Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023170.1 Corchorus olitorius cultivar O-4 contig23203, 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: 76673
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1035 original size:30 final size:27
Alignment explanation
Indices: 1002--1084 Score: 112
Period size: 30 Copynumber: 3.0 Consensus size: 27
992 ATACCACTAA
* *
1002 TAATTATTATTATTATAATAATAAGTT
1 TAATAATTATTATAATAATAATAAGTT
*
1029 TAATAATTATAATACCACTAATAATAAGTT
1 TAATAATTATTATA--A-TAATAATAAGTT
1059 TAATAATTATTATAATAATAATAAGT
1 TAATAATTATTATAATAATAATAAGT
1085 CTAAATTAAC
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
27 22 0.45
28 1 0.02
29 1 0.02
30 25 0.51
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (27 bp):
TAATAATTATTATAATAATAATAAGTT
Found at i:3166 original size:22 final size:22
Alignment explanation
Indices: 3124--3166 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
3114 AAGGGTCCCT
* *
3124 AAGTTGGTTTAGGTATTTTTCC
1 AAGTTGGTTTAGGAATCTTTCC
3146 AAGTTGG-TTAGGAATGCTTTC
1 AAGTTGGTTTAGGAAT-CTTTC
3167 AAAACTGTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.21, C:0.09, G:0.26, T:0.44
Consensus pattern (22 bp):
AAGTTGGTTTAGGAATCTTTCC
Found at i:3608 original size:13 final size:12
Alignment explanation
Indices: 3590--3632 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
3580 TGTCCCTTTT
3590 AAAAATTCTTCAA
1 AAAAATTCTT-AA
*
3603 AAAAATTCCTAA
1 AAAAATTCTTAA
*
3615 AAAAAATCTTTAA
1 AAAAATTC-TTAA
3628 AAAAA
1 AAAAA
3633 AAAAAGGAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
12 9 0.35
13 17 0.65
ACGTcount: A:0.63, C:0.12, G:0.00, T:0.26
Consensus pattern (12 bp):
AAAAATTCTTAA
Found at i:7420 original size:19 final size:18
Alignment explanation
Indices: 7396--7431 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
7386 TGAAGATTTC
7396 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
7415 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
7432 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:15552 original size:28 final size:27
Alignment explanation
Indices: 15490--15551 Score: 81
Period size: 28 Copynumber: 2.3 Consensus size: 27
15480 AAAGAAGGAG
*
15490 AAGAGAAGAAAAGAAGGAAAAATTGAAA
1 AAGAAAAGAAAAGAA-GAAAAATTGAAA
*
15518 AAGAAAAGAAAAGAA-AGAAATTGAAA
1 AAGAAAAGAAAAGAAGAAAAATTGAAA
15544 AAGTAAAA
1 AAG-AAAA
15552 ATGGAGGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
26 13 0.42
27 4 0.13
28 14 0.45
ACGTcount: A:0.71, C:0.00, G:0.21, T:0.08
Consensus pattern (27 bp):
AAGAAAAGAAAAGAAGAAAAATTGAAA
Found at i:17034 original size:54 final size:54
Alignment explanation
Indices: 16930--18071 Score: 638
Period size: 54 Copynumber: 21.3 Consensus size: 54
16920 CGATCTTTTA
* * *
16930 AAGTTTTCAGAGATCTAAGATGA-CGTTC--ATGGCCCTGTGCGGTCTGTCATAG
1 AAGTTTTCAGAGATCTAAGTTGATC-TTCAGATGACCCTGTGCGGTCTTTCATAG
* * * *
16982 AAGTTTTCAGAGGTTTAAGTTGATCTTCAGATAACCATGTGCGGTCTTTCATAG
1 AAGTTTTCAGAGATCTAAGTTGATCTTCAGATGACCCTGTGCGGTCTTTCATAG
* * *
17036 AAGTTTTCAGAGATTTAAGTTGATGTTCAGATGACCTTGTGCGGTCTTTCATAG
1 AAGTTTTCAGAGATCTAAGTTGATCTTCAGATGACCCTGTGCGGTCTTTCATAG
* * * *
17090 AAGTTTTCAGAAATCTAAGATTGATTTTAAGATGACCCCGTGCGGTCTTTCATAG
1 AAGTTTTCAGAGATCTAAG-TTGATCTTCAGATGACCCTGTGCGGTCTTTCATAG
* *** * * * *
17145 AAGCTTTT-AGAGATCTAGGTTGATCTTCAGGCAACCGTATACGGTCTTTCACAG
1 AAG-TTTTCAGAGATCTAAGTTGATCTTCAGATGACCCTGTGCGGTCTTTCATAG
* *
17199 AAGTTTTCAGAGATCTAAGTTGATCTTCAGCTGACCCTGTGCGCTCTTTCATAG
1 AAGTTTTCAGAGATCTAAGTTGATCTTCAGATGACCCTGTGCGGTCTTTCATAG
* *
17253 AAGTTTTCAGAGATTTAAGTTGATCTTCAGATGATCCTGTGCGGTCTTTCATAG
1 AAGTTTTCAGAGATCTAAGTTGATCTTCAGATGACCCTGTGCGGTCTTTCATAG
* * *
17307 AAGTTTTCAGAAATCTAAGTTGATTTTAAGATGACCCTGTGCGGTCTTTCATAG
1 AAGTTTTCAGAGATCTAAGTTGATCTTCAGATGACCCTGTGCGGTCTTTCATAG
** * * * *
17361 AACCTTTCAGAGATCTAAGTTGATCTTCAGATGACTC-G-GCATTGTCATTCGTAG
