Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011037.1 Corchorus capsularis cultivar CVL-1 contig11058, whole genome shotgun sequence
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: 18287
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.34
Found at i:39 original size:31 final size:31
Alignment explanation
Indices: 1--332 Score: 359
Period size: 31 Copynumber: 10.7 Consensus size: 31
1 TTGGCGTCGGCATTTGCCGATGCCCATGGCC
1 TTGGCGTCGGCATTTGCCGATGCCCATGGCC
32 TTGGCGTCGGCATTTGCCGATGCCCATGGCC
1 TTGGCGTCGGCATTTGCCGATGCCCATGGCC
* * *
63 TAGGCGTCGGCATTTGCCGATGGCCCGTTGCC
1 TTGGCGTCGGCATTTGCCGAT-GCCCATGGCC
** ** **
95 TTGGTATCGGCATTTGCCGATTG-CGTTGGAA
1 TTGGCGTCGGCATTTGCCGA-TGCCCATGGCC
* * * * * * *
126 TTTG-AT--G-ATGTCCCTTATCCCCTTGGCC
1 TTGGCGTCGGCATTTGCC-GATGCCCATGGCC
* * *
154 TAGGGGTCGGCATTTGCTGATGCCCATGGCC
1 TTGGCGTCGGCATTTGCCGATGCCCATGGCC
* *
185 TTGGCGTCGGTATTTGCCGATGGCCCTTGGCC
1 TTGGCGTCGGCATTTGCCGAT-GCCCATGGCC
* *
217 TTGGCGTCGGCATTTGCTGATGCCCATGTCC
1 TTGGCGTCGGCATTTGCCGATGCCCATGGCC
*
248 TTGACGTCGGCATTTGCCGATGCCCATGGCC
1 TTGGCGTCGGCATTTGCCGATGCCCATGGCC
*
279 TTGGCGTCGGCATTTGCCGATGGCCCTTGGCC
1 TTGGCGTCGGCATTTGCCGAT-GCCCATGGCC
311 TTGGCGTCGGCATTTGCCGATG
1 TTGGCGTCGGCATTTGCCGATG
333 TCCCTTGGTG
Statistics
Matches: 249, Mismatches: 42, Indels: 20
0.80 0.14 0.06
Matches are distributed among these distances:
27 6 0.02
28 9 0.04
29 1 0.00
30 2 0.01
31 142 0.57
32 88 0.35
33 1 0.00
ACGTcount: A:0.10, C:0.29, G:0.32, T:0.30
Consensus pattern (31 bp):
TTGGCGTCGGCATTTGCCGATGCCCATGGCC
Found at i:113 original size:63 final size:62
Alignment explanation
Indices: 1--332 Score: 336
Period size: 63 Copynumber: 5.4 Consensus size: 62
*
1 TTGGCGTCGGCATTTGCCGATGCCCATGGCCTTGGCGTCGGCATTTGCCGATGCCCATGGCC
1 TTGGCGTCGGCATTTGCCGATGCCCATTGCCTTGGCGTCGGCATTTGCCGATGCCCATGGCC
* * ** ** **
63 TAGGCGTCGGCATTTGCCGATGGCCCGTTGCCTTGGTATCGGCATTTGCCGATTG-CGTTGGAA
1 TTGGCGTCGGCATTTGCCGAT-GCCCATTGCCTTGGCGTCGGCATTTGCCGA-TGCCCATGGCC
* * * * * * * * *
126 TTTG-AT--G-ATGTCCCTTAT-CCCCTTGGCCTAGGGGTCGGCATTTGCTGATGCCCATGGCC
1 TTGGCGTCGGCATTTGCC-GATGCCCATT-GCCTTGGCGTCGGCATTTGCCGATGCCCATGGCC
* * *
185 TTGGCGTCGGTATTTGCCGATGGCCC-TTGGCCTTGGCGTCGGCATTTGCTGATGCCCATGTCC
1 TTGGCGTCGGCATTTGCCGAT-GCCCATT-GCCTTGGCGTCGGCATTTGCCGATGCCCATGGCC
* * *
248 TTGACGTCGGCATTTGCCGATGCCCATGGCCTTGGCGTCGGCATTTGCCGATGGCCCTTGGCC
1 TTGGCGTCGGCATTTGCCGATGCCCATTGCCTTGGCGTCGGCATTTGCCGAT-GCCCATGGCC
311 TTGGCGTCGGCATTTGCCGATG
1 TTGGCGTCGGCATTTGCCGATG
333 TCCCTTGGTG
Statistics
Matches: 218, Mismatches: 39, Indels: 25
0.77 0.14 0.09
Matches are distributed among these distances:
58 7 0.03
59 31 0.14
60 4 0.02
62 51 0.23
63 120 0.55
64 5 0.02
ACGTcount: A:0.10, C:0.29, G:0.32, T:0.30
Consensus pattern (62 bp):
TTGGCGTCGGCATTTGCCGATGCCCATTGCCTTGGCGTCGGCATTTGCCGATGCCCATGGCC
Found at i:793 original size:22 final size:23
Alignment explanation
Indices: 768--818 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 23
758 CTTGGGGCCA
768 CTTGGGGCAACCTCGGGGGC-GC
1 CTTGGGGCAACCTCGGGGGCAGC
**
790 CTTGGGGCCTCCTCGGGGGCAGC
1 CTTGGGGCAACCTCGGGGGCAGC
*
813 TTTGGG
1 CTTGGG
819 CCCTAACGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 18 0.72
23 7 0.28
ACGTcount: A:0.06, C:0.29, G:0.45, T:0.20
Consensus pattern (23 bp):
CTTGGGGCAACCTCGGGGGCAGC
Found at i:1144 original size:91 final size:91
Alignment explanation
Indices: 952--1275 Score: 407
Period size: 91 Copynumber: 3.5 Consensus size: 91
942 AGTCCCGATG
* * * * * * *
952 TGGCGTCGGCATTTGCCGATGGCCCATGGCCTTGGCGTCGACATTTGCCGATGGCCTTGTCGGAA
1 TGGCATCGGCATTTGACGATGGCACATGGCCTTGGTGTCGGCATTTGCTGATTG-C--GTCGGAA
*
1017 TTTGATGATGTCCCTTGT-TACATTGGCGT
63 TTTGATGATGTCCCTTGTCTAC-TTGGCAT
**
1046 TGGCATCGGCATTTGACGATGGCATGTGGCCTTGGTGTCGGCATTTGCTGATTGCGTCGGAATTT
1 TGGCATCGGCATTTGACGATGGCACATGGCCTTGGTGTCGGCATTTGCTGATTGCGTCGGAATTT
* *
1111 GATGATGTCCCTTGTCTGCTTGGCAC
66 GATGATGTCCCTTGTCTACTTGGCAT
* * *
1137 TGGCATCGGCTTTTGACGATGGCACGTGGCCTTGGTGTCGGCATTTGCTGATTGCGTCGAAATTT
