Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010872.1 Corchorus capsularis cultivar CVL-1 contig10893, 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: 57437
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1112 original size:318 final size:320
Alignment explanation
Indices: 1--1379 Score: 1961
Period size: 315 Copynumber: 4.3 Consensus size: 320
* *
1 TTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTAGGATGCTCGAAAAAACAAATACTT
1 TTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTGGGATGCTC-AAAAAACAAATCCTT
* * *
66 ATATCCAATATGACTGATATTTGCTTCGATGAAAATAGATATTTCAAGGAGTCTTTGCGTCAAAA
65 ATATCCAATATGACTGAGATTTGGTTCGATGAAAATAGATATTTCAAGGAGTCTTTGCGCCAAAA
* * * * * *
131 ATCATGTAAAATTGAGTCAGGGCTCCGGAATGCGTTTTTAGCCAAAAAT--AGA-A---CGTACA
130 ATCATGCAAAATTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAAATCGTGATAGTTAGTACA
*
190 CG-TTTGCGGCTAAAAACTGATCCGAAGAGTTTTATCTCAATTTTTTGCCACAATACTCAGAAAA
195 CGATTT-CGGCTAAAAACTGATCCGAAGAGTTTTATCTCAATTTTTTGCCACAATACTCACAAAA
*
254 AATATATAACTT-AATGCCAAAAATATTGATGGGCTTTTCACGCTTCTAATATCGTTTTCCCA
259 AATATATAA-TTCAATGCCAAAAAGATTGATGGGCTTTTCACGCTTCTAATATCGTTTTCCCA
*
316 TTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTAGGATGCTCGAAAAAACAAATCCTT
1 TTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTGGGATGCTC-AAAAAACAAATCCTT
* *
381 ATATCCAATATGACTGATATTTGGTTCGATGAAAATAGATATTTCAAGGAGTCTTTGCGACAAAA
65 ATATCCAATATGACTGAGATTTGGTTCGATGAAAATAGATATTTCAAGGAGTCTTTGCGCCAAAA
* *
446 ATCATGCAAAATTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAAA-CGTAATGGTTAGTACA
130 ATCATGCAAAATTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAAATCGTGATAGTTAGTACA
*
510 CGATTGCGGCTAAAAACTGATCC---GA-TTTT-TCTCAATTTTTTGCCACAATACTCACAAAAA
195 CGATTTCGGCTAAAAACTGATCCGAAGAGTTTTATCTCAATTTTTTGCCACAATACTCACAAAAA
* *
570 ATATATAATTCAACT-CCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATTGTTTTCCCA
260 ATATATAATTCAA-TGCCAAAAAGATTGATGGGCTTTTCACGCTTCTAATATCGTTTTCCCA
* * ** **
631 TTTTTTCTGAATTAATTTCTAATTAAGTCGAAACAAGATTGAAATGCTCAGAAAAACAAATTATT
1 TTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTGGGATGCTCA-AAAAACAAATCCTT
* * * * * *
696 TTCTCCAATATGATTGAGATTTGGTTCGATGAATATAGATATTTCAAAGAGTTTTTGCGCCAAAA
65 ATATCCAATATGACTGAGATTTGGTTCGATGAAAATAGATATTTCAAGGAGTCTTTGCGCCAAAA
*
761 ATCATGAAAAATTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAAATCGTGATAGTTAGTACA
130 ATCATGCAAAATTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAAATCGTGATAGTTAGTACA
* * *
826 CGATTTCGGCTAAAAATTGATCCGAAAAGTTTTATCTCAATTTTTTTGCCACAATACTCAGAAAA
195 CGATTTCGGCTAAAAACTGATCCGAAGAGTTTTATCTCAA-TTTTTTGCCACAATACTCACAAAA
* *
891 AATATATAATTTAATGCCAAAAAGATTGATGGGCTTTTCACGCTTCTAATATCGTTTTTCCA
259 AATATATAATTCAATGCCAAAAAGATTGATGGGCTTTTCACGCTTCTAATATCGTTTTCCCA
*
953 -TTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTGGGATACT-AAAAAA-AAATCCTTA
1 TTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTGGGATGCTCAAAAAACAAATCCTTA
* *
1015 TATACAATATGGA-TGAGATTTGGTTCAATGAAAATAGATATTTCAAGGAGTCTTTGCGCCAAAA
66 TATCCAATAT-GACTGAGATTTGGTTCGATGAAAATAGATATTTCAAGGAGTCTTTGCGCCAAAA
* * *
1079 ATCATGCAAAATTGAGCCGGGACTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACA
130 ATCATGCAAAATTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAAATCGTGATAGTTAGTACA
*
1144 CGATTTCGGCTAAAAACTGATCCGAAGAGTTTTTTCTCAATTTTTTGCCACAATACTCACAAAAA
195 CGATTTCGGCTAAAAACTGATCCGAAGAGTTTTATCTCAATTTTTTGCCACAATACTCACAAAAA
* * * * *
1209 ATATATAATTCAACGCCAAAAAGATTGAGGGGCTTTTCACGCTTCTAATATTGTTTTTCTA
260 ATATATAATTCAATGCCAAAAAGATTGATGGGCTTTTCACGCTTCTAATATCGTTTTCCCA
* * * * *
1270 TTTTTTTTTCTGAATTAATTTCTAATTAAGTCGAAACAAGATTGAGATGCTAAAAAAAACAAATT
1 ---TTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTGGGATGCT-CAAAAAACAAATC
* * * *
1335 ATTATCTCCAATAT-AGCTGAGATTTGTTTCGATGAATATAGATAT
62 CTTATATCCAATATGA-CTGAGATTTGGTTCGATGAAAATAGATAT
1380 ACAATATGGC
Statistics
Matches: 956, Mismatches: 80, Indels: 47
0.88 0.07 0.04
Matches are distributed among these distances:
314 3 0.00
315 414 0.43
316 41 0.04
317 82 0.09
318 159 0.17
319 8 0.01
320 29 0.03
321 94 0.10
322 80 0.08
323 6 0.01
324 40 0.04
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (320 bp):
TTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTGGGATGCTCAAAAAACAAATCCTTA
