Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_4047
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: 16225
ACGTcount: A:0.23, C:0.29, G:0.27, T:0.21
Found at i:1056 original size:42 final size:42
Alignment explanation
Indices: 997--1449 Score: 421
Period size: 42 Copynumber: 10.7 Consensus size: 42
987 CATTCGTTGT
* * ** *
997 CGATGGTGCCCAAGGCTCCTGCAC-ATCCAAGCACCAAGGTGC
1 CGATGGTGCCCGAGGCTCCCGCACGA-CCAAGGGCCTAGGTGC
**
1039 CGATGGTGCCCGAGGCTCCCGCACGACTTAGGGCCTAGGTGC
1 CGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTAGGTGC
*
1081 CGATGGTGCCCGAGGCTCTCGCACGACCAAGGGCCTAGGTTGC
1 CGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTAGG-TGC
* * ** *
1124 CGATGGTGGCCGAAGCTCCTACATGACC-AGGGCCTAGGTGC
1 CGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTAGGTGC
* * *
1165 CGAT-GTGGCCGAGGCTCCTGCACGACCAAGCGCCTAGGTTGC
1 CGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTAGG-TGC
* * *
1207 CGATGGTGGCCGAGGCTCCCGCACGACCAGGGGCCTAGGTTC
1 CGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTAGGTGC
* *
1249 CGATGGTGCCCGAGGGTCTCGCACGACCAAGGGCCTAGGTTGC
1 CGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTAGG-TGC
** * * *
1292 CGATGGT-ATCGAGGCTCCCGCGCGACCAGGGGCCTAGGTTAC
1 CGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTAGG-TGC
* * * ** *
1334 CGATGGTACCTGAGGCTCCCGCAC-ATCCTAGCACCAAGGTGC
1 CGATGGTGCCCGAGGCTCCCGCACGA-CCAAGGGCCTAGGTGC
* * * * * *
1376 GGGTGGTGCCCGAGGCTCCCGCACGACAAACGTCCTAGGTTAC
1 CGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTAGG-TGC
* * * * *
1419 CGATGGCGTCCAAGGCTCCAGCACGTCCAAG
1 CGATGGTGCCCGAGGCTCCCGCACGACCAAG
1450 CAGCAATGTG
Statistics
Matches: 335, Mismatches: 66, Indels: 19
0.80 0.16 0.05
Matches are distributed among these distances:
40 20 0.06
41 16 0.05
42 188 0.56
43 111 0.33
ACGTcount: A:0.18, C:0.33, G:0.33, T:0.16
Consensus pattern (42 bp):
CGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTAGGTGC
Found at i:1327 original size:168 final size:169
Alignment explanation
Indices: 1009--1402 Score: 530
Period size: 168 Copynumber: 2.3 Consensus size: 169
999 ATGGTGCCCA
*
1009 AGGCTCCTGCACATCCAAGCACCAAGGTGCCGATGGTGCCCGAGGCTCCCGCACGACTTAGGGCC
1 AGGCTCCTGCACATCCAAGCACCAAGGTGCCGATGGTGCCCGAGGCTCCCGCACGACTCAGGGCC
*
1074 TAGGTGCCGATGGTGCCCGAGGCTCTCGCACGACCAAGGGCCTAGGTTGCCGATGGTGGCCGAAG
66 TAGGTGCCGATGGTGCCCGAGGCTCTCGCACGACCAAGGGCCTAGGTTGCCGATGGTGACCGAAG
* * * *
1139 CTCCTACATGACCAGGGCCTAGG-TGCCGAT-GTGGCC-G
131 CTCCCACACGACCAGGGCCTAGGTTACCGATGGT-ACCTG
* * *
1176 AGGCTCCTGCACGA-CCAAGCGCCTAGGTTGCCGATGGTGGCCGAGGCTCCCGCACGAC-CAGGG
1 AGGCTCCTGCAC-ATCCAAGCACCAAGG-TGCCGATGGTGCCCGAGGCTCCCGCACGACTCA-GG