1 TGGCATCGGCATTTGACGATGGCACATGGCCTTGGTGTCGGCATTTGCTGATTGCGTCGGAATTT
*
1202 GATGATGTCCCTTGTCCACTTGGCAT
66 GATGATGTCCCTTGTCTACTTGGCAT
* * * * **
1228 TAGCATCAGCATTTGCCGATGGCCCATGGCCTTGGAATCGGCATTTGC
1 TGGCATCGGCATTTGACGATGGCACATGGCCTTGGTGTCGGCATTTGC
1276 CGATGCCCAT
Statistics
Matches: 203, Mismatches: 26, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
91 155 0.76
92 2 0.01
93 1 0.00
94 45 0.22
ACGTcount: A:0.14, C:0.23, G:0.30, T:0.32
Consensus pattern (91 bp):
TGGCATCGGCATTTGACGATGGCACATGGCCTTGGTGTCGGCATTTGCTGATTGCGTCGGAATTT
GATGATGTCCCTTGTCTACTTGGCAT
Found at i:1277 original size:32 final size:32
Alignment explanation
Indices: 1236--1561 Score: 285
Period size: 32 Copynumber: 10.4 Consensus size: 32
1226 ATTAGCATCA
**
1236 GCATTTGCCGATGGCCCATGGCCTTGGAATCG
1 GCATTTGCCGATGGCCCATGGCCTTGGCGTCG
1268 GCATTTGCCGAT-GCCCATGGCCTTGGCGTCG
1 GCATTTGCCGATGGCCCATGGCCTTGGCGTCG
* *
1299 GTATTTGCCGATGGTCCATGGCCTTGGCGTCG
1 GCATTTGCCGATGGCCCATGGCCTTGGCGTCG
* * *
1331 GCATTTGCTGATGGCCCATTGCCTTGGCATCG
1 GCATTTGCCGATGGCCCATGGCCTTGGCGTCG
* * ** * **
1363 CCATTTGCCGATTGTGTCC---GAATT---TTAT
1 GCATTTGCCGA-TG-GCCCATGGCCTTGGCGTCG
* ** * * ** *
1391 G-ATGT-CCCTTGTCCCCTTGGAATTGGCATCG
1 GCATTTGCCGATG-GCCCATGGCCTTGGCGTCG
*
1422 GCATTTGCCGATGGCCCTTGGCCTTGGCGTCG
1 GCATTTGCCGATGGCCCATGGCCTTGGCGTCG
* * *
1454 GTAGTTGCCGAT-GCCCATGGCCTTGACGTCG
1 GCATTTGCCGATGGCCCATGGCCTTGGCGTCG
* *
1485 GCACTTGCCGATGGCCCATGGTCTTGGCGTCG
1 GCATTTGCCGATGGCCCATGGCCTTGGCGTCG
*
1517 GCATTTGCCGATGGCCCTTGGCCTTGGCGTCG
1 GCATTTGCCGATGGCCCATGGCCTTGGCGTCG
*
1549 GCATTTGCTGATG
1 GCATTTGCCGATG
1562 TCCCTTGGTG
Statistics
Matches: 237, Mismatches: 45, Indels: 24
0.77 0.15 0.08
Matches are distributed among these distances:
25 5 0.02
26 2 0.01
27 3 0.01
28 6 0.03
31 60 0.25
32 152 0.64
33 6 0.03
34 3 0.01
ACGTcount: A:0.11, C:0.28, G:0.31, T:0.30
Consensus pattern (32 bp):
GCATTTGCCGATGGCCCATGGCCTTGGCGTCG
Found at i:1355 original size:95 final size:95
Alignment explanation
Indices: 1236--1561 Score: 294
Period size: 95 Copynumber: 3.5 Consensus size: 95
1226 ATTAGCATCA
* *
1236 GCATTTGCCGATGGCCCATGGCCTTGGAATCGGCATTTGCCGATGCCCATGGCCTTGGCGTCGGT
1 GCATTTGCCGATGGCCCTTGGCCTTGGCATCGGCATTTGCCGATGCCCATGGCCTTGGCGTCGGT
*
1301 ATTTGCCGATGGTCCATGGCCTTGGCGTCG
66 ATTTGCCGATGGTCCATGGACTTGGCGTCG
* * * ** *
1331 GCATTTGCTGATGGCCCATT-GCCTTGGCATCGCCATTTGCCGATTG----TGTCC---GAAT-T
1 GCATTTGCCGATGGCCC-TTGGCCTTGGCATCGGCATTTGCCGA-TGCCCATGGCCTTGGCGTCG
* * * * * * *
1387 TTATGATGTCC-CTTGTCCCCTTGGAATTGGCATCG
64 GTAT-TTG-CCGATGGT--CCATGGACTTGGCGTCG
* * * * *
1422 GCATTTGCCGATGGCCCTTGGCCTTGGCGTCGGTAGTTGCCGATGCCCATGGCCTTGACGTCGGC
1 GCATTTGCCGATGGCCCTTGGCCTTGGCATCGGCATTTGCCGATGCCCATGGCCTTGGCGTCGGT
* * *
1487 ACTTGCCGATGGCCCATGGTCTTGGCGTCG
66 ATTTGCCGATGGTCCATGGACTTGGCGTCG
* *
1517 GCATTTGCCGATGGCCCTTGGCCTTGGCGTCGGCATTTGCTGATG
1 GCATTTGCCGATGGCCCTTGGCCTTGGCATCGGCATTTGCCGATG
1562 TCCCTTGGTG
Statistics
Matches: 175, Mismatches: 40, Indels: 32
0.71 0.16 0.13
Matches are distributed among these distances:
88 3 0.02
89 7 0.04
90 6 0.03
91 48 0.27
92 4 0.02
94 4 0.02
95 92 0.53
96 5 0.03
97 5 0.03
98 1 0.01
ACGTcount: A:0.11, C:0.28, G:0.31, T:0.30
Consensus pattern (95 bp):
GCATTTGCCGATGGCCCTTGGCCTTGGCATCGGCATTTGCCGATGCCCATGGCCTTGGCGTCGGT
ATTTGCCGATGGTCCATGGACTTGGCGTCG
Found at i:1428 original size:186 final size:186
Alignment explanation
Indices: 1137--1556 Score: 556
Period size: 186 Copynumber: 2.3 Consensus size: 186
1127 TGCTTGGCAC
* * * * * ** * *
1137 TGGCATCGGCTTTTGACGATGGCACGTGGCCTTGGTGTCGGCATTTGCTGATTGCGTCGAAATTT
1 TGGCGTCGGCATTTGCCGATGGCCCTTGGCCTTGGCATCGCCATTTGCCGATTGCGTCGAAATTT
*
1202 GATGATGTCCCTTGTCCACTTGGCATTAGCATCAGCATTTGCCGATGGCCCATGGCCTTGGAATC
66 GATGATGTCCCTTGTCCACTTGGAATTAGCATCAGCATTTGCCGATGGCCCATGGCCTTGGAATC
* * * * *
1267 GGCATTTGCCGATGCCCATGGCCTTGGCGTCGGTATTTGCCGATGGTCCATGGCCT
131 GGCAGTTGCCGATGCCCATGGCCTTGACGTCGGCACTTGCCGATGGCCCATGGCCT
* *