TATCCAATATGACTGAGATTTGGTTCGATGAAAATAGATATTTCAAGGAGTCTTTGCGCCAAAAA
TCATGCAAAATTGAGCCGGGGCTCCGGAACGCGTTTTTAGCCAAAAATCGTGATAGTTAGTACAC
GATTTCGGCTAAAAACTGATCCGAAGAGTTTTATCTCAATTTTTTGCCACAATACTCACAAAAAA
TATATAATTCAATGCCAAAAAGATTGATGGGCTTTTCACGCTTCTAATATCGTTTTCCCA
Found at i:1386 original size:38 final size:38
Alignment explanation
Indices: 1343--1417 Score: 96
Period size: 38 Copynumber: 2.0 Consensus size: 38
1333 TTATTATCTC
* * * *
1343 CAATATAGCTGAGATTTGTTTCGATGAATATAGATATA
1 CAATATAGCCGAGATTTGGTTCAATGAAAATAGATATA
* *
1381 CAATATGGCCGAGATTTGGTTCAATGAAAATATATAT
1 CAATATAGCCGAGATTTGGTTCAATGAAAATAGATAT
1418 TTCACGGAGT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.35
Consensus pattern (38 bp):
CAATATAGCCGAGATTTGGTTCAATGAAAATAGATATA
Found at i:2153 original size:323 final size:322
Alignment explanation
Indices: 1445--2521 Score: 936
Period size: 322 Copynumber: 3.4 Consensus size: 322
1435 CCAAAAATCA
* *
1445 ATCGTTTTTCCATTTTTTTTCCGAATTAATTTCTAATTAAGTCGAAACAAGATTCAGATGCTCGT
1 ATCGTTTTTCCA-ATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGT
* * * * * * * *
1510 AAAAACAAATCTTTATATCCATTGTGGCTGACATTTGGTTCGATGAATATATATATTTCATGGAG
65 AAAAACAAATCCTTATATCCAATATCGCTGACAATCGGTTCGATGAATATAGATATTTCAAGGAG
** * *
1575 TCCTTGCATTAAAAATCATGCAAAATTGAGTCAGGGCTCCAGAACGCGTTTTTAGCCAAAAACCG
130 TCCTTGCAGCAAAAATCATGCAAAATTGAGCCAGGGATCCAGAACGCGTTTTTAGCCAAAAACCG
* * ** ** *
1640 TGATGGTTAGTGCACGATTTCGGCTAAAAACTGAACCGAAAAGTTTTTTCTCAATTTTTTGCCAC
195 TAACGGTTAGAACAAAATTTCGGCTAAAAACTGAACCGAAAAGTTTTTTCTCAATTCTTTGCCAC
* * * *
1705 AATACTCAGAAAAAATATATAATTCAATGCCAAAAAGATTGATGGGTTTTTCACACTTCTAAT
260 AATACCCAGAAAAAATATATAATTCAATCCCAAAAAGATTGATAGGTTTTTCACACTTCGAAT
* * * * * *
1768 ATCATTTTTCC-ATTTTCATACGAATTAATTTCTAATTAAATCGAAACAAGATTGAAATGCTCGA
1 ATCGTTTTTCCAATTTT-TTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGT
*
1832 AAAAACAAATCCTTATATCCAATATCGCTGAGAATCGGTTCGATGAATATAGATATTTCAAGGAG
65 AAAAACAAATCCTTATATCCAATATCGCTGACAATCGGTTCGATGAATATAGATATTTCAAGGAG
* * * * *
1897 TCTTTGC-GCCAAAATCTTGCAAAATTGAGCCGGGGATCCGGAACG-GTTTTTAGCCAAAAACCG
130 TCCTTGCAGCAAAAATCATGCAAAATTGAGCCAGGGATCCAGAACGCGTTTTTAGCCAAAAACCG
* * * * *
1960 TAACAAACGATTTCGAATAAAATTT-TGC-AAAAACTGATCCGAAAA-TTTTTTCCTCAATTCTT
195 T----AACG-GTTAGAACAAAATTTCGGCTAAAAACTGAACCGAAAAGTTTTTT-CTCAATTCTT
* *
2022 T-CCACAATACCCAGAAAAAAATATATAATTCAA-CCCGAAAAGATTGA-AGGTTTTTCA-AGTT
254 TGCCACAATACCCAG-AAAAAATATATAATTCAATCCCAAAAAGATTGATAGGTTTTTCACA-CT
2083 TCGAAT
317 TCGAAT
2089 ATCGTTTTTCCAAATTTGTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCG
1 ATCGTTTTTCC-AATTT-TTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCG
* * * * * * * *
2154 TAAAAACAAATCTTTGTATTCAATGTGGCTGAC-AT---TT-G--G--T-TTG--A-TCCACGGA
64 TAAAAACAAATCCTTATATCCAATATCGCTGACAATCGGTTCGATGAATATAGATATTTCAAGGA
** * * * * *
2206 GTTTTTGC-GCTAAAAATCATGCAAAATTGAGTCGGGGCTCC-GAAATGCATTTTTAGCCAAAAA
129 GTCCTTGCAGC-AAAAATCATGCAAAATTGAGCCAGGGATCCAG-AACGCGTTTTTAGCCAAAAA
* * * *
2269 ---T--C--AT-GATAC--GATTTCGGCTAAAAACTGACCCGAAAAGTTCTTTTATCAATT-TTT
192 CCGTAACGGTTAGA-ACAAAATTTCGGCTAAAAACTGAACCGAAAAGTT-TTTTCTCAATTCTTT
* * * ** * *
2323 GGCCACAATTCTCAGAAAAAATATATAATTCAA-CGCCAATAAGATTGACGGGCTTTTCACGCTT
255 -GCCACAATACCCAGAAAAAATATATAATTCAATC-CCAAAAAGATTGATAGGTTTTTCACACTT
*
2387 CTAAT
318 CGAAT
* * * *
2392 ATCATTTTTCC-ATTTTTTCCCGAATTAATTTTTAATTAAATCGAAATAAGATTCAGATGCTTGT
1 ATCGTTTTTCCAATTTTTT-CCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGT
* * * * * * * * **
2456 GAAAACAAATACTTAAATCGAATGTGGCT-AGGATTTTGTTCGATGAATATAGATATTTCAAGGA
65 AAAAACAAATCCTTATATCCAATATCGCTGA-CAATCGGTTCGATGAATATAGATATTTCAAGGA
2520 GT
129 GT
2522 ATTTACGCAA
Statistics
Matches: 617, Mismatches: 97, Indels: 89
0.77 0.12 0.11
Matches are distributed among these distances:
298 4 0.01
299 4 0.01
300 25 0.04
301 95 0.15
302 27 0.04
303 25 0.04
305 2 0.00
306 1 0.00
308 1 0.00
309 1 0.00
310 17 0.03
311 32 0.05
312 14 0.02
313 3 0.00
314 9 0.01
316 1 0.00
318 1 0.00
319 2 0.00
320 20 0.03
321 59 0.10
322 135 0.22
323 126 0.20
324 5 0.01
325 8 0.01
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (322 bp):
ATCGTTTTTCCAATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTA
AAAACAAATCCTTATATCCAATATCGCTGACAATCGGTTCGATGAATATAGATATTTCAAGGAGT
CCTTGCAGCAAAAATCATGCAAAATTGAGCCAGGGATCCAGAACGCGTTTTTAGCCAAAAACCGT
AACGGTTAGAACAAAATTTCGGCTAAAAACTGAACCGAAAAGTTTTTTCTCAATTCTTTGCCACA
ATACCCAGAAAAAATATATAATTCAATCCCAAAAAGATTGATAGGTTTTTCACACTTCGAAT
Found at i:4006 original size:22 final size:22
Alignment explanation
Indices: 3965--4006 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
3955 AAACCGTTGT
*
3965 TATCAAAATTTCGTAAGGAAAC
1 TATCAAAATTTCATAAGGAAAC
*
3987 TATCAAAATTTCATAGGGAA
1 TATCAAAATTTCATAAGGAA
4007 GGGAGGTTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.29
Consensus pattern (22 bp):
TATCAAAATTTCATAAGGAAAC
Found at i:4199 original size:22 final size:22
Alignment explanation
Indices: 4143--4257 Score: 151
Period size: 22 Copynumber: 5.2 Consensus size: 22
4133 GTATTTTTAA
*
4143 GTTACCAAAATTTTCATAGTGAGG
1 GTTACCAAAA-TTTCATAGGGA-G
* * *
4167 GTT-TCAGAATTGCATAGGGAG
1 GTTACCAAAATTTCATAGGGAG
*
4188 GTTACCAAAATTTCATAGGGAA
1 GTTACCAAAATTTCATAGGGAG
*
4210 GTTACCAAAATTTCATAGGGAA
1 GTTACCAAAATTTCATAGGGAG
4232 GTTACCAAAATTTCATAGGGAG
1 GTTACCAAAATTTCATAGGGAG
4254 GTTA
1 GTTA
4258 TTAGAATAGT
Statistics
Matches: 81, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
21 4 0.05
22 70 0.86
23 4 0.05
24 3 0.04
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.30
Consensus pattern (22 bp):
GTTACCAAAATTTCATAGGGAG
Found at i:11949 original size:22 final size:22
Alignment explanation
Indices: 11921--11962 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
11911 GACATGTGTC
11921 ACTTTTTGATACATGTGGCACG
1 ACTTTTTGATACATGTGGCACG
*
11943 ACTTTTTGGTACATGTGGCA
1 ACTTTTTGATACATGTGGCA
11963 TGCCACATGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.17, G:0.24, T:0.38
Consensus pattern (22 bp):
ACTTTTTGATACATGTGGCACG
Found at i:21787 original size:30 final size:29
Alignment explanation
Indices: 21725--21794 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
21715 ACCGAACCGT
****
21725 CAAATAAGCCCCTGAACTATTATTTCGGC
1 CAAATAAGCCCCTGAACTATTAAAAAGGC
*
21754 CAAATAAGCCCCTGAACTCTTAAAAAAGGC
1 CAAATAAGCCCCTGAACTATT-AAAAAGGC
21784 CAAATAAGCCC
1 CAAATAAGCCC
21795 TGTTGCCAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
29 20 0.57
30 15 0.43
ACGTcount: A:0.39, C:0.29, G:0.13, T:0.20
Consensus pattern (29 bp):
CAAATAAGCCCCTGAACTATTAAAAAGGC
Found at i:24150 original size:14 final size:15
Alignment explanation
Indices: 24121--24149 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
24111 ATAAATTAAT
24121 TTGTACCAAAAAAAA
1 TTGTACCAAAAAAAA
24136 TTGTACCAAAAAAA
1 TTGTACCAAAAAAA
24150 TATAGCAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.59, C:0.14, G:0.07, T:0.21
Consensus pattern (15 bp):
TTGTACCAAAAAAAA
Found at i:44089 original size:9 final size:9
Alignment explanation
Indices: 44075--44099 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
44065 TCAACTCAAA
44075 AGTCAAAAC
1 AGTCAAAAC
44084 AGTCAAAAC
1 AGTCAAAAC
44093 AGTCAAA
1 AGTCAAA
44100 CTCAAAAGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.56, C:0.20, G:0.12, T:0.12
Consensus pattern (9 bp):
AGTCAAAAC
Found at i:48810 original size:21 final size:21
Alignment explanation
Indices: 48784--48875 Score: 87
Period size: 21 Copynumber: 4.2 Consensus size: 21
48774 AGGCCCTGGC
*
48784 CCCGGCCTTCCTGGCGGTCCT
1 CCCGGCCTTCCTGGAGGTCCT
*
48805 CCCGGCCTTCCAGGAGGTCCT
1 CCCGGCCTTCCTGGAGGTCCT
* * *
48826 CCTCCTGGCCTTCCCGGTGGCCCT
1 -C-CC-GGCCTTCCTGGAGGTCCT
*
48850 CCTGGCCTT-CTCGGAGGTCCT
1 CCCGGCCTTCCT-GGAGGTCCT
48871 CCCGG
1 CCCGG
48876 TCCACCTGGC
Statistics
Matches: 57, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
20 1 0.02
21 36 0.63
22 2 0.04
23 3 0.05
24 15 0.26
ACGTcount: A:0.03, C:0.46, G:0.28, T:0.23
Consensus pattern (21 bp):
CCCGGCCTTCCTGGAGGTCCT
Found at i:48835 original size:24 final size:23
Alignment explanation
Indices: 48801--48872 Score: 78
Period size: 24 Copynumber: 3.1 Consensus size: 23
48791 TTCCTGGCGG
*
48801 TCCTCCCGGCCTTCCAGGAGGTCC
1 TCCTCCTGGCCTTCC-GGAGGTCC
*
48825 TCCTCCTGGCCTTCCCGGTGG--C
1 TCCTCCTGGCCTT-CCGGAGGTCC
48847 -CCTCCTGGCCTTCTCGGAGGTCC
1 TCCTCCTGGCCTTC-CGGAGGTCC
48870 TCC
1 TCC
48873 CGGTCCACCT
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
20 1 0.03
21 17 0.43
22 1 0.03