* * *
1239 GCCTAGGTTCCGATGGTGCCCGAGGGTCTCGCACGACCAAGGGCCTAGGTTGCCGATGGT-ATCG
63 GCCTAGGTGCCGATGGTGCCCGAGGCTCTCGCACGACCAAGGGCCTAGGTTGCCGATGGTGACCG
* * *
1303 AGGCTCCCGCGCGACCAGGGGCCTAGGTTACCGATGGTACCTG
128 AAGCTCCCACACGACCA-GGGCCTAGGTTACCGATGGTACCTG
* * * *
1346 AGGCTCCCGCACATCCTAGCACCAAGGTGCGGGTGGTGCCCGAGGCTCCCGCACGAC
1 AGGCTCCTGCACATCCAAGCACCAAGGTGCCGATGGTGCCCGAGGCTCCCGCACGAC
1403 AAACGTCCTA
Statistics
Matches: 197, Mismatches: 22, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
167 38 0.19
168 99 0.50
169 36 0.18
170 24 0.12
ACGTcount: A:0.17, C:0.33, G:0.34, T:0.16
Consensus pattern (169 bp):
AGGCTCCTGCACATCCAAGCACCAAGGTGCCGATGGTGCCCGAGGCTCCCGCACGACTCAGGGCC
TAGGTGCCGATGGTGCCCGAGGCTCTCGCACGACCAAGGGCCTAGGTTGCCGATGGTGACCGAAG
CTCCCACACGACCAGGGCCTAGGTTACCGATGGTACCTG
Found at i:1388 original size:127 final size:128
Alignment explanation
Indices: 997--1450 Score: 381
Period size: 127 Copynumber: 3.6 Consensus size: 128
987 CATTCGTTGT
* * ** * *
997 CGATGGTGCCCAAGGCTCCTGCAC-ATCCAAGCACCAAGG-TGCCGATGGTGCCCGAGGCTCCCG
1 CGATGGTGCCCGAGGCTCCCGCACGA-CCAAGGGCCTAGGTTGCCGATGGTGACCGAGGCTCCCG
** * * * * * *
1060 CACGACTTAGGGCCTAGG-TGCCGATGGTGCCCGAGGCTCTCGCACGACCAAGG-GCCTAGGTTG
65 CACGACCAAGCGCCTAGGTTACCGATGGTGACCGAGGCTCCCGCACGACC-AGGCACCAAGG-TG
1123 C
128 C
* * ** * * *
1124 CGATGGTGGCCGAAGCTCCTACATGACC-AGGGCCTAGG-TGCCGAT-GTGGCCGAGGCTCCTGC
1 CGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTAGGTTGCCGATGGTGACCGAGGCTCCCGC
* * ** * *
1186 ACGACCAAGCGCCTAGGTTGCCGATGGTGGCCGAGGCTCCCGCACGACCAGGGGCCTAGGTTC
66 ACGACCAAGCGCCTAGGTTACCGATGGTGACCGAGGCTCCCGCACGACCAGGCACCAAGGTGC
* * *
1249 CGATGGTGCCCGAGGGTCTCGCACGACCAAGGGCCTAGGTTGCCGATGGT-ATCGAGGCTCCCGC
1 CGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTAGGTTGCCGATGGTGACCGAGGCTCCCGC
* * *
1313 GCGACCAGGGGCCTAGGTTACCGATGGT-ACCTGAGGCTCCCGCAC-ATCCTA-GCACCAAGGTG
66 ACGACCAAGCGCCTAGGTTACCGATGGTGACC-GAGGCTCCCGCACGA-CC-AGGCACCAAGGTG
1375 C
128 C
* * * * * * * * * *
1376 GGGTGGTGCCCGAGGCTCCCGCACGACAAACGTCCTAGGTTACCGATGGCGTCCAAGGCTCCAGC
1 CGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTAGGTTGCCGATGGTGACCGAGGCTCCCGC
*
1441 ACGTCCAAGC
66 ACGACCAAGC
1451 AGCAATGTGC
Statistics
Matches: 265, Mismatches: 52, Indels: 19
0.79 0.15 0.06
Matches are distributed among these distances:
125 55 0.21
126 63 0.24
127 127 0.48
128 20 0.08
ACGTcount: A:0.18, C:0.33, G:0.33, T:0.16
Consensus pattern (128 bp):
CGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTAGGTTGCCGATGGTGACCGAGGCTCCCGC
ACGACCAAGCGCCTAGGTTACCGATGGTGACCGAGGCTCCCGCACGACCAGGCACCAAGGTGC
Found at i:1396 original size:85 final size:85
