Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021135.1 Corchorus olitorius cultivar O-4 contig21168, 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: 151667
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:579 original size:2 final size:2
Alignment explanation
Indices: 572--598 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
562 TCACTGAAGA
572 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
599 AACATAAAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4909 original size:18 final size:17
Alignment explanation
Indices: 4877--4925 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
4867 TTACCTTCTC
*
4877 TTTTCTTTTCTTTTTCAGT
1 TTTTCTTTTC-TTTTCA-A
4896 TTTTCTTTTCTTTTCAA
1 TTTTCTTTTCTTTTCAA
*
4913 TTTTGTTTTCTTT
1 TTTTCTTTTCTTT
4926 ATTTATTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 12 0.43
18 6 0.21
19 10 0.36
ACGTcount: A:0.06, C:0.14, G:0.04, T:0.76
Consensus pattern (17 bp):
TTTTCTTTTCTTTTCAA
Found at i:14031 original size:29 final size:29
Alignment explanation
Indices: 13989--14047 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
13979 AGTTTTTTTG
*
13989 TATGCTTATCTAAAATTTCGTTGTTCTTT
1 TATGCTTATCTAAAATTTCCTTGTTCTTT
14018 TATGCTTATCTAAAATTTCCTTGTTCTTT
1 TATGCTTATCTAAAATTTCCTTGTTCTTT
14047 T
1 T
14048 TTCTTGTGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.20, C:0.15, G:0.08, T:0.56
Consensus pattern (29 bp):
TATGCTTATCTAAAATTTCCTTGTTCTTT
Found at i:26515 original size:36 final size:35
Alignment explanation
Indices: 26464--26535 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 35
26454 AGATCTATGG
*
26464 TTCAAATAAATTAATTCACCTTATTTATTTTATTT
1 TTCAAATAAATTAATTCACCCTATTTATTTTATTT
26499 TTCAGAATAAATTAATTCACCCTATTTATTTTATTT
1 TTCA-AATAAATTAATTCACCCTATTTATTTTATTT
26535 T
1 T
26536 CCAGTTATAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
35 4 0.11
36 31 0.89
ACGTcount: A:0.33, C:0.12, G:0.01, T:0.53
Consensus pattern (35 bp):
TTCAAATAAATTAATTCACCCTATTTATTTTATTT
Found at i:28731 original size:19 final size:21
Alignment explanation
Indices: 28706--28761 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 21
28696 GTGAGATTTT
28706 TAATAATAATTATTCAA-TAA
1 TAATAATAATTATTCAATTAA
* *
28726 -AATAATTATTATTTAATTAA
1 TAATAATAATTATTCAATTAA
28746 TAATTAATTAATTATT
1 TAA-TAA-TAATTATT
28762 TCAGCCCTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 14 0.48
20 3 0.10
21 2 0.07
22 3 0.10
23 7 0.24
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (21 bp):
TAATAATAATTATTCAATTAA
Found at i:29713 original size:53 final size:53
Alignment explanation
Indices: 29650--29766 Score: 189
Period size: 53 Copynumber: 2.2 Consensus size: 53
29640 ATCGTGTCAG
* *
29650 ACACGATTAAAATTATCGTGTTTCCTTTCATAATTGTGTCGTTGACACGTTTA
1 ACACGTTTAAAATTATCGTGTTTCCTGTCATAATTGTGTCGTTGACACGTTTA
* *
29703 ATACGTTTAAAATTATCGTGTTTCGTGTCATAATTGTGTCGTTGACACGTTTA
1 ACACGTTTAAAATTATCGTGTTTCCTGTCATAATTGTGTCGTTGACACGTTTA
*
29756 ACACGTCTAAA
1 ACACGTTTAAA
29767 CTTAAAACCC
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
53 58 1.00
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.40
Consensus pattern (53 bp):
ACACGTTTAAAATTATCGTGTTTCCTGTCATAATTGTGTCGTTGACACGTTTA
Found at i:30175 original size:8 final size:7
Alignment explanation
Indices: 30157--30195 Score: 53
Period size: 8 Copynumber: 5.4 Consensus size: 7
30147 ACTAAACGGG
30157 AAAA-AA
1 AAAACAA
30163 AAAACATA
1 AAAACA-A
30171 AAAACAA
1 AAAACAA
30178 AAAACAAA
1 AAAAC-AA
30186 AAAACAA
1 AAAACAA
30193 AAA
1 AAA
30196 CGTAAACTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
6 4 0.13
7 12 0.40
8 14 0.47
ACGTcount: A:0.87, C:0.10, G:0.00, T:0.03
Consensus pattern (7 bp):
AAAACAA
Found at i:30181 original size:15 final size:15
Alignment explanation
Indices: 30157--30195 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
30147 ACTAAACGGG
*
30157 AAAA-AAAAAACATA
1 AAAACAAAAAACAAA
30171 AAAACAAAAAACAAA
1 AAAACAAAAAACAAA
30186 AAAACAAAAA
1 AAAACAAAAA
30196 CGTAAACTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 4 0.17
15 19 0.83
ACGTcount: A:0.87, C:0.10, G:0.00, T:0.03
Consensus pattern (15 bp):
AAAACAAAAAACAAA
Found at i:35986 original size:14 final size:14
Alignment explanation
Indices: 35967--35993 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
35957 GAAATACTAC
35967 TCCTTAGTCCTTCG
1 TCCTTAGTCCTTCG
35981 TCCTTAGTCCTTC
1 TCCTTAGTCCTTC
35994 CTGCAGGGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.37, G:0.11, T:0.44
Consensus pattern (14 bp):
TCCTTAGTCCTTCG
Found at i:40591 original size:21 final size:20
Alignment explanation
