Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1178
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: 21629
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Found at i:1050 original size:21 final size:22
Alignment explanation
Indices: 1014--1055 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1004 TTGCATTTGT
*
1014 TTTTTTTTTTTATTATCATATA
1 TTTTTTTTGTTATTATCATATA
*
1036 TTTTTTTTGTT-TTATTATAT
1 TTTTTTTTGTTATTATCATAT
1056 GTATATATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.76
Consensus pattern (22 bp):
TTTTTTTTGTTATTATCATATA
Found at i:7405 original size:15 final size:15
Alignment explanation
Indices: 7385--7414 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
7375 CCGTAATCCT
7385 AAAAAAAAAAAAACC
1 AAAAAAAAAAAAACC
7400 AAAAAAAAAAAAACC
1 AAAAAAAAAAAAACC
7415 TTTTCACCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAACC
Found at i:8477 original size:27 final size:27
Alignment explanation
Indices: 8447--9441 Score: 1566
Period size: 27 Copynumber: 36.6 Consensus size: 27
8437 TTTAAAGCCC
*
8447 CAACTTCGTGGCACCCTTTTAAGTCCA
1 CAACTCCGTGGCACCCTTTTAAGTCCA
8474 CAACTCCGTGGCACCCTTTTAAAGTCCA
1 CAACTCCGTGGCACCCTTTT-AAGTCCA
*
8502 CAACTCCGTGGCATCCTTTTAAGTCCA
1 CAACTCCGTGGCACCCTTTTAAGTCCA
*
8529 CAACTCTGTGG-ACCCTTTTAAAGTCCA
1 CAACTCCGTGGCACCCTTTT-AAGTCCA
8556 CAACTCCGTGGCACCCTTTTAAAGTCCA
1 CAACTCCGTGGCACCCTTTT-AAGTCCA
*
8584 CAACTCCGTGGCACCCTTTTTAGTCCA
1 CAACTCCGTGGCACCCTTTTAAGTCCA
*
8611 CAACTCTGTGGCACCCTTTTAAGTCCA
1 CAACTCCGTGGCACCCTTTTAAGTCCA
*
8638 CAACTCTGTGGCACCCTTTTAAGTCCA
1 CAACTCCGTGGCACCCTTTTAAGTCCA
8665 CAACTCCGTGGCACCCTTTTAAGTCCA
1 CAACTCCGTGGCACCCTTTTAAGTCCA
8692 -AACTCCGTGGCACCCTTTTAAGTCCA
1 CAACTCCGTGGCACCCTTTTAAGTCCA
* *
8718 CAACTCCGTGACACCCTTTTAAAGACCA
1 CAACTCCGTGGCACCCTTTT-AAGTCCA
8746 CAACTCCGTGGCACCCTTTTAAGTCCA
1 CAACTCCGTGGCACCCTTTTAAGTCCA
8773 CAACTCCGTGGCACCCTTTTAAGTCCA
1 CAACTCCGTGGCACCCTTTTAAGTCCA
* *
8800 TAACTCCGTGGCATCTCTTTTAAGTCCA
1 CAACTCCGTGGCA-CCCTTTTAAGTCCA
*
8828 CAACTCTGTGGCACCCTTTTAAAGTCCA
1 CAACTCCGTGGCACCCTTTT-AAGTCCA
*
8856 CAACTCCGTGGCACCCTTTTTAGTCCA
1 CAACTCCGTGGCACCCTTTTAAGTCCA
*
8883 CAACTCTGTGGCACCCTTTTAAGTCCA
1 CAACTCCGTGGCACCCTTTTAAGTCCA
8910 CAACTCCGTGGCACCCTTTTAAGTCCA
1 CAACTCCGTGGCACCCTTTTAAGTCCA
*
8937 CAACTCTGTGGCACCCTTTTAAGTCCA
1 CAACTCCGTGGCACCCTTTTAAGTCCA
* *
8964 CAACTCTGTGGCACCCTTTTAAAGACCA
1 CAACTCCGTGGCACCCTTTT-AAGTCCA
8992 CAACTCC-TGGCACCCTTTTAAGTCCA
1 CAACTCCGTGGCACCCTTTTAAGTCCA
9018 CAACTCCGTGGCACCCTTTTAAGTCCA
1 CAACTCCGTGGCACCCTTTTAAGTCCA
9045 CAACTCCGTGGCACCCTTTTAAGTCCA
1 CAACTCCGTGGCACCCTTTTAAGTCCA
* *
9072 TAACTCCGTGGCATCTCTTTTAAGTCCA
1 CAACTCCGTGGCA-CCCTTTTAAGTCCA
*
9100 CAACTCTGTGGCACCCTTTTAAAGTCCA
1 CAACTCCGTGGCACCCTTTT-AAGTCCA
*
9128 CAACTCCGTGGCACCCTTTTTAGTCCA
1 CAACTCCGTGGCACCCTTTTAAGTCCA
**
9155 CAACTTTGTGGCACCCTTTTAAGTCCA
1 CAACTCCGTGGCACCCTTTTAAGTCCA
*
9182 CAACTCCGTGGCACCCTTTTAAGACCA