1 AAGTTTTCAGAGATCTAAGTTGATCTTCAGATGACCCTGTGC--GGTCTTTCATAG
* * * * *
17415 AAG-TTTCTAGAGATC-AGAGTTGATC-CCTAGATGATCCAGTGCGATCATTC-TAAG
1 AAGTTTTC-AGAGATCTA-AGTTGATCTTC-AGATGACCCTGTGCGGTCTTTCAT-AG
* * * * *
17469 AAGTTTT-GGATGATC-AGAGTTGATC-ACTAAATGA-TCTAGTGCGATCATTTCA-AG
1 AAGTTTTCAGA-GATCTA-AGTTGATCTTC-AGATGACCCT-GTGCGGTC-TTTCATAG
** * *
17523 AAGTTTTCAG-G-----AGTTGATCCCCAGATGATCCAGTGCGGTCATTTCA-AG
1 AAGTTTTCAGAGATCTAAGTTGATCTTCAGATGACCCTGTGCGGTC-TTTCATAG
*** * * * *
17571 AAGTTTTCTTTGATC-AAGATTTAATC-CCAGATGACCCAGTGCGGTCATTCCA-AG
1 AAGTTTTCAGAGATCTAAG--TTGATCTTCAGATGACCCTGTGCGGTC-TTTCATAG
* * * * * *
17625 AAGTTTTTAGAGATC-AGAGTTGATC-CCTAGATGATCCAGTGCGGTCATTCCAAAG
1 AAGTTTTCAGAGATCTA-AGTTGATCTTC-AGATGACCCTGTGCGGTC-TTTCATAG
* *
17680 AAGTTTTCA-ATGATC-AGAGTTGATC-CCTAGATGA-TCTAGTGCGGTCATTTCA-AG
1 AAGTTTTCAGA-GATCTA-AGTTGATCTTC-AGATGACCCT-GTGCGGTC-TTTCATAG
* * * * * *
17734 AAGTTTTCAGTGAT-TAGAGTTGATC-CCTGATGATCCAGTGCGGTCATTCCA-AG
1 AAGTTTTCAGAGATCTA-AGTTGATCTTCAGATGACCCTGTGCGGTC-TTTCATAG
* * * * * * *
17787 AAGTTTTCTGTGATC-AGAGTTGATC-CCAGATGATCCAGTGCAGTCATTCCA-AG
1 AAGTTTTCAGAGATCTA-AGTTGATCTTCAGATGACCCTGTGCGGTC-TTTCATAG
* * * * ** *
17840 AAGTTTTCA-ATGATCAAAGTTGATCTCCATATGATCCAATGCGGTCGTTCCA-AG
1 AAGTTTTCAGA-GATCTAAGTTGATCTTCAGATGACCCTGTGCGGTC-TTTCATAG
* * * *
17894 AAATTTTC-GATGATC-AGAGTTGATCTCCAGATGA-TCTAGTGCGGTCATTCCA-AG
1 AAGTTTTCAGA-GATCTA-AGTTGATCTTCAGATGACCCT-GTGCGGTC-TTTCATAG
* * * ** * *
17948 AAGTTTTTAGAGATC-AGAGTTGATCCCTCA-ATGATCCAATGCGGTCATTCGAAAG
1 AAGTTTTCAGAGATCTA-AGTTGAT-CTTCAGATGACCCTGTGCGGTCTTTC-ATAG
** * * *
18003 AAGTTTTCA-ATGATC-AGAGTTGATCCCCAGATAATCCAGTGAC-GTCATTTCA-AG
1 AAGTTTTCAGA-GATCTA-AGTTGATCTTCAGATGACCCTGTG-CGGTC-TTTCATAG
*
18057 AAGTTTTCAGTGATC
1 AAGTTTTCAGAGATC
18072 AGAATTGATC
Statistics
Matches: 912, Mismatches: 124, Indels: 106
0.80 0.11 0.09
Matches are distributed among these distances:
48 36 0.04
49 3 0.00
52 25 0.03
53 119 0.13
54 573 0.63
55 146 0.16
56 10 0.01
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (54 bp):
AAGTTTTCAGAGATCTAAGTTGATCTTCAGATGACCCTGTGCGGTCTTTCATAG
Found at i:17420 original size:162 final size:160
Alignment explanation
Indices: 16930--17398 Score: 577
Period size: 163 Copynumber: 2.9 Consensus size: 160
16920 CGATCTTTTA
* * *
16930 AAGTTTTCAGAGATCTAAGATGA-CGTTC--ATGGCCCTGTGCGGTCTGTCATAGAAGTTTTCAG
1 AAGTTTTCAGAGATCTAAGTTGATC-TTCAGATGACCCTGTGCGGTCTTTCATAGAAGTTTTCAG
* * *
16992 AGGTTTAAGTTGATCTTCAGATAACCATGTGCGGTCTTTCATAGAAGTTTTCAGAGATTTAAGTT
65 AGATCTAAGTTGATCTTCAGATAACCATGTGCGGTCTTTCATAGAAGTTTTCAGAGATCTAAGTT
* *
17057 GATGTTCAGATGACCTTGTGCGGTCTTTCATAG
130 GATCTTCAGATGA-CTCGTGC-GTCTTTCATAG
* * * *
17090 AAGTTTTCAGAAATCTAAGATTGATTTTAAGATGACCCCGTGCGGTCTTTCATAGAAGCTTTT-A
1 AAGTTTTCAGAGATCTAAG-TTGATCTTCAGATGACCCTGTGCGGTCTTTCATAGAAG-TTTTCA
* ** * * * *
17154 GAGATCTAGGTTGATCTTCAGGCAACCGTATACGGTCTTTCACAGAAGTTTTCAGAGATCTAAGT
64 GAGATCTAAGTTGATCTTCAGATAACCATGTGCGGTCTTTCATAGAAGTTTTCAGAGATCTAAGT
* *
17219 TGATCTTCAGCTGACCCTGTGCGCTCTTTCATAG
129 TGATCTTCAGATGACTC-GTGCG-TCTTTCATAG
* *
17253 AAGTTTTCAGAGATTTAAGTTGATCTTCAGATGATCCTGTGCGGTCTTTCATAGAAGTTTTCAGA
1 AAGTTTTCAGAGATCTAAGTTGATCTTCAGATGACCCTGTGCGGTCTTTCATAGAAGTTTTCAGA
* * * * * **
17318 AATCTAAGTTGATTTTAAGATGACCCTGTGCGGTCTTTCATAGAACCTTTCAGAGATCTAAGTTG
66 GATCTAAGTTGATCTTCAGATAACCATGTGCGGTCTTTCATAGAAGTTTTCAGAGATCTAAGTTG
17383 ATCTTCAGATGACTCG
131 ATCTTCAGATGACTCG
17399 GCATTGTCAT
Statistics
Matches: 259, Mismatches: 42, Indels: 15
0.82 0.13 0.05
Matches are distributed among these distances:
160 18 0.07
161 10 0.04
162 104 0.40
163 123 0.47
164 4 0.02
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (160 bp):
AAGTTTTCAGAGATCTAAGTTGATCTTCAGATGACCCTGTGCGGTCTTTCATAGAAGTTTTCAGA
GATCTAAGTTGATCTTCAGATAACCATGTGCGGTCTTTCATAGAAGTTTTCAGAGATCTAAGTTG
