Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015083.1 Corchorus olitorius cultivar O-4 contig15116, 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: 58022
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:92 original size:15 final size:15
Alignment explanation
Indices: 69--111 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
59 AGAAAAATAG
*
69 AAAGGAAAAGAAAGA
1 AAAGAAAAAGAAAGA
*
84 AAAGAAAAAGGAAGA
1 AAAGAAAAAGAAAGA
*
99 AAAAAAAGAAGAA
1 AAAGAAA-AAGAA
112 GAAGAAGGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
15 19 0.83
16 4 0.17
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (15 bp):
AAAGAAAAAGAAAGA
Found at i:98 original size:19 final size:18
Alignment explanation
Indices: 76--122 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
66 TAGAAAGGAA
76 AAGAAAGAAAAGAAAAAGG
1 AAGAAAGAAAAGAAAAA-G
* *
95 AAGAAAAAAAAGAAGAAG
1 AAGAAAGAAAAGAAAAAG
*
113 AAGAAGGAAA
1 AAGAAAGAAA
123 TAAGGAAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (18 bp):
AAGAAAGAAAAGAAAAAG
Found at i:3133 original size:23 final size:23
Alignment explanation
Indices: 3107--3158 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
3097 GAGGTTATCT
*
3107 AAATTTTATAGGGA-GGTTTATAA
1 AAATTTTATA-GGATGGTTGATAA
*
3130 AAATTTTATAGGATGGTTGATCA
1 AAATTTTATAGGATGGTTGATAA
3153 AAATTT
1 AAATTT
3159 CATATCGAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 3 0.12
23 23 0.88
ACGTcount: A:0.38, C:0.02, G:0.19, T:0.40
Consensus pattern (23 bp):
AAATTTTATAGGATGGTTGATAA
Found at i:3316 original size:23 final size:23
Alignment explanation
Indices: 3078--3383 Score: 144
Period size: 22 Copynumber: 13.7 Consensus size: 23
3068 AAAATTTGTA
* *
3078 GTTATCAAGATTTCATA-AGGAG
1 GTTATCAAAATTTCATAGTGGAG
* *
3100 GTTATCTAAATTTTATAG-GGAG
1 GTTATCAAAATTTCATAGTGGAG
* *
3122 GTTTATAAAAATTTTATA--GGATG
1 G-TTATCAAAATTTCATAGTGGA-G
*
3145 GTTGATCAAAATTTCATA-TCGAG
1 GTT-ATCAAAATTTCATAGTGGAG
* *
3168 ATTATCACAATTTCATAGTGTGA-
1 GTTATCAAAATTTCATAGTG-GAG
*
3191 -TTATCAAAATTT--TAG-GGTG
1 GTTATCAAAATTTCATAGTGGAG
* *
3210 TGATAGCTAACAA-TTCATA-TGGAG
1 -GTTATC-AA-AATTTCATAGTGGAG
* * * ** *
3234 GTTTTTAAATTTTCATA-ACGTG
1 GTTATCAAAATTTCATAGTGGAG
* *
3256 GTTATCAATATATCATA-TGGAG
1 GTTATCAAAATTTCATAGTGGAG
* * **
3278 GTTATCAACATCTCATAGTGTTG
1 GTTATCAAAATTTCATAGTGGAG
* *
3301 GTTATCAAAATTTCATTG-GGAA
1 GTTATCAAAATTTCATAGTGGAG
3323 GTTATCAAAATTTCATAGT-GAG
1 GTTATCAAAATTTCATAGTGGAG
* * *
3345 GTCT-TCAAAATTCCTTAG-GAAG
1 GT-TATCAAAATTTCATAGTGGAG
*
3367 GTTAACAAAATTTCATA
1 GTTATCAAAATTTCATA
3384 AGTTAAAAAA
Statistics
Matches: 213, Mismatches: 50, Indels: 42
0.70 0.16 0.14
Matches are distributed among these distances:
18 1 0.00
19 1 0.00
20 3 0.01
21 5 0.02
22 139 0.65
23 55 0.26
24 9 0.04
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.38
Consensus pattern (23 bp):
GTTATCAAAATTTCATAGTGGAG
Found at i:3327 original size:45 final size:45