Indices: 40551--40601 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 20
40541 CCGTTTAGTA
*
40551 ATATT-TATA-ATTAAATAT
1 ATATTATATATATAAAATAT
40569 ATATTATATATATAAAATA-
1 ATATTATATATATAAAATAT
*
40588 ATATTAAATATATA
1 ATATTATATATATA
40602 TAATTACATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 5 0.17
19 17 0.59
20 7 0.24
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATATTATATATATAAAATAT
Found at i:40618 original size:21 final size:19
Alignment explanation
Indices: 40549--40625 Score: 55
Period size: 21 Copynumber: 3.6 Consensus size: 19
40539 GACCGTTTAG
*
40549 TAATATTTATAATTAAATAT
1 TAATATATATAATT-AATAT
*
40569 ATATTATATATATAAAATAATAT
1 -TA--ATATATAT-AATTAATAT
40592 TAAATATATATAATTACATAT
1 T-AATATATATAATTA-ATAT
40613 CTAATAATATATA
1 -TAAT-ATATATA
40626 TAATTATTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
20 4 0.09
21 17 0.37
22 9 0.20
23 13 0.28
24 3 0.07
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (19 bp):
TAATATATATAATTAATAT
Found at i:46166 original size:2 final size:2
Alignment explanation
Indices: 46159--46192 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
46149 AGTAGTACAG
46159 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
46193 GACACGCCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48981 original size:4 final size:4
Alignment explanation
Indices: 48972--48996 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
48962 ATTTAAAAAG
48972 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
48997 TTTCTAGTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:54506 original size:61 final size:61
Alignment explanation
Indices: 54431--54550 Score: 231
Period size: 61 Copynumber: 2.0 Consensus size: 61
54421 TTCAGCCACA
54431 GATTCCTTTTGGATCTCTAAAGGAATCAAGCCCTGGAAGTAAACCCAAGTATATGTAAATG
1 GATTCCTTTTGGATCTCTAAAGGAATCAAGCCCTGGAAGTAAACCCAAGTATATGTAAATG
*
54492 GATTCCTTTTGGATCTCTAAAGGAATCAAGCCCTGGAAGTAAGCCCAAGTATATGTAAA
1 GATTCCTTTTGGATCTCTAAAGGAATCAAGCCCTGGAAGTAAACCCAAGTATATGTAAA
54551 GGAAAGCTTG
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 58 1.00
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (61 bp):
GATTCCTTTTGGATCTCTAAAGGAATCAAGCCCTGGAAGTAAACCCAAGTATATGTAAATG
Found at i:56190 original size:95 final size:95
Alignment explanation
Indices: 56027--56309 Score: 539
Period size: 95 Copynumber: 3.0 Consensus size: 95
56017 AGCTCTTAAT
56027 GACTTAACTGTGCTTTCCATAGGAAAATACGAAATGGCTTACAACACTTCCTCAACCACATTTAA
1 GACTTAACTGTGCTTTCCATAGGAAAATACGAAATGGCTTACAACACTTCCTCAACCACATTTAA
56092 ATTTGGTTAACCCACAAATCCGTAATTTTA
66 ATTTGGTTAACCCACAAATCCGTAATTTTA
56122 GACTTAACTGTGCTTTCCATAGGAAAATACGAAATGGCTTACAACACTTCCTCAACCACATTTAA
1 GACTTAACTGTGCTTTCCATAGGAAAATACGAAATGGCTTACAACACTTCCTCAACCACATTTAA
56187 ATTTGGTTAACCCACAAATCCGTAATTTTA
66 ATTTGGTTAACCCACAAATCCGTAATTTTA
* *
56217 GACTTAACTGTGCTTTCCATAGGAAAAAGACGAATTGGCTTACAACACTTCCTCAACCACATTTA
1 GACTTAACTGTGCTTTCCATAGG-AAAATACGAAATGGCTTACAACACTTCCTCAACCACATTTA
56282 AATTTGGTTAACCCACAAATCCGTAATT
65 AATTTGGTTAACCCACAAATCCGTAATT
56310 AGGTTAACCA
Statistics
Matches: 185, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
95 118 0.64
96 67 0.36
ACGTcount: A:0.35, C:0.23, G:0.12, T:0.30
Consensus pattern (95 bp):
GACTTAACTGTGCTTTCCATAGGAAAATACGAAATGGCTTACAACACTTCCTCAACCACATTTAA
ATTTGGTTAACCCACAAATCCGTAATTTTA
Found at i:56314 original size:24 final size:24
Alignment explanation
Indices: 56282--56333 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
56272 ACCACATTTA
* *
56282 AATTTGGTTAACCCACAAATCCGT
1 AATTAGGTTAACCAACAAATCCGT
56306 AATTAGGTTAACCAACAAATCCGT
1 AATTAGGTTAACCAACAAATCCGT
56330 AATT
1 AATT
56334 TTAGACGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.29
Consensus pattern (24 bp):
AATTAGGTTAACCAACAAATCCGT
Found at i:58424 original size:4 final size:4
Alignment explanation
Indices: 58415--58457 Score: 50
Period size: 4 Copynumber: 10.5 Consensus size: 4
58405 TGGAATCTTC
* * *
58415 TTCT TTCT TTCT CTCT TTCT CTCT TTCT CTCT TTCTT TTCT TT
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTC-T TTCT TT
58458 TATTTTCCAT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
4 28 0.88
5 4 0.12
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (4 bp):
TTCT
Found at i:58431 original size:8 final size:8
Alignment explanation
Indices: 58415--58450 Score: 63
Period size: 8 Copynumber: 4.5 Consensus size: 8
58405 TGGAATCTTC
*
58415 TTCTTTCT
1 TTCTCTCT
58423 TTCTCTCT
1 TTCTCTCT
58431 TTCTCTCT
1 TTCTCTCT
58439 TTCTCTCT
1 TTCTCTCT
58447 TTCT
1 TTCT
58451 TTTCTTTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (8 bp):