1323 TGGCGTCGGCATTTGCTGATGGCCCATT-GCCTTGGCATCGCCATTTGCCGATTGTGTCCG-AAT
1 TGGCGTCGGCATTTGCCGATGGCCC-TTGGCCTTGGCATCGCCATTTGCCGATTGCGT-CGAAAT
* * * * * **
1386 TTTATGATGTCCCTTGTCCCCTTGGAATTGGCATCGGCATTTGCCGATGGCCCTTGGCCTTGGCG
64 TTGATGATGTCCCTTGTCCACTTGGAATTAGCATCAGCATTTGCCGATGGCCCATGGCCTTGGAA
* *
1451 TCGGTAGTTGCCGATGCCCATGGCCTTGACGTCGGCACTTGCCGATGGCCCATGGTCT
129 TCGGCAGTTGCCGATGCCCATGGCCTTGACGTCGGCACTTGCCGATGGCCCATGGCCT
* *
1509 TGGCGTCGGCATTTGCCGATGGCCCTTGGCCTTGGCGTCGGCATTTGC
1 TGGCGTCGGCATTTGCCGATGGCCCTTGGCCTTGGCATCGCCATTTGC
1557 TGATGTCCCT
Statistics
Matches: 202, Mismatches: 29, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
185 2 0.01
186 197 0.98
187 3 0.01
ACGTcount: A:0.12, C:0.27, G:0.30, T:0.30
Consensus pattern (186 bp):
TGGCGTCGGCATTTGCCGATGGCCCTTGGCCTTGGCATCGCCATTTGCCGATTGCGTCGAAATTT
GATGATGTCCCTTGTCCACTTGGAATTAGCATCAGCATTTGCCGATGGCCCATGGCCTTGGAATC
GGCAGTTGCCGATGCCCATGGCCTTGACGTCGGCACTTGCCGATGGCCCATGGCCT
Found at i:1446 original size:91 final size:91
Alignment explanation
Indices: 952--1465 Score: 403
Period size: 91 Copynumber: 5.6 Consensus size: 91
942 AGTCCCGATG
* * * * *
952 TGGCGTCGGCATTTGCCGATGGCCCATGGCCTTGGCGTCGACATTTGCCGATGGCCTTGTCGGAA
1 TGGCATCGGCATTTGCCGATGGCCCTTGGCCTTGGCGTCGGCATTTGCCGATTG---TGTCCGAA
** * *
1017 TTTGATGATGTCCCTTGTTACATTGGCGT
63 TTTGATGATGTCCCTTGTCCCCTTGGCAT
* * * * * *
1046 TGGCATCGGCATTTGACGATGG-CATGTGGCCTTGGTGTCGGCATTTGCTGATTGCGTCGGAATT
1 TGGCATCGGCATTTGCCGATGGCCCT-TGGCCTTGGCGTCGGCATTTGCCGATTGTGTCCGAATT
** *
1110 TGATGATGTCCCTTGTCTGCTTGGCAC
65 TGATGATGTCCCTTGTCCCCTTGGCAT
* * * * * * *
1137 TGGCATCGGCTTTTGACGATGGCACGTGGCCTTGGTGTCGGCATTTGCTGATTGCGT-CGAAATT
1 TGGCATCGGCATTTGCCGATGGCCCTTGGCCTTGGCGTCGGCATTTGCCGATTGTGTCCG-AATT
*
1201 TGATGATGTCCCTTGTCCACTTGGCAT
65 TGATGATGTCCCTTGTCCCCTTGGCAT
* * * ** *
1228 TAGCATCAGCATTTGCCGATGGCCCATGGCCTTGGAATCGGCATTTGCCGA-TGCCCATGGCCTT
1 TGGCATCGGCATTTGCCGATGGCCCTTGGCCTTGGCGTCGGCATTTGCCGATTG----TGTCC--
*** * * * * * * *
1292 GGCGTCGGT-ATTTGCCGATGGT--CCATGGCCT
60 GAATTTGATGATGT-CC-CTTGTCCCCTTGGCAT
* * * *
1323 TGGCGTCGGCATTTGCTGATGGCCCATT-GCCTTGGCATCGCCATTTGCCGATTGTGTCCGAATT
1 TGGCATCGGCATTTGCCGATGGCCC-TTGGCCTTGGCGTCGGCATTTGCCGATTGTGTCCGAATT
* *
1387 TTATGATGTCCCTTGTCCCCTTGGAAT
65 TGATGATGTCCCTTGTCCCCTTGGCAT
* *
1414 TGGCATCGGCATTTGCCGATGGCCCTTGGCCTTGGCGTCGGTAGTTGCCGAT
1 TGGCATCGGCATTTGCCGATGGCCCTTGGCCTTGGCGTCGGCATTTGCCGAT
1466 GCCCATGGCC
Statistics
Matches: 331, Mismatches: 71, Indels: 39
0.75 0.16 0.09
Matches are distributed among these distances:
89 3 0.01
90 10 0.03
91 204 0.62
92 4 0.01
93 1 0.00
94 45 0.14
95 52 0.16
96 8 0.02
97 4 0.01
ACGTcount: A:0.13, C:0.25, G:0.30, T:0.32
Consensus pattern (91 bp):
TGGCATCGGCATTTGCCGATGGCCCTTGGCCTTGGCGTCGGCATTTGCCGATTGTGTCCGAATTT
GATGATGTCCCTTGTCCCCTTGGCAT
Found at i:2028 original size:22 final size:22
Alignment explanation
Indices: 1973--2029 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
1963 CATGCACCTC
1973 GCACCTTGGGGCCTCCTCGGGG
1 GCACCTTGGGGCCTCCTCGGGG
*
1995 GCGCCTTGGGGCCTCCTCGGGG
1 GCACCTTGGGGCCTCCTCGGGG
* *
2017 GCACTTTTGGGCC
1 GCACCTTGGGGCC
2030 CTAACGTGGG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.04, C:0.35, G:0.40, T:0.21
Consensus pattern (22 bp):
GCACCTTGGGGCCTCCTCGGGG
Found at i:3278 original size:21 final size:21
Alignment explanation
Indices: 3254--3298 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
3244 TTCCAAAACG
*
3254 GTTAGTTCTTCAT-CTTTTGGT
1 GTTAGTTATTC-TCCTTTTGGT
*
3275 GTTAGTTATTCTCCTTTTGTT
1 GTTAGTTATTCTCCTTTTGGT
3296 GTT
1 GTT
3299 CAATCTTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.09, C:0.13, G:0.18, T:0.60
Consensus pattern (21 bp):
GTTAGTTATTCTCCTTTTGGT
Found at i:4504 original size:325 final size:323
Alignment explanation
Indices: 3844--4584 Score: 704
Period size: 325 Copynumber: 2.3 Consensus size: 323
3834 TGTACTCGAC
* * * * * *
3844 TTCGACTAAAAAATGACCCGAATTTTTTTTTCTCATTTTTTTTACACAATATTCAGAAAAAATAT
1 TTCGGCTAAAAACTGACCCAAATTTTTTTTTCTCATCTTTTGTACACAATACTCAGAAAAAATAT