1 CAACTCCGTGGCACCCTTTTAAGTCCA
9209 CAACTCCGTGGCACCCTTTTAAGTCCA
1 CAACTCCGTGGCACCCTTTTAAGTCCA
9236 C-ACTCCGTGGCACCCTTTTAAGTCCA
1 CAACTCCGTGGCACCCTTTTAAGTCCA
* *
9262 TAACTCCGTGGCATCTCTTTTAAGTCCA
1 CAACTCCGTGGCA-CCCTTTTAAGTCCA
*
9290 CAACTCTGTGGCACCCTTTTAAAGTCCA
1 CAACTCCGTGGCACCCTTTT-AAGTCCA
*
9318 CAACTCCGTGGCACCCTTTTTAGTCCA
1 CAACTCCGTGGCACCCTTTTAAGTCCA
* *
9345 CAACTCTGTGACACCCTTTTAAGTCCA
1 CAACTCCGTGGCACCCTTTTAAGTCCA
9372 CAACTCCGTGGCACCCTTTTAAGTCCA
1 CAACTCCGTGGCACCCTTTTAAGTCCA
** *
9399 CAACTCCGTGGCGTCCTTTTAAATCCA
1 CAACTCCGTGGCACCCTTTTAAGTCCA
*
9426 CAACTCTGTGGCACCC
1 CAACTCCGTGGCACCC
9442 ATTTCAAAGC
Statistics
Matches: 895, Mismatches: 59, Indels: 28
0.91 0.06 0.03
Matches are distributed among these distances:
26 71 0.08
27 575 0.64
28 249 0.28
ACGTcount: A:0.23, C:0.35, G:0.14, T:0.28
Consensus pattern (27 bp):
CAACTCCGTGGCACCCTTTTAAGTCCA
Found at i:8950 original size:272 final size:271
Alignment explanation
Indices: 8447--9441 Score: 1640
Period size: 272 Copynumber: 3.7 Consensus size: 271
8437 TTTAAAGCCC
*
8447 CAACTTCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTG
1 CAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTG
* *
8512 GCATCCTTTTAAGTCCACAACTCTGTGG-ACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTT
66 GCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACCCTTTT
8576 AAAGTCCACAACTCCGTGGCACCCTTTTTAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAA
130 AAAGTCCACAACTCCGTGGCACCCTTTTTAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAA
*
8641 CTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCAAACTCCGTGGCACC
195 CTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCAAACTCCGTGGCACC
8706 CTTTTAAGTCCA
260 CTTTTAAGTCCA
* *
8718 CAACTCCGTGACACCCTTTTAAAGACCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGT
1 CAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGT
* * *
8782 GGCACCCTTTTAAGTCCATAACTCCGTGGCATCTCTTTTAAGTCCACAACTCTGTGGCACCCTTT
65 GGCACCCTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACCCTTT
8847 TAAAGTCCACAACTCCGTGGCACCCTTTTTAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACA
129 TAAAGTCCACAACTCCGTGGCACCCTTTTTAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACA
* *
8912 ACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCTGTGGCA
194 ACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCA-AACTCCGTGGCA
*
8977 CCCTTTTAAAGACCA
258 CCCTTTT-AAGTCCA
8992 CAACTCC-TGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTG
1 CAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTG
* * *
9055 GCACCCTTTTAAGTCCATAACTCCGTGGCATCTCTTTTAAGTCCACAACTCTGTGGCACCCTTTT
66 GCACCCTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT
*
9120 AAAGTCCACAACTCCGTGGCACCCTTTTTAGTCCACAACTTTGTGGCACCCTTTTAAGTCCACAA
130 AAAGTCCACAACTCCGTGGCACCCTTTTTAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAA
* *
9185 CTCCGTGGCACCCTTTTAAGACCACAACTCCGTGGCACCCTTTTAAGTCCACACTCCGTGGCACC
195 CTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCAAACTCCGTGGCACC
9250 CTTTTAAGTCCA
260 CTTTTAAGTCCA
* * *
9262 TAACTCCGTGGCATCTCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAAGTCCACAACTCCGT
1 CAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGT
* * *
9327 GGCACCCTTTTTAGTCCACAACTCTGTGACACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT
65 GGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT
** * *
9392 -AAGTCCACAACTCCGTGGCGTCCTTTTAAATCCACAACTCTGTGGCACCC
130 AAAGTCCACAACTCCGTGGCACCCTTTTTAGTCCACAACTCTGTGGCACCC
9442 ATTTCAAAGC
Statistics
Matches: 682, Mismatches: 34, Indels: 16
0.93 0.05 0.02
Matches are distributed among these distances:
270 12 0.02
271 127 0.19
272 452 0.66
273 78 0.11
274 13 0.02
ACGTcount: A:0.23, C:0.35, G:0.14, T:0.28
Consensus pattern (271 bp):
CAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTG
GCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTA
AAGTCCACAACTCCGTGGCACCCTTTTTAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAAC
TCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCAAACTCCGTGGCACCC
TTTTAAGTCCA
Found at i:9482 original size:32 final size:32
Alignment explanation
Indices: 9424--9954 Score: 816
Period size: 32 Copynumber: 16.8 Consensus size: 32
9414 CTTTTAAATC
* *
9424 CACAACTCTGTGGC-ACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
9455 CACAAGTTGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
9487 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
9519 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
9551 CACAAGTCGGTGGC-ACCCATTTCAAAG-CC-
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
9580 CAC-A-TCGGTGGCAA-CCATTTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCA-TTTCAAAGCCCA
9610 C-CAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
9641 CACAAGTC-TTGGCAACCCATTTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCA-TTTCAAAGCCCA
9673 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
9705 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
9737 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
9769 CACAGGTC-GTGGCAACCCA-TTCTAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTC-AAAGCCCA
*
9800 CACAAGTAGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
**
9832 CACAAGTCGGTGGCAACCTTTTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
9864 CACAAGTCGGTGGCAACCCATTTAAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
9896 CGA-AAGTCGGTGGCAACCCATTTAAAAGCCCA
1 C-ACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* * *
9928 CGCAAGTCAGTGGCAACCCTTTTCAAA
1 CACAAGTCGGTGGCAACCCATTTCAAA
9955 TCACCATTTT
Statistics
Matches: 463, Mismatches: 21, Indels: 31
0.90 0.04 0.06
Matches are distributed among these distances:
27 11 0.02
28 10 0.02
29 6 0.01
30 7 0.02
31 82 0.18