TTCTCTCT
Found at i:60235 original size:27 final size:27
Alignment explanation
Indices: 60194--60269 Score: 125
Period size: 27 Copynumber: 2.8 Consensus size: 27
60184 CAATCTCCAG
60194 CTTTTGAGTTGGCAACTCTTTCCCCTT
1 CTTTTGAGTTGGCAACTCTTTCCCCTT
*
60221 CTTTTGAGTTTGCAACTCTTTCCCCTT
1 CTTTTGAGTTGGCAACTCTTTCCCCTT
* *
60248 CTTTTGAGTTGGAAAATCTTTC
1 CTTTTGAGTTGGCAACTCTTTC
60270 TCCACACCCG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.14, C:0.25, G:0.14, T:0.46
Consensus pattern (27 bp):
CTTTTGAGTTGGCAACTCTTTCCCCTT
Found at i:60394 original size:45 final size:45
Alignment explanation
Indices: 60330--60465 Score: 238
Period size: 45 Copynumber: 3.0 Consensus size: 45
60320 ACGTCCAAGA
*
60330 GTAAGGTTAGTTGAAACGCCAGAGCGAACCAACTCATCAGCAACG
1 GTAAGCTTAGTTGAAACGCCAGAGCGAACCAACTCATCAGCAACG
*
60375 GTAAGCTTAGTTGAAACGCCGGAGCGAACCAACTCATCAGCAACG
1 GTAAGCTTAGTTGAAACGCCAGAGCGAACCAACTCATCAGCAACG
60420 GTAAGCTTAGTTGAAACGCCAGAGCGAACCAGA-TCATCAGCAACG
1 GTAAGCTTAGTTGAAACGCCAGAGCGAACCA-ACTCATCAGCAACG
60465 G
1 G
60466 ACGTCAATCC
Statistics
Matches: 87, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
45 86 0.99
46 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.25, T:0.15
Consensus pattern (45 bp):
GTAAGCTTAGTTGAAACGCCAGAGCGAACCAACTCATCAGCAACG
Found at i:67084 original size:105 final size:105
Alignment explanation
Indices: 66884--67140 Score: 326
Period size: 105 Copynumber: 2.5 Consensus size: 105
66874 TTTAACCTTG
* * *
66884 ATTTCACTAAGTTTAGCCCAAAATTAAATTTTTATTTTATTTT-AAGAGTAAATTTCAAAATTAA
1 ATTTCACTAAGTTTAGCCCAAAATTAAAATTTTATTTTATTTTAAAGAGAAAATTCCAAAATTAA
*
66948 TAATTTATTGTTACAGGGTTTTAGAAAAAAATACAAAACTA
66 TAA-TTATTATTACAGGGTTTTAGAAAAAAATACAAAACTA
* *
66989 ATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAAG-GAAAATTCCATAATTA
1 ATTTCACTAAGTTTAGCCCAAAATTAAAATTTTA-TTTTATTTTAAAGAGAAAATTCCAAAATTA
* *
67053 ATAA-TATTATTACAGGGTTTTAGAAATAAAATATATAACTA
65 ATAATTATTATTACAGGGTTTTAGAAA-AAAATACAAAACTA
* * * **
67094 A-TTCACTAAGTTTAG-ACTAAACTAAAATTAAAATTTTATTTTAAAGA
1 ATTTCACTAAGTTTAGCCCAAAATTAAAATT-TTATTTTATTTTAAAGA
67141 TTAGAAAAAT
Statistics
Matches: 134, Mismatches: 13, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
103 24 0.18
104 36 0.27
105 45 0.34
106 26 0.19
107 3 0.02
ACGTcount: A:0.44, C:0.09, G:0.08, T:0.40
Consensus pattern (105 bp):
ATTTCACTAAGTTTAGCCCAAAATTAAAATTTTATTTTATTTTAAAGAGAAAATTCCAAAATTAA
TAATTATTATTACAGGGTTTTAGAAAAAAATACAAAACTA
Found at i:87178 original size:19 final size:19
Alignment explanation
Indices: 87154--87211 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 19
87144 CTTTTTGGCA
87154 ACTGTACAGATGAGATTAC
1 ACTGTACAGATGAGATTAC
* *
87173 ACTGTACAGATTAGATTATAT
1 ACTGTACAGATGAGA-T-TAC
87194 ACTGTACAGATGAGATTA
1 ACTGTACAGATGAGATTA
87212 TTAGAGCAGC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 16 0.47
20 2 0.06
21 16 0.47
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (19 bp):
ACTGTACAGATGAGATTAC
Found at i:87199 original size:21 final size:21
Alignment explanation
Indices: 87154--87212 Score: 86
Period size: 21 Copynumber: 2.9 Consensus size: 21
87144 CTTTTTGGCA
87154 ACTGTACAGATGAGA-T-TAC
1 ACTGTACAGATGAGATTATAC
* *
87173 ACTGTACAGATTAGATTATAT
1 ACTGTACAGATGAGATTATAC
87194 ACTGTACAGATGAGATTAT
1 ACTGTACAGATGAGATTAT
87213 TAGAGCAGCG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
19 14 0.40
20 1 0.03
21 20 0.57
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.32
Consensus pattern (21 bp):
ACTGTACAGATGAGATTATAC
Found at i:89990 original size:14 final size:14
Alignment explanation
Indices: 89971--90004 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
89961 AACATAGATA
89971 GAACAAAAAAAGGG
1 GAACAAAAAAAGGG
89985 GAACAAAAAAAGGG
1 GAACAAAAAAAGGG
89999 GAACAA
1 GAACAA
90005 TAACAATGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.65, C:0.09, G:0.26, T:0.00
Consensus pattern (14 bp):
GAACAAAAAAAGGG
Found at i:96567 original size:1 final size:1
Alignment explanation
Indices: 96561--96605 Score: 90
Period size: 1 Copynumber: 45.0 Consensus size: 1
96551 GTTCTTTTAC
96561 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
96606 CGGGGGATAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:103454 original size:23 final size:23
Alignment explanation
Indices: 103425--103468 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
103415 CGGTACTTTC
103425 TTTCAATCTCTCCCTCATTTTTT
1 TTTCAATCTCTCCCTCATTTTTT
103448 TTTCAATCTCTCCCTCATTTT
1 TTTCAATCTCTCCCTCATTTT
103469 GGCCAATTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.14, C:0.32, G:0.00, T:0.55
Consensus pattern (23 bp):