23 1 0.03
24 18 0.45
25 2 0.05
ACGTcount: A:0.04, C:0.46, G:0.25, T:0.25
Consensus pattern (23 bp):
TCCTCCTGGCCTTCCGGAGGTCC
Found at i:48851 original size:45 final size:45
Alignment explanation
Indices: 48787--48872 Score: 120
Period size: 45 Copynumber: 1.9 Consensus size: 45
48777 CCCTGGCCCC
* *
48787 GGCCTTCCTGGCGGTCCTCCCGGCCTTC-CAGGAGGTCCTCCTCCT
1 GGCCTTCCCGGCGGCCCTCCCGGCCTTCTC-GGAGGTCCTCCTCCT
* *
48832 GGCCTTCCCGGTGGCCCTCCTGGCCTTCTCGGAGGTCCTCC
1 GGCCTTCCCGGCGGCCCTCCCGGCCTTCTCGGAGGTCCTCC
48873 CGGTCCACCT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
45 35 0.97
46 1 0.03
ACGTcount: A:0.03, C:0.44, G:0.28, T:0.24
Consensus pattern (45 bp):
GGCCTTCCCGGCGGCCCTCCCGGCCTTCTCGGAGGTCCTCCTCCT
Found at i:48886 original size:30 final size:30
Alignment explanation
Indices: 48850--48907 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 30
48840 CGGTGGCCCT
48850 CCTGGCCTT-CTCGGAGGTCCTCCCGGTCCA
1 CCTGGCCTTCCT-GGAGGTCCTCCCGGTCCA
48880 CCTGGCCTTCCTGGAGGTCCTCCCGGTC
1 CCTGGCCTTCCTGGAGGTCCTCCCGGTC
48908 TGAACCCGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 25 0.93
31 2 0.07
ACGTcount: A:0.05, C:0.43, G:0.28, T:0.24
Consensus pattern (30 bp):
CCTGGCCTTCCTGGAGGTCCTCCCGGTCCA
Found at i:55255 original size:324 final size:324
Alignment explanation
Indices: 54455--55686 Score: 1467
Period size: 324 Copynumber: 3.8 Consensus size: 324
54445 AAAAACTAAT
* *
54455 AAAAATATATATAATTCAATG-CAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCGTTTTTC
1 AAAAA-ATATATAATTCAACGTCAAAAAGATTGACGGACTTTTCACGCTTTTAATATCGTTTTTC
* * * **
54519 ATATTTTTTTTTCTGAATTAATTTCTATTTAAATCGAAACAAGATTCTA-ATGCAAGTAAAAACA
65 -CA--TTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTC-AGATGCTCGTAAAAACA
* * * * * ***
54583 AATCCTTAAATTCAATATGGCTAAGATTTGATTAGACT-AATAAAGATATTTCAAGGAGTCTCGG
126 AATCCTTATATCCAATATGGCTGAGATTTGATTCGA-TGAATATAGATATTTCAAGGAGTCTTTA
* * ** * * * ** *
54647 CGCCAAAAACCATACAAAACAGAGCCGTGGCCCCAGAAGGCGTTTTTAGTGAAAAACCGTGATGA
190 CGCCAAAAATCATGCAAAATTGAGCCGGGGCTCCAGAACGCGTTTTTAGCCAAAAACCGTGATGG
* * * * ** ** *
54712 TTGGTAC-CTGAGTTCGGCTAAAAGCTGACGCGAAAAG--TTTACCATCATTTTTTTTTACCACA
255 TTAGTACAC-GATTTCGGCTAAAAACTGACCCGAAAAGTTTTTTTC-TCA-AATTTTTTGCCACA
54774 ATACTCAG
317 ATACTCAG
* * ** * * *
54782 AAAAAATATAAAATTCTAACGCCAAAAAGATTGGTGAACTTTTCACGCTTGTAATATTGTTTTTC
1 AAAAAATATATAATTC-AACGTCAAAAAGATTGACGGACTTTTCACGCTTTTAATATCGTTTTTC
* * *
54847 CATTTTTTTCCGAATTAATTTCTAATTAAATCCAAACCAGATTGAGATGCTCGTAAAAACAAATC
65 CATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATC
* * *
54912 CTTATATCCAATATGGCTGAGATTTGATTCGATGAATATAGACATTTCAAGAAGTCTTTACGCCT
130 CTTATATCCAATATGGCTGAGATTTGATTCGATGAATATAGATATTTCAAGGAGTCTTTACGCCA
* * * * *
54977 AAAATTATGCAAAATTGAGTCGGGGCTCCGGAACGCTTTTTTAGCCAAAAACCGTGATGGTTATT
195 AAAATCATGCAAAATTGAGCCGGGGCTCCAGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGT
*
55042 ACACGATTTCGGCTAAAAACTGACCCGAATAGTTTTTTTCTCAAATTTTTTGCCACAATACTCAG
260 ACACGATTTCGGCTAAAAACTGACCCGAAAAGTTTTTTTCTCAAATTTTTTGCCACAATACTCAG
* * * * * *
55107 AATAAGTATATAATTCAACGTCAAAAAAATTGACGGATTTTTCACACTTTTAATATCATTTTTCC
1 AAAAAATATATAATTCAACGTCAAAAAGATTGACGGACTTTTCACGCTTTTAATATCGTTTTT-C
**
55172 CA-TTTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATC
65 CATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATC
* * * * * *
55236 CTTATATCCAATGTGGCTGACATTTCG-TTCAATAAATATAGATATTTCAAGGAGTTTTTGCGCC
130 CTTATATCCAATATGGCTGAGATTT-GATTCGATGAATATAGATATTTCAAGGAGTCTTTACGCC
* * * *
55300 AAAAATCATGCAAAATTGACCCGGGACTCCGGAACGCGTTTTTAGCCAAACACCGTGATGGTTAG
194 AAAAATCATGCAAAATTGAGCCGGGGCTCCAGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAG
* * *
55365 TACACGATTTCGGCTAAAAACTAACCCAAAAACTTTTTTTCTC-AATTTTTTGCCACAATACTCA
259 TACACGATTTCGGCTAAAAACTGACCCGAAAAGTTTTTTTCTCAAATTTTTTGCCACAATACTCA
55429 G
324 G
* * * *
55430 AAAAAATATATAATTCAACGGT-AAAACGATTGGCGGGCTTTTCACGCTTCTAATATCGTTTTTC
1 AAAAAATATATAATTCAAC-GTCAAAAAGATTGACGGACTTTTCACGCTTTTAATATCGTTTTTC
* *
55494 CATTTTTTTTCCGAATTAATTTCTCATTAAATCGAAACAAGATTGAGATGCTCGTAAAAACAAAT
65 CA-TTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAAT
* * * * *
55559 CCTTATATCCAATATAGTTGAGATTTGGTTCGATGAATATAAATATTTCAATGAGTCTTTACGCC
129 CCTTATATCCAATATGGCTGAGATTTGATTCGATGAATATAGATATTTCAAGGAGTCTTTACGCC