32 333 0.72
33 14 0.03
ACGTcount: A:0.31, C:0.34, G:0.18, T:0.17
Consensus pattern (32 bp):
CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
Found at i:10034 original size:45 final size:46
Alignment explanation
Indices: 9975--10104 Score: 129
Period size: 45 Copynumber: 2.8 Consensus size: 46
9965 TGTCATCTTA
* * *
9975 AAGTCCGATATCGCTGGCCTTGAATCAGCATATTGG-CACCTTT-CT
1 AAGTCCAATGTCGCTGGCCTTGAATC-GCACATTGGCCACCTTTCCT
* *
10020 AAGTCCAATGTCGCTGGCCTTGAGTCGCACATTGGTCCACTTTTCCCT
1 AAGTCCAATGTCGCTGGCCTTGAATCGCACATTGG-CCACCTTT-CCT
* * * *
10068 TAGTCCAATGTCGTTGACCTTGAAATGGCACATTGGC
1 AAGTCCAATGTCGCTGGCCTTG-AATCGCACATTGGC
10105 ACTCCTCTCA
Statistics
Matches: 70, Mismatches: 10, Indels: 7
0.80 0.11 0.08
Matches are distributed among these distances:
44 8 0.11
45 23 0.33
46 6 0.09
48 22 0.31
49 11 0.16
ACGTcount: A:0.21, C:0.27, G:0.22, T:0.31
Consensus pattern (46 bp):
AAGTCCAATGTCGCTGGCCTTGAATCGCACATTGGCCACCTTTCCT
Found at i:10993 original size:9 final size:10
Alignment explanation
Indices: 10965--10998 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
10955 TCTCTTGTAG
10965 ATCTAGAAAA
1 ATCTAGAAAA
*
10975 ATCTAAAAAA
1 ATCTAGAAAA
10985 AT-TAGAAAA
1 ATCTAGAAAA
10994 ATCTA
1 ATCTA
10999 ATTTCGGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.62, C:0.09, G:0.06, T:0.24
Consensus pattern (10 bp):
ATCTAGAAAA
Found at i:13316 original size:95 final size:96
Alignment explanation
Indices: 13097--13338 Score: 452
Period size: 95 Copynumber: 2.5 Consensus size: 96
13087 TATTTGATTG
13097 AAAAACGGGGTTGGAGTATCCCCTCGGAGGAATGGGGTTGGAGTGTCCCCGACAATGATACTTTA
1 AAAAACGGGGTTGGAGTATCCCCTCGGAGGAATGGGGTTGGAGTGTCCCCGACAATGATACTTTA
13162 AGTAAAAATAAGAATTATCTTTGGCAAGTTT
66 AGTAAAAATAAGAATTATCTTTGGCAAGTTT
13193 AAAAACGGGGTTGGAGTATCCCCTCGGAGGAATGGGGTTGGAGTGTCCCCGACAATGATAC-TTA
1 AAAAACGGGGTTGGAGTATCCCCTCGGAGGAATGGGGTTGGAGTGTCCCCGACAATGATACTTTA
13257 AGTAAAAATAAGAATTATCTTTGGCAAGTTT
66 AGTAAAAATAAGAATTATCTTTGGCAAGTTT
* *
13288 AAAAACGGGGTTGGAGTATCCCCTCGGA-GAATGGGGTAGGAGTATCCCCGA
1 AAAAACGGGGTTGGAGTATCCCCTCGGAGGAATGGGGTTGGAGTGTCCCCGA
13339 TGAATAAAAA
Statistics
Matches: 144, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
94 21 0.15
95 62 0.43
96 61 0.42
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.25
Consensus pattern (96 bp):
AAAAACGGGGTTGGAGTATCCCCTCGGAGGAATGGGGTTGGAGTGTCCCCGACAATGATACTTTA
AGTAAAAATAAGAATTATCTTTGGCAAGTTT
Found at i:14634 original size:22 final size:23
Alignment explanation
Indices: 14588--14643 Score: 105
Period size: 23 Copynumber: 2.5 Consensus size: 23
14578 TGGACATGTT
14588 AAAAATGCATGAAACATAATAAA
1 AAAAATGCATGAAACATAATAAA
14611 AAAAATGCATGAAACATAAT-AA
1 AAAAATGCATGAAACATAATAAA
14633 AAAAATGCATG
1 AAAAATGCATG
14644 GTCAAAGGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 13 0.39
23 20 0.61
ACGTcount: A:0.62, C:0.09, G:0.11, T:0.18
Consensus pattern (23 bp):
