Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1893
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: 28092
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Found at i:476 original size:28 final size:30
Alignment explanation
Indices: 439--532 Score: 144
Period size: 28 Copynumber: 3.3 Consensus size: 30
429 CTAGCCTTTG
439 CCACC-CCAACTCCACTA-CCA-ACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
466 CCACCACCAACTCCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
*
496 -CA-CACCTACTCCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
524 CCACCACCA
1 CCACCACCA
533 CTTGTACCTA
Statistics
Matches: 60, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
27 5 0.08
28 37 0.62
29 7 0.12
30 11 0.18
ACGTcount: A:0.27, C:0.51, G:0.05, T:0.17
Consensus pattern (30 bp):
CCACCACCAACTCCACTAGCCACACTTGCT
Found at i:996 original size:17 final size:17
Alignment explanation
Indices: 974--1008 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
964 TCTCCTCTTT
*
974 TTTTTTATTATTATATA
1 TTTTTTAATATTATATA
991 TTTTTTAATATTATATA
1 TTTTTTAATATTATATA
1008 T
1 T
1009 ATATATTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTTTTAATATTATATA
Found at i:1103 original size:25 final size:25
Alignment explanation
Indices: 979--1187 Score: 91
Period size: 25 Copynumber: 8.6 Consensus size: 25
969 TCTTTTTTTT
* *
979 TATTAT-TATATATTTTTTAATATTA
1 TATTATGTATATA-TCTTTAATACTA
* *
1004 TA-TATATATAT-TCTTT--TAATA
1 TATTATGTATATATCTTTAATACTA
* * *
1025 TATTAGGTATAT-TC-TAAATTCTA
1 TATTATGTATATATCTTTAATACTA
* *
1048 TATTACGTATATATATATT-ATACTA
1 TATTATGTATATATCT-TTAATACTA
*
1073 TTTTATGTATATATCTTTAATACTA
1 TATTATGTATATATCTTTAATACTA
* * * **
1098 TATTATTTATATTTTTTTTTCTACATGTTA
1 TATTATGTATA---TATCTT-TA-ATACTA
*
1128 TCTTATGTATATAT-TTTAAT--TA
1 TATTATGTATATATCTTTAATACTA
* * *
1150 TATTATGTATGTAT-TTTTACACTA
1 TATTATGTATATATCTTTAATACTA
*
1174 TATTATGTACATAT
1 TATTATGTATATAT
1188 TTTTTTTATA
Statistics
Matches: 140, Mismatches: 29, Indels: 31
0.70 0.14 0.16
Matches are distributed among these distances:
21 7 0.05
22 27 0.19
23 18 0.13
24 22 0.16
25 42 0.30
26 3 0.02
27 2 0.01
28 4 0.03
29 2 0.01
30 13 0.09
ACGTcount: A:0.33, C:0.06, G:0.04, T:0.56
Consensus pattern (25 bp):
TATTATGTATATATCTTTAATACTA
Found at i:1150 original size:22 final size:23
Alignment explanation
Indices: 1125--1190 Score: 80
Period size: 22 Copynumber: 2.9 Consensus size: 23
1115 TTTCTACATG
*
1125 TTATCTTATGTATATATTTTA-A
1 TTATATTATGTATATATTTTACA
*
1147 TTATATTATGTATGTATTTTTACA
1 TTATATTATGTATATA-TTTTACA
* *
1171 CTATATTATGTACATATTTT
1 TTATATTATGTATATATTTT
1191 TTTTATATCT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
22 14 0.38
23 9 0.24
24 14 0.38
ACGTcount: A:0.30, C:0.06, G:0.06, T:0.58
Consensus pattern (23 bp):
TTATATTATGTATATATTTTACA
Found at i:1180 original size:24 final size:23
Alignment explanation
Indices: 1130--1191 Score: 81
Period size: 24 Copynumber: 2.7 Consensus size: 23
1120 ACATGTTATC
*
1130 TTATGTATATA-TTTTAATTATA
1 TTATGTATATATTTTTAACTATA
*
1152 TTATGTATGTATTTTTACACTATA
1 TTATGTATATATTTTTA-ACTATA
*
1176 TTATGTACATATTTTT
1 TTATGTATATATTTTT
1192 TTTATATCTA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 10 0.29
23 5 0.15
24 19 0.56
ACGTcount: A:0.31, C:0.05, G:0.06, T:0.58
Consensus pattern (23 bp):
TTATGTATATATTTTTAACTATA
Found at i:1282 original size:25 final size:24
Alignment explanation