ATCTTCAGATGACTCGTGCGTCTTTCATAG
Found at i:17438 original size:162 final size:159
Alignment explanation
Indices: 16930--18142 Score: 570
Period size: 163 Copynumber: 7.5 Consensus size: 159
16920 CGATCTTTTA
* ** *
16930 AAGTTTTCAGAGATCTAAGATGA-CGTTC--ATGGCCCTGTGCGGTCTGTCATAGAAGTTTTCAG
1 AAGTTTTCAGAGATC-AAGTTGATC-TTCAGATGATCCTGTGCGGTCTTTCATAGAAGTTTTCAG
* * *
16992 AGGTTTAAGTTGATCTTCAGATAACCATGTGCGGTCTTTCATAGAAGTTTTCAGAGATTTAAGTT
64 AGATCTAAGTTGATCTTCAGATAACCATGTGCGGTCTTTCATAGAAGTTTTCAGAGATCTAAGTT
* *
17057 GATGTTCAGATGACCTTGTGCGGTCTTTCATAG
129 GATCTTCAGATGA-CTCGTGC-GTCTTTCATAG
* * * * *
17090 AAGTTTTCAGAAATCTAAGATTGATTTTAAGATGACCCCGTGCGGTCTTTCATAGAAGCTTTT-A
1 AAGTTTTCAGAGATC-AAG-TTGATCTTCAGATGATCCTGTGCGGTCTTTCATAGAAG-TTTTCA
* ** * * * *
17154 GAGATCTAGGTTGATCTTCAGGCAACCGTATACGGTCTTTCACAGAAGTTTTCAGAGATCTAAGT
63 GAGATCTAAGTTGATCTTCAGATAACCATGTGCGGTCTTTCATAGAAGTTTTCAGAGATCTAAGT
* *
17219 TGATCTTCAGCTGACCCTGTGCGCTCTTTCATAG
128 TGATCTTCAGATGACTC-GTGCG-TCTTTCATAG
*
17253 AAGTTTTCAGAGATTTAAGTTGATCTTCAGATGATCCTGTGCGGTCTTTCATAGAAGTTTTCAGA
1 AAGTTTTCAGAGA-TCAAGTTGATCTTCAGATGATCCTGTGCGGTCTTTCATAGAAGTTTTCAGA
* * * * * **
17318 AATCTAAGTTGATTTTAAGATGACCCTGTGCGGTCTTTCATAGAACCTTTCAGAGATCTAAGTTG
65 GATCTAAGTTGATCTTCAGATAACCATGTGCGGTCTTTCATAGAAGTTTTCAGAGATCTAAGTTG
* *
17383 ATCTTCAGATGACTCG-GCATTGTCATTCGTAG
130 ATCTTCAGATGACTCGTGC---GTCTTTCATAG
* * * *
17415 AAG-TTTCTAGAGATCAGAGTTGATC-CCTAGATGATCCAGTGCGATCATTC-TAAGAAGTTTT-
1 AAGTTTTC-AGAGATCA-AGTTGATCTTC-AGATGATCCTGTGCGGTCTTTCAT-AGAAGTTTTC
* * * * * *
17476 GGATGATC-AGAGTTGATC-ACTAAATGATC-TAGTGCGATCATTTCA-AGAAGTTTTCAG-G--
62 AGA-GATCTA-AGTTGATCTTC-AGATAACCAT-GTGCGGTC-TTTCATAGAAGTTTTCAGAGAT
**
17534 ---AGTTGATCCCCAGATGA-TCCAGTGCGGTCATTTCA-AG
122 CTAAGTTGATCTTCAGATGACT-C-GTGC-GTC-TTTCATAG
*** * * * * * *
17571 AAGTTTTCTTTGATCAAGATTTAATC-CCAGATGACCCAGTGCGGTCATTCCA-AGAAGTTTTTA
1 AAGTTTTCAGAGATCAAG--TTGATCTTCAGATGATCCTGTGCGGTC-TTTCATAGAAGTTTTCA
* * * *
17634 GAGATC-AGAGTTGATC-CCTAGATGATCCA-GTGCGGTCATTCCAAAGAAGTTTTCA-ATGATC
63 GAGATCTA-AGTTGATCTTC-AGAT-AACCATGTGCGGTC-TTTCATAGAAGTTTTCAGA-GATC
* *
17695 -AGAGTTGATC-CCTAGATGATCTAGTGCGGTCATTTCA-AG
123 TA-AGTTGATCTTC-AGATGA-CTCGTGC-GTC-TTTCATAG
* * * * * * *
17734 AAGTTTTCAGTGATTAGAGTTGATC-CCTGATGATCCAGTGCGGTCATTCCA-AGAAGTTTTCTG
1 AAGTTTTCAGAGATCA-AGTTGATCTTCAGATGATCCTGTGCGGTC-TTTCATAGAAGTTTTCAG
* * * * * *
17797 TGATC-AGAGTTGATC-CCAGATGATCCA-GTGCAGTCATTCCA-AGAAGTTTTCA-ATGATCAA
64 AGATCTA-AGTTGATCTTCAGAT-AACCATGTGCGGTC-TTTCATAGAAGTTTTCAGA-GATCTA
* * * *
17857 AGTTGATCTCCATATGA-TCCAATGCGGTCGTTCCA-AG
125 AGTTGATCTTCAGATGACT-C-GTGC-GTC-TTTCATAG
* * * *
17894 AAATTTTC-GATGATCAGAGTTGATCTCCAGATGAT-CTAGTGCGGTCATTCCA-AGAAGTTTTT
1 AAGTTTTCAGA-GATCA-AGTTGATCTTCAGATGATCCT-GTGCGGTC-TTTCATAGAAGTTTTC
* * * * *
17956 AGAGATC-AGAGTTGATCCCTCA-ATGATCCA-ATGCGGTCATTCGAAAGAAGTTTTCA-ATGAT
62 AGAGATCTA-AGTTGAT-CTTCAGAT-AACCATGTGCGGTCTTTC-ATAGAAGTTTTCAGA-GAT
** *
18017 C-AGAGTTGATCCCCAGAT-AATCCAGTGACGTCATTTCA-AG
122 CTA-AGTTGATCTTCAGATGACT-C-GTG-CGTC-TTTCATAG
* * ** * * *
18057 AAGTTTTCAGTGATCAGAATTGATCCCCAGATGAT-CTAGTGTGGTCATTCCA-AAAAGTTTTCA
1 AAGTTTTCAGAGATCA-AGTTGATCTTCAGATGATCCT-GTGCGGTC-TTTCATAGAAGTTTTCA
*
18120 -ATGAT-TATAGTTGATCTCCAGAT
63 GA-GATCTA-AGTTGATCTTCAGAT
18143 GATTCAGTGT
Statistics
Matches: 866, Mismatches: 124, Indels: 123
0.78 0.11 0.11
Matches are distributed among these distances:
155 3 0.00
156 85 0.10
157 31 0.04
158 4 0.00
159 1 0.00
160 84 0.10
161 96 0.11
162 268 0.31
163 284 0.33
164 9 0.01
165 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (159 bp):
AAGTTTTCAGAGATCAAGTTGATCTTCAGATGATCCTGTGCGGTCTTTCATAGAAGTTTTCAGAG
ATCTAAGTTGATCTTCAGATAACCATGTGCGGTCTTTCATAGAAGTTTTCAGAGATCTAAGTTGA
TCTTCAGATGACTCGTGCGTCTTTCATAG
Found at i:17953 original size:323 final size:321