AAAAATGCATGAAACATAATAAA
Found at i:15592 original size:20 final size:19
Alignment explanation
Indices: 15542--15617 Score: 66
Period size: 20 Copynumber: 3.9 Consensus size: 19
15532 GGTAAAAAGA
15542 CATAATGTATCGATACATT
1 CATAATGTATCGATACATT
* *
15561 -GTAGA-ATATCGATACATT
1 CATA-ATGTATCGATACATT
*
15579 CATACATGTATCGATATATT
1 CATA-ATGTATCGATACATT
* *
15599 GAAAAATGTATCGATACAT
1 -CATAATGTATCGATACAT
15618 CAAGGTAAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
18 14 0.32
19 4 0.09
20 24 0.55
21 2 0.05
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.34
Consensus pattern (19 bp):
CATAATGTATCGATACATT
Found at i:16323 original size:28 final size:28
Alignment explanation
Indices: 16209--16867 Score: 624
Period size: 28 Copynumber: 22.9 Consensus size: 28
16199 TGAAAAAAGT
* *
16209 TGCCACTGACACATGTGGGCTTTGAAAAGA
1 TGCCACTGACTC--GTGGGCTTTGAAAGGA
** * * *
16239 GTGTTACTGACTTGCGTGGGCATTAAAAGGG
1 -TGCCACTGAC-T-CGTGGGCTTTGAAAGGA
16270 TGCCACTGACTTGCGTGGGCTTTGAAAGGA
1 TGCCACTGAC-T-CGTGGGCTTTGAAAGGA
16300 TGCCACTGACTCGTGGGCTTTGAAA-GA
1 TGCCACTGACTCGTGGGCTTTGAAAGGA
*
16327 GTGCCACTGACTTGTGGGC-TTGAAAGG-
1 -TGCCACTGACTCGTGGGCTTTGAAAGGA
16354 TGCCACTGACTCGTGGGCTTTGAAAAGG-
1 TGCCACTGACTCGTGGGCTTTG-AAAGGA
* *
16382 TACCACTGACTCGTGGGC--TGAAAGGG
1 TGCCACTGACTCGTGGGCTTTGAAAGGA
*
16408 TGCCACTGACTTGTGGGCTTTGAAA-GA
1 TGCCACTGACTCGTGGGCTTTGAAAGGA
16435 GTGCCACTGACTCGTGGGCTTTGAAAAGG-
1 -TGCCACTGACTCGTGGGCTTTG-AAAGGA
16464 TGCCACTGACTTGCGTGGGCTTTGAAAGGA
1 TGCCACTGAC-T-CGTGGGCTTTGAAAGGA
* *
16494 GTGCCACTGACTTGTGTGGGCTTTGAAAGGG
1 -TGCCACTGAC-T-CGTGGGCTTTGAAAGGA
*
16525 TGCCACTAACTCGTGGGCTTTGAAAGGA
1 TGCCACTGACTCGTGGGCTTTGAAAGGA
*
16553 TGCCACTGACTTGTGGGCTTTGAAA-GA
1 TGCCACTGACTCGTGGGCTTTGAAAGGA
16580 TGCCAC-GACTCGTGGGCTTTGAAAAGG-
1 TGCCACTGACTCGTGGGCTTTG-AAAGGA
* *
16607 TACCACTGACTCGTGGGC-TTGAAAGGG
1 TGCCACTGACTCGTGGGCTTTGAAAGGA
*
16634 TGCCACTGACTTGTGGGCTTTGAAA-GA
1 TGCCACTGACTCGTGGGCTTTGAAAGGA
*
16661 GTGCCACTGACTCGTGGGCTTTGAAAAGA
1 -TGCCACTGACTCGTGGGCTTTGAAAGGA
* * * *
16690 GTGCCACTAACTTGTGGGCTTTAAAAGGG
1 -TGCCACTGACTCGTGGGCTTTGAAAGGA
* *
16719 TGCCACTAACTTGCGTGGGCTTTGAAAGGGG
1 TGCCACTGAC-T-CGTGGGCTTTGAAA-GGA
* *
16750 TGCCACTGACTTGTGGGCTTTGAAAGGG
1 TGCCACTGACTCGTGGGCTTTGAAAGGA
* * * *
16778 TGCCACCGACTTGTGTGGGTTTGAAAAGTGT
1 TGCCACTGACTCGTG-GGCTTTG-AAAG-GA
* * *
16809 TGCCACCGACTTGTGTGGGCTTTGAAATGGGT
1 TGCCACTGAC-T-CGTGGGCTTTGAAA--GGA
* *
16841 TGCCACCGACTTGTATGGGCTTTGAAA
1 TGCCACTGACTCG--TGGGCTTTGAAA
16868 TGGGTTGCCA
Statistics
Matches: 548, Mismatches: 45, Indels: 69
0.83 0.07 0.10
Matches are distributed among these distances:
25 5 0.01
26 54 0.10
27 48 0.09
28 197 0.36
29 57 0.10
30 75 0.14
31 75 0.14
32 31 0.06
33 6 0.01
ACGTcount: A:0.21, C:0.19, G:0.32, T:0.27
Consensus pattern (28 bp):
TGCCACTGACTCGTGGGCTTTGAAAGGA
Found at i:16614 original size:225 final size:227