Indices: 1254--1309 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
1244 GTTATATTTT
*
1254 CACTATTTTAT-GTATATACTTCAAA
1 CACTATTATATAGTATAT--TTCAAA
*
1279 CACTA-TATATAGTATATTTCTAA
1 CACTATTATATAGTATATTTCAAA
1302 CACTATTA
1 CACTATTA
1310 CTATTTATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 10 0.37
24 6 0.22
25 11 0.41
ACGTcount: A:0.38, C:0.16, G:0.04, T:0.43
Consensus pattern (24 bp):
CACTATTATATAGTATATTTCAAA
Found at i:11565 original size:73 final size:73
Alignment explanation
Indices: 11468--11841 Score: 601
Period size: 73 Copynumber: 5.1 Consensus size: 73
11458 TGATGTTTTT
* * ** * * *
11468 ATTTCTATTT-TCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
1 ATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGG
11532 TAATTTCA
66 TAATTTCA
*
11540 ATTTCTGTTTGTCAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGG
1 ATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGG
11605 TAATTTCA
66 TAATTTCA
*
11613 ATTTCTGTTTGTCAAAACA-CAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAG
1 ATTTCTGTTTGTCAAAA-ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAG
11677 GTAATTTCA
65 GTAATTTCA
* *
11686 ATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTAGGGCACGCTAAGG
1 ATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGG
11751 TAATTTCA
66 TAATTTCA
*
11759 ATTTCTGTTTGTCAAAACA-CAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGTACGCTGAG
1 ATTTCTGTTTGTCAAAA-ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAG
11823 GTAATTTCA
65 GTAATTTCA
11832 ATTTCTGTTT
1 ATTTCTGTTT
11842 TTTTCAATTT
Statistics
Matches: 282, Mismatches: 16, Indels: 7
0.92 0.05 0.02
Matches are distributed among these distances:
72 10 0.04
73 270 0.96
74 2 0.01
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (73 bp):
ATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGG
TAATTTCA
Found at i:11910 original size:89 final size:89
Alignment explanation
Indices: 11754--12076 Score: 488
Period size: 89 Copynumber: 3.6 Consensus size: 89
11744 GCTAAGGTAA
* * * **
11754 TTTCAATTTCTGTTTGTCAAAACA-CAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGTACG
1 TTTCAATTTATATTTTTCAAAA-ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACG
*
11818 CTGAGGTAATTTCAATTTCTGTTTT
65 CTGAGGTATTTTCAATTTCTGTTTT
* *
11843 TTTCAATTTATATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTTAGCCTCAGGACATGC
1 TTTCAATTTATATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
*
11908 TGAGGTATTTTCAATTTTTGTTTT
66 TGAGGTATTTTCAATTTCTGTTTT
*
11932 TTTCAATTTATATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTTAGCCTCAGGACACGC
1 TTTCAATTTATATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
*
11997 TGAGGTATTTTCAATTTCTATTTTT
66 TGAGGTATTTTCAATTTCT-GTTTT
* * *
12022 TTTCAATTTATA-TTTTCAAAAATTAATTCATATTGCGAGAGATGAGTTGAGCCTC
1 TTTCAATTTATATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
12077 GGGGCACATG
Statistics
Matches: 216, Mismatches: 16, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
88 1 0.00
89 199 0.92
90 16 0.07
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (89 bp):
TTTCAATTTATATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
TGAGGTATTTTCAATTTCTGTTTT
Found at i:11947 original size:16 final size:16
Alignment explanation
Indices: 11915--11948 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
11905 TGCTGAGGTA
* *
11915 TTTTCAATTTTTGTTT
1 TTTTCAATTTATATTT