Alignment explanation
Indices: 17413--18191 Score: 995
Period size: 323 Copynumber: 2.4 Consensus size: 321
17403 TGTCATTCGT
* * *
17413 AGAAG-TTTCTAGAGATCAGAGTTGATCCCTAGATGATCCAGTGCGATCATTCTAAGAAGTTTT-
1 AGAAGTTTTC-AGTGATCAGAGTTGATCCCT-GATGATCCAGTGCGGTCATTCCAAGAAGTTTTC
* * * * *
17476 GGATGATCAGAGTTGATCACTAAATGATCTAGTGCGATCATTTCAAGAAGTTTTC-AG---GAGT
64 AG-TGATCAGAGTTGATCACCAGATGATCCAGTGCG-TCATTCCAAGAAGTTTTCAAGACAGAGT
* * * * ** *
17537 TGATCCCCAGATGATCCAGTGCGGTCATTTCAAGAAGTTTTCTTTGATCAAGATTTAATCCCAGA
127 TGATCTCCAGATGATCCAATGCGGTCATTCCAAGAAATTTTCGATGATCAAGAGTTAATCCCAGA
*
17602 TGACCCAGTGCGGTCATTCCAAGAAGTTTTTAGAGATCAGAGTTGATCCCT-AGATGATCCAGTG
192 TGACCCAGTGCGGTCATTCCAAGAAGTTTTTAGAGATCAGAGTTGATCCCTCA-ATGATCCAATG
* * *
17666 CGGTCATTCCAAAGAAGTTTTCAATGATCAGAGTTGATCCCTAGATGATCTAGTG-CGGTCATTT
256 CGGTCATTCCAAAGAAGTTTTCAATGATCAGAGTTGATCCCCAGATAATCCAGTGAC-GTCATTT
17730 CA
320 CA
* *
17732 AGAAGTTTTCAGTGATTAGAGTTGATCCCTGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCTG
1 AGAAGTTTTCAGTGATCAGAGTTGATCCCTGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCAG
*
17797 TGATCAGAGTTGATC-CCAGATGATCCAGTGCAGTCATTCCAAGAAGTTTTCAATGATCAAAGTT
66 TGATCAGAGTTGATCACCAGATGATCCAGTGC-GTCATTCCAAGAAGTTTTCAA-GA-CAGAGTT
* * *
17861 GATCTCCATATGATCCAATGCGGTCGTTCCAAGAAATTTTCGATGATC-AGAGTTGATCTCCAGA
128 GATCTCCAGATGATCCAATGCGGTCATTCCAAGAAATTTTCGATGATCAAGAGTTAATC-CCAGA
* *
17925 TGATCTAGTGCGGTCATTCCAAGAAGTTTTTAGAGATCAGAGTTGATCCCTCAATGATCCAATGC
192 TGACCCAGTGCGGTCATTCCAAGAAGTTTTTAGAGATCAGAGTTGATCCCTCAATGATCCAATGC
*
17990 GGTCATTCGAAAGAAGTTTTCAATGATCAGAGTTGATCCCCAGATAATCCAGTGACGTCATTTCA
257 GGTCATTCCAAAGAAGTTTTCAATGATCAGAGTTGATCCCCAGATAATCCAGTGACGTCATTTCA
* * * * *
18055 AGAAGTTTTCAGTGATCAGAATTGATCCCCAGATGATCTAGTGTGGTCATTCCAAAAAGTTTTCA
1 AGAAGTTTTCAGTGATCAGAGTTGAT-CCCTGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCA
* * * * * *
18120 ATGATTATAGTTGATCTCCAGATGATTCAGTGTGCTTC-TTCCAAGAAGTTTTCGAAGAACAGAG
65 GTGATCAGAGTTGATCACCAGATGATCCA--GTGCGTCATTCCAAGAAGTTTTC-AAG-ACAGAG
18184 TTGATCTC
126 TTGATCTC
18192 ATTTCAAAAA
Statistics
Matches: 402, Mismatches: 40, Indels: 30
0.85 0.08 0.06
Matches are distributed among these distances:
317 30 0.07
318 47 0.12
319 25 0.06
320 4 0.01
322 8 0.02
323 192 0.48
324 48 0.12
325 39 0.10
326 5 0.01
327 4 0.01
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (321 bp):
AGAAGTTTTCAGTGATCAGAGTTGATCCCTGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCAG
TGATCAGAGTTGATCACCAGATGATCCAGTGCGTCATTCCAAGAAGTTTTCAAGACAGAGTTGAT
CTCCAGATGATCCAATGCGGTCATTCCAAGAAATTTTCGATGATCAAGAGTTAATCCCAGATGAC
CCAGTGCGGTCATTCCAAGAAGTTTTTAGAGATCAGAGTTGATCCCTCAATGATCCAATGCGGTC
ATTCCAAAGAAGTTTTCAATGATCAGAGTTGATCCCCAGATAATCCAGTGACGTCATTTCA
Found at i:18191 original size:54 final size:52
Alignment explanation
Indices: 17425--18189 Score: 781
Period size: 54 Copynumber: 14.3 Consensus size: 52
17415 AAGTTTCTAG
* * *
17425 AGATCAGAGTTGATCCCTAGATGATCCAGTGCGATCATTCTAAGAAGTTTTGGA
1 AGATCAGAGTTGATCCC-AGATGATCCAGTGCGGTCATTCCAAGAAGTTTT-CA
* * * * * *
17479 TGATCAGAGTTGATCACTAAATGATCTAGTGCGATCATTTCAAGAAGTTTTC-
1 AGATCAGAGTTGATC-CCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCA
* *
17531 AG----GAGTTGATCCCCAGATGATCCAGTGCGGTCATTTCAAGAAGTTTTCTT
1 AGATCAGAGTTGAT-CCCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTC-A
* * * * *
17581 TGATCAAGATTTAATCCCAGATGACCCAGTGCGGTCATTCCAAGAAGTTTTTA
1 AGATC-AGAGTTGATCCCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCA
17634 GAGATCAGAGTTGATCCCTAGATGATCCAGTGCGGTCATTCCAAAGAAGTTTTCA
1 -AGATCAGAGTTGATCCC-AGATGATCCAGTGCGGTCATTCC-AAGAAGTTTTCA
* *
17689 ATGATCAGAGTTGATCCCTAGATGATCTAGTGCGGTCATTTCAAGAAGTTTTCA
1 A-GATCAGAGTTGATCCC-AGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCA
* * * *
17743 GTGATTAGAGTTGATCCCTGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCTG
1 -AGATCAGAGTTGATCCCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTC-A
* *
17797 TGATCAGAGTTGATCCCAGATGATCCAGTGCAGTCATTCCAAGAAGTTTTCA
1 AGATCAGAGTTGATCCCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCA
* * * * *
17849 ATGATCAAAGTTGATCTCCATATGATCCAATGCGGTCGTTCCAAGAAATTTTCGA
1 A-GATCAGAGTTGATC-CCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTC-A
* * *
17904 TGATCAGAGTTGATCTCCAGATGATCTAGTGCGGTCATTCCAAGAAGTTTTTA
1 AGATCAGAGTTGATC-CCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCA
* *
17957 GAGATCAGAGTTGATCCCTCA-ATGATCCAATGCGGTCATTCGAAAGAAGTTTTCA
1 -AGATCAGAGTTGAT-CC-CAGATGATCCAGTGCGGTCATTC-CAAGAAGTTTTCA
* *
18012 ATGATCAGAGTTGATCCCCAGATAATCCAGTGAC-GTCATTTCAAGAAGTTTTCA
1 A-GATCAGAGTTGAT-CCCAGATGATCCAGTG-CGGTCATTCCAAGAAGTTTTCA
* * * * *
18066 GTGATCAGAATTGATCCCCAGATGATCTAGTGTGGTCATTCCAAAAAGTTTTCA
1 -AGATCAGAGTTGAT-CCCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCA
* * * * *
18120 ATGATTATAGTTGATCTCCAGATGATTCAGTGTGCTTC-TTCCAAGAAGTTTTCGA
1 A-GATCAGAGTTGATC-CCAGATGATCCAGTGCG-GTCATTCCAAGAAGTTTTC-A
*
18175 AGAACAGAGTTGATC
1 AGATCAGAGTTGATC
18190 TCATTTCAAA
Statistics
Matches: 602, Mismatches: 78, Indels: 62
0.81 0.11 0.08
Matches are distributed among these distances:
48 40 0.07
49 1 0.00
50 1 0.00
52 1 0.00
53 104 0.17
54 348 0.58
55 106 0.18
56 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.31
Consensus pattern (52 bp):
AGATCAGAGTTGATCCCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCA
Found at i:18218 original size:35 final size:35
Alignment explanation
Indices: 18161--18436 Score: 453
Period size: 35 Copynumber: 7.9 Consensus size: 35
18151 GTGCTTCTTC
* *
18161 CAAGAAGTTTTCGAAGAACAGAGTTGATCTCATTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCATTT
*
18196 CAAAAAGTTTTCGATGATCAGAGTTGATCTCATTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCATTT
* **
18231 CAAGAAGTTTTCAACAATCAGAGTTGATCTCATTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCATTT
*
18266 CAAGAGGTTTTCGATGATCAGAGTTGATCTCATTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCATTT
*
18301 CAAGAGGTTTTCGATGATCAGAGTTGATCTCATTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCATTT
* *
18336 CAAGAAGTTTTCGATGATCAGAATTAATCTCATTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCATTT
*
18371 CAAGAAGTTTTTGATGATCAGAGTTGATCTCATTT
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTCATTT
18406 CAAGAAGTTTTCGATGATCAGAGTTGATCTC
1 CAAGAAGTTTTCGATGATCAGAGTTGATCTC
18437 TAATTGATCC
Statistics
Matches: 223, Mismatches: 18, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 223 1.00
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.36
Consensus pattern (35 bp):
CAAGAAGTTTTCGATGATCAGAGTTGATCTCATTT
Found at i:21714 original size:73 final size:73
Alignment explanation
Indices: 21595--21737 Score: 286
Period size: 73 Copynumber: 2.0 Consensus size: 73
21585 ATGGGCTTAG
21595 CTTTTCTATTGGTTTCCATTTCTATGTGTGTTTTTACAGGAATTTCTTTCTTGGTAAAATTATTT
1 CTTTTCTATTGGTTTCCATTTCTATGTGTGTTTTTACAGGAATTTCTTTCTTGGTAAAATTATTT
21660 TGGAAGAA
66 TGGAAGAA
21668 CTTTTCTATTGGTTTCCATTTCTATGTGTGTTTTTACAGGAATTTCTTTCTTGGTAAAATTATTT
1 CTTTTCTATTGGTTTCCATTTCTATGTGTGTTTTTACAGGAATTTCTTTCTTGGTAAAATTATTT
21733 TGGAA
66 TGGAA
21738 AAAAGTTAAA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 70 1.00
ACGTcount: A:0.21, C:0.11, G:0.16, T:0.52
Consensus pattern (73 bp):
CTTTTCTATTGGTTTCCATTTCTATGTGTGTTTTTACAGGAATTTCTTTCTTGGTAAAATTATTT
TGGAAGAA
Found at i:28988 original size:21 final size:22
Alignment explanation
Indices: 28962--29009 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
28952 TAAAAAGGAT
28962 TAAAAA-AATAAAATGAAGACA
1 TAAAAAGAATAAAATGAAGACA
* *
28983 TAAAAAGGATTAAATGAAGACA
1 TAAAAAGAATAAAATGAAGACA
29005 TAAAA
1 TAAAA