* * * *
55624 AAAAATCTTGCAAAATTAAGTCGGGGCGCCAGAACGCGTTTTTAGCCAAAAACCGTGATGGTT
194 AAAAATCATGCAAAATTGAGCCGGGGCTCCAGAACGCGTTTTTAGCCAAAAACCGTGATGGTT
55687 TAATATAATT
Statistics
Matches: 771, Mismatches: 121, Indels: 29
0.84 0.13 0.03
Matches are distributed among these distances:
322 3 0.00
323 73 0.09
324 413 0.54
325 217 0.28
326 14 0.02
327 13 0.02
328 38 0.05
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.33
Consensus pattern (324 bp):
AAAAAATATATAATTCAACGTCAAAAAGATTGACGGACTTTTCACGCTTTTAATATCGTTTTTCC
ATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCC
TTATATCCAATATGGCTGAGATTTGATTCGATGAATATAGATATTTCAAGGAGTCTTTACGCCAA
AAATCATGCAAAATTGAGCCGGGGCTCCAGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTA
CACGATTTCGGCTAAAAACTGACCCGAAAAGTTTTTTTCTCAAATTTTTTGCCACAATACTCAG
Found at i:55853 original size:205 final size:206
Alignment explanation
Indices: 55489--55880 Score: 608
Period size: 205 Copynumber: 1.9 Consensus size: 206
55479 CTAATATCGT
* * *
55489 TTTTCCATTTTTTTTCCGAATTAATTTCTCATTAAATCGAAACAAGATTGAGATGCTCGTAAAAA
1 TTTTCCATTTTTTTTCCGAATTAATTTCTAATGAAATCGAAACAAGATTGAGATGCTCGAAAAAA
* * *
55554 CAAATCCTTATATCCAATATAGTTGAGATTTGGTTCGATGAATATAAATATTTCAATGAGTCTTT
66 CAAATCCTTATATCCAATATAGCTGAGATTTGCTTCGATGAATATAAATATTTCAAGGAGTCTTT
* *
55619 ACGCCAAAAATCTTGCAAAATTAAGTCGGGGCGCCAGAACGCGTTTTTAGCCAAAAACCGTGATG
131 ACGCCAAAAATCATGCAAAATTAAGTCGGGGCGCCAGAACGCGCTTTTAGCCAAAAACCGTGATG
55684 GTTTAATATAA
196 GTTTAATATAA
* *
55695 TTTTCCA-TTTTTTTCCTAATTAATTTCTAATGAAATCGAAACAAGATTGAGATTCTCGAAAAAA
1 TTTTCCATTTTTTTTCCGAATTAATTTCTAATGAAATCGAAACAAGATTGAGATGCTCGAAAAAA
* *
55759 CAAAT-CTTCATATCCAATATAGCTGAGATTTGCTTTGATGAATATAGATATTTCAAGGAGTCTT
66 CAAATCCTT-ATATCCAATATAGCTGAGATTTGCTTCGATGAATATAAATATTTCAAGGAGTCTT
* * * * *
55823 TGCGCTAAAAATCATGCAAAATTGAGTCGGGGCTCCGGAACGCGCTTTTAGCCAAAAA
130 TACGCCAAAAATCATGCAAAATTAAGTCGGGGCGCCAGAACGCGCTTTTAGCCAAAAA
55881 TCGTAACGTA
Statistics
Matches: 168, Mismatches: 17, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
204 3 0.02
205 158 0.94
206 7 0.04
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Consensus pattern (206 bp):
TTTTCCATTTTTTTTCCGAATTAATTTCTAATGAAATCGAAACAAGATTGAGATGCTCGAAAAAA
CAAATCCTTATATCCAATATAGCTGAGATTTGCTTCGATGAATATAAATATTTCAAGGAGTCTTT
ACGCCAAAAATCATGCAAAATTAAGTCGGGGCGCCAGAACGCGCTTTTAGCCAAAAACCGTGATG
GTTTAATATAA
Found at i:56167 original size:524 final size:526
Alignment explanation
Indices: 55155--56214 Score: 1420
Period size: 524 Copynumber: 2.0 Consensus size: 526
55145 TTTTCACACT
* *
55155 TTTAATATCATTTTTCCCATTTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATG
1 TTTAATATCAATTTTCCCATTTTTTCTAAATTAATTTCTAATGAAATCGAAACAAGATTCAGATG
* * *
55220 CTCGTAAAAACAAATCCTTATATCCAATGTGGCTGACATTTCGTTCAATAAATATAGATATTTCA
66 CTCGAAAAAACAAATCCTTATATCCAATATAGCTGACATTTCGTTCAATAAATATAGATATTTCA
* *
55285 AGGAGTTTTTGCGCCAAAAATCATGCAAAATTGACCCGGGACTCCGGAACGCGTTTTTAGCCAAA
131 AGGAGTCTTTGCGCCAAAAATCATGCAAAATTGACCCGGGACTCCGGAACGCGCTTTTAGCCAAA
* * *
55350 CACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTAACCCAAAAACTTTTTTTCTCAATTTTT
196 CA-C---ATCGTAAGTACACGATTTCGGCTAAAAACTAACACAAAAACTTTTTTTCTCAATTTTT
* ** * * * *
55415 TGCCACAATACTCAGAAAAAATATATAATTCAACGGTAAAACGATTGGCGGGCTTTTCACGCTTC
257 TCCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACAGGCTTTTCACACTTC
* * * * *
55480 TAATATCGTTTTTCCATTTTTTTTCCGAATTAATTTCTCATTAAATCGAAACAAGATTGAGATGC
322 TAATATCGTTTTGCCATTTTTGTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAAATGC
* * * *
55545 TCGTAAAAACAAATCCTTATATCCAATATAGTTGAGATTTGGTTCGATGAATATAAATATTTCAA
387 TCGTAAAAACAAATCCTTATATCCAATATAGCTGACATTTCGTTCGATAAATATAAATATTTCAA
* * * * *
55610 TGAGTCTTTACGCCAAAAATCTTGCAAAATTAAGTCGGGGCGCCAGAACGCGTTTTTAGCCAAAA
452 GGAGTCTTTACGACAAAAATCATGCAAAATTAAGTCGGAGCGCCAAAACGCGTTTTTAGCCAAAA
55675 ACCGTGATGG
517 ACCGTGATGG
*
55685 TTTAATAT-AATTTT-CCATTTTTTTCCT-AATTAATTTCTAATGAAATCGAAACAAGATTGAGA
1 TTTAATATCAATTTTCCCA-TTTTTT-CTAAATTAATTTCTAATGAAATCGAAACAAGATTCAGA
* * ** *
55747 TTCTCGAAAAAACAAAT-CTTCATATCCAATATAGCTGAGATTT-GCTTTGATGAATATAGATAT
64 TGCTCGAAAAAACAAATCCTT-ATATCCAATATAGCTGACATTTCG-TTCAATAAATATAGATAT
* ** *
55810 TTCAAGGAGTCTTTGCGCTAAAAATCATGCAAAATTGAGTCGGGGCTCCGGAACGCGCTTTTAGC