Alignment explanation
Indices: 16176--16803 Score: 957
Period size: 225 Copynumber: 2.8 Consensus size: 227
16166 TAAAAAAAAT
* *
16176 GTGCCACT-AGCTTGTGTAGGCTTTGAAAAAAGTTGCCACTGACACATGTGGGCTTTGAAAAGAG
1 GTGCCACTGA-CTTGTG--GGCTTTG-AAAGAG-TGCCACTGACTC--GTGGGCTTTGAAAAGAG
** * *
16240 TGTTACTGACTTGCGTGGGCATTAAAAGGGTGCCACTGACTTGCGTGGGCTTTGAAAGGATGCCA
59 TGCCACTGACTTGCGTGGGCTTTAAAAGGGTGCCACTGACTTGCGTGGGCTTTGAAAGGGTGCCA
*
16305 CTGACTCGTGGGCTTTGAAA-GAGTGCCACTGACTTGTGGGC-TTGAAAGGTGCCACTGACTCGT
124 CTGACTCGTGGGCTTTGAAAGGA-TGCCACTGACTTGTGGGCTTTGAAAGATGCCACTGACTCGT
16368 GGGCTTTGAAAAGGTACCACTGACTCGTGGGC-TGAAAGG
188 GGGCTTTGAAAAGGTACCACTGACTCGTGGGCTTGAAAGG
16407 GTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAG-GTGCCACT
1 GTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGAGTGCCACT
* * *
16471 GACTTGCGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTAACT
66 GACTTGCGTGGGCTTTAAAAGG-GTGCCACTGACTTGCGTGGGCTTTGAAAGGGTGCCACTGACT
16536 CGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGATGCCAC-GACTCGTGGGCTTT
130 CGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGATGCCACTGACTCGTGGGCTTT
16600 GAAAAGGTACCACTGACTCGTGGGCTTGAAAGG
195 GAAAAGGTACCACTGACTCGTGGGCTTGAAAGG
16633 GTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGAGTGCCACT
1 GTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGAGTGCCACT
* *
16698 AACTT--GTGGGCTTTAAAAGGGTGCCACTAACTTGCGTGGGCTTTGAAAGGGGTGCCACTGACT
66 GACTTGCGTGGGCTTTAAAAGGGTGCCACTGACTTGCGTGGGCTTTGAAA-GGGTGCCACTGACT
* * * *
16761 TGTGGGCTTTGAAAGGGTGCCACCGACTTGTGTGGGTTTGAAA
130 CGTGGGCTTTGAAAGGATGCCACTGACTTGTG-GGCTTTGAAA
16804 AGTGTTGCCA
Statistics
Matches: 370, Mismatches: 19, Indels: 21
0.90 0.05 0.05
Matches are distributed among these distances:
224 52 0.14
225 181 0.49
226 87 0.24
227 23 0.06
228 5 0.01
229 7 0.02
231 14 0.04
232 1 0.00
ACGTcount: A:0.22, C:0.19, G:0.32, T:0.26
Consensus pattern (227 bp):
GTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGAGTGCCACT
GACTTGCGTGGGCTTTAAAAGGGTGCCACTGACTTGCGTGGGCTTTGAAAGGGTGCCACTGACTC
GTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGATGCCACTGACTCGTGGGCTTTG
AAAAGGTACCACTGACTCGTGGGCTTGAAAGG
Found at i:16709 original size:255 final size:253
Alignment explanation
Indices: 16176--16835 Score: 855
Period size: 255 Copynumber: 2.6 Consensus size: 253
16166 TAAAAAAAAT
* * **** *
16176 GTGCCACTAGCTTGTGTAGGCTTTGAAAAAAGTTGCCACTGACACATGTGGGCTTTGAAAAGAGT
1 GTGCCACTAACTTGTG--GGCTTTG--AAAAGGTGCCACTGACTTGCGTGGGCTTTGAAAGGAGT
** * * *
16241 GTTACTGACTTGCGTGGGCATTAAAAGGGTGCCACTGACTTGCGTGGGCTTTGAAAGGATGCCAC
62 GCCACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTGAC-T-CGTGGGCTTTGAAAGGATGCCAC
* * *
16306 TGACTCGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTGAAAGGTGCCACTGACTCGTGGG
125 TGACTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTGAAAGGTACCACTGACTCGTGGG
* *