TTTCAATCTCTCCCTCATTTTTT
Found at i:103475 original size:21 final size:22
Alignment explanation
Indices: 103428--103475 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 22
103418 TACTTTCTTT
***
103428 CAATCTCTCCCTCATTTTTTTTT
1 CAATCTCTCCCTCA-TTTTTGGC
103451 CAATCTCTCCCTCA-TTTTGGC
1 CAATCTCTCCCTCATTTTTGGC
103472 CAAT
1 CAAT
103476 TACATTTCCT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 8 0.36
23 14 0.64
ACGTcount: A:0.17, C:0.33, G:0.04, T:0.46
Consensus pattern (22 bp):
CAATCTCTCCCTCATTTTTGGC
Found at i:106839 original size:75 final size:75
Alignment explanation
Indices: 106716--106862 Score: 276
Period size: 75 Copynumber: 2.0 Consensus size: 75
106706 CAGAACTTCA
106716 TAGTAATTCACAAATGAACTTGTTAGATTCTAATCTTCATTTCCCGTTTGATCAAGTCCAAAATA
1 TAGTAATTCACAAATGAACTTGTTAGATTCTAATCTTCATTTCCCGTTTGATCAAGTCCAAAATA
106781 GTAGGAAATG
66 GTAGGAAATG
* *
106791 TAGTAATTCACAAATGAACTTGTTAGATTCTACTCTTCATTTCCCGTTTGATCAAGTCCAACATA
1 TAGTAATTCACAAATGAACTTGTTAGATTCTAATCTTCATTTCCCGTTTGATCAAGTCCAAAATA
106856 GTAGGAA
66 GTAGGAA
106863 TTGAAAATTG
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 70 1.00
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (75 bp):
TAGTAATTCACAAATGAACTTGTTAGATTCTAATCTTCATTTCCCGTTTGATCAAGTCCAAAATA
GTAGGAAATG
Found at i:118806 original size:20 final size:19
Alignment explanation
Indices: 118758--118807 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
118748 TATTCTTGGC
118758 CTTTTTGTTTTCATAGTTTT
1 CTTTTT-TTTTCATAGTTTT
** *
118778 CTTGGTTTTTCACTTGTTTT
1 CTTTTTTTTTCA-TAGTTTT
118798 CTTTTTTTTT
1 CTTTTTTTTT
118808 TTTTCAAGTT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.06, C:0.12, G:0.10, T:0.72
Consensus pattern (19 bp):
CTTTTTTTTTCATAGTTTT
Found at i:121203 original size:61 final size:60
Alignment explanation
Indices: 121124--121244 Score: 165
Period size: 61 Copynumber: 2.0 Consensus size: 60
121114 TGCCTCAAAA
* *
121124 TTTTTGTTCCTATCGGCTGATTTCTTCACTTAATG-AAAACAATCAAAAGTCAAAACCCAC
1 TTTTTGTTCCTATCGGCTGATTTCCTCAC-CAATGAAAAACAATCAAAAGTCAAAACCCAC
* *
121184 TTTTTCGTTCCTTAT-GGCTGATTTCCTCACCAATGAAAAACAGTCAAAAGTCAAAAGCCAC
1 TTTTT-GTTCC-TATCGGCTGATTTCCTCACCAATGAAAAACAATCAAAAGTCAAAACCCAC
121245 GAGGGCGGCA
Statistics
Matches: 54, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
60 9 0.17
61 42 0.78
62 3 0.06
ACGTcount: A:0.33, C:0.24, G:0.12, T:0.31
Consensus pattern (60 bp):
TTTTTGTTCCTATCGGCTGATTTCCTCACCAATGAAAAACAATCAAAAGTCAAAACCCAC
Found at i:126170 original size:133 final size:133
Alignment explanation
Indices: 126004--126261 Score: 480
Period size: 133 Copynumber: 1.9 Consensus size: 133
125994 CTTTTGACAC
*
126004 AAACCATGATTTATTTGATATTGCGTTTGGGTTCAAAAGCAGCTTTTTTATCTTCAAACGCAATG
1 AAACCAGGATTTATTTGATATTGCGTTTGGGTTCAAAAGCAGCTTTTTTATCTTCAAACGCAATG
* *
126069 CCAAAACCAGGCCATAGTCCATTTTACCAACAAGTGGTTGGTTCAAGTGGTTTGTCACTTGTTTG
66 CCAAAACCAAGCCATAGTCCATTTTACCAACAAGTGATTGGTTCAAGTGGTTTGTCACTTGTTTG
126134 CCA
131 CCA
*
126137 AAACCAGGATTTATTTGATATTGCGTTTGGGTTCAAAAGCAGCTTTTTTATCTTTAAACGCAATG
1 AAACCAGGATTTATTTGATATTGCGTTTGGGTTCAAAAGCAGCTTTTTTATCTTCAAACGCAATG
126202 CCAAAACCAAGCCATAGTCCATTTTACCAACAAGTGATTGGTTCAAGTGGTTTGTCACTT
66 CCAAAACCAAGCCATAGTCCATTTTACCAACAAGTGATTGGTTCAAGTGGTTTGTCACTT
126262 ATTTCCCCTA
Statistics
Matches: 121, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
133 121 1.00
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.34
Consensus pattern (133 bp):
AAACCAGGATTTATTTGATATTGCGTTTGGGTTCAAAAGCAGCTTTTTTATCTTCAAACGCAATG
CCAAAACCAAGCCATAGTCCATTTTACCAACAAGTGATTGGTTCAAGTGGTTTGTCACTTGTTTG
CCA
Found at i:126568 original size:13 final size:13
Alignment explanation
Indices: 126552--126578 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
126542 TTTATGACTT
126552 ATAATTATAATAA
1 ATAATTATAATAA
126565 ATAATTATAATAA
1 ATAATTATAATAA
126578 A
1 A
126579 GGAGGATGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
ATAATTATAATAA
Found at i:131075 original size:24 final size:24
Alignment explanation
Indices: 131048--131123 Score: 125
Period size: 24 Copynumber: 3.2 Consensus size: 24
131038 GCAATAATAA
*
131048 CAACGGAAATGGTGGCAACAACGG
1 CAACGGCAATGGTGGCAACAACGG
131072 CAACGGCAATGGTGGCAACAACGG
1 CAACGGCAATGGTGGCAACAACGG
* *
131096 AAACGGCAATGGTGGCAACAATGG
1 CAACGGCAATGGTGGCAACAACGG
131120 CAAC
1 CAAC
131124 AACGGAAACG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.37, C:0.22, G:0.32, T:0.09
Consensus pattern (24 bp):
CAACGGCAATGGTGGCAACAACGG
Found at i:131162 original size:6 final size:6
Alignment explanation
Indices: 131153--131179 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