*
3909 ATAATTCAACGCCAAAAAGATTGAAGGGTTTTACACACTTCTAATACTGTTTTTCTTTTTTTTTT
66 ATAATTCAACGCCAAAAAGATTGAAGGCTTTTACACACTTCTAATACTGTTTTTCTTTTTTTTTT
*
3974 CCTAAATTTATTTCTAATTAAATCGAAAAAAGATTTAGATGTTCGTAAAAACAAACAAATCCTTA
131 CCTAAATTTATTTCTAATTAAATCGAAAAAAGATTTAGATGCTCGT--AAACAAACAAATCCTTA
* * * * * * *
4039 ATTCCAATGTGATTGTAATTTGGTTCGATGAATATAACTATTTCGATGAGTCTTTTTGCCAAAAA
194 AATCCAATGTGATTGTAATTTAGTTCGATGAATATAACCATTTCGAGGAATCTTTCTACCAAAAA
* * * ** * * *
4104 TCATGAAAATTGAGCTGCGGCCACGGAACGCGGAGTTAGCCAAAACCATGATGGTTCGTACATAA
259 TCATGAAAACTGAGCT-CGGCCACGAAACGCGGAGTTAGCAAAAAAAATGATGGCTAGTACACAA
4169 T
323 T
*
4170 TTTGGCTAAAAACTGA-CCAAATTTTTTTTTCTCAATCTTTTGT-CACAATACTCAG-AAAAATA
1 TTCGGCTAAAAACTGACCCAAATTTTTTTTTCTC-ATCTTTTGTACACAATACTCAGAAAAAATA
* * * *
4232 TGTAATTCAACGTCAAAATA-ATTAGAAGGCTTTT-CTCGCTTCTAATA-TAGTTTTTCCTTTTA
65 TATAATTCAACGCCAAAA-AGATT-GAAGGCTTTTACACACTTCTAATACT-GTTTTT-CTTTT-
* *
4294 TTTCTTT-C-GAATTTATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGT-AA-AAA-AAAT
125 TTT-TTTCCTAAATTTATTTCTAATTAAATCGAAAAAAGATTTAGATGCTCGTAAACAAACAAAT
* * * * **
4354 -GTTAAATCCATTGTGGTTG-AGATTTAGTTCGATGAATGTCGCCATTTCGAGGAATCTTTCTAC
189 CCTTAAATCCAATGTGATTGTA-ATTTAGTTCGATGAATATAACCATTTCGAGGAATCTTTCTAC
* * * ***
4417 CAAAAATCATTAAAACTGAG-TCATGGCCTCGAAAACGTGTTTTTAGCAAAAAAAAAAATGTCAT
253 CAAAAATCATGAAAACTGAGCTC--GGCCACG-AAACGCGGAGTTAGC---AAAAAAAATG--AT
4481 GGCTAGTACACAAT
310 GGCTAGTACACAAT
* * * * * *
4495 TTCGGCTAAAAACTTACCCGAAAGATGTTCTTTCTCAAT-TTTTTTACAAAATACTC-GAAGAAA
1 TTCGGCTAAAAACTGACCC-AAA-TTTTTTTTTCTC-ATCTTTTGTACACAATACTCAGAA-AAA
* *
4558 ATAAATAATTCAACGCAAAAAAAGATT
62 ATATATAATTCAACGC-CAAAAAGATT
4585 AAATTCAAAC
Statistics
Matches: 338, Mismatches: 53, Indels: 44
0.78 0.12 0.10
Matches are distributed among these distances:
317 1 0.00
318 2 0.01
319 72 0.21
320 14 0.04
321 3 0.01
322 2 0.01
323 8 0.02
324 43 0.13
325 109 0.32
326 26 0.08
327 12 0.04
328 22 0.07
329 17 0.05
330 7 0.02
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (323 bp):
TTCGGCTAAAAACTGACCCAAATTTTTTTTTCTCATCTTTTGTACACAATACTCAGAAAAAATAT
ATAATTCAACGCCAAAAAGATTGAAGGCTTTTACACACTTCTAATACTGTTTTTCTTTTTTTTTT
CCTAAATTTATTTCTAATTAAATCGAAAAAAGATTTAGATGCTCGTAAACAAACAAATCCTTAAA
TCCAATGTGATTGTAATTTAGTTCGATGAATATAACCATTTCGAGGAATCTTTCTACCAAAAATC
ATGAAAACTGAGCTCGGCCACGAAACGCGGAGTTAGCAAAAAAAATGATGGCTAGTACACAAT
Found at i:4947 original size:376 final size:371
Alignment explanation
Indices: 4263--4954 Score: 921
Period size: 376 Copynumber: 1.8 Consensus size: 371
4253 TTAGAAGGCT
* * *
4263 TTTCTCGCTTCTAATATAGTTTTTCCTTTTATTTCTTTCGAATTTATTTCTAATTAAATCGAAAC
1 TTTCACGCTTCTAATATAGTTTTTCCATTTATTTC--TCGAATTAATTTCTAATTAAATCGAAAC
* * *
4328 AAGATTTAGATGCTCGTAAAAAAAATGTTAAATCCATTGTGGTTGAGATTTAGTTCGATGAATGT
64 AAGATTCAGATGCTCGTAAAAAAAATCTTAAATCCATTGTAGTTGAGATTTAGTTCGATGAATGT
* **
4393 CGCCATTTCGAGGAATCTTTCTACCAAAAATCATTAAAACTGAGTCATGGCCTCGAAAACGTGTT
129 AGCCATTTCGAGGAATCTTTCTACCAAAAATCATTAAAACTGAGTCATGGCCTCGAAAACGCATT
*
4458 TTTAGCAAAAAAAAAAATGTCATGGCTAGTACACAATTTCGGCTAAAAACTTACCCGAAAGATGT
194 TTTAGC---AAAAAAAACGTCATGGCTAGTACACAATTTCGGCTAAAAACTTACCCGAAAGATGT
*
4523 TCTTTCTCAATTTTTTTACAAAATACTCGAAGAAAATAAATAATTCAACGCAAAAAAAGATTAAA
256 TCTTTCTCAATTTTTTTACAAAATACTCGAAAAAAATAAATAATTCAACGCAAAAAAAGATTAAA
4588 TTCAAACAAGATCATTAATATCGTATTTTTTTACAAAATACCCGAAGGGCA
321 TTCAAACAAGATCATTAATATCGTATTTTTTTACAAAATACCCGAAGGGCA
*
4639 TTTCACGCTTCTAATATCGTTTTTCCATTT-TTTC-CGAATTAATTT-TAATTAAATTC-AAACA
1 TTTCACGCTTCTAATATAGTTTTTCCATTTATTTCTCGAATTAATTTCTAATTAAA-TCGAAACA
* * *
4700 AGATTCAGTTGCTCGTTAAAACAAATCCTTAAATCCATTGTAGTTGAGATTTGGTTCGATGAATG
65 AGATTCAGATGCTCG-TAAAAAAAAT-CTTAAATCCATTGTAGTTGAGATTTAGTTCGATGAATG
** * * **
4765 TAGTTATTTCGAGGAGTTTTTCTGTCAAAAATCATTAAAACTAAGCTGAGTCTCATGGCCTCG-A
128 TAGCCATTTCGAGGAATCTTTCTACCAAAAATCATT--AA--AA-CTGAG--TCATGGCCTCGAA
* * * * *
4829 AACGCATTTTTAGC-AAAAAACCGTCATGGTTAGTACACGATTTCGGCTAAAAGCTTACTCGAAA