16371 CTTTGAAAAGGTACCACTGACTCGTGGGCTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGA
190 CTTTGAAAAGGTACCACTGACTCGTGGGCTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAGA
* *
16435 GTGCCACTGACTCGTGGGCTTTGAAAAGGTGCCACTGACTTGCGTGGGCTTTGAAAGGAGTGCCA
1 GTGCCACTAACTTGTGGGCTTTGAAAAGGTGCCACTGACTTGCGTGGGCTTTGAAAGGAGTGCCA
*
16500 CTGACTTGTGTGGGCTTTGAAAGGGTGCCACTAACTCGTGGGCTTTGAAAGGATGCCACTGACTT
66 CTGACTTGTGTGGGCTTTGAAAGGGTGCCACTGACTCGTGGGCTTTGAAAGGATGCCACTGACTT
16565 GTGGGCTTTGAAAGA-TGCCAC-GACTCGTGGGCTTTGAAAAGGTACCACTGACTCGTGGGC-TT
131 GTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGC-TTG-AAAGGTACCACTGACTCGTGGGCTTT
* * *
16627 GAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGA
194 GAAAAGGTACCACTGACTCGTGGGC--TGAAAGAGTGCCACTGACTCGTGGGCTTTG-AAAGA
* *
16690 GTGCCACTAACTTGTGGGCTTT-AAAAGGGTGCCACTAACTTGCGTGGGCTTTGAAAGGGGTGCC
1 GTGCCACTAACTTGTGGGCTTTGAAAA-GGTGCCACTGACTTGCGTGGGCTTTGAAAGGAGTGCC
* * * * *
16754 ACTGAC-T-TGTGGGCTTTGAAAGGGTGCCACCGACTTGTGTGGGTTTGAAAAGTGTTGCCACCG
65 ACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTGACTCGTG-GGCTTTG-AAAG-GATGCCACTG
16817 ACTTGTGTGGGCTTTGAAA
127 AC-T-TGTGGGCTTTGAAA
16836 TGGGTTGCCA
Statistics
Matches: 357, Mismatches: 33, Indels: 23
0.86 0.08 0.06
Matches are distributed among these distances:
251 10 0.03
252 33 0.09
253 94 0.26
254 40 0.11
255 135 0.38
256 10 0.03
257 8 0.02
258 14 0.04
259 13 0.04
ACGTcount: A:0.22, C:0.19, G:0.32, T:0.27
Consensus pattern (253 bp):
GTGCCACTAACTTGTGGGCTTTGAAAAGGTGCCACTGACTTGCGTGGGCTTTGAAAGGAGTGCCA
CTGACTTGTGTGGGCTTTGAAAGGGTGCCACTGACTCGTGGGCTTTGAAAGGATGCCACTGACTT
GTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTGAAAGGTACCACTGACTCGTGGGCTTTGA
AAAGGTACCACTGACTCGTGGGCTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAGA
Found at i:16961 original size:27 final size:27
Alignment explanation
Indices: 16901--17471 Score: 824
Period size: 27 Copynumber: 21.0 Consensus size: 27
16891 GCTTTGAAAT
* *
16901 GGGTGCCACAGAGTTGTGGATTTTAAAA
1 GGGTGCCACGGAGTTGTGGA-CTTAAAA
** *
16929 AAGTGCCACGGAGTTGTGGATTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
16956 GGGTGCCATGGAGTTGTGGATTTTAAAA
1 GGGTGCCACGGAGTTGTGGA-CTTAAAA
* * *
16984 GGGTGCCAC-AAGTTATGGACTCAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
17010 GAGATGCCACGGAGTTATGGACTTAAAA
1 G-GGTGCCACGGAGTTGTGGACTTAAAA
*
17038 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
17065 GTGTTCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
17092 -GGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
17118 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
17145 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
17172 GGGTGCCACGGAGTTGTGGACTAAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
17199 GGGTGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
17227 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