131143 ATGGTGGCAA
131153 CAATGG CAATGG CAATGG CAATGG CAA
1 CAATGG CAATGG CAATGG CAATGG CAA
131180 CCACCCTCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.37, C:0.19, G:0.30, T:0.15
Consensus pattern (6 bp):
CAATGG
Found at i:134883 original size:24 final size:24
Alignment explanation
Indices: 134856--134966 Score: 123
Period size: 24 Copynumber: 4.4 Consensus size: 24
134846 GCAATAATAA
*
134856 CAACGGTAATGGTGGCAACAACGG
1 CAACGGCAATGGTGGCAACAACGG
*
134880 CAACGGCAATGGTGGCAACAATGG
1 CAACGGCAATGGTGGCAACAACGG
*
134904 CAACGGCAATGGTGGAAACAACGGTAATGG
1 CAACGGCAATGGTGG---CAAC---AACGG
*
134934 CAACGGTAATGGTGGCAACAACGG
1 CAACGGCAATGGTGGCAACAACGG
*
134958 CAATGGCAA
1 CAACGGCAA
134967 CGGTAATGGT
Statistics
Matches: 75, Mismatches: 6, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
24 48 0.64
27 8 0.11
30 19 0.25
ACGTcount: A:0.35, C:0.20, G:0.32, T:0.13
Consensus pattern (24 bp):
CAACGGCAATGGTGGCAACAACGG
Found at i:134910 original size:30 final size:30
Alignment explanation
Indices: 134898--134978 Score: 126
Period size: 30 Copynumber: 2.7 Consensus size: 30
134888 ATGGTGGCAA
*
134898 CAATGGCAACGGCAATGGTGGAAACAACGG
1 CAATGGCAACGGCAATGGTGGCAACAACGG
* *
134928 TAATGGCAACGGTAATGGTGGCAACAACGG
1 CAATGGCAACGGCAATGGTGGCAACAACGG
*
134958 CAATGGCAACGGTAATGGTGG
1 CAATGGCAACGGCAATGGTGG
134979 TCATAATTAC
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.33, C:0.17, G:0.35, T:0.15
Consensus pattern (30 bp):
CAATGGCAACGGCAATGGTGGCAACAACGG
Found at i:135044 original size:30 final size:29
Alignment explanation
Indices: 135010--135082 Score: 87
Period size: 27 Copynumber: 2.5 Consensus size: 29
135000 GACACCTCCA
135010 CCAACTACTTATACTCCTCCACCATCCACT
1 CCAACTA-TTATACTCCTCCACCATCCACT
* *
135040 CCAACTATT-TA-TACTCCACCATCCATT
1 CCAACTATTATACTCCTCCACCATCCACT
*
135067 CCAACTGTTTATACTC
1 CCAACT-ATTATACTC
135083 ATCCGTCGCC
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
27 20 0.56
28 4 0.11
29 4 0.11
30 8 0.22
ACGTcount: A:0.27, C:0.40, G:0.01, T:0.32
Consensus pattern (29 bp):
CCAACTATTATACTCCTCCACCATCCACT
Found at i:135056 original size:27 final size:27
Alignment explanation
Indices: 135026--135082 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
135016 ACTTATACTC
135026 CTCCACCATCCACTCCAACTATTTATA
1 CTCCACCATCCACTCCAACTATTTATA
* *
135053 CTCCACCATCCATTCCAACTGTTTATA
1 CTCCACCATCCACTCCAACTATTTATA
135080 CTC
1 CTC
135083 ATCCGTCGCC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.26, C:0.40, G:0.02, T:0.32
Consensus pattern (27 bp):
CTCCACCATCCACTCCAACTATTTATA
Found at i:138993 original size:24 final size:24
Alignment explanation
Indices: 138966--139089 Score: 212
Period size: 24 Copynumber: 5.2 Consensus size: 24
138956 GCAATAATAA
138966 CAACGGTAATGGTGGCAACAACGG
1 CAACGGTAATGGTGGCAACAACGG
*
138990 CAACGGCAATGGTGGCAACAACGG
1 CAACGGTAATGGTGGCAACAACGG
*
139014 AAACGGTAATGGTGGCAACAACGG
1 CAACGGTAATGGTGGCAACAACGG
139038 CAACGGTAATGGTGGCAACAACGG
1 CAACGGTAATGGTGGCAACAACGG
* *
139062 AAACGGTAATGGTGGCAACAATGG
1 CAACGGTAATGGTGGCAACAACGG
139086 CAAC
1 CAAC
139090 AACGGAAACG
Statistics
Matches: 93, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 93 1.00
ACGTcount: A:0.35, C:0.20, G:0.32, T:0.12
Consensus pattern (24 bp):
CAACGGTAATGGTGGCAACAACGG
Found at i:139133 original size:30 final size:30
Alignment explanation
Indices: 138985--139139 Score: 100
Period size: 24 Copynumber: 5.5 Consensus size: 30
138975 TGGTGGCAAC
138985 AACGGCAACGGCAATGGTGGCAACAACGG-
1 AACGGCAACGGCAATGGTGGCAACAACGGA
*
139014 -A----AACGGTAATGGTGGCAACAAC-G-
1 AACGGCAACGGCAATGGTGGCAACAACGGA
*
139037 ----GCAACGGTAATGGTGGCAACAACGGA
1 AACGGCAACGGCAATGGTGGCAACAACGGA
* * ***
139063 AACGGTAATGGTGGCAACAATGGCAACAACGGA
1 AACGGCAA---CGGCAATGGTGGCAACAACGGA
* *
139096 AACGGCAACGGCAATGGTGGCAACAATGGC
1 AACGGCAACGGCAATGGTGGCAACAACGGA
* *
139126 AATGGCAATGGCAA
1 AACGGCAACGGCAA
139140 CAACCCTCCA
Statistics
Matches: 99, Mismatches: 16, Indels: 21
0.73 0.12 0.15
Matches are distributed among these distances:
23 1 0.01
24 41 0.41
25 1 0.01
28 1 0.01
30 31 0.31
33 24 0.24
ACGTcount: A:0.37, C:0.20, G:0.32, T:0.11
Consensus pattern (30 bp):
AACGGCAACGGCAATGGTGGCAACAACGGA
Found at i:144748 original size:6 final size:6
Alignment explanation
Indices: 144737--144762 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
144727 ACGTCGTGGC
144737 TTGCCA TTGCCA TTGCCA TTGCCA TT
1 TTGCCA TTGCCA TTGCCA TTGCCA TT
144763 TTGGGGATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.31, G:0.15, T:0.38
Consensus pattern (6 bp):
TTGCCA
Found at i:145972 original size:19 final size:19