11931 TTTTCAATTTATATTT
1 TTTTCAATTTATATTT
11947 TT
1 TT
11949 CAAAAATCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.18, C:0.06, G:0.03, T:0.74
Consensus pattern (16 bp):
TTTTCAATTTATATTT
Found at i:12026 original size:17 final size:17
Alignment explanation
Indices: 12004--12037 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
11994 CGCTGAGGTA
*
12004 TTTTCAATTTCTATTTT
1 TTTTCAATTTATATTTT
12021 TTTTCAATTTATATTTT
1 TTTTCAATTTATATTTT
12038 CAAAAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.09, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTCAATTTATATTTT
Found at i:12940 original size:18 final size:18
Alignment explanation
Indices: 12917--12971 Score: 50
Period size: 18 Copynumber: 3.4 Consensus size: 18
12907 CCACCACCAA
12917 CTCCACTAACCACACTTG
1 CTCCACTAACCACACTTG
*
12935 CTCCAC-CACCA-A----
1 CTCCACTAACCACACTTG
*
12947 CTCCACTAGCCACACTTG
1 CTCCACTAACCACACTTG
12965 CTCCACT
1 CTCCACT
12972 TACCTACTCC
Statistics
Matches: 28, Mismatches: 3, Indels: 12
0.65 0.07 0.28
Matches are distributed among these distances:
12 6 0.21
13 3 0.11
14 1 0.04
16 1 0.04
17 4 0.14
18 13 0.46
ACGTcount: A:0.25, C:0.49, G:0.05, T:0.20
Consensus pattern (18 bp):
CTCCACTAACCACACTTG
Found at i:12984 original size:31 final size:30
Alignment explanation
Indices: 12907--13006 Score: 164
Period size: 30 Copynumber: 3.3 Consensus size: 30
12897 CTAGCCTTTG
*
12907 CCACCACCAACTCCACTAACCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
12937 CCACCACCAACTCCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
* *
12967 CCACTTACCTACTCCACTAGCCACACTTGCT
1 CCAC-CACCAACTCCACTAGCCACACTTGCT
12998 CCACCACCA
1 CCACCACCA
13007 CTTGTACCTA
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
30 36 0.56
31 28 0.44
ACGTcount: A:0.27, C:0.50, G:0.05, T:0.18
Consensus pattern (30 bp):
CCACCACCAACTCCACTAGCCACACTTGCT
Found at i:13001 original size:18 final size:18
Alignment explanation
Indices: 12947--13001 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
12937 CCACCACCAA
12947 CTCCACTAGCCACACTTG
1 CTCCACTAGCCACACTTG
* *
12965 CTCCACT---TAC-C-TA
1 CTCCACTAGCCACACTTG
12978 CTCCACTAGCCACACTTG
1 CTCCACTAGCCACACTTG
12996 CTCCAC
1 CTCCAC
13002 CACCACTTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 10
0.67 0.10 0.24
Matches are distributed among these distances:
13 8 0.29
14 1 0.04
15 2 0.07
16 2 0.07
17 1 0.04
18 14 0.50
ACGTcount: A:0.22, C:0.47, G:0.07, T:0.24
Consensus pattern (18 bp):
CTCCACTAGCCACACTTG
Found at i:13591 original size:27 final size:26
Alignment explanation
Indices: 13551--13622 Score: 94
Period size: 25 Copynumber: 2.8 Consensus size: 26
13541 ATTCTAAATT
*
13551 CTATATTACGTATATATATATT-ATA
1 CTATATTATGTATATATATATTAATA
* *
13576 CTATTTTATGTATATATCT-TTAATA
1 CTATATTATGTATATATATATTAATA
*
13601 CTATATTATTTATATATATATT
1 CTATATTATGTATATATATATT
13623 TTTCTACATG
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
24 2 0.05
25 35 0.90
26 2 0.05
ACGTcount: A:0.36, C:0.07, G:0.03, T:0.54
Consensus pattern (26 bp):
CTATATTATGTATATATATATTAATA
Found at i:13646 original size:28 final size:28
Alignment explanation
Indices: 13580--13688 Score: 104
Period size: 28 Copynumber: 4.0 Consensus size: 28
13570 ATTATACTAT
13580 TTTATGTATATATCTTTAATACTATATTA
1 TTTATGTATATAT-TTTAATACTATATTA
* ** *
13609 TTTATATATATATTTTTCTAC-ATGTTA
1 TTTATGTATATATTTTAATACTATATTA
13636 TCTTATGTATATATTTTAAT--TATATTA