Alignment explanation
Indices: 997--1450 Score: 449
Period size: 85 Copynumber: 5.4 Consensus size: 85
987 CATTCGTTGT
* * * *
997 CGATGGTGCCCAAGGCTCCTGCAC-ATCCAAGCACCAAGG-TGCCGATGGTGCCCGAGGCTCCCG
1 CGATGGTGCCCGAGGCTCCCGCACGA-CCAAGCGCCTAGGTTGCCGATGGTGCCCGAGGCTCCCG
* *
1060 CACGACTTAGGGCCTAGG-TGC
65 CACGAC-CAGGGCCTAGGTTAC
* * * * **
1081 CGATGGTGCCCGAGGCTCTCGCACGACCAAGGGCCTAGGTTGCCGATGGTGGCCGAAGCTCCTAC
1 CGATGGTGCCCGAGGCTCCCGCACGACCAAGCGCCTAGGTTGCCGATGGTGCCCGAGGCTCCCGC
* *
1146 ATGACCAGGGCCTAGG-TGC
66 ACGACCAGGGCCTAGGTTAC
* * *
1165 CGAT-GTGGCCGAGGCTCCTGCACGACCAAGCGCCTAGGTTGCCGATGGTGGCCGAGGCTCCCGC
1 CGATGGTGCCCGAGGCTCCCGCACGACCAAGCGCCTAGGTTGCCGATGGTGCCCGAGGCTCCCGC
1229 ACGACCAGGGGCCTAGGTT-C
66 ACGACCA-GGGCCTAGGTTAC
* * * **
1249 CGATGGTGCCCGAGGGTCTCGCACGACCAAGGGCCTAGGTTGCCGATGGT-ATCGAGGCTCCCGC
1 CGATGGTGCCCGAGGCTCCCGCACGACCAAGCGCCTAGGTTGCCGATGGTGCCCGAGGCTCCCGC
*
1313 GCGACCAGGGGCCTAGGTTAC
66 ACGACCA-GGGCCTAGGTTAC
* * * * * * *
1334 CGATGGTACCTGAGGCTCCCGCAC-ATCCTAGCACCAAGG-TGCGGGTGGTGCCCGAGGCTCCCG
1 CGATGGTGCCCGAGGCTCCCGCACGA-CCAAGCGCCTAGGTTGCCGATGGTGCCCGAGGCTCCCG
* * *
1397 CACGACAAACGTCCTAGGTTAC
65 CACGAC-CAGGGCCTAGGTTAC
* * * * *
1419 CGATGGCGTCCAAGGCTCCAGCACGTCCAAGC
1 CGATGGTGCCCGAGGCTCCCGCACGACCAAGC
1451 AGCAATGTGC
Statistics
Matches: 308, Mismatches: 52, Indels: 19
0.81 0.14 0.05
Matches are distributed among these distances:
83 59 0.19
84 101 0.33
85 147 0.48
86 1 0.00
ACGTcount: A:0.18, C:0.33, G:0.33, T:0.16
Consensus pattern (85 bp):
CGATGGTGCCCGAGGCTCCCGCACGACCAAGCGCCTAGGTTGCCGATGGTGCCCGAGGCTCCCGC
ACGACCAGGGCCTAGGTTAC
Found at i:1688 original size:23 final size:23
Alignment explanation
Indices: 1632--1706 Score: 123
Period size: 23 Copynumber: 3.2 Consensus size: 23
1622 TTTCAATATT
1632 CCGGATGGCTCGCCGGAGCACCG
1 CCGGATGGCTCGCCGGAGCACCG
1655 CCAGGATGGCTCGCCGGAGCACCG
1 CC-GGATGGCTCGCCGGAGCACCG
**
1679 CCGGATGGCTCGCTAGAGCACCG
1 CCGGATGGCTCGCCGGAGCACCG
1702 CCGGA
1 CCGGA
1707 ACCTAACCGG
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
23 26 0.53
24 23 0.47
ACGTcount: A:0.16, C:0.37, G:0.37, T:0.09
Consensus pattern (23 bp):
CCGGATGGCTCGCCGGAGCACCG
Found at i:2210 original size:57 final size:59
Alignment explanation
Indices: 2099--2218 Score: 172
Period size: 57 Copynumber: 2.1 Consensus size: 59
2089 GGGAGGGACA
* * * *
2099 GGGACGATTCATTCATTGTTGGGTATCGGACATGCAACGGTATCTGAATCCTACC-TTT
1 GGGACGATTCATTCATTATTGGGTACCGAACATGCAACGGTATCCGAATCCTACCTTTT
* *
2157 GGGACGATTCATTCATTATT-GGTACCGAACATGTAACGGTATCCGAATTCTACCTTTT
1 GGGACGATTCATTCATTATTGGGTACCGAACATGCAACGGTATCCGAATCCTACCTTTT
2215 GGGA
1 GGGA
2219 TTGGGGAGGG