127 TTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGACCCGGGACTCCGGAACGCGCTTTTAGC
* * * *
55875 CAAA-A-ATCGTAACGTACACGATTTTCGGCTAAAAGCTGACAC-GAAATTTTTTTTCTCAATTT
192 CAAACACATCGTAA-GTACACGA-TTTCGGCTAAAAACTAACACAAAAACTTTTTTTCTCAATTT
* * *
55937 TTTCCCACAATACTCA-TAAAAATATATAATTCATCGCCAAAAAGATTGACATGCTTTTCACACT
255 TTTCCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACAGGCTTTTCACACT
* *
56001 TTTAATATCGTTTTGCCTATTTTTGTTCCGAATTAATTTCTAATTAAATCGAAATAAGATTCAAA
320 TCTAATATCGTTTTGCC-ATTTTTGTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAAA
* * * **
56066 TGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGACATTTCGTTCTATAAATATTGATATTT
384 TGCTCGTAAAAACAAATCCTTATATCCAATATAGCTGACATTTCGTTCGATAAATATAAATATTT
** *
56131 CAAGGAGTCTTTGTGACAAAAATCATGCAAAATTAAGTCGGAGCTCCAAAACGCGTTTTTAGCCA
449 CAAGGAGTCTTTACGACAAAAATCATGCAAAATTAAGTCGGAGCGCCAAAACGCGTTTTTAGCCA
*
56196 AAAACTGTGATGG
514 AAAACCGTGATGG
56209 -TTAATA
1 TTTAATA
56215 CATGATTTCG
Statistics
Matches: 464, Mismatches: 59, Indels: 21
0.85 0.11 0.04
Matches are distributed among these distances:
523 65 0.14
524 208 0.45
525 17 0.04
528 8 0.02
529 156 0.34
530 10 0.02
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (526 bp):
TTTAATATCAATTTTCCCATTTTTTCTAAATTAATTTCTAATGAAATCGAAACAAGATTCAGATG
CTCGAAAAAACAAATCCTTATATCCAATATAGCTGACATTTCGTTCAATAAATATAGATATTTCA
AGGAGTCTTTGCGCCAAAAATCATGCAAAATTGACCCGGGACTCCGGAACGCGCTTTTAGCCAAA
CACATCGTAAGTACACGATTTCGGCTAAAAACTAACACAAAAACTTTTTTTCTCAATTTTTTCCC
ACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACAGGCTTTTCACACTTCTAAT
ATCGTTTTGCCATTTTTGTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAAATGCTCGT
AAAAACAAATCCTTATATCCAATATAGCTGACATTTCGTTCGATAAATATAAATATTTCAAGGAG
TCTTTACGACAAAAATCATGCAAAATTAAGTCGGAGCGCCAAAACGCGTTTTTAGCCAAAAACCG
TGATGG
Found at i:56990 original size:647 final size:635
Alignment explanation
Indices: 55687--57437 Score: 2017
Period size: 647 Copynumber: 2.7 Consensus size: 635
55677 CGTGATGGTT
* *
55687 TAATATAATTTTCCATTTTTTTCCTAATTAATTTCTAATGAAATCGAAACAAGATTGAGATTCTC
1 TAATATCATTTTCCATTTTTTTCC--ATTAATTTCTAATTAAATCGAAACAAGATTGAGATTCTC
* * * * * *
55752 GAAAAAACAAAT-CTTCATATCCAATATAGCTGAGATTTGCTTTGATGAATATAGATATTTCAAG
64 GTAAAAACAAATCCTT-ATATCCAATGTGGCTGACATTTGGTTCGATGAATATAGATATTTCAAG
* *
55816 GAGTCTTTGCGCTAAAAATCATGCAAAATTGAGTCGGGGCTCCGGAACGCGCTTTTAGCCAAAA-
128 GAGTCTTTGCGCCAAAAAT-ATGCAAAATTGAGTCGGGGCTCCGGAACGCGTTTTTAGCCAAAAC
* * * * *
55880 ---ATCGTAACGTACACGATTTTCGGCTAAAAGCTGACACGAAATTTTTTTTCTCAATTTTTTCC
192 CTGATGGTTA-GTACACGA-TTTCGGCTAAAAGCTAACCCGAAATTTTTTTTCTCAATTTTTTGC
* * ** *
55942 CACAATACTCATAAAAATATATAATTCATCGCCAAAAAGATTGACATGCTTTTCACACTTTTAAT
255 CACAATACTAATAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTTTTCACACTTCTAAT
* * * *
56007 ATCGTTTTGCCTATTTTTGTTCCGAATTAATTTCTAATTAAATCGAAATAAGATTCAAATGCTCG
320 ATCGTTTTTCC-A--TTT-TTCCGAATTAATTTCTAATTAAATCGAAATAAGATTGAGATGATCG
* * *
56072 TAAAAACAAATCCTTATATCCAATGTGGCTGACATTT-CGTTCT-ATAAATATTGATATTTCAAG
381 TAAAAAAAAATCCTTATATCCAATATGGCTGAGATTTGC-TT-TGATAAATATTGATATTTCAAG
* *
56135 GAGTCTTTGTGACAAAAATCATGCAAAATTAAGTCGGAGCTCCAAAACGCGTTTTTAGCCAAAAA
444 GAGTCTTTGTGCCAAAAATCATGCAAAATTAAGTCGGAGCTCCAAAACACGTTTTTAGCCAAAAA
* *
56200 CTGTGATGGTTAATACATGATTTCGGCTAAAAACTGACCCGAAAGGTTTTTTCTCGATTTTTTCC
509 CCGTGATGGTTAATACACGATTTCGGCTAAAAACTGACCCGAAAGGTTTTTTCTCGATTTTTTCC
** * *
56265 ACAATATACAGAAAAAAATAAATAATTCAAAACCAAAAATTTTGACGGGCTTTTCAGACTTC
574 ACAATATACAGAAAAAAATAAATAATTCAAAACCAAAAAGATTGACAGGCTTTTCACACTTC
* *
56327 TAATATCATCTTTCCATTTTTTTCCGAGTTAATTTCTAATTAAATCGGAAA-AAGATTTAGATGC
1 TAATATCAT-TTTCCATTTTTTTCC-A-TTAATTTCTAATTAAATC-GAAACAAGATTGAGATTC
56391 TCGTAAAAACAAATCCATT-TATCCAATGTGGCTGACATTTGGTTCGATGAATATAGATATTTCA
62 TCGTAAAAACAAATCC-TTATATCCAATGTGGCTGACATTTGGTTCGATGAATATAGATATTTCA
* *
56455 AGGAGTCTTTGCGCCAAAAATATGCAAAATTGAGTCAGGGCTCCGGAACACGTTTTTAGCCAAAC
126 AGGAGTCTTTGCGCCAAAAATATGCAAAATTGAGTCGGGGCTCCGGAACGCGTTTTTAGCCAAA-
* *
56520 ACCGTGATGGTTAGTACACGATTTCAGCTAAAAGCTAACCCGAATTTTTTTTTCTTTTCAATTTT
190 ACC-TGATGGTTAGTACACGATTTCGGCTAAAAGCTAACCCGAAATTTTTTTTC---TCAA-TTT
* * *
56585 TTTGCCACAATACTAAAAATTAAAAATATATAATTCAACGTCAAAAAGATTGACGGGCTTTTGAT