Alignment explanation
Indices: 145932--145968 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
145922 AATTTTTAAG
145932 TAAAAATATAATATATAAA
1 TAAAAATATAATATATAAA
145951 TAAAAATATAATAT-TAAA
1 TAAAAATATAATATATAAA
145969 ATAATTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAAAATATAATATATAAA
Found at i:146821 original size:5 final size:5
Alignment explanation
Indices: 146811--146837 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
146801 ATATTACATA
146811 TATCT TATCT TATCT TATCT TATCT TA
1 TATCT TATCT TATCT TATCT TATCT TA
146838 ATACTATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.22, C:0.19, G:0.00, T:0.59
Consensus pattern (5 bp):
TATCT
Found at i:148270 original size:317 final size:316
Alignment explanation
Indices: 147694--148277 Score: 759
Period size: 317 Copynumber: 1.8 Consensus size: 316
147684 ATTTTGCATG
* *
147694 GAGTATTTTAGCCAAAAATTGAGGAAATATCTTTCGGGTCAATTTTTGCAAAATTCTAGCCGAAA
1 GAGTATTTTAGCCAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTCTAGCCAAAA
* *
147759 TCATGTACCATCACGGTTTTTGGGCAAAAAACGCGTTCTGGGGCCCTGGCTTAGTTTTGCATGAT
66 TCATGTACCATCACGGTTTTTGGCCAAAAAACGCGTTCTGGGGCCCTGACTTAGTTTTGCATGAT
* * * ** *
147824 TTTTGCCGACAAGGCTTCTTGAGATATCCATATTCATCTAATTAAATCTCAGATTCATTGGATTT
131 TTTTGCCGACAAGGCTCCTTGAAATATCCATATTCATCTAATAAAATCTCAGACACATTGCATTT
* *
147889 AAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTAAATTAGAAATTAATTAAAAAAAAT
196 AAGAATTTGTTTTCACGAGCATCTGAATCATGTTTCGATTAAATTAGAAATTAATTAAAAAAAAT
147954 ATGAAAAGCATGAAAAGTCCTCCAATCATTTTCGTGTTAAATTACATATATTTTAT
261 ATGAAAAGCATGAAAAGTCCTCCAATCATTTTCGTGTTAAATTACATATATTTTAT
* * *
148010 GAGTATTTTATCCAAAAATTGAGGAAAAAT-TATTCGGGTC-ATTTTTTCAAAATTTTAGCCAAA
1 GAGTATTTTAGCCAAAAATTGAGGAAAAATCT-TTCGGGTCAATTTTTGCAAAATTCTAGCCAAA
* * * * * *
148073 ATCGTGTACTAATTATCACGGTTTTT-GCCTAAAAGCGCATT-TCGGGG-ACTCGACTTAGTTTT
65 ATCATGTAC----CATCACGGTTTTTGGCCAAAAAACGCGTTCT-GGGGCCCT-GACTTAGTTTT
* * * * * *
148135 GCAT-ATTTTTGGC-ACCGAGTCTCCTTGAAATATCTATATTCATCTAATAAAATCTTAGCCACA
124 GCATGATTTTTGCCGA-CAAGGCTCCTTGAAATATCCATATTCATCTAATAAAATCTCAGACACA
* * * *
148198 TTGCATTTAAGGATTTGTTTTCACGAGCATTTGAATCATGTTTCGATTTAATTAGAAATTAATTT
188 TTGCATTTAAGAATTTGTTTTCACGAGCATCTGAATCATGTTTCGATTAAATTAGAAATTAATTA
*
148263 GAAAAAATATGAAAA
253 AAAAAAATATGAAAA
148278 ACGATATTAA
Statistics
Matches: 228, Mismatches: 32, Indels: 15
0.83 0.12 0.05
Matches are distributed among these distances:
315 29 0.13
316 37 0.16
317 121 0.53
318 29 0.13
319 12 0.05
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.37
Consensus pattern (316 bp):
GAGTATTTTAGCCAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTCTAGCCAAAA
TCATGTACCATCACGGTTTTTGGCCAAAAAACGCGTTCTGGGGCCCTGACTTAGTTTTGCATGAT
TTTTGCCGACAAGGCTCCTTGAAATATCCATATTCATCTAATAAAATCTCAGACACATTGCATTT
AAGAATTTGTTTTCACGAGCATCTGAATCATGTTTCGATTAAATTAGAAATTAATTAAAAAAAAT
ATGAAAAGCATGAAAAGTCCTCCAATCATTTTCGTGTTAAATTACATATATTTTAT
Found at i:148500 original size:2 final size:2
Alignment explanation
Indices: 148493--148517 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
148483 AATCCTTTAA
148493 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
148518 CACACATTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:151252 original size:653 final size:642
Alignment explanation
Indices: 149822--151371 Score: 1529
Period size: 653 Copynumber: 2.4 Consensus size: 642
149812 TTAAGGGCAT
* * * * *
149822 CGACTCA-ATTTTGCATGATCT-TTGGCATAAAGACTTCTTGAAATATCTATAATCA-CTTAACT
1 CGACTCACA-TTTGCATGAT-TATTGGCCTAAAGACTCCTTGAAATATCTATATTCATC-AAACC
** * * * * * * *
149884 AAATTTCAGCCACATTGGATTTAAAGATTT--TTTTTACGAGCATCTGAATCTTCTTTCAATTTA
63 AAATCCCAACCACACTCGATTTAACGATTTGGTTTTT-CGAACATCTGAATCTTGTTTCGATTTA
** * * * * *
149947 ATTAGAAATAAAT-TTGGAAAAAATGGAAAGACAATATTAGAAGCGTGAAAAGTCCTTCAATTTT
127 ATTAGAAATAAATGCGGGAAAAAATGGAAA-ACGATACTAGAAGCGTGAAAAATCCCTCAATCTT
* * * * * * *
150011 TTTGGCGTTGAATTATAT-ATTTATT-ATGAGTATTATGACAAAAAATTGAGGA-AAAAATTTTC
191 ATTGGCATTGAATAATATAATTT-TTCA-GAGTATTGTGGCAGAAAATTGA-GATTAAAATTTTC
* * * **
150073 GTGTCAGTTTTAGCAAAATTTTAGCCGAAATCGTGTACTAACTAACCAATACGG-TTTT-AAGCT
253 G-G---G-TCT-G----TTTTTAGCTGAAATCGTG---T-ACTAA-C---ACGGTTTTTCTGGCT
* * * * * *
150136 AAAAACGCATTCCGAGG-CCCCGACTCAGTTTTGCATGATATTTTGTGCAAAGACTCTTTGAAAT
300 TAAAATGCGTTTCG-GGACCCCGACTCAGTTTTGCATAATATTTTGTGCAAAGACTCCTTGAAAT
* * * *
150200 ATCTATATTCATCGAAACAAATCTCAGCCACATCGGATTTAGGGATTTGTTTTTATGAACATCTG
364 ATCTATATTCATCGAAACAAATCTCAACCACATCGGAATTAAGCATTTGTTTTTATGAACATCTG
* * * * *
150265 AATCTTGTTTCGATTTAATAAGAAATAAATGCGGGAAAAATGATGTCAAAAGCATGAAAAATCCT