29010 TTATCGGGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 6 0.25
22 18 0.75
ACGTcount: A:0.67, C:0.04, G:0.12, T:0.17
Consensus pattern (22 bp):
TAAAAAGAATAAAATGAAGACA
Found at i:32527 original size:115 final size:115
Alignment explanation
Indices: 32397--32645 Score: 417
Period size: 115 Copynumber: 2.2 Consensus size: 115
32387 TTTATTTAAA
* *
32397 AAATTTATCCACTGTTATACAATTAGTTTCTGAAATTGACTTCCATTTACATCTGATTTTACTTT
1 AAATTTATGCACTGTTATACAATTAGTTTCTGAAATTGACTTCCATTTACATCTAATTTTACTTT
*
32462 CTTAATGACTTTACTTTACATACATAATAAATTTAAGTTACATTTTTTAC
66 CTTAATGACTTTACTTTACATACATAATAAATTTAAGTTACATATTTTAC
* *
32512 ACATTTATGCACTGTTATACAATTAGTTTTTGAAATTGACTTCCATTTACATCTAATTTTACTTT
1 AAATTTATGCACTGTTATACAATTAGTTTCTGAAATTGACTTCCATTTACATCTAATTTTACTTT
* * *
32577 GTTAATTACTTTACTTTACTTACATAATAAATTTAAGTTACATATTTTAC
66 CTTAATGACTTTACTTTACATACATAATAAATTTAAGTTACATATTTTAC
*
32627 AAATTTATGCATTGTTATA
1 AAATTTATGCACTGTTATA
32646 GGTAGTTAAC
Statistics
Matches: 124, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
115 124 1.00
ACGTcount: A:0.33, C:0.14, G:0.06, T:0.47
Consensus pattern (115 bp):
AAATTTATGCACTGTTATACAATTAGTTTCTGAAATTGACTTCCATTTACATCTAATTTTACTTT
CTTAATGACTTTACTTTACATACATAATAAATTTAAGTTACATATTTTAC
Found at i:33919 original size:22 final size:22
Alignment explanation
Indices: 33889--33949 Score: 88
Period size: 22 Copynumber: 2.8 Consensus size: 22
33879 TTGAATATTT
*
33889 TTATGAAATTTTGATAACTATCG
1 TTATGAAATTTTGATAACCA-CG
*
33912 -TATTAAATTTTGATAACCACG
1 TTATGAAATTTTGATAACCACG
33933 TTATGAAATTTTGATAA
1 TTATGAAATTTTGATAA
33950 TTTACCTATG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
21 2 0.06
22 32 0.94
ACGTcount: A:0.38, C:0.08, G:0.11, T:0.43
Consensus pattern (22 bp):
TTATGAAATTTTGATAACCACG
Found at i:33959 original size:22 final size:21
Alignment explanation
Indices: 33890--33963 Score: 76
Period size: 22 Copynumber: 3.4 Consensus size: 21
33880 TGAATATTTT
*
33890 TATGAAATTTTGATAACTATCG
1 TATGAAATTTTGATAACTA-CC
* * *
33912 TATTAAATTTTGATAACCACGT
1 TATGAAATTTTGATAACTAC-C
*
33934 TATGAAATTTTGATAATTTACC
1 TATGAAATTTTGATAA-CTACC
33956 TATGAAAT
1 TATGAAAT
33964 ATGAAACTTA
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
21 1 0.02
22 40 0.93
23 2 0.05
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.42
Consensus pattern (21 bp):
TATGAAATTTTGATAACTACC
Found at i:37714 original size:2 final size:2
Alignment explanation
Indices: 37707--37737 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
37697 GGCTCCCTCC
37707 CT CT CT CT CT CT CT CAT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT C-T CT CT CT CT CT CT CT
37738 GTTAAAAGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.03, C:0.48, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:37728 original size:13 final size:13
Alignment explanation
Indices: 37710--37734 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
37700 TCCCTCCCTC
37710 TCTCTCTCTCTCA
1 TCTCTCTCTCTCA
37723 TCTCTCTCTCTC
1 TCTCTCTCTCTC
37735 TCTGTTAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.04, C:0.48, G:0.00, T:0.48
Consensus pattern (13 bp):
TCTCTCTCTCTCA
Found at i:37728 original size:15 final size:15
Alignment explanation
Indices: 37708--37736 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
37698 GCTCCCTCCC
37708 TCTCTCTCTCTCTCA
1 TCTCTCTCTCTCTCA
37723 TCTCTCTCTCTCTC
1 TCTCTCTCTCTCTC
37737 TGTTAAAAGC
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:0.03, C:0.48, G:0.00, T:0.48
Consensus pattern (15 bp):
TCTCTCTCTCTCTCA
Found at i:38168 original size:3 final size:3
Alignment explanation
Indices: 38160--38214 Score: 92
Period size: 3 Copynumber: 18.3 Consensus size: 3
38150 TGGGAGCTAG
* *
38160 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAG GAA GAA GAG
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
