACTTGATGGAATTACCGTTCG
GAGAATTCGATTTGATTCTAGAGATGGACTGGTTGACCAAGCAAAGGGCAACTCTGGATTGTGCA
GCTAA
Found at i:37341 original size:15 final size:16
Alignment explanation
Indices: 37306--37343 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
37296 CTTCTTCTCT
37306 TTTTTCTCCATTTTTC
1 TTTTTCTCCATTTTTC
37322 TTTTT-TCC-TTTTTGC
1 TTTTTCTCCATTTTT-C
37337 TTTTTCT
1 TTTTTCT
37344 TCTAGTCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 5 0.25
15 9 0.45
16 6 0.30
ACGTcount: A:0.03, C:0.21, G:0.03, T:0.74
Consensus pattern (16 bp):
TTTTTCTCCATTTTTC
Found at i:42400 original size:30 final size:31
Alignment explanation
Indices: 42355--42417 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 31
42345 AAAATTTAAA
* *
42355 GACATGTTCAGAGGCCAAATTGCCTTGGCTT
1 GACATGTTCAGAGGCCAAATAGCCTTAGCTT
*
42386 GACA-GTTGAGAGGCCAAATAGCCTTAGCTT
1 GACATGTTCAGAGGCCAAATAGCCTTAGCTT
42416 GA
1 GA
42418 TAGTCAGTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 25 0.86
31 4 0.14
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (31 bp):
GACATGTTCAGAGGCCAAATAGCCTTAGCTT
Done.