186 AACGCATTTTTAGCAAAAAAAACGTCATGGCTAGTACACAATTTCGGCTAAAAACTTACCCGAAA
* * *
4893 GATTTTTTTTTCTCAATTTTTTTACAAAATACTC-AAAAAAATTACATAATTCAACGCAAAAA
251 GA-TGTTCTTTCTCAATTTTTTTACAAAATACTCGAAAAAAA-TAAATAATTCAACGCAAAAA
4955 TGATTGAAGG
Statistics
Matches: 275, Mismatches: 29, Indels: 24
0.84 0.09 0.07
Matches are distributed among these distances:
371 26 0.09
372 21 0.08
373 64 0.23
375 58 0.21
376 75 0.27
377 2 0.01
378 5 0.02
379 13 0.05
380 11 0.04
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (371 bp):
TTTCACGCTTCTAATATAGTTTTTCCATTTATTTCTCGAATTAATTTCTAATTAAATCGAAACAA
GATTCAGATGCTCGTAAAAAAAATCTTAAATCCATTGTAGTTGAGATTTAGTTCGATGAATGTAG
CCATTTCGAGGAATCTTTCTACCAAAAATCATTAAAACTGAGTCATGGCCTCGAAAACGCATTTT
TAGCAAAAAAAACGTCATGGCTAGTACACAATTTCGGCTAAAAACTTACCCGAAAGATGTTCTTT
CTCAATTTTTTTACAAAATACTCGAAAAAAATAAATAATTCAACGCAAAAAAAGATTAAATTCAA
ACAAGATCATTAATATCGTATTTTTTTACAAAATACCCGAAGGGCA
Found at i:6874 original size:630 final size:638
Alignment explanation
Indices: 6095--7306 Score: 1589
Period size: 630 Copynumber: 1.9 Consensus size: 638
6085 AACAAACCCG
* * * * * *
6095 AAAATTTTTTTTCTCAATTTTTTGCCACAATGCTCAGGAAAAAATATATAATTCAGCGCCAAAAG
1 AAAAATTTTTTTCTCAATTTTTTGACACAATGCTCAGGAAAAAATATATAATGCAACACCAAAAA
**
6160 GATTGAAGGGTTTTTCACGCTTCTAATATCATTTTCCACATTTTTCCTAATTAATTTCTAATAAA
66 GATTGAAGGACTTTTCACGCTTCTAATATCATTTTCCACATTTTTCCTAATTAATTTCTAATAAA
* * *
6225 ATCAAAACAAACTTCAGATGCTCGTTAAAACAAATCCTTAAATCCAATGTGGCTTAGATTTGGTT
131 ATCAAAACAAAATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTT
6290 CGATGAATATAGACAGTTCAAAGAGTCATTACGCCAAAAATCATGCAAAACTGAGCCAT-GGCCC
196 CGATGAATATAGACAGTTCAAAGAGTCATTACGCCAAAAATCATGCAAAACTGAG-C-TGGGCCC
* * *
6354 TGA-AACGCATTTTTAACCAAAAATAGCG-T-T-C-AC-A-ATTTCGGCTAAAATTCT-G-TAAA
259 TCAGAACGCATTTTTAACCAAAAATAGCGATGTACGACTAGATTTCGCCTAAAATACTCGATAAA
* *
6410 AATTGTCCCGAAAATTTTTTCCTCAATT-TTTGCCACAATACTT-AGAAAAAAATATATAATTCA
324 AACTGACCCG-AAATTTTTTCCTCAATTCTTTGCCACAATA-TTCAG-AAAAAATATATAATTCA
* * * * *
6473 ATGCCAAAAAAATTGAAAGGTTTTTCACGTTTTTAATGTCGTTTTTC-CATTTTTCCAAGTTAAT
386 ACGCCAAAAAAATTGAAAGGTTTTTCACGCTTCTAATATCGTTTCTCTCATTTTTCCAA-TTAAT
6537 TTCTAAGTAAATCGAAACAAGATTCA-ATGCTCGTAAAAACAAATAC-TTAAATCCAATGTGACT
450 TTCTAAGTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAAT-CTTTAAATCCAATGTGACT
* * * **
6600 GAGATTT-GTTAAGATTAATATAAATATTTCATGGAGTCTTTATGCCAAAAATCATGCAAAACTG
514 GAGATTTCGTTAA-ATGAATATAAATATTTCAAGGAGTCCTTACCCCAAAAATCATGCAAAACTG
6664 AGTCGGGGTCCCGAAACGCGTTTTTACCCAAAGTAGACGATTTTCGGCTAAAAACTGACTC
578 AGTCGGGGTCCCGAAACGCGTTTTTACCCAAAGTAGACGATTTTCGGCTAAAAACTGACTC
* * * *
6725 AAAAATTTTTTTCTCAATTTTTTTACACAATTCTCA-GAAAAAATATATTATGCAACACTAAAAA
1 AAAAATTTTTTTCTCAATTTTTTGACACAATGCTCAGGAAAAAATATATAATGCAACACCAAAAA
* *
6789 GATTGAAGGACTTTTCACGCTTCTAATATCGTTTTTC-CATTTTT-CTGAGAATTAATTTCTAAT
66 GATTGAAGGACTTTTCACGCTTCTAATATCATTTTCCACATTTTTCCT---AATTAATTTCTAAT
* *
6852 TAAATCGAAACAAAATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTG
128 AAAATCAAAACAAAATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTG
* * * * * * *
6917 GTTCGATGATTATAGATATTTCAAGGAGTCGTTACGTCAAAAATCATGCAAAACTGAGCTGGGGC
193 GTTCGATGAATATAGACAGTTCAAAGAGTCATTACGCCAAAAATCATGCAAAACTGAGCTGGGCC
* * * * * * * *
6982 CTCAGAATGCGTTTTTATCCAACAATCGTGATGTAACGTGCTAGATTTCGCCTAAACTACTCGAA
258 CTCAGAACGCATTTTTAACCAAAAATAGCGATGT-ACG-ACTAGATTTCGCCTAAAATACTCG-A
*
7047 TAAAAACTGACCCGAAATTTTTTCTTCAATTCTTTGCCACAATATTCAGAAAAAATATATAATTC
320 TAAAAACTGACCCGAAATTTTTTCCTCAATTCTTTGCCACAATATTCAGAAAAAATATATAATTC
* * ** *
7112 AACGCCAAAAATATTGAAGGGTTTTTCACGCTTCTAATATCGTTTCTCTTTTTTTTCGAATTAAT
385 AACGCCAAAAAAATTGAAAGGTTTTTCACGCTTCTAATATCGTTTCTCTCATTTTTCCAATTAAT
* * * **
7177 TTCTAATTTAATCGAAACCAGATTCAGATGCTCGTAAAAACAAATCTTTAAATCCAATGTGGGTG
450 TTCTAAGTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCTTTAAATCCAATGTGACTG
* * * *
7242 AGATTTCGTTTAATGAATATAGATATTTTAAGGTGTCCTTACCCCAAAAATCATGCAAAACTGAG
515 AGATTTCGTTAAATGAATATAAATATTTCAAGGAGTCCTTACCCCAAAAATCATGCAAAACTGAG