38208 GAA GAA G
1 GAA GAA G
38215 GAAAAAAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:38374 original size:18 final size:18
Alignment explanation
Indices: 38352--38391 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
38342 TAAAAAAATA
* *
38352 AAAAAAAAATAGAAAAGGG
1 AAAAGAAAA-AGAAAAAGG
38371 AAAAGAAAAAGAAAAAGG
1 AAAAGAAAAAGAAAAAGG
38389 AAA
1 AAA
38392 TAAGGAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.03
Consensus pattern (18 bp):
AAAAGAAAAAGAAAAAGG
Found at i:38374 original size:19 final size:19
Alignment explanation
Indices: 38332--38391 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 19
38322 GCCCAAGACC
* *
38332 GAAAAAAAAATAAAAAAAT
1 GAAAAAAAAATAGAAAAAG
* *
38351 AAAAAAAAAATAGAAAAGG
1 GAAAAAAAAATAGAAAAAG
*
38370 GAAAAGAAAA-AGAAAAAG
1 GAAAAAAAAATAGAAAAAG
38388 GAAA
1 GAAA
38392 TAAGGAATAA
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
18 11 0.32
19 23 0.68
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (19 bp):
GAAAAAAAAATAGAAAAAG
Found at i:38432 original size:31 final size:29
Alignment explanation
Indices: 38374--38433 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 29
38364 AAAAGGGAAA
*
38374 AGAAAAAGAAAAAGGAAATAAGGAATAAG
1 AGAAAAAGAAAAAGGAAATAAGAAATAAG
* *
38403 AGAAAAATGAAAAATTGAAATAATAAATAAG
1 AGAAAAA-GAAAAA-GGAAATAAGAAATAAG
38434 TAGATGAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 7 0.27
30 6 0.23
31 13 0.50
ACGTcount: A:0.68, C:0.00, G:0.18, T:0.13
Consensus pattern (29 bp):
AGAAAAAGAAAAAGGAAATAAGAAATAAG
Found at i:40619 original size:14 final size:14
Alignment explanation
Indices: 40600--40632 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
40590 GGGCGTGACA
40600 ATATATATATATAC
1 ATATATATATATAC
40614 ATATATATATATAC
1 ATATATATATATAC
40628 ATATA
1 ATATA
40633 AAACTTAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (14 bp):
ATATATATATATAC
Found at i:47509 original size:16 final size:15
Alignment explanation
Indices: 47451--47509 Score: 64
Period size: 16 Copynumber: 3.7 Consensus size: 15
47441 AATCGAAATC
47451 AAACCCGAACCCGACA
1 AAACCCGAACCCGA-A
*
47467 GAACCCGAACCCGAA
1 AAACCCGAACCCGAA
* *
47482 TAAATCCAAACCCGAA
1 -AAACCCGAACCCGAA
47498 AAAGCCCGAACC
1 AAA-CCCGAACC
47510 TGAAGTACCC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
15 4 0.11
16 31 0.89
ACGTcount: A:0.44, C:0.39, G:0.14, T:0.03
Consensus pattern (15 bp):
AAACCCGAACCCGAA
Found at i:47599 original size:30 final size:30
Alignment explanation
Indices: 47557--47648 Score: 175
Period size: 30 Copynumber: 3.0 Consensus size: 30
47547 TATTAGAAAA
47557 TATATATTTTATCTAAAACACCTAGTTTTTT
1 TATAT-TTTTATCTAAAACACCTAGTTTTTT
47588 TATATTTTTATCTAAAACACCTAGTTTTTT
1 TATATTTTTATCTAAAACACCTAGTTTTTT
47618 TATATTTTTATCTAAAACACCTAGTTTTTT
1 TATATTTTTATCTAAAACACCTAGTTTTTT
47648 T
1 T
47649 GTTTGTTTTT
Statistics
Matches: 61, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
30 56 0.92
31 5 0.08
ACGTcount: A:0.30, C:0.13, G:0.03, T:0.53
Consensus pattern (30 bp):
TATATTTTTATCTAAAACACCTAGTTTTTT
Found at i:53922 original size:21 final size:21
Alignment explanation
Indices: 53879--53922 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
53869 CCAATTTAGG
* *
53879 TTTAGATTTCAATTTCTTGTT
1 TTTAGATTTAAATTTATTGTT
53900 TTTAGATTTAAGATTTATT-TT
1 TTTAGATTTAA-ATTTATTGTT
53921 TT
1 TT
53923 ATGCATCTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.23, C:0.05, G:0.09, T:0.64
Consensus pattern (21 bp):
TTTAGATTTAAATTTATTGTT
Found at i:57356 original size:51 final size:51
Alignment explanation
Indices: 57274--57376 Score: 118
Period size: 51 Copynumber: 2.0 Consensus size: 51
57264 CATATTTTTC
** * *
57274 TTGTTTAGATCTTGTCTCAGGACACCCAAACACTCTTTTAGTGTTTTTCTT
1 TTGTTTAGATCTTGTCTCAGGACACAAAAACACTCTATTAGTGTTTCTCTT
* * * *