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
57 29 0.53
58 26 0.47
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (59 bp):
GGGACGATTCATTCATTATTGGGTACCGAACATGCAACGGTATCCGAATCCTACCTTTT
Found at i:2479 original size:26 final size:27
Alignment explanation
Indices: 2450--2501 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
2440 GACATTCATG
*
2450 TGTCTGAAACAGGGACA-TGTTTCAGA
1 TGTCTAAAACAGGGACACTGTTTCAGA
*
2476 TGTCTAAAACAGGGACACTTTTTCAG
1 TGTCTAAAACAGGGACACTGTTTCAG
2502 CCCAACGCTC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 16 0.70
27 7 0.30
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (27 bp):
TGTCTAAAACAGGGACACTGTTTCAGA
Found at i:4278 original size:85 final size:84
Alignment explanation
Indices: 4167--4488 Score: 305
Period size: 85 Copynumber: 3.8 Consensus size: 84
4157 TTTTCTTTAG
* * ** * * *
4167 CCCGCACATCCGAGCCACCAGGGTGCCCCTGCTGCTCGAGGCACCCGCACATCCAACGTCCTAGG
1 CCCGCACATCCAAGCCACCAAGGTGCCAATGCTGCTCGAGGCTCCCGCACATCCAA-GACCAAGG
4232 TTGCCGATGGTGTCCGAGGCT
65 TTGCCGATGGTG-CCGAGGCT
*
4253 CCCGCACATCCAAG-CACCAAGGTGCCAATGCTTCTCGAGGCTCCCGCACATCCAAGCACCAAGG
1 CCCGCACATCCAAGCCACCAAGGTGCCAATGCTGCTCGAGGCTCCCGCACATCCAAG-ACCAAGG
* *
4317 -TGCCAATGCTGCTCGAGGCT
65 TTGCCGATGGTGC-CGAGGCT
* * *
4337 CCCGCACATCCAAGCCACCAAGGTGCCGATGGC-GCCCGAGGCTCCCGCACGA-CCAAGGGCCAA
1 CCCGCACATCCAAGCCACCAAGGTGCCAAT-GCTGCTCGAGGCTCCCGCAC-ATCCAA-GACCAA
*
4400 GGTTGCCGATGGTACCCGAGGCT
63 GGTTGCCGATGGT-GCCGAGGCT
** * * * * * * *
4423 CCCGCACGA-CCAAG-GGCCGAGGTTGTCGATGGTGTTCGAGGCTCCCGCACATCCAAGCCCGAG
1 CCCGCAC-ATCCAAGCCACCAAGG-TGCCAATGCTGCTCGAGGCTCCCGCACATCCAAGACCAAG
4486 GTT
64 GTT
4489 CTCGCACGAT
Statistics
Matches: 198, Mismatches: 26, Indels: 25
0.80 0.10 0.10
Matches are distributed among these distances:
83 1 0.01
84 31 0.16
85 95 0.48
86 69 0.35
87 2 0.01
ACGTcount: A:0.20, C:0.38, G:0.28, T:0.15
Consensus pattern (84 bp):
CCCGCACATCCAAGCCACCAAGGTGCCAATGCTGCTCGAGGCTCCCGCACATCCAAGACCAAGGT
TGCCGATGGTGCCGAGGCT
Found at i:4300 original size:42 final size:42
Alignment explanation
Indices: 4167--4480 Score: 296
Period size: 43 Copynumber: 7.4 Consensus size: 42
4157 TTTTCTTTAG
* * ** *
4167 CCCGCACATCCGAGCCACCAGGGTGCCCCTGCTGCTCGAGGCA
1 CCCGCACATCCAAG-CACCAAGGTGCCGATGCTGCTCGAGGCT
* * *
4210 CCCGCACATCCAA-CGTCCTAGGTTGCCGATGGTG-TCCGAGGCT
1 CCCGCACATCCAAGC-ACCAAGG-TGCCGATGCTGCT-CGAGGCT
* *
4253 CCCGCACATCCAAGCACCAAGGTGCCAATGCTTCTCGAGGCT
1 CCCGCACATCCAAGCACCAAGGTGCCGATGCTGCTCGAGGCT
*
4295 CCCGCACATCCAAGCACCAAGGTGCCAATGCTGCTCGAGGCT
1 CCCGCACATCCAAGCACCAAGGTGCCGATGCTGCTCGAGGCT
*
4337 CCCGCACATCCAAGCCACCAAGGTGCCGATGGC-GCCCGAGGCT