250 TTTGCCACAATACT---AA-TAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTTTTCAC
* *
56650 GCTTCTAATATCGTTTTTCCATTTTTCCTAATTAATTTCTAATTAAATCGAAATAAGATTGAGAT
311 ACTTCTAATATCGTTTTTCCATTTTTCCGAATTAATTTCTAATTAAATCGAAATAAGATTGAGAT
* * *
56715 GATCG-AAAAAGAAATCGTTATATCCAATATGGCTGAGATTTGCTTTGATGAATATTGATATTTC
376 GATCGTAAAAAAAAATCCTTATATCCAATATGGCTGAGATTTGCTTTGATAAATATTGATATTTC
* * * * * ** ** *
56779 AAAGATTCTTTGTGCCAGAAATCATGCAAAATTGAG-CTGGGGCTCCGGAACATTTTTTTAGCGA
441 AAGGAGTCTTTGTGCCAAAAATCATGCAAAATTAAGTC-GGAGCTCCAAAACACGTTTTTAGCCA
** * * *
56843 AAAACCGTGATGGTTTGTACACGATTTCGGCTAAAAATTGACCCGAAA-TTATTGTTTCT-TATT
505 AAAACCGTGATGGTTAATACACGATTTCGGCTAAAAACTGACCCGAAAGGT-TT-TTTCTCGATT
* * * * *
56906 TTTTAGTCACAATACT-CAGAAAAAAGTATA-AATTCAATGA-TAAAAAGATTGACAGGCTTTTC
568 TTTT--CCACAATA-TACAGAAAAAAATAAATAATTCAA-AACCAAAAAGATTGACAGGCTTTTC
56968 ACACTTC
629 ACACTTC
* *
56975 TAATATCGTTTTCCA-TTTTTTCC--------CTAATTAAATTGAAACAAGATTGAGATTCTCGT
1 TAATATCATTTTCCATTTTTTTCCATTAATTTCTAATTAAATCGAAACAAGATTGAGATTCTCGT
** * * * *
57031 TTAAACAAATCCTTATATCGAATGTGGCTGACATTTCGTTCCATGAATATAGTTATTTCAAGGAG
66 AAAAACAAATCCTTATATCCAATGTGGCTGACATTTGGTTCGATGAATATAGATATTTCAAGGAG
* * ** * * * * *
57096 TATTTACGCCAAAAATCGGAAAAAATTGAGCCGGGGCTCCGGATCGGGTTTTTAGTCAAAAACCA
131 TCTTTGCGCCAAAAATATG-CAAAATTGAGTCGGGGCTCCGGAACGCGTTTTTAG-CCAAAACC-
* * * * **
57161 TGATGGTTAGTACACTATTTCGGCAAAAAACTAATCCGAAAACTTTTTTCTCAATTTTTTGCCAC
193 TGATGGTTAGTACACGATTTCGGCTAAAAGCTAACCCGAAATTTTTTTTCTCAATTTTTTGCCAC
* * * * *
57226 AATATTAAGAAAAATTTATAATTCAACGCCAAAATA-ATTGGCGGGCTTTTCACCCTTCTAATAT
258 AATACTAATAAAAATATATAATTCAACGCCAAAA-AGATTGACGGGCTTTTCACACTTCTAATAT
* *
57290 CGTTTTTCCATTTTTCCGAATTGATTTCTAATTAAATCGAAACAAGATTGAGAT-ACTCGTAAAA
322 CGTTTTTCCATTTTTCCGAATTAATTTCTAATTAAATCGAAATAAGATTGAGATGA-TCGTAAAA
* * * *
57354 AAAAATCCTTATATCCAATATAGCTGAGATTTGGTTTGATTAATATAGATATTTCAAGGAGTCTT
386 AAAAATCCTTATATCCAATATGGCTGAGATTTGCTTTGATAAATATTGATATTTCAAGGAGTCTT
* *
57419 TGCGCTAAAAATCATGCAA
451 TGTGCCAAAAATCATGCAA
Statistics
Matches: 955, Mismatches: 121, Indels: 80
0.83 0.10 0.07
Matches are distributed among these distances:
628 1 0.00
629 101 0.11
630 80 0.08
633 16 0.02
634 4 0.00
635 6 0.01
636 96 0.10
637 74 0.08
638 4 0.00
640 49 0.05
641 117 0.12
642 5 0.01
643 2 0.00
644 29 0.03
645 8 0.01
646 16 0.02
647 162 0.17
648 103 0.11
649 23 0.02
650 1 0.00
651 2 0.00
652 56 0.06
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (635 bp):
TAATATCATTTTCCATTTTTTTCCATTAATTTCTAATTAAATCGAAACAAGATTGAGATTCTCGT
AAAAACAAATCCTTATATCCAATGTGGCTGACATTTGGTTCGATGAATATAGATATTTCAAGGAG
TCTTTGCGCCAAAAATATGCAAAATTGAGTCGGGGCTCCGGAACGCGTTTTTAGCCAAAACCTGA
TGGTTAGTACACGATTTCGGCTAAAAGCTAACCCGAAATTTTTTTTCTCAATTTTTTGCCACAAT
ACTAATAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTTTTCACACTTCTAATATCGTT
TTTCCATTTTTCCGAATTAATTTCTAATTAAATCGAAATAAGATTGAGATGATCGTAAAAAAAAA
TCCTTATATCCAATATGGCTGAGATTTGCTTTGATAAATATTGATATTTCAAGGAGTCTTTGTGC
CAAAAATCATGCAAAATTAAGTCGGAGCTCCAAAACACGTTTTTAGCCAAAAACCGTGATGGTTA
ATACACGATTTCGGCTAAAAACTGACCCGAAAGGTTTTTTCTCGATTTTTTCCACAATATACAGA
AAAAAATAAATAATTCAAAACCAAAAAGATTGACAGGCTTTTCACACTTC
Found at i:57414 original size:319 final size:319
Alignment explanation
Indices: 55695--57437 Score: 1817
Period size: 319 Copynumber: 5.5 Consensus size: 319
55685 TTTAATATAA
* * * *
55695 TTTTCCATTTTTTTCCTAATTAATTTCTAATGAAATCGAAACAAGATTGAGATTCTCGAAAAAAC
1 TTTTCCA-TTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTGAGATACTCGTAAAAAC
* * *
55760 AAAT-CTTCATATCCAATATAGCTGAGATTTGCTTTGATGAATATAGATATTTCAAGGAGTCTTT
65 AAATCCTT-ATATCCAATATGGCTGACATTTGGTTTGATGAATATAGATATTTCAAGGAGTCTTT
* * *
55824 GCGCTAAAAATCATGCAAAATTGAGTCGGGGCTCCGGAACGCGCTTTTAGCCAAAAATCGT-A--
129 GCGCCAAAAATCATGCAAAATTGAGTCGGGGCTCCGGAACGCGTTTTTAG-CAAAAACCGTGATG
* * * *
55886 ---ACGTACACGATTTTCGGCTAAAAGCTGACACGAAATTTTTTTTCTCAATTTTTTCCCACAAT
193 GTTA-GTACACGA-TTTCGGCTAAAAACTGACCCGAAAATTTTTTTCTCAATTTTTTGCCACAAT
* * * ** *
55948 ACTCATAAAAATATATAATTCATCGCCAAAAAGATTGACATGCTTTTCACACTTTTAATATCGT
256 ACTAAGAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTTTTCACACTTCTAATATCGT
* * * * *
56012 TTTGCCTATTTTTGTTCCGAATTAATTTCTAATTAAATCGAAATAAGATTCAAATGCTCGTAAAA
1 TTTTCC-A-TTTT-TTCCGAATTAATTTCTAATTAAATCGAAACAAGATTGAGATACTCGTAAAA