Alignment explanation
Indices: 3254--3342 Score: 117
Period size: 45 Copynumber: 2.0 Consensus size: 45
3244 TTTCATAACG
* * *
3254 TGGTTATCAATATATCATATGGAGGTTATCAACATCTCATAGTGT
1 TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTCATAGTGT
* *
3299 TGGTTATCAAAATTTCAT-TGGGAAGTTATCAAAATTTCATAGTG
1 TGGTTATCAAAATATCATAT-GGAAGTTATCAAAATCTCATAGTG
3343 AGGTCTTCAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
44 1 0.03
45 37 0.97
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.38
Consensus pattern (45 bp):
TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTCATAGTGT
Found at i:3486 original size:23 final size:22
Alignment explanation
Indices: 3437--3484 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
3427 TATCGTTATT
*
3437 AAAATTTCATAGGAAGATTATC
1 AAAATTTCATAGGAAGATCATC
*
3459 AAAATTTCATAAGG-AGGTCATC
1 AAAATTTCAT-AGGAAGATCATC
3481 AAAA
1 AAAA
3485 ATAGTGTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 20 0.87
23 3 0.13
ACGTcount: A:0.48, C:0.10, G:0.15, T:0.27
Consensus pattern (22 bp):
AAAATTTCATAGGAAGATCATC
Found at i:8330 original size:13 final size:12
Alignment explanation
Indices: 8311--8341 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
8301 ACTTTTTGGC
8311 CAAAAAAAAAAA
1 CAAAAAAAAAAA
8323 CAAAAAAAAAAA
1 CAAAAAAAAAAA
8335 CAAAAAA
1 CAAAAAA
8342 CGCAACCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (12 bp):
CAAAAAAAAAAA
Found at i:26535 original size:37 final size:38
Alignment explanation
Indices: 26489--26567 Score: 151
Period size: 38 Copynumber: 2.1 Consensus size: 38
26479 ATTCTAAATA
26489 AACAACATAAAATTTTGGCC-AAAAAAAATATATAAAC
1 AACAACATAAAATTTTGGCCAAAAAAAAATATATAAAC
26526 AACAACATAAAATTTTGGCCAAAAAAAAATATATAAAC
1 AACAACATAAAATTTTGGCCAAAAAAAAATATATAAAC
26564 AACA
1 AACA
26568 TAAAATAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
37 20 0.49
38 21 0.51
ACGTcount: A:0.61, C:0.14, G:0.05, T:0.20
Consensus pattern (38 bp):
AACAACATAAAATTTTGGCCAAAAAAAAATATATAAAC
Found at i:27198 original size:13 final size:13
Alignment explanation
Indices: 27176--27205 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
27166 TAACATTTAC
*
27176 AAAAATGAAAAAA
1 AAAAAAGAAAAAA
27189 AAAAAAGAAAAAA
1 AAAAAAGAAAAAA
27202 AAAA
1 AAAA
27206 TGCAGCTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.90, C:0.00, G:0.07, T:0.03
Consensus pattern (13 bp):
AAAAAAGAAAAAA
Found at i:27826 original size:22 final size:22
Alignment explanation
Indices: 27801--28184 Score: 138
Period size: 22 Copynumber: 17.3 Consensus size: 22
27791 GGAGATTAAT
*
27801 AATTTCATAGTGTAGTTATCCA
1 AATTTCATAGTGTAGTTATCAA
* ** *
27823 AATTTCATGGTGCGGTTACCAA
1 AATTTCATAGTGTAGTTATCAA
* *
27845 AATTTCATA-TGCAGGTTATGAA
1 AATTTCATAGTGTA-GTTATCAA
* **
27867 AATTTCTTAG-AAAGGTTATCAA
1 AATTTCATAGTGTA-GTTATCAA
*
27889 AATTTCATAGTGTGGTTA-CTAA
1 AATTTCATAGTGTAGTTATC-AA
* * *
27911 AATTACACA-TGAAGGTTAT-AA