17254 GAGATGCCACGGAGTTATGGACTTAAAA
1 G-GGTGCCACGGAGTTGTGGACTTAAAA
*
17282 GGGTGCCACGAAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
17309 GGGTGCCACGGAGTTGTGGTCTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
17336 GGGATGCCACGGAGTTGTGGACTTAAAA
1 GGG-TGCCACGGAGTTGTGGACTTAAAA
17364 GGGTGCCACGGAGTTGTGGACTT-AAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* * *
17390 GAGTGTCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
17417 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
17444 GGGTGCCACGGAGTTGTGGGCTTTAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
17471 G
1 G
17472 AGGTAACACT
Statistics
Matches: 491, Mismatches: 44, Indels: 17
0.89 0.08 0.03
Matches are distributed among these distances:
26 53 0.11
27 315 0.64
28 123 0.25
ACGTcount: A:0.28, C:0.14, G:0.34, T:0.24
Consensus pattern (27 bp):
GGGTGCCACGGAGTTGTGGACTTAAAA
Found at i:17023 original size:82 final size:81
Alignment explanation
Indices: 16901--17471 Score: 844
Period size: 82 Copynumber: 7.0 Consensus size: 81
16891 GCTTTGAAAT
* * * *
16901 GGGTGCCACAGAGTTGTGGATTTTAAAA-AAGTGCCACGGAGTTGTGGATTTAAAAGGGTGCCAT
1 GGGTGCCACAGAGTTGTGGA-CTTAAAAGGA-TGCCACGGAGTTGTGGACTTAAAAGGGTGCCAC
*
16965 GGAGTTGTGGATTTTAAAA
64 GGAGTTGTGGA-CTTAAAA
* * * *
16984 GGGTGCCACA-AGTTATGGACTCAAAAGAGATGCCACGGAGTTATGGACTTAAAAGGGTGCCACA
1 GGGTGCCACAGAGTTGTGGACTTAAAAG-GATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACG
17048 GAGTTGTGGACTTAAAA
65 GAGTTGTGGACTTAAAA
* * *
17065 GTGTTCCACGGAGTTGTGGACTTAAAAGG-TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
1 GGGTGCCACAGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
17129 AGTTGTGGACTTAAAA
66 AGTTGTGGACTTAAAA
* *
17145 GGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTAAAAAGGGTGCCACGG
1 GGGTGCCACAGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
17210 AGTTGTGGACTTTAAAA
66 AGTTGTGGAC-TTAAAA
*
17227 GGGTGCCACAGAGTTGTGGACTTAAAAGAGATGCCACGGAGTTATGGACTTAAAAGGGTGCCACG
1 GGGTGCCACAGAGTTGTGGACTTAAAAG-GATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACG
*
17292 AAGTTGTGGACTTAAAA
65 GAGTTGTGGACTTAAAA
* *
17309 GGGTGCCACGGAGTTGTGGTCTTAAAAGGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACG
1 GGGTGCCACAGAGTTGTGGACTTAAAA-GGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACG
17374 GAGTTGTGGACTT-AAA
65 GAGTTGTGGACTTAAAA
* * *
17390 GAGTGTCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
1 GGGTGCCACAGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
* *
17455 AGTTGTGGGCTTTAAA
66 AGTTGTGGACTTAAAA
17471 G
1 G
17472 AGGTAACACT
Statistics
Matches: 446, Mismatches: 34, Indels: 18
0.90 0.07 0.04
Matches are distributed among these distances:
80 123 0.28
81 93 0.21
82 175 0.39
83 55 0.12
ACGTcount: A:0.28, C:0.14, G:0.34, T:0.24
Consensus pattern (81 bp):
GGGTGCCACAGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
AGTTGTGGACTTAAAA
Done.