* * * *
56077 ACAAATCCTTATATCCAATGTGGCTGACATTTCGTTCT-ATAAATATTGATATTTCAAGGAGTCT
63 ACAAATCCTTATATCCAATATGGCTGACATTTGGTT-TGATGAATATAGATATTTCAAGGAGTCT
* * * * ** *
56141 TTGTGACAAAAATCATGCAAAATTAAGTCGGAGCTCCAAAACGCGTTTTTAGCCAAAAACTGTGA
127 TTGCGCCAAAAATCATGCAAAATTGAGTCGGGGCTCCGGAACGCGTTTTTAG-CAAAAACCGTGA
* * ** *
56206 TGGTTAATACATGATTTCGGCTAAAAACTGACCCGAAAGGTTTTTTCTCGATTTTTT-CCACAAT
191 TGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAATTTTTTTCTCAATTTTTTGCCACAAT
* ** ** *
56270 A-TACAGAAAAAAATAAATAATTCAAAACCAAAAATTTTGACGGGCTTTTCAGACTTCTAATATC
256 ACTA-AG--AAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTTTTCACACTTCTAATATC
*
56334 AT
318 GT
* * * *
56336 CTTTCCATTTTTTTCCGAGTTAATTTCTAATTAAATCGGAAA-AAGATTTAGATGCTCGTAAAAA
1 TTTTCCA-TTTTTTCCGAATTAATTTCTAATTAAATC-GAAACAAGATTGAGATACTCGTAAAAA
* *
56400 CAAATCCATT-TATCCAATGTGGCTGACATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTT
64 CAAATCC-TTATATCCAATATGGCTGACATTTGGTTTGATGAATATAGATATTTCAAGGAGTCTT
* * *
56464 TGCGCCAAAAAT-ATGCAAAATTGAGTCAGGGCTCCGGAACACGTTTTTAGCCAAACACCGTGAT
128 TGCGCCAAAAATCATGCAAAATTGAGTCGGGGCTCCGGAACGCGTTTTTAG-CAAAAACCGTGAT
* * * **
56528 GGTTAGTACACGATTTCAGCTAAAAGCTAACCCGAATTTTTTTTTCTTTTCAATTTTTTTGCCAC
192 GGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAATTTTTTTC---TCAA-TTTTTTGCCAC
* * * **
56593 AATACTAAAAATTAAAAATATATAATTCAACGTCAAAAAGATTGACGGGCTTTTGATGCTTCTAA
253 AATACT---AA-GAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTTTTCACACTTCTAA
56658 TATCGT
314 TATCGT
* * *
56664 TTTTCCA-TTTTTCCTAATTAATTTCTAATTAAATCGAAATAAGATTGAGATGA-TCG-AAAAAG
1 TTTTCCATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTGAGAT-ACTCGTAAAAAC
* * * * * *
56726 AAATCGTTATATCCAATATGGCTGAGATTTGCTTTGATGAATATTGATATTTCAAAGATTCTTTG
65 AAATCCTTATATCCAATATGGCTGACATTTGGTTTGATGAATATAGATATTTCAAGGAGTCTTTG
* * ***
56791 TGCCAGAAATCATGCAAAATTGAG-CTGGGGCTCCGGAACATTTTTTTAGCGAAAAACCGTGATG
130 CGCCAAAAATCATGCAAAATTGAGTC-GGGGCTCCGGAACGCGTTTTTAGC-AAAAACCGTGATG
* * * *
56855 GTTTGTACACGATTTCGGCTAAAAATTGACCCG-AAATTATTGTTTCT-TATTTTTTAGTCACAA
193 GTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAATT-TT-TTTCTCAATTTTTT-GCCACAA
* * ** *
56918 TACTCAGAAAAA-AGTATAAATTCAATGATAAAAAGATTGACAGGCTTTTCACACTTCTAATATC
255 TACTAAGAAAAATA-TAT-AATTCAACGCCAAAAAGATTGACGGGCTTTTCACACTTCTAATATC
56982 G-
318 GT
* * **
56983 TTTTCCATTTTTTCC----------CTAATTAAATTGAAACAAGATTGAGATTCTCGTTTAAACA
1 TTTTCCATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTGAGATACTCGTAAAAACA
* * * ** * * *
57038 AATCCTTATATCGAATGTGGCTGACATTTCGTTCCATGAATATAGTTATTTCAAGGAGTATTTAC
66 AATCCTTATATCCAATATGGCTGACATTTGGTTTGATGAATATAGATATTTCAAGGAGTCTTTGC
* * * * * *
57103 GCCAAAAATC-GGAAAAAATTGAGCCGGGGCTCCGGATCGGGTTTTTAGTCAAAAACCATGATGG
131 GCCAAAAATCATG-CAAAATTGAGTCGGGGCTCCGGAACGCGTTTTTAG-CAAAAACCGTGATGG
* * * * * *
57167 TTAGTACACTATTTCGGCAAAAAACTAATCCGAAAACTTTTTTCTCAATTTTTTGCCACAATATT
194 TTAGTACACGATTTCGGCTAAAAACTGACCCGAAAATTTTTTTCTCAATTTTTTGCCACAATACT
* * *
57232 AAGAAAAATTTATAATTCAACGCCAAAATA-ATTGGCGGGCTTTTCACCCTTCTAATATCGT
259 AAGAAAAATATATAATTCAACGCCAAAA-AGATTGACGGGCTTTTCACACTTCTAATATCGT
* *
57293 TTTTCCA-TTTTTCCGAATTGATTTCTAATTAAATCGAAACAAGATTGAGATACTCGTAAAAAAA
1 TTTTCCATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTGAGATACTCGTAAAAACA
* * *
57357 AATCCTTATATCCAATATAGCTGAGATTTGGTTTGATTAATATAGATATTTCAAGGAGTCTTTGC
66 AATCCTTATATCCAATATGGCTGACATTTGGTTTGATGAATATAGATATTTCAAGGAGTCTTTGC
*
57422 GCTAAAAATCATGCAA
131 GCCAAAAATCATGCAA
Statistics
Matches: 1179, Mismatches: 188, Indels: 116
0.80 0.13 0.08
Matches are distributed among these distances:
309 46 0.04
310 61 0.05
311 139 0.12
312 6 0.01
317 5 0.00
318 7 0.01
319 263 0.22
320 54 0.05
321 83 0.07
322 125 0.11
323 61 0.05
324 63 0.05
325 83 0.07
326 122 0.10
327 5 0.00
328 54 0.05
329 1 0.00
330 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (319 bp):
TTTTCCATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTGAGATACTCGTAAAAACA
AATCCTTATATCCAATATGGCTGACATTTGGTTTGATGAATATAGATATTTCAAGGAGTCTTTGC
GCCAAAAATCATGCAAAATTGAGTCGGGGCTCCGGAACGCGTTTTTAGCAAAAACCGTGATGGTT
AGTACACGATTTCGGCTAAAAACTGACCCGAAAATTTTTTTCTCAATTTTTTGCCACAATACTAA
GAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTTTTCACACTTCTAATATCGT
Done.