1 CCCGCACATCCAAG-CACCAAGGTGCCGAT-GCTGCTCGAGGCT
** * * *
4380 CCCGCACGA-CCAAGGGCCAAGGTTGCCGATGGTACCCGAGGCT
1 CCCGCAC-ATCCAAGCACCAAGG-TGCCGATGCTGCTCGAGGCT
** * * * *
4423 CCCGCACGA-CCAAGGGCCGAGGTTGTCGATGGTGTTCGAGGCT
1 CCCGCAC-ATCCAAGCACCAAGG-TGCCGATGCTGCTCGAGGCT
4466 CCCGCACATCCAAGC
1 CCCGCACATCCAAGC
4481 CCGAGGTTCT
Statistics
Matches: 234, Mismatches: 26, Indels: 22
0.83 0.09 0.08
Matches are distributed among these distances:
41 1 0.00
42 83 0.35
43 146 0.62
44 4 0.02
ACGTcount: A:0.20, C:0.38, G:0.28, T:0.14
Consensus pattern (42 bp):
CCCGCACATCCAAGCACCAAGGTGCCGATGCTGCTCGAGGCT
Found at i:4502 original size:23 final size:23
Alignment explanation
Indices: 4459--4553 Score: 56
Period size: 23 Copynumber: 4.3 Consensus size: 23
4449 CGATGGTGTT
* *
4459 CGAGGCTCCCGCAC-ATCCAAGCC
1 CGAGGTTCTCGCACGAT-CAAGCC
*
4482 CGAGGTTCTCGCACGATCAAGGC
1 CGAGGTTCTCGCACGATCAAGCC
* ***
4505 CTAGG-T-T-GC-CGATGGTGCC
1 CGAGGTTCTCGCACGATCAAGCC
* *
4524 CGAGGTTCTCGTACGATCAAGGC
1 CGAGGTTCTCGCACGATCAAGCC
*
4547 CTAGGTT
1 CGAGGTT
4554 GCCGATGGTG
Statistics
Matches: 52, Mismatches: 15, Indels: 10
0.68 0.19 0.13
Matches are distributed among these distances:
19 10 0.19
20 3 0.06
21 2 0.04
22 2 0.04
23 33 0.63
24 2 0.04
ACGTcount: A:0.19, C:0.32, G:0.29, T:0.20
Consensus pattern (23 bp):
CGAGGTTCTCGCACGATCAAGCC
Found at i:4525 original size:42 final size:42
Alignment explanation
Indices: 4479--5094 Score: 599
Period size: 42 Copynumber: 14.6 Consensus size: 42
4469 GCACATCCAA
* * *
4479 GCCCGAGGTTCTCGCACGATCAAGGCCTAGGTTGCCGATGGT
1 GCCCGAGGCTCCCGCACGACCAAGGCCTAGGTTGCCGATGGT
* * * *
4521 GCCCGAGGTTCTCGTACGATCAAGGCCTAGGTTGCCGATGGT
1 GCCCGAGGCTCCCGCACGACCAAGGCCTAGGTTGCCGATGGT
* * *
4563 GCCCGAGGCTCCCGTACAACCAGGGGCCTAGGTTGCCGATGGT
1 GCCCGAGGCTCCCGCACGACCA-AGGCCTAGGTTGCCGATGGT
* *
4606 GCCCGATGCTCCCCCAC-ATCCAAGGGCCTAGG-TGCCGATGGT
1 GCCCGAGGCTCCCGCACGA-CCAA-GGCCTAGGTTGCCGATGGT
* *
4648 GGCCGAGGCTCCCGCACGACCAAGGGCCTAGG-TGCCAATGGT
1 GCCCGAGGCTCCCGCACGACCAA-GGCCTAGGTTGCCGATGGT
* *
4690 -CCCAAGGCTCTCGCACGACCAAGGGCCTAGGTTGCCGATGGT
1 GCCCGAGGCTCCCGCACGACCAA-GGCCTAGGTTGCCGATGGT
* * *
4732 GCCCGAGGCTACCGCACGACCAGGGGCCTAAGTTGCCGATGGT
1 GCCCGAGGCTCCCGCACGACCA-AGGCCTAGGTTGCCGATGGT
* * * *
4775 GCCCTAGG-TCCCGCAC-ATGCAAGCACCAAGG-TGCCGATGGT
1 GCCCGAGGCTCCCGCACGA-CCAAG-GCCTAGGTTGCCGATGGT
* *
4816 GCCCGAGGCTTCTGCACGACCAAGGGCCTAGGTTGCCGATGGT
1 GCCCGAGGCTCCCGCACGACCAA-GGCCTAGGTTGCCGATGGT
* *
4859 GCCCGAGGCTCCCGCACGACCAGGGGCCTAAGTTGCCGATGGT
1 GCCCGAGGCTCCCGCACGACCA-AGGCCTAGGTTGCCGATGGT
* * * * *
4902 GCCCTAGGGTCCCGCAC-ATGCAAGCACCAAGG-TGCCGATGGT
1 GCCCGAGGCTCCCGCACGA-CCAAG-GCCTAGGTTGCCGATGGT
*