57325 TTGTTTCA-ATCTTGTCTCCGGACATAAAAACACTGTATTCGTGTTTCTCTT
1 TTGTTT-AGATCTTGTCTCAGGACACAAAAACACTCTATTAGTGTTTCTCTT
57376 T
1 T
57377 CAGAAATAAC
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
51 42 0.98
52 1 0.02
ACGTcount: A:0.20, C:0.21, G:0.14, T:0.45
Consensus pattern (51 bp):
TTGTTTAGATCTTGTCTCAGGACACAAAAACACTCTATTAGTGTTTCTCTT
Found at i:64056 original size:25 final size:25
Alignment explanation
Indices: 64006--64057 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
63996 TAACTCTCAC
* * *
64006 TCAATCTCTAAACCCAATCTAACAA
1 TCAATCTCTAAACCAAACCCAACAA
64031 TCAATC-CTAAACCAAACCCAACCAA
1 TCAATCTCTAAACCAAACCCAA-CAA
64056 TC
1 TC
64058 TTGAGCACTC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 12 0.52
25 11 0.48
ACGTcount: A:0.44, C:0.37, G:0.00, T:0.19
Consensus pattern (25 bp):
TCAATCTCTAAACCAAACCCAACAA
Found at i:66564 original size:17 final size:17
Alignment explanation
Indices: 66542--66575 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
66532 AAGCAATTTT
66542 TTGGAA-AAGATTTATTC
1 TTGGAATAAG-TTTATTC
66559 TTGGAATAAGTTTATTC
1 TTGGAATAAGTTTATTC
66576 CCCTTCTCTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.81
18 3 0.19
ACGTcount: A:0.32, C:0.06, G:0.18, T:0.44
Consensus pattern (17 bp):
TTGGAATAAGTTTATTC
Found at i:66908 original size:16 final size:17
Alignment explanation
Indices: 66877--66909 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
66867 AAGGAAAAAA
66877 GAAAATAAAAGAAAGAG
1 GAAAATAAAAGAAAGAG
*
66894 GAAAA-AAAAGGAAGAG
1 GAAAATAAAAGAAAGAG
66910 CAATTAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.70, C:0.00, G:0.27, T:0.03
Consensus pattern (17 bp):
GAAAATAAAAGAAAGAG
Found at i:69202 original size:22 final size:21
Alignment explanation
Indices: 69161--69205 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
69151 CCAAAGAGAG
69161 TTGCTATTAACCGCCCCCTTT
1 TTGCTATTAACCGCCCCCTTT
*
69182 TTGCTACTT-ACCGCCCCCCTT
1 TTGCTA-TTAACCGCCCCCTTT
69203 TTG
1 TTG
69206 ACATTTTTGC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 20 0.91
22 2 0.09
ACGTcount: A:0.11, C:0.40, G:0.11, T:0.38
Consensus pattern (21 bp):
TTGCTATTAACCGCCCCCTTT
Found at i:69436 original size:32 final size:33
Alignment explanation
Indices: 69377--69474 Score: 119
Period size: 32 Copynumber: 3.0 Consensus size: 33
69367 GATGACCGTG
* * *
69377 TCGCCTTGTGAGGACGGCAAGCAATGGTGGTGC
1 TCGCCTTGTCAGGACGGCACGCCATGGTGGTGC
*
69410 -CGCCCTGTCAGGACGGCACGCCATGGTGGT-C
1 TCGCCTTGTCAGGACGGCACGCCATGGTGGTGC
* * *
69441 TCGTCTTGTCCGGACGGCACGCCATGGTTGTGC
1 TCGCCTTGTCAGGACGGCACGCCATGGTGGTGC
69474 T
1 T
69475 GTCCTAGCAG
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
31 1 0.02
32 52 0.95
33 2 0.04
ACGTcount: A:0.13, C:0.29, G:0.36, T:0.22
Consensus pattern (33 bp):
TCGCCTTGTCAGGACGGCACGCCATGGTGGTGC
Found at i:73899 original size:21 final size:21
Alignment explanation
Indices: 73849--73899 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
73839 GTGACACTGC
* *
73849 CCATCTGGGTTCTCAAGCAAA
1 CCATATGGGTGCTCAAGCAAA
*
73870 CCACATGGGTGCTCAAGGC-AA
1 CCATATGGGTGCTCAA-GCAAA
*
73891 CCATGTGGG
1 CCATATGGG
73900 CGCCCAGGAG
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
21 22 0.92
22 2 0.08
ACGTcount: A:0.25, C:0.27, G:0.27, T:0.20
Consensus pattern (21 bp):
CCATATGGGTGCTCAAGCAAA
Found at i:76322 original size:23 final size:21
Alignment explanation
Indices: 76289--76337 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 21
76279 AATTAAAACT
* *
76289 AATAAACATTATTGATTAGTA
1 AATAAACATTAATAATTAGTA
*
76310 AATAAACTAATTAATAATTATTA
1 AATAAAC--ATTAATAATTAGTA
76333 AATAA
1 AATAA
76338 TCAAAGAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 7 0.30
23 16 0.70
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.37
Consensus pattern (21 bp):
AATAAACATTAATAATTAGTA
Done.