429 AATCTTGTTTCGATTTAATAAGAAATAAATGAGGAAAAAACGATATCAAAAGCATGAAAAACCCT
* * * * *
150330 TCCATTTTTTTGGCATTAAATAATATATTTTTTTTGAGTATTTTGGCAGAAAATTGAGGAACATT
494 TCAATTTTTTTGGCATTAAATAATATATTTTTTCTGAGTATTATGGCAAAAAATTGAGGAACAAT
* * * * *
150395 TTTTTTGGTCAGTTTTTGCAAAATTTCAGTCGAAATGGTGTATTAACCATCACGATTTTTGGCTA
559 TTTTTCGGTCAGTTTTTGCAAAATTTCAGCCAAAATCGTGTATTAACAATCACGATTTTTGGCTA
150460 AAAACGCGTTCCGAGACCC
624 AAAACGCGTTCCGAGACCC
* * * * *
150479 TGACTTAGATTTGCATGATTATTGGCGTAAAGACTCCTTGAAATATCTATATTCATTAAACCAAA
1 CGACTCACATTTGCATGATTATTGGCCTAAAGACTCCTTGAAATATCTATATTCATCAAACCAAA
* * * **
150544 TCCCAACCACATTCTATTTAACGATTTGGTTTTTTGAGTATCTGAATCTTGTTTCGATTTAATTA
66 TCCCAACCACACTCGATTTAACGATTTGGTTTTTCGAACATCTGAATCTTGTTTCGATTTAATTA
* * ** *
150609 GGAATTAAT-TTGG-AAAAATGGAAAAACGATACTGGAAGCGTGAAAAATCCCTCAATCTTATTG
131 GAAATAAATGCGGGAAAAAATGG-AAAACGATACTAGAAGCGTGAAAAATCCCTCAATCTTATTG
* * *
150672 GCCATTGAATTATTTAATTTTTCAGAGTGTTGTGGCA-AAATATTGAGATTAAAATTTTCGGGTC
195 G-CATTGAATAATATAATTTTTCAGAGTATTGTGGCAGAAA-ATTGAGATTAAAATTTTCGGGTC
150736 TGTTTTTAGCTGAAATCGTGTACTAACACGGTTTTTCTGGCTTAAAATGCGTTTCGGGACCCCGA
258 TGTTTTTAGCTGAAATCGTGTACTAACACGGTTTTTCTGGCTTAAAATGCGTTTCGGGACCCCGA
* * *
150801 CTCAGTTTTGCATAAT-TTTTG-GCATAAATACTCCTTGAAATATCTATATTCATCTAACCAAAT
323 CTCAGTTTTGCATAATATTTTGTGC--AAAGACTCCTTGAAATATCTATATTCATCGAAACAAAT
* * * * *
150864 CTTAACCACTTTGGAATTAAGCATTTGTTTTTATGAGCATCTGAATCTTGTTTCGATTTAATTAG
386 CTCAACCACATCGGAATTAAGCATTTGTTTTTATGAACATCTGAATCTTGTTTCGATTTAATAAG
* *
150929 AAATAAATTTGAAAAAAAAAGGAAAAAACGATATCAGAAGCGTGAAAAACCCTTCAATTTTTTTG
451 AAATAAA--TG--------AGGAAAAAACGATATCAAAAGCATGAAAAACCCTTCAATTTTTTTG
** *
150994 GTGTTTAATAATATATTTTTTCTGAGTATTATGGCAAAAAAAATTGAGGAA-AATTTTTTCGGTC
506 GCATTAAATAATATATTTTTTCTGAGTATTATGGC--AAAAAATTGAGGAACAATTTTTTCGGTC
* * ** * *
151058 TGTTTTTGCAAAATTTTAGCCAAAATCGTGTATTGGCAATCACGGTTTTTTGCTAAAAACGCGTT
569 AGTTTTTGCAAAATTTCAGCCAAAATCGTGTATTAACAATCACGATTTTTGGCTAAAAACGCGTT
151123 CC-AGGACCC
634 CCGA-GACCC
* * * *
151132 CGACTCACTTTTGCATGATTGTTGGCCTAAAGACTCCTTGAAATATCTATATTCATCGAGCCAAA
1 CGACTCACATTTGCATGATTATTGGCCTAAAGACTCCTTGAAATATCTATATTCATCAAACCAAA
* * * * *
151197 TTCTAGCCAGACTCGATTTAAGGATTT-GTTTTTACGAACATCTGAATCTTGTTTCGATTTAATT
66 TCCCAACCACACTCGATTTAACGATTTGGTTTTT-CGAACATCTGAATCTTGTTTCGATTTAATT
* * * * * * *
151261 AGAAATAAATGCGGGAAAAAATGGAAATCGATATTAGATGTGTGAAAAATCCTTCAATTTTTTTG
130 AGAAATAAATGCGGGAAAAAATGGAAAACGATACTAGAAGCGTGAAAAATCCCTCAATCTTATTG
* *
151326 GCATTGAATAATATATTTTTTCTGAGTATTGTGGCAGAAAATTGAG
195 GCATTGAATAATATAATTTTTCAGAGTATTGTGGCAGAAAATTGAG
151372 GAAAAATTTT
Statistics
Matches: 742, Mismatches: 118, Indels: 70
0.80 0.13 0.08
Matches are distributed among these distances:
640 6 0.01
641 11 0.01
642 131 0.18
643 1 0.00
644 7 0.01
645 1 0.00
648 16 0.02
652 76 0.10
653 222 0.30
654 53 0.07
655 8 0.01
656 1 0.00
657 119 0.16
658 80 0.11
659 10 0.01
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.36
Consensus pattern (642 bp):
CGACTCACATTTGCATGATTATTGGCCTAAAGACTCCTTGAAATATCTATATTCATCAAACCAAA
TCCCAACCACACTCGATTTAACGATTTGGTTTTTCGAACATCTGAATCTTGTTTCGATTTAATTA
GAAATAAATGCGGGAAAAAATGGAAAACGATACTAGAAGCGTGAAAAATCCCTCAATCTTATTGG
CATTGAATAATATAATTTTTCAGAGTATTGTGGCAGAAAATTGAGATTAAAATTTTCGGGTCTGT
TTTTAGCTGAAATCGTGTACTAACACGGTTTTTCTGGCTTAAAATGCGTTTCGGGACCCCGACTC
AGTTTTGCATAATATTTTGTGCAAAGACTCCTTGAAATATCTATATTCATCGAAACAAATCTCAA
CCACATCGGAATTAAGCATTTGTTTTTATGAACATCTGAATCTTGTTTCGATTTAATAAGAAATA
AATGAGGAAAAAACGATATCAAAAGCATGAAAAACCCTTCAATTTTTTTGGCATTAAATAATATA
TTTTTTCTGAGTATTATGGCAAAAAATTGAGGAACAATTTTTTCGGTCAGTTTTTGCAAAATTTC
AGCCAAAATCGTGTATTAACAATCACGATTTTTGGCTAAAAACGCGTTCCGAGACCC
Found at i:151496 original size:331 final size:330
Alignment explanation
Indices: 149822--151665 Score: 1749
Period size: 334 Copynumber: 5.6 Consensus size: 330
149812 TTAAGGGCAT
* * * * * * *
149822 CGACTCAATTTTGCATGATCT-TTGGCATAAAGACTTCTTGAAATATCTATAATCA-CTTAACTA
1 CGACTCAGTTTTGCATGAT-TATTTGCGTAAAGACTCCTTGAAATATCTATATTCATC-GAACCA
* * * * *
149885 AATT-TCAGCCACATTGGATTTAAAGATTT-TTTTTACGAGCATCTGAATCTTCTTTCAATTTAA
64 AATTCT-AGCCACATTCGATTTAAGGATTTGTTTTTATGAGCATCTGAATCTTGTTTCGATTTAA
* * * *
149948 TTAGAAATAAATTTGGAAAAAATGGAAAGACAATATTAGAAGCGTGAAAAGTCCTTCAATTTTTT
128 TTAGAAATAAA-TTGGGAAAAATGGAAAAACGATATTAGAAGCGTGAAAAATCCTTCAATTTTTT
* * * * * *
150013 TGGCGTTGAATTATATATTTATTATGAGTATTATGACAAAAAATTGAGGAAAAA-ATTTTCGTGT
192 TGGCATTGAATAATATATTTTTTCTGAGTATTATGGCAAAAAATTGAGGAAAAATTTTTTCG-GT
* * **
150077 CAGTTTTAGCAAAATTTTAGCCGAAATCGTGTACTAACTAACCAAT-ACGGTTTTAAGCTAAAAA
256 CAGTTTTTGCAAAATTTTAGCCGAAATCGTGTA-T---TAACC-ATCACGATTTTTGGCTAAAAA