7307 CCAAGATCTC
Statistics
Matches: 496, Mismatches: 64, Indels: 33
0.84 0.11 0.06
Matches are distributed among these distances:
627 2 0.00
628 8 0.02
629 62 0.12
630 177 0.36
631 1 0.00
632 1 0.00
634 1 0.00
636 1 0.00
637 1 0.00
638 14 0.03
639 1 0.00
640 104 0.21
641 119 0.24
642 4 0.01
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.33
Consensus pattern (638 bp):
AAAAATTTTTTTCTCAATTTTTTGACACAATGCTCAGGAAAAAATATATAATGCAACACCAAAAA
GATTGAAGGACTTTTCACGCTTCTAATATCATTTTCCACATTTTTCCTAATTAATTTCTAATAAA
ATCAAAACAAAATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTT
CGATGAATATAGACAGTTCAAAGAGTCATTACGCCAAAAATCATGCAAAACTGAGCTGGGCCCTC
AGAACGCATTTTTAACCAAAAATAGCGATGTACGACTAGATTTCGCCTAAAATACTCGATAAAAA
CTGACCCGAAATTTTTTCCTCAATTCTTTGCCACAATATTCAGAAAAAATATATAATTCAACGCC
AAAAAAATTGAAAGGTTTTTCACGCTTCTAATATCGTTTCTCTCATTTTTCCAATTAATTTCTAA
GTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCTTTAAATCCAATGTGACTGAGATTT
CGTTAAATGAATATAAATATTTCAAGGAGTCCTTACCCCAAAAATCATGCAAAACTGAGTCGGGG
TCCCGAAACGCGTTTTTACCCAAAGTAGACGATTTTCGGCTAAAAACTGACTC
Found at i:9522 original size:14 final size:14
Alignment explanation
Indices: 9477--9514 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
9467 GGACTAGCCG
*
9477 CTCCTCTCTCCCCTT
1 CTCC-CTCTCCTCTT
9492 CTCCCTCTCCTCTT
1 CTCCCTCTCCTCTT
9506 CTCCCTCTC
1 CTCCCTCTC
9515 TAGTTCTCGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 18 0.82
15 4 0.18
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (14 bp):
CTCCCTCTCCTCTT
Found at i:11214 original size:326 final size:318
Alignment explanation
Indices: 10601--11344 Score: 816
Period size: 326 Copynumber: 2.3 Consensus size: 318
10591 TAGATTTCGA
* * * * * *
10601 CTAATTAGATCAAAACAAAATTTAGCTTCTCATAAAAACAAATCCTTAAATCCAATGTGACTT-A
1 CTAATTAAATCAAAAC-AAATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTG-GTTGA
* * * *
10665 GATTTGGTTCGATGAATTTAGATATTTTAAAGAGTTCTTATGCCAAAAATCAGGCAAAATTGAGC
64 GATTTGGTTCGATGAATATAGATA-TTTCAAG-GTTCTTATGCCAAAAACCAGGCAAAACTGAGC
* * * *
10730 CAAAGTCCCAAAACGGTTTTTAGCCAAAAACCGTAATGGTTATTACACGAACTCGGTTAAAAACT
127 CAAAGCCCCAAAACGGTTCTTAGCCAAAAACCGTAATGGTTAATACACGAACTCGGCTAAAAACT
* * *
10795 AACCTGAAAATTTTTTTTCTCATTTTCTTGCCACAATAGTCAATAAAAATATATAATTGAACGCC
192 AACCCGAAAATTTTTTTTCTAATTTTCTTGCCACAATACTCAATAAAAATATATAATTGAACGCC
* * * * * *
10860 AATGTGATTGAAGTGCTTTTCTCGCTTCTAATATCGCTTTTCCATTTTTTTTGTTCCGAATTTAT
257 AA-GAGATTGAAGGGATTTTCACGCTTCTAATATCG-TTTTCCA--ATTTTT-TTCCGAATTAAT
10925 TT
317 TT
*
10927 CTAATTAAATCAAAACAAGATTCAGATGCTCGTAAAAACAAATCTTTAAATCCAATGTGGTTGAG
1 CTAATTAAATCAAAACAA-ATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGTTGAG
* * * ** * *
10992 ATCTGGTTAGATGAATATAGATATTTCAAGGTGTCGTTATGCCAACAACCATTCGAAACTGAGTC
65 ATTTGGTTCGATGAATATAGATATTTCAAGGT-TC-TTATGCCAAAAACCAGGCAAAACTGAGCC
* * * * * * **
11057 -GAGACCCCGAAACGCGTTCTTAGCTAAAAATCGTGATGGTTAATGCACGATTTCGGCTAAAAAC
128 AAAG-CCCCAAAACG-GTTCTTAGCCAAAAACCGTAATGGTTAATACACGAACTCGGCTAAAAAC
* **
11121 TAACCCG-AAATTTTTTTTCTTAATTTT-TTGCCACAATACTCAGA-AAAAATATATAATTTAGT
191 TAACCCGAAAATTTTTTTTC-TAATTTTCTTGCCACAATACTCA-ATAAAAATATATAATTGAAC
* * *
11183 GCCTTAA-AGATTGATGGGATTTTCACGCTTCTAATATCGTTTTTCAATTTTTTTCCTAATTAAT
254 GCC--AAGAGATTGAAGGGATTTTCACGCTTCTAATATCGTTTTCCAATTTTTTTCCGAATTAAT
11247 TT
317 TT
* * * * *
11249 CTAATTAAATCGAAACAAACTTCAGATGCTCGTAAAAATAAATCCTTGAATCCAATGTAGCTGAG
1 CTAATTAAATCAAAACAAA-TTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGTTGAG
*
11314 ATTTGTTTCGATGAATATAGATATTTCAAGG
65 ATTTGGTTCGATGAATATAGATATTTCAAGG
11345 AGTCCATACC
Statistics
Matches: 353, Mismatches: 54, Indels: 26
0.82 0.12 0.06
Matches are distributed among these distances:
321 1 0.00
322 97 0.27
323 5 0.01
324 2 0.01
325 20 0.06
326 173 0.49
327 53 0.15
328 2 0.01
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.35
Consensus pattern (318 bp):
CTAATTAAATCAAAACAAATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGTTGAGA
TTTGGTTCGATGAATATAGATATTTCAAGGTTCTTATGCCAAAAACCAGGCAAAACTGAGCCAAA
GCCCCAAAACGGTTCTTAGCCAAAAACCGTAATGGTTAATACACGAACTCGGCTAAAAACTAACC
CGAAAATTTTTTTTCTAATTTTCTTGCCACAATACTCAATAAAAATATATAATTGAACGCCAAGA
GATTGAAGGGATTTTCACGCTTCTAATATCGTTTTCCAATTTTTTTCCGAATTAATTT
Found at i:16206 original size:330 final size:323
Alignment explanation
Indices: 15716--16954 Score: 1197
Period size: 330 Copynumber: 3.8 Consensus size: 323
15706 AATTCTTCAG
* * * *
15716 TTCTTTGCCACAATACTCAG-AAAAAGATATAATTTAACGCCAAAAAGATT-AA-AGATTTTCAC
1 TTCTTTGCCACAATACTCAGAAAAAATATATAATTCAATGCCAAAAAGATTGAAGAGTTTTTCAC
* * * * *
15778 GCTTCTAATATCGTTTCTCTTTTTCTTTTTTTTTTGAATTAATTTCTAATTTAATCGAAACCAGA
66 GCTTCTAATATCG------TTTTTCCTTTTTATTCGAATTAATTTCTAATTAAATCGAAACAAGA
* * * * ** *
15843 TTCAGATACTAGTAAAAAAAAATCCTCAAATCCAATGTGGTTGAGATTTCATTTAATGAATATAG
125 TTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGTTGAGATTTGGTTCAATGAATATAG
* * * * *
15908 ATATTTCAATGAAACCTTACCCCAAAAATCATGCACAACTGAGCCGTGGTCC-CGGAACGCGTTT
190 ATATTTCAAGGAATCCTTACGCCAAAAATCATGCAAAACTGAGCCG-GGGCCTCGGAACGCGTTT
* * * *
15972 TTAG-CAAAAGCCGTGATAGTTAATATACGATTTCAGCTAATATTTTGCAAAAACTGACCTAATT
254 TTAGCCAAAAACCGTGATGGTTAATACACGATTTCAGCTAA-A---T-CAAAAACTGA-CAAATT
*
16036 TTTTTTTTCAA
313 TTTTTTCTCAA
* * *
16047 TTCTTTGCCACGATACTTAGAAAAAATATATAATTCAAAT-CCAAAAAAATTGAAGAGTTTTTCA
1 TTCTTTGCCACAATACTCAGAAAAAATATATAATTC-AATGCCAAAAAGATTGAAGAGTTTTTCA
** *
16111 CGCAGCTAATATCGTTTTTCCATTTTTATTCTGAATTTATTTCTAATTAAATCGAAACAAGATTC
65 CGCTTCTAATATCGTTTTTCC-TTTTTATTC-GAATTAATTTCTAATTAAATCGAAACAAGATTC
*
16176 AGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTCAATGAATATAGATA
128 AGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGTTGAGATTTGGTTCAATGAATATAGATA
* * * * ***
16241 TTTTAAGGAATCCTTACACCAAAAATCATGCAAAACTAAGTCGGGGCCAAAGAACGCGTTTTTAG
193 TTTCAAGGAATCCTTACGCCAAAAATCATGCAAAACTGAGCCGGGGCCTCGGAACGCGTTTTTAG
* * * * *
16306 CCAAAAACCGTGATGGTT-GTACACGAATTCGGC----T-AAAAACTGTCGAATATTTTTATTCT
258 CCAAAAACCGTGATGGTTAATACACGATTTCAGCTAAATCAAAAACTGAC-AA-ATTTTTTTTCT
16365 C-A
321 CAA
* * * * *
16367 TTTTTTGCCACAATAATCAGAAAAAATATATAATTCAATGCCTAAATGATTGAAGGGCCTTTTT-
1 TTCTTTGCCACAATACTCAGAAAAAATATATAATTCAATGCCAAAAAGATTGAAGAG--TTTTTC
* * * * *
16431 -CGCTTCTTATATCATTTTTCCTTTTTTTTCGAATTTATTTCTAATCAAATCGAAACAAGATTCA
64 ACGCTTCTAATATCGTTTTTCCTTTTTATTCGAATTAATTTCTAATTAAATCGAAACAAGATTCA
* * **
16495 GATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGTTGAAATCTGGTTGGATGAATATAGATAT
129 GATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGTTGAGATTTGGTTCAATGAATATAGATAT
** * ** ** * * * * *
16560 TTCAAGGTGT-CTCTATGCCAAAAATGCATTTAAAACTGAGTTGAGACCTTGAAACGCGTTCTTA
194 TTCAAGGAATCCT-TACGCCAAAAAT-CATGCAAAACTGAGCCGGGGCCTCGGAACGCGTTTTTA
* * * * *****
16624 GCCAAAAACCATGATGGTTAATACACGATTT-AGTTAAA--AACAAACCCGAAAAAAAAAATTTC
257 GCCAAAAACCGTGATGGTTAATACACGATTTCAGCTAAATCAA-AAA-CTGACAAATTTTTTTTC
16686 TCAA
320 TCAA
* * * * * *
16690 TTTTTTGCCACAATGCTCAGGAAAAATATATAATTCAGTGCCAAAAGGATTGAAGGGTTTTTCAC
1 TTCTTTGCCACAATACTCAGAAAAAATATATAATTCAATGCCAAAAAGATTGAAGAGTTTTTCAC
* * *
16755 GCTTCTAATATCGTTTTTCCACTTTTTA-TCGAATTAATTTCTAATTAAATAGAAATAAGCTTCA
66 GCTTCTAATATCGTTTTT-C-CTTTTTATTCGAATTAATTTCTAATTAAATCGAAACAAGATTCA
* * * * *
16819 GATGCTCATCAAAACAAATCCTTGAATCCAATGTGGCTT-AGATTTGGTTCGATGAATATAGACA
129 GATGCTCGTAAAAACAAATCCTTAAATCCAATGTGG-TTGAGATTTGGTTCAATGAATATAGATA
* * * * *
16883 TTTCAAGGAGTCCTTAAGTCAAAAATCATGCAAAACTGAGCCGGGGCCTCGGAATGCGTTTTTAT
193 TTTCAAGGAATCCTTACGCCAAAAATCATGCAAAACTGAGCCGGGGCCTCGGAACGCGTTTTTAG
16948 CCAAAAA
258 CCAAAAA
16955 TCGTAATGCA
Statistics
Matches: 752, Mismatches: 127, Indels: 66
0.80 0.13 0.07
Matches are distributed among these distances:
317 2 0.00
318 110 0.15
319 58 0.08
320 81 0.11
321 15 0.02
322 14 0.02
323 109 0.14
324 108 0.14
325 10 0.01
328 6 0.01
329 11 0.01
330 148 0.20
331 33 0.04
332 23 0.03
333 4 0.01
334 20 0.03
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (323 bp):