4944 GTCCGAGGCTCCCGCACGACCAAGGGCCTAGG-TGCCGATGGT
1 GCCCGAGGCTCCCGCACGACCAA-GGCCTAGGTTGCCGATGGT
* * * * *
4986 GCCCGAAGCTCTCGCAC-ATCCAAGCACCAAGG-TGCCGGTGGT
1 GCCCGAGGCTCCCGCACGA-CCAAG-GCCTAGGTTGCCGATGGT
* * *
5028 GCCCGAGGCTCCCGCACGACAAACGTCCTAGGTTGCCGATGGC
1 GCCCGAGGCTCCCGCACGACCAA-GGCCTAGGTTGCCGATGGT
* * * *
5071 GTCCAAGGCTCCAGCACGTCCAAG
1 GCCCGAGGCTCCCGCACGACCAAG
5095 CAGCAATGTG
Statistics
Matches: 480, Mismatches: 71, Indels: 46
0.80 0.12 0.08
Matches are distributed among these distances:
41 49 0.10
42 242 0.50
43 189 0.39
ACGTcount: A:0.19, C:0.33, G:0.32, T:0.16
Consensus pattern (42 bp):
GCCCGAGGCTCCCGCACGACCAAGGCCTAGGTTGCCGATGGT
Found at i:4863 original size:127 final size:129
Alignment explanation
Indices: 4479--5046 Score: 667
Period size: 127 Copynumber: 4.5 Consensus size: 129
4469 GCACATCCAA
* * * * * * * *
4479 GCCCGAGGTTCTCGCACGATCA-AGGCCTAGGTTGCCGATGGTGCCCGAGGTTCTCGTACGAT-C
1 GCCCGAGGCTCCCGCACGACCAGGGGCCTAAGTTGCCGATGGTGCCCGAGGCTCCCGCACGATGC
* * * * *
4542 AAG-GCCTAGGTTGCCGATGGTGCCCGAGGCTCCCGTACAACCAGGGGCCTAGGTTGCCGATGGT
66 AAGCACCAAGG-TGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTAGGTTGCCGATGGT
* * * * * *
4606 GCCCGATGCTCCCCCAC-ATCCAAGGGCCT-AGGTGCCGATGGTGGCCGAGGCTCCCGCACGA-C
1 GCCCGAGGCTCCCGCACGA-CCAGGGGCCTAAGTTGCCGATGGTGCCCGAGGCTCCCGCACGATG
** * * * *
4668 CAAGGGCCTAGGTGCCAATGGT-CCCAAGGCTCTCGCACGACCAAGGGCCTAGGTTGCCGATGGT
65 CAAGCACCAAGGTGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTAGGTTGCCGATGGT
* *
4732 GCCCGAGGCTACCGCACGACCAGGGGCCTAAGTTGCCGATGGTGCCCTAGG-TCCCGCAC-ATGC
1 GCCCGAGGCTCCCGCACGACCAGGGGCCTAAGTTGCCGATGGTGCCCGAGGCTCCCGCACGATGC
* *
4795 AAGCACCAAGGTGCCGATGGTGCCCGAGGCTTCTGCACGACCAAGGGCCTAGGTTGCCGATGGT
66 AAGCACCAAGGTGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTAGGTTGCCGATGGT
* *
4859 GCCCGAGGCTCCCGCACGACCAGGGGCCTAAGTTGCCGATGGTGCCCTAGGGTCCCGCAC-ATGC
1 GCCCGAGGCTCCCGCACGACCAGGGGCCTAAGTTGCCGATGGTGCCCGAGGCTCCCGCACGATGC
*
4923 AAGCACCAAGGTGCCGATGGTGTCCGAGGCTCCCGCACGACCAAGGGCCTAGG-TGCCGATGGT
66 AAGCACCAAGGTGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTAGGTTGCCGATGGT
* * * ** * *
4986 GCCCGAAGCTCTCGCAC-ATCCAAGCACC-AAGGTGCCGGTGGTGCCCGAGGCTCCCGCACGA
1 GCCCGAGGCTCCCGCACGA-CCAGGGGCCTAAGTTGCCGATGGTGCCCGAGGCTCCCGCACGA
5047 CAAACGTCCT
Statistics
Matches: 383, Mismatches: 47, Indels: 22
0.85 0.10 0.05
Matches are distributed among these distances:
125 1 0.00
126 115 0.30
127 193 0.50
128 74 0.19
ACGTcount: A:0.18, C:0.33, G:0.33, T:0.16
Consensus pattern (129 bp):
GCCCGAGGCTCCCGCACGACCAGGGGCCTAAGTTGCCGATGGTGCCCGAGGCTCCCGCACGATGC
AAGCACCAAGGTGCCGATGGTGCCCGAGGCTCCCGCACGACCAAGGGCCTAGGTTGCCGATGGT