* *
150141 CGCATTCCGAGG-CCC
316 CGCGTT-CTAGGACCC
* * * *
150156 CGACTCAGTTTTGCATGA-TATTTTGTGCAAAGACTCTTTGAAATATCTATATTCATCGAAACAA
1 CGACTCAGTTTTGCATGATTA-TTTGCGTAAAGACTCCTTGAAATATCTATATTCATCGAACCAA
* *
150220 A-TCTCAGCCACA-TCGGATTTAGGGATTTGTTTTTATGAACATCTGAATCTTGTTTCGATTTAA
65 ATTCT-AGCCACATTC-GATTTAAGGATTTGTTTTTATGAGCATCTGAATCTTGTTTCGATTTAA
* * * * * * * *
150283 TAAGAAATAAA-TGCG------GGAAAAATGATGTCAAAAGCATGAAAAATCCTTCCATTTTTTT
128 TTAGAAATAAATTGGGAAAAATGGAAAAACGATATTAGAAGCGTGAAAAATCCTTCAATTTTTTT
* * * * * * *
150341 GGCATTAAATAATATATTTTTTTTGAGTATTTTGGCAGAAAATTGAGGAACATTTTTTTTGGTCA
193 GGCATTGAATAATATATTTTTTCTGAGTATTATGGCAAAAAATTGAGGAAAAATTTTTTCGGTCA
* * *
150406 GTTTTTGCAAAATTTCAGTCGAAATGGTGTATTAACCATCACGATTTTTGGCTAAAAACGCGTTC
258 GTTTTTGCAAAATTTTAGCCGAAATCGTGTATTAACCATCACGATTTTTGGCTAAAAACGCGTTC
*
150471 -CGAGACCC
323 TAG-GACCC
* * * * **
150479 TGACTTAGATTTGCATGATTATTGGCGTAAAGACTCCTTGAAATATCTATATTCATTAAACCAAA
1 CGACTCAGTTTTGCATGATTATTTGCGTAAAGACTCCTTGAAATATCTATATTCATCGAACCAAA
* * * * * *
150544 TCCCAACCACATTCTATTTAACGATTTGGTTTTT-TGAGTATCTGAATCTTGTTTCGATTTAATT
66 TTCTAGCCACATTCGATTTAAGGATTT-GTTTTTATGAGCATCTGAATCTTGTTTCGATTTAATT
* * * * * * * *
150608 AGGAATTAATTTGGAAAAATGGAAAAACGATACTGGAAGCGTGAAAAATCCCTCAATCTTATTGG
130 AGAAATAAATTGGGAAAAATGGAAAAACGATATTAGAAGCGTGAAAAATCCTTCAATTTTTTTGG
* * * * * * *
150673 CCATTGAATTATTTAATTTTTCAGAGTGTTGTGGCAAAATATTGA-GATTAAAA--TTTTCGG--
195 -CATTGAATAATATATTTTTTCTGAGTATTATGGCAAAAAATTGAGGA--AAAATTTTTTCGGTC
* * * * * * * *
150733 -G--TCTG----TTTTTAGCTGAAATCGTGTACTAA-CA-C-GGTTTTTCTGGCTTAAAATGCGT
257 AGTTTTTGCAAAATTTTAGCCGAAATCGTGTATTAACCATCACGATTTT-TGGCTAAAAACGCGT
*
150788 T-TCGGGACCC
321 TCT-AGGACCC
* * * *
150798 CGACTCAGTTTTGCATAATT-TTTGGCATAAATACTCCTTGAAATATCTATATTCATCTAACCAA
1 CGACTCAGTTTTGCATGATTATTT-GCGTAAAGACTCCTTGAAATATCTATATTCATCGAACCAA
* * * * *
150862 A-TCTTAACCACTTTGGAATTAAGCATTTGTTTTTATGAGCATCTGAATCTTGTTTCGATTTAAT
65 ATTC-TAGCCACATTCGATTTAAGGATTTGTTTTTATGAGCATCTGAATCTTGTTTCGATTTAAT
** * * *
150926 TAGAAATAAATTTGAAAAAAAAAGGAAAAAACGATATCAGAAGCGTGAAAAACCCTTCAATTTTT
129 TAGAAATAAA-TTG-GGAAAAATGG-AAAAACGATATTAGAAGCGTGAAAAATCCTTCAATTTTT
** *
150991 TTGGTGTTTAATAATATATTTTTTCTGAGTATTATGGCAAAAAAAATTGAGG-AAAATTTTTTCG
191 TTGGCATTGAATAATATATTTTTTCTGAGTATTATGGC--AAAAAATTGAGGAAAAATTTTTTCG
* * ** * * *
151055 GTCTGTTTTTGCAAAATTTTAGCCAAAATCGTGTATTGGCAATCACGGTTTTTTGCTAAAAACGC
254 GTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTATTAACCATCACGATTTTTGGCTAAAAACGC
*
151120 GTTCCAGGACCC
319 GTTCTAGGACCC
* * * * *
151132 CGACTCACTTTTGCATGATTGTTGGCCTAAAGACTCCTTGAAATATCTATATTCATCGAGCCAAA
1 CGACTCAGTTTTGCATGATTATTTGCGTAAAGACTCCTTGAAATATCTATATTCATCGAACCAAA
* * * *
151197 TTCTAGCCAGACTCGATTTAAGGATTTGTTTTTACGAACATCTGAATCTTGTTTCGATTTAATTA
66 TTCTAGCCACATTCGATTTAAGGATTTGTTTTTATGAGCATCTGAATCTTGTTTCGATTTAATTA
* * * *
151262 GAAATAAATGCGGGAAAAAATGG-AAATCGATATTAGATGTGTGAAAAATCCTTCAATTTTTTTG
131 GAAATAAAT-TGGG-AAAAATGGAAAAACGATATTAGAAGCGTGAAAAATCCTTCAATTTTTTTG
* * *
151326 GCATTGAATAATATATTTTTTCTGAGTATTGTGGCAGAAAATTGAGGAAAAATTTTTTAGGTCAG
194 GCATTGAATAATATATTTTTTCTGAGTATTATGGCAAAAAATTGAGGAAAAATTTTTTCGGTCAG
*
151391 TTTTTGCAAAATTTTAGCCGAAATCGTGTATTAACCATCACGATTTTTGGCTAAAAACACGTTCT
259 TTTTTGCAAAATTTTAGCCGAAATCGTGTATTAACCATCACGATTTTTGGCTAAAAACGCGTTCT
151456 AGGACCC
324 AGGACCC
* * * *
151463 TGGCTTAG-TTTGACATGATTATTTGCGTAAAGAC-CTCGTGAAATATCTATATTCAAT-GAACC
1 CGACTCAGTTTTG-CATGATTATTTGCGTAAAGACTC-CTTGAAATATCTATATTC-ATCGAACC
* * * * * *
151525 AAATCCCAGCCACATTCGATTTAACGATTTGTTTTT-TTAGTATCTAAATCTTGTTTCGATTTAA
63 AAATTCTAGCCACATTCGATTTAAGGATTTGTTTTTATGAGCATCTGAATCTTGTTTCGATTTAA
* * * * * *
151589 TTAGGAATTAATTTGGAAAAATGGAAAAACGATATTGGAAGCGTGAAAAAATCCCTCAATCTTTT
128 TTAGAAATAAATTGGGAAAAATGGAAAAACGATATTAGAAGCGTG-AAAAATCCTTCAATTTTTT
151654 TGGACATTGAAT
192 TGG-CATTGAAT
151666 TA
Statistics
Matches: 1213, Mismatches: 235, Indels: 127
0.77 0.15 0.08
Matches are distributed among these distances:
318 14 0.01
319 126 0.10
320 5 0.00
321 55 0.05
322 40 0.03
323 146 0.12
324 14 0.01
325 3 0.00
326 2 0.00
327 109 0.09
328 16 0.01
329 18 0.01
330 111 0.09
331 195 0.16
332 90 0.07
333 6 0.00
334 213 0.18
335 50 0.04
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (330 bp):
CGACTCAGTTTTGCATGATTATTTGCGTAAAGACTCCTTGAAATATCTATATTCATCGAACCAAA
TTCTAGCCACATTCGATTTAAGGATTTGTTTTTATGAGCATCTGAATCTTGTTTCGATTTAATTA
GAAATAAATTGGGAAAAATGGAAAAACGATATTAGAAGCGTGAAAAATCCTTCAATTTTTTTGGC
ATTGAATAATATATTTTTTCTGAGTATTATGGCAAAAAATTGAGGAAAAATTTTTTCGGTCAGTT
TTTGCAAAATTTTAGCCGAAATCGTGTATTAACCATCACGATTTTTGGCTAAAAACGCGTTCTAG
GACCC
Done.