1 T-TTATGTATATATTTTAATACTATATTA
* *
13663 TGTATGTAT-T-TTTT-ACACTATATTA
1 TTTATGTATATATTTTAATACTATATTA
13688 T
1 T
13689 GTACATATTT
Statistics
Matches: 66, Mismatches: 10, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
23 1 0.02
24 4 0.06
25 9 0.14
26 7 0.11
27 12 0.18
28 21 0.32
29 12 0.18
ACGTcount: A:0.31, C:0.06, G:0.05, T:0.58
Consensus pattern (28 bp):
TTTATGTATATATTTTAATACTATATTA
Found at i:13689 original size:25 final size:24
Alignment explanation
Indices: 13639--13701 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 24
13629 CATGTTATCT
*
13639 TATGTATATATTTTAATTATATTATG
1 TATGTAT-T-TTTTAACTATATTATG
13665 TATGTATTTTTTACACTATATTATG
1 TATGTATTTTTTA-ACTATATTATG
**
13690 TACATATTTTTT
1 TATGTATTTTTT
13702 TATATCTATT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
24 5 0.15
25 21 0.64
26 7 0.21
ACGTcount: A:0.30, C:0.05, G:0.06, T:0.59
Consensus pattern (24 bp):
TATGTATTTTTTAACTATATTATG
Found at i:13790 original size:25 final size:24
Alignment explanation
Indices: 13762--13817 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
13752 GTTATATTTT
*
13762 CACTATTTTAT-GTATATACTTCAAA
1 CACTATTATATAGTATAT--TTCAAA
*
13787 CACTA-TATATAGTATATTTCTAA
1 CACTATTATATAGTATATTTCAAA
13810 CACTATTA
1 CACTATTA
13818 CTATTTATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 10 0.37
24 6 0.22
25 11 0.41
ACGTcount: A:0.38, C:0.16, G:0.04, T:0.43
Consensus pattern (24 bp):
CACTATTATATAGTATATTTCAAA
Found at i:19171 original size:39 final size:40
Alignment explanation
Indices: 19121--19237 Score: 184
Period size: 39 Copynumber: 3.0 Consensus size: 40
19111 TTATATTACC
* *
19121 AGCACAAAGCCTGCGGGACTTTAGCCCGGATACATTTCCT
1 AGCACGAAGCCTACGGGACTTTAGCCCGGATACATTTCCT
*
19161 -GCTCGAAGCCTACGGGACTTTAGCCCGGATACATTT-CT
1 AGCACGAAGCCTACGGGACTTTAGCCCGGATACATTTCCT
*
19199 AGCACGAAGCCTACGAGACTTTAGCCCGGATACATTTCC
1 AGCACGAAGCCTACGGGACTTTAGCCCGGATACATTTCC
19238 AGTGTCTTTC
Statistics
Matches: 70, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
38 2 0.03
39 67 0.96
40 1 0.01
ACGTcount: A:0.25, C:0.30, G:0.22, T:0.23
Consensus pattern (40 bp):
AGCACGAAGCCTACGGGACTTTAGCCCGGATACATTTCCT
Found at i:23563 original size:99 final size:99
Alignment explanation
Indices: 23338--23596 Score: 281
Period size: 99 Copynumber: 2.7 Consensus size: 99
23328 GCCGATGCCG
* * * **
23338 TGTCCCAGACATGGTCTTACACT-G-GCTCATCTATT-AAGCCGATGCCATGTCCCATACATGGT
1 TGTCCCAAACATGGTCTTACACTAGCTCTCATATATTCGTGCCGATGCCATGTCCCATACATGGT
*
23400 CTTACATTGACTATCAAAATCGAGGTCGACGCCA
66 CTTACACTGACTATCAAAATCGAGGTCGACGCCA
23434 TGTCCCAAACATGGTCTTACACTAGCTCTCATATATTCGTGCCGATGCCATGTCCCATACATGGT
1 TGTCCCAAACATGGTCTTACACTAGCTCTCATATATTCGTGCCGATGCCATGTCCCATACATGGT
** *
23499 CTTACACTGAC-A-C-ATCTCGTA-GTCGATG-CA
66 CTTACACTGACTATCAAAATCG-AGGTCGACGCCA
* * * * * *
23529 TGTCCCATACAT-GTCTTACACTAGCTCTC--GT-CTCAATGCCAATGCCATGTCCCAAACATGG
1 TGTCCCAAACATGGTCTTACACTAGCTCTCATATATTC-GTGCCGATGCCATGTCCCATACATGG
23590 TCTTACA
65 TCTTACA
23597 TTGGCTCTCA
Statistics
Matches: 143, Mismatches: 15, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
91 2 0.01
92 31 0.22
94 17 0.12
95 13 0.09
96 32 0.22
97 3 0.02
98 10 0.07
99 35 0.24
ACGTcount: A:0.25, C:0.30, G:0.17, T:0.29
Consensus pattern (99 bp):
TGTCCCAAACATGGTCTTACACTAGCTCTCATATATTCGTGCCGATGCCATGTCCCATACATGGT
CTTACACTGACTATCAAAATCGAGGTCGACGCCA
Found at i:23636 original size:94 final size:94