Found at i:5315 original size:24 final size:24
Alignment explanation
Indices: 5283--5334 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
5273 TTGATATTCT
5283 GGGATGGCTCGCTGCAGCACCGCC
1 GGGATGGCTCGCTGCAGCACCGCC
*
5307 GGGATGGCTCGCTGGAGCACCGCC
1 GGGATGGCTCGCTGCAGCACCGCC
5331 GGGA
1 GGGA
5335 ACCTAACCGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.13, C:0.33, G:0.42, T:0.12
Consensus pattern (24 bp):
GGGATGGCTCGCTGCAGCACCGCC
Found at i:5820 original size:58 final size:59
Alignment explanation
Indices: 5729--5849 Score: 190
Period size: 58 Copynumber: 2.1 Consensus size: 59
5719 GGGAGGGACA
* * *
5729 GGGACGATTCATTCATTGTTGGGTACCGGACATGCAACGGTATCCGAATCCTACC-TTT
1 GGGACGATTCATTCATTATTGGGTACCGAACATGCAACGGTACCCGAATCCTACCTTTT
* *
5787 GGGACGATTCATTCATTATTGGGTACCGAACATGTAACGGTACCCGAATTCTACCTTTT
1 GGGACGATTCATTCATTATTGGGTACCGAACATGCAACGGTACCCGAATCCTACCTTTT
5846 GGGA
1 GGGA
5850 TGGCTCGCCA
Statistics
Matches: 57, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
58 50 0.88
59 7 0.12
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (59 bp):
GGGACGATTCATTCATTATTGGGTACCGAACATGCAACGGTACCCGAATCCTACCTTTT
Found at i:6485 original size:10 final size:10
Alignment explanation
Indices: 6472--6505 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
6462 CAAGAAGTAT
*
6472 GGCATGGCAT
1 GGCATGGCAC
6482 GGCATGGCAC
1 GGCATGGCAC
*
6492 GGCACGGCAC
1 GGCATGGCAC
6502 GGCA
1 GGCA
6506 GAAAATTGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.21, C:0.29, G:0.41, T:0.09
Consensus pattern (10 bp):
GGCATGGCAC
Found at i:13725 original size:39 final size:38
Alignment explanation
Indices: 13600--13818 Score: 220
Period size: 39 Copynumber: 5.7 Consensus size: 38
13590 TCACCAAGGT
*
13600 GCCGATGGTGCCGAGGCTTCGCACGACC-AGGCCT--G
1 GCCGATGGTGCCGAGGCTCCGCACGACCAAGGCCTAGG
* * *
13635 GACGATGGTGCCGA-GCTCC-CATGA-CAGGGGCCTAGG
1 GCCGATGGTGCCGAGGCTCCGCACGACCA-AGGCCTAGG
13671 TGCCGATGGTGGGCCGAGGCTCCGCACGACCAAGGCCTAGG
1 -GCCGATGGT--GCCGAGGCTCCGCACGACCAAGGCCTAGG
13712 GCCGATGGTGGCCGAGGCTCCCGCACGA-CAAGGGCCTAGG
1 GCCGATGGT-GCCGAGGCT-CCGCACGACCAA-GGCCTAGG
*
13752 TCCGATGGTGCCGAGGCTCTCGCACGACCAAGGCCTAGG
1 GCCGATGGTGCCGAGGCTC-CGCACGACCAAGGCCTAGG
** *
13791 TTGCCGATGGTATCGAGGCCCCGC-CGAC
1 --GCCGATGGTGCCGAGGCTCCGCACGAC
13819 AGAGCCTAGT
Statistics
Matches: 156, Mismatches: 12, Indels: 28
0.80 0.06 0.14
Matches are distributed among these distances:
32 1 0.01
33 4 0.03
34 9 0.06
35 13 0.08
36 1 0.01
37 8 0.05
38 1 0.01
39 46 0.29
40 44 0.28
41 27 0.17
42 2 0.01
ACGTcount: A:0.17, C:0.32, G:0.37, T:0.14
Consensus pattern (38 bp):
GCCGATGGTGCCGAGGCTCCGCACGACCAAGGCCTAGG