TTCTTTGCCACAATACTCAGAAAAAATATATAATTCAATGCCAAAAAGATTGAAGAGTTTTTCAC
GCTTCTAATATCGTTTTTCCTTTTTATTCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGA
TGCTCGTAAAAACAAATCCTTAAATCCAATGTGGTTGAGATTTGGTTCAATGAATATAGATATTT
CAAGGAATCCTTACGCCAAAAATCATGCAAAACTGAGCCGGGGCCTCGGAACGCGTTTTTAGCCA
AAAACCGTGATGGTTAATACACGATTTCAGCTAAATCAAAAACTGACAAATTTTTTTTCTCAA
Found at i:17651 original size:323 final size:320
Alignment explanation
Indices: 16981--18089 Score: 1064
Period size: 323 Copynumber: 3.4 Consensus size: 320
16971 TAGATTTTGA
** * * *
16981 CTAATTAGGTCAAAACAAAATTCAGATTCTCGTAAAAACAAATCCTTAAATCCAATGTGACTTAG
1 CTAATTAAATCAAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTG-GTTAG
** * * *
17046 ATTTCTTCGATGAATATAGATATTTTAAGGAGTTCTTACGCCAAAAATC-ATGCAAAACTGAGCC
65 ATTGGTTAGATGAATATAGATATTTCAAGGTG-TCTTACGCCAAAAA-CAATGCAAAACTGAGCC
* * * * * * **
17110 G-GAGTCTCAAAACG-GTTTTTAGCCAAAAACCGTGATGGTTAGTACACGAATTCGGTTAAAAAC
128 GAGA-CCTCGAGACGCGTTTTTAGCCAAAAACCGTGATGGTTAATGCACGATTTCGACTAAAAAC
* ** * * *
17173 TGA-CATGAAATTTTTTTTTCTCATTTTTTTGCCACAATAGTCA-ATAAAAATATATAATTCAAC
192 TAATCCCGAAA-ATTTTTTTCTCAATTTTTTGCCACAATACTCAGA-AAAAATATATAATTCAAC
* * * * * * * *
17236 GCC-AATGTGATTGAAGTGCTTTTCTCACTTCTAATATCATTTTTCC-ATTTTTTTCCGAATTTA
255 GCCAAAAG-GATTGAAGGGTTTTTCACGCTTATAATATC-GTTTTCCTATTTTTTTCCGAATTAA
17299 TTT
318 TTT
*
17302 CTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGTTGAG
1 CTAATTAAATCAAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGTT-AG
* * * *
17367 ATCTGGTTAGATGAATATAGATATTTCAAGGTGTCGTTATGCCAAAAACAATTCGAAACTGAGTC
65 AT-TGGTTAGATGAATATAGATATTTCAAGGTGTC-TTACGCCAAAAACAATGCAAAACTGAGCC
*
17432 GAGACCCCGAGACGCGTTTTTAGCC-AAAACCGTGATGGTTAATGCACGATTTCGACTAAAAACT
128 GAGACCTCGAGACGCGTTTTTAGCCAAAAACCGTGATGGTTAATGCACGATTTCGACTAAAAACT
*
17496 AATCCCGAAAATTTTTTTCTCAATTTTTTGCCACAATACTCAGGAAAAAATATATAATTCAGCGC
193 AATCCCGAAAATTTTTTTCTCAATTTTTTGCCACAATACTCA-GAAAAAATATATAATTCAACGC
* * * *
17561 CAAAAGGTTTGAAGGGTTTTTCACGCTTTTAATATCGTTTTCCTACTTTTTTCTGAATTAATTT
257 CAAAAGGATTGAAGGGTTTTTCACGCTTATAATATCGTTTTCCTATTTTTTTCCGAATTAATTT
* * *
17625 CTAATTAAATCAAAACAAGCTTCAGATGCTCATAAAAACAAATCCTTGAATCCAATGTGGCTTAG
1 CTAATTAAATCAAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGG-TTAG
* * * * *
17690 ATTTGGTTCGATGAATATAGATAGTTCAAGGGGTCCTTACGCCAAAGATAATGCAAAACTGAGCC
65 A-TTGGTTAGATGAATATAGATATTTCAAGGTGT-CTTACGCCAAAAACAATGCAAAACTGAGCC
* * * * * *
17755 GCCAGGGCCTCG-GAATGCGTTTCTATCCAAAAATCGTGAT--TGAACGTGCTA-GATTTCGACT
128 G--A-GACCTCGAG-ACGCGTTTTTAGCCAAAAACCGTGATGGTTAA--TGC-ACGATTTCGACT
** * * *
17816 AAAATTTTGCAAAAACTGACCCGAAAA-TTTTTTCTTCAATTCTTTGCCATAATACTCAG-ACAA
186 AAAA------ACTAA-T--CCCGAAAATTTTTTTC-TCAATTTTTTGCCACAATACTCAGAAAAA
* * * * *
17879 ATATATAATTCAACGCTAAAAAGATTGAAGGGTTTTTCATGCTTATAATATCG-TTTCTGTTTTT
241 ATATATAATTCAACGCCAAAAGGATTGAAGGGTTTTTCACGCTTATAATATCGTTTTC-CTATTT
17943 TTTTCCGAATTAATTT
305 TTTTCCGAATTAATTT
* * * * *
17959 CTAATTTAATCGAAACCAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGAGGGTGAG
1 CTAATTAAATCAAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATG-TGGTTAG
** * * *
18024 AATTCATCTA-ATGTATATAGATATTTTAAGGTGTCCTTACCCCAAAAATC-ATGCAAAACTGAG
65 -ATTGGT-TAGATGAATATAGATATTTCAAGGTGT-CTTACGCCAAAAA-CAATGCAAAACTGAG
18087 CCG
126 CCG
18090 GGATCCTGGA
Statistics
Matches: 656, Mismatches: 95, Indels: 61
0.81 0.12 0.08
Matches are distributed among these distances:
320 2 0.00
321 61 0.09
322 125 0.19
323 189 0.29
324 8 0.01
325 5 0.01
326 16 0.02
327 27 0.04
328 1 0.00
333 7 0.01
334 174 0.27
335 12 0.02
336 29 0.04
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (320 bp):
CTAATTAAATCAAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGTTAGA
TTGGTTAGATGAATATAGATATTTCAAGGTGTCTTACGCCAAAAACAATGCAAAACTGAGCCGAG
ACCTCGAGACGCGTTTTTAGCCAAAAACCGTGATGGTTAATGCACGATTTCGACTAAAAACTAAT
CCCGAAAATTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAA
AGGATTGAAGGGTTTTTCACGCTTATAATATCGTTTTCCTATTTTTTTCCGAATTAATTT
Done.