Alignment explanation
Indices: 23338--23621 Score: 274
Period size: 96 Copynumber: 3.0 Consensus size: 94
23328 GCCGATGCCG
* * * *
23338 TGTCCCAGACATGGTCTTACACTGGCTCATC-TAT-TAAGCCGATGCCATGTCCCATACATGGTC
1 TGTCCCAAACAT-GTCTTACACTAGCTC-TCATATATATGCCAATGCCATGTCCCATACATGGTC
* * * *
23401 TTACATTGACTATCAAAATCGAGGTCGACGCCA
64 TTACATTGACTCTCATAAT-GTGGTCGATG-CA
* *
23434 TGTCCCAAACATGGTCTTACACTAGCTCTCATATATTCGTGCCGATGCCATGTCCCATACATGGT
1 TGTCCCAAACAT-GTCTTACACTAGCTCTCATATA-T-ATGCCAATGCCATGTCCCATACATGGT
* * * *
23499 CTTACACTGACACATC-T--CGTAGTCGATGCA
63 CTTACATTGACTC-TCATAATGTGGTCGATGCA
* * * *
23529 TGTCCCATACATGTCTTACACTAGCTCTCGTCTCA-ATGCCAATGCCATGTCCCAAACATGGTCT
1 TGTCCCAAACATGTCTTACACTAGCTCTCATAT-ATATGCCAATGCCATGTCCCATACATGGTCT
*
23593 TACATTGGCTCTCATAATGTGGTCGATGC
65 TACATTGACTCTCATAATGTGGTCGATGC
23622 TAGTTCCAGG
Statistics
Matches: 156, Mismatches: 23, Indels: 20
0.78 0.12 0.10
Matches are distributed among these distances:
91 2 0.01
92 35 0.22
94 29 0.19
95 16 0.10
96 36 0.23
98 1 0.01
99 35 0.22
100 2 0.01
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (94 bp):
TGTCCCAAACATGTCTTACACTAGCTCTCATATATATGCCAATGCCATGTCCCATACATGGTCTT
ACATTGACTCTCATAATGTGGTCGATGCA
Found at i:26677 original size:22 final size:21
Alignment explanation
Indices: 26652--26717 Score: 66
Period size: 19 Copynumber: 3.2 Consensus size: 21
26642 TATAAATTAA
26652 ATCTCTAAGATTACAAAATCAT
1 ATCTCTAAGATTAC-AAATCAT
* *
26674 ATCTTCTAAGATTGCATATCAT
1 ATC-TCTAAGATTACAAATCAT
*
26696 A--TCTAAGATTGC-AATCAT
1 ATCTCTAAGATTACAAATCAT
26714 ATCT
1 ATCT
26718 AAGATTGCAT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
18 6 0.16
19 11 0.29
20 1 0.03
22 10 0.26
23 10 0.26
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.36
Consensus pattern (21 bp):
ATCTCTAAGATTACAAATCAT
Found at i:26685 original size:23 final size:22
Alignment explanation
Indices: 26655--26699 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
26645 AAATTAAATC
26655 TCTAAGATTACAAAATCATATCT
1 TCTAAGATTAC-AAATCATATCT
* *
26678 TCTAAGATTGCATATCATATCT
1 TCTAAGATTACAAATCATATCT
26700 AAGATTGCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.38
Consensus pattern (22 bp):
TCTAAGATTACAAATCATATCT
Found at i:26702 original size:19 final size:19
Alignment explanation
Indices: 26678--26751 Score: 132
Period size: 19 Copynumber: 3.9 Consensus size: 19
26668 AATCATATCT
26678 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
26697 TCTAAGATTGCA-ATCATA
1 TCTAAGATTGCATATCATA
*
26715 TCTAAGATTGCATATCACA
1 TCTAAGATTGCATATCATA
26734 TCTAAGATTGCATATCAT
1 TCTAAGATTGCATATCAT
26752 TGAAGATTAT
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
18 18 0.35
19 34 0.65
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.35
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:26724 original size:37 final size:38
Alignment explanation
Indices: 26671--26751 Score: 132
Period size: 37 Copynumber: 2.2 Consensus size: 38
26661 ATTACAAAAT
*
26671 CATATC-T-TCTAAGATTGCATATCATATCTAAGATTG
1 CATATCATATCTAAGATTGCATATCACATCTAAGATTG
26707 CA-ATCATATCTAAGATTGCATATCACATCTAAGATTG
1 CATATCATATCTAAGATTGCATATCACATCTAAGATTG
26744 CATATCAT
1 CATATCAT
26752 TGAAGATTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
35 3 0.07
36 3 0.07
37 30 0.73
38 5 0.12
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.36
Consensus pattern (38 bp):
CATATCATATCTAAGATTGCATATCACATCTAAGATTG
Done.