Found at i:13750 original size:81 final size:75
Alignment explanation
Indices: 13596--13801 Score: 267
Period size: 81 Copynumber: 2.7 Consensus size: 75
13586 AGCCTCACCA
* * *
13596 AGGTGCCGATGGTGCCGAGGCTTCGCACGACC-AGGCCT--GGACGATGGTGCCGAGCTCCCATG
1 AGGTGCCGATGGTGCCGAGGCTCCGCACGACCAAGGCCTAGGGCCGATGGTGCCGAGCTCCCACG
*
13658 ACAGGGGCCT
66 ACAAGGGCCT
13668 AGGTGCCGATGGTGGGCCGAGGCTCCGCACGACCAAGGCCTAGGGCCGATGGTGGCCGAGGCTCC
1 AGGTGCCGATGGT--GCCGAGGCTCCGCACGACCAAGGCCTAGGGCCGATGGT-GCCGA-GCT-C
13733 CGCACGACAAGGGCCT
61 C-CACGACAAGGGCCT
13749 AGGT-CCGATGGTGCCGAGGCTCTCGCACGACCAAGGCCTAGGTTGCCGATGGT
1 AGGTGCCGATGGTGCCGAGGCTC-CGCACGACCAAGGCCTAGG--GCCGATGGT
13802 ATCGAGGCCC
Statistics
Matches: 118, Mismatches: 4, Indels: 15
0.86 0.03 0.11
Matches are distributed among these distances:
72 13 0.11
74 18 0.15
75 6 0.05
77 9 0.08
78 15 0.13
79 22 0.19
80 10 0.08
81 25 0.21
ACGTcount: A:0.17, C:0.31, G:0.38, T:0.15
Consensus pattern (75 bp):
AGGTGCCGATGGTGCCGAGGCTCCGCACGACCAAGGCCTAGGGCCGATGGTGCCGAGCTCCCACG
ACAAGGGCCT
Found at i:13814 original size:79 final size:78
Alignment explanation
Indices: 13596--13827 Score: 277
Period size: 79 Copynumber: 3.0 Consensus size: 78
13586 AGCCTCACCA
* *
13596 AGGTGCCGATGGTGCCGAGGCT-TCGCACGACC-AGGCCT--GGACGATGGTGCCGA-GCTCC-C
1 AGGTGCCGATGGTGCCGAGGCTCTCGCACGACCAAGGCCTAGGGCCGATGGTGCCGAGGCCCCGC
* *
13655 ATGACAGGGGCCT
66 ACGACAAGGGCCT
13668 AGGTGCCGATGGTGGGCCGAGGCTC-CGCACGACCAAGGCCTAGGGCCGATGGTGGCCGAGGCTC
1 AGGTGCCGATGGT--GCCGAGGCTCTCGCACGACCAAGGCCTAGGGCCGATGGT-GCCGAGGC-C
13732 CCGCACGACAAGGGCCT
62 CCGCACGACAAGGGCCT
**
13749 AGGT-CCGATGGTGCCGAGGCTCTCGCACGACCAAGGCCTAGGTTGCCGATGGTATCGAGGCCCC
1 AGGTGCCGATGGTGCCGAGGCTCTCGCACGACCAAGGCCTAGG--GCCGATGGTGCCGAGGCCCC
*
13813 GC-CGAC-AGAGCCT
64 GCACGACAAGGGCCT
13826 AG
1 AG
13828 TCGTGGTCCG
Statistics
Matches: 140, Mismatches: 7, Indels: 21
0.83 0.04 0.12
Matches are distributed among these distances:
72 13 0.09
74 18 0.13
75 6 0.04
77 17 0.12
78 19 0.14
79 26 0.19
80 16 0.11
81 25 0.18
ACGTcount: A:0.18, C:0.31, G:0.37, T:0.14
Consensus pattern (78 bp):
AGGTGCCGATGGTGCCGAGGCTCTCGCACGACCAAGGCCTAGGGCCGATGGTGCCGAGGCCCCGC
ACGACAAGGGCCT
Found at i:14130 original size:24 final size:24
Alignment explanation
Indices: 14098--14151 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
14088 TTTCGATATT
*
14098 CCGGGATGGCTCGCTGGAGCACCG
1 CCGGGATGGCTCACTGGAGCACCG
14122 CCGGGATGGCTCACTGGAGCACCG
1 CCGGGATGGCTCACTGGAGCACCG
14146 CCGGGA
1 CCGGGA
14152 ACCTAACCGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.15, C:0.33, G:0.41, T:0.11
Consensus pattern (24 bp):
CCGGGATGGCTCACTGGAGCACCG
Done.