1 AATTTCATAGTGTA-GTTATCAA
* * *
27932 AAATTCGATAGTATGGTTATCAA
1 AATTTC-ATAGTGTAGTTATCAA
* * *
27955 AATTACATAG-GGAGATTAACAA
1 AATTTCATAGTGTAG-TTATCAA
* **
27977 AATTTCATAG-GGAGGTTATCGT
1 AATTTCATAGTGTA-GTTATCAA
*
27999 AATTTTATAGTGTAGTTATCAA
1 AATTTCATAGTGTAGTTATCAA
* * *
28021 AATTTCATAGTATTGTTTTCAA
1 AATTTCATAGTGTAGTTATCAA
* **
28043 AA-TTC-T-GTAAGGAGATTAAAAA
1 AATTTCATAGT--GTAG-TTATCAA
*
28065 AATTTCGTAAG-G-ATGTTATCAA
1 AATTTCAT-AGTGTA-GTTATCAA
* * *
28087 AAATTCATAAAGCGT--TTATCCA
1 AATTTCAT--AGTGTAGTTATCAA
28109 AATTTCATA-TGGTAGTTATCAA
1 AATTTCATAGT-GTAGTTATCAA
*
28131 AATTTCATGAG-GT-GATTATCGA
1 AATTTCAT-AGTGTAG-TTATCAA
28153 AATTTCATGAG-GATCAGATTATCAA
1 AATTTCAT-AGTG-T-AG-TTATCAA
28178 AATTTCA
1 AATTTCA
28185 AAGGAGGGTT
Statistics
Matches: 269, Mismatches: 61, Indels: 61
0.69 0.16 0.16
Matches are distributed among these distances:
19 2 0.01
20 4 0.01
21 18 0.07
22 207 0.77
23 20 0.07
24 2 0.01
25 15 0.06
26 1 0.00
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (22 bp):
AATTTCATAGTGTAGTTATCAA
Found at i:27996 original size:44 final size:44
Alignment explanation
Indices: 27594--28184 Score: 170
Period size: 44 Copynumber: 13.4 Consensus size: 44
27584 TTCACGGTGT
* * * * * * * **
27594 GGTTATAAAAATTTCACAAGAAGTTTATCAAAAATTCATATTGA
1 GGTTATCAAAATTTCATAGGGAGATTAACAAAATTTCATAGGGA
* * * * * * * *
27638 GGTCATCTAAATTTCTTAGTGTGATT-ACAAAAATTCGATAGTGT
1 GGTTATCAAAATTTCATAGGGAGATTAACAAAATTTC-ATAGGGA
* *
27682 GGTTATCAAAATTACATATAGGGAGATTAACAAAATTTCATATGGA
1 GGTTATCAAAATTTC--ATAGGGAGATTAACAAAATTTCATAGGGA
** * * * **
27728 GGTTATCGTAATTTCATCGTGTAG-TTATCAAAATTTCATA-ATA
1 GGTTATCAAAATTTCATAG-GGAGATTAACAAAATTTCATAGGGA
* * * * * * *
27771 TGATTTTTAAAATCTCGTAGGGAGATT-A-ATAATTTCATAGTGTA
1 -GGTTATCAAAATTTCATAGGGAGATTAACAAAATTTCATAG-GGA
* * * * * *
27815 -GTTATCCAAATTTCAT-GGTGCGGTTACCAAAATTTCATATGCA
1 GGTTATCAAAATTTCATAGG-GAGATTAACAAAATTTCATAGGGA
* * ** * * * *
27858 GGTTATGAAAATTTCTTAGAAAGGTTATCAAAATTTCATAGTGT
1 GGTTATCAAAATTTCATAGGGAGATTAACAAAATTTCATAGGGA
* * * * * *
27902 GGTTA-CTAAAATTACACATGAAGGTTATA-AAAA-TTCGATA-GTA
1 GGTTATC-AAAATTTCATAGGGAGATTA-ACAAAATTTC-ATAGGGA
*
27945 TGGTTATCAAAATTACATAGGGAGATTAACAAAATTTCATAGGGA
1 -GGTTATCAAAATTTCATAGGGAGATTAACAAAATTTCATAGGGA
** * * * *
27990 GGTTATCGTAATTTTATAGTGTAG-TTATCAAAATTTCATA-GTA
1 GGTTATCAAAATTTCATAG-GGAGATTAACAAAATTTCATAGGGA
* * * * * * *
28033 TTGTTTTCAAAA-TTCTGTAAGGAGATTAAAAAAATTTCGTAAGGA
1 -GGTTATCAAAATTTC-ATAGGGAGATTAACAAAATTTCATAGGGA
* * ** * * * * *
28078 TGTTATCAAAAATTCATAAAGCGTTTATCCAAATTTCATATGGTA
1 GGTTATCAAAATTTCATAGGGAGATTAACAAAATTTCATA-GGGA
* * * *
28123 -GTTATCAAAATTTCAT-GAGGTGATTATCGAAATTTCATGAGGATCA
1 GGTTATCAAAATTTCATAG-GGAGATTAACAAAATTTCAT-AGG--GA
*
28169 GATTATCAAAATTTCA
1 GGTTATCAAAATTTCA
28185 AAGGAGGGTT
Statistics
Matches: 394, Mismatches: 119, Indels: 65
0.68 0.21 0.11
Matches are distributed among these distances:
41 2 0.01
42 24 0.06
43 26 0.07
44 273 0.69
45 21 0.05
46 25 0.06
47 23 0.06
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (44 bp):
GGTTATCAAAATTTCATAGGGAGATTAACAAAATTTCATAGGGA
Found at i:28009 original size:66 final size:65
Alignment explanation
Indices: 27675--28030 Score: 263
Period size: 66 Copynumber: 5.4 Consensus size: 65
27665 CAAAAATTCG
* *
27675 ATAGTGTGGTTATCAAAATTACATATAGGGAGATTAACAAAATTTCATATGGAGGTTATCGTAAT
1 ATAGTGTAGTTATCAAAATTTC--ATAGGGAGATTAACAAAATTTCATATGGAGGTTAT-GTAAT
27740 TTC
63 TTC
* ** *** * * * * *
27743 ATCGTGTAGTTATCAAAATTTCATA-ATATGATTTTTAAAATCTCGTAGGGAGATTA-ATAATTT
1 ATAGTGTAGTTATCAAAATTTCATAGGGA-GATTAACAAAATTTCATATGGAGGTTATGTAATTT
27806 C
65 C
* * * * * *
27807 ATAGTGTAGTTATCCAAATTTCAT-GGTGCGGTTACCAAAATTTCATATGCAGGTTATGAAAATT
1 ATAGTGTAGTTATCAAAATTTCATAGG-GAGATTAACAAAATTTCATATGGAGGTTATG-TAATT
27871 TC
64 TC
* ** * * * * * * ** *
27873 TTAG-AAAGGTTATCAAAATTTCATAGTGTGGTT-ACTAAAATTACACATGAAGGTTATAAAAAT
1 ATAGTGTA-GTTATCAAAATTTCATAGGGAGATTAAC-AAAATTTCATATGGAGGTTATGTAATT
27936 TC
64 TC
* * * *
27938 GATAGTATGGTTATCAAAATTACATAGGGAGATTAACAAAATTTCATAGGGAGGTTATCGTAATT
1 -ATAGTGTAGTTATCAAAATTTCATAGGGAGATTAACAAAATTTCATATGGAGGTTAT-GTAATT
*
28003 TT
64 TC
28005 ATAGTGTAGTTATCAAAATTTCATAG
1 ATAGTGTAGTTATCAAAATTTCATAG
28031 TATTGTTTTC
Statistics
Matches: 217, Mismatches: 59, Indels: 26
0.72 0.20 0.09
Matches are distributed among these distances:
64 47 0.22
65 9 0.04
66 134 0.62
67 8 0.04
68 19 0.09
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (65 bp):
ATAGTGTAGTTATCAAAATTTCATAGGGAGATTAACAAAATTTCATATGGAGGTTATGTAATTTC
Found at i:28360 original size:44 final size:44
Alignment explanation
Indices: 28309--28434 Score: 153
Period size: 44 Copynumber: 2.9 Consensus size: 44
28299 TATGATTATA
* * *
28309 TACCAACATTTTATAGGGAGGTTATCAAAATTTCGTAGTGTGCT
1 TACCAACATTTCATATGGAGGTTATCAAAATTTCGTAATGTGCT
* * * * *
28353 TACCAACATTCCATATGGTGGTTATTAAAATATCATAATGTGCT
1 TACCAACATTTCATATGGAGGTTATCAAAATTTCGTAATGTGCT
* * *
28397 TATCAAAATTTGATATGGAGGTTATCAAAATTTCGTAA
1 TACCAACATTTCATATGGAGGTTATCAAAATTTCGTAA
28435 GGAGCTTATT
Statistics
Matches: 66, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
44 66 1.00
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.37
Consensus pattern (44 bp):
TACCAACATTTCATATGGAGGTTATCAAAATTTCGTAATGTGCT
Found at i:28438 original size:22 final size:22
Alignment explanation
Indices: 28394--28452 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
28384 ATCATAATGT
*
28394 GCTTATCAAAATTT-GATATGGA
1 GCTTATCAAAATTTCG-TAAGGA
*
28416 GGTTATCAAAATTTCGTAAGGA
1 GCTTATCAAAATTTCGTAAGGA
* *
28438 GCTTATTAAATTTTC
1 GCTTATCAAAATTTC
28453 ATAGTTTCGT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 30 0.97
23 1 0.03
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.39
Consensus pattern (22 bp):
GCTTATCAAAATTTCGTAAGGA
Found at i:28442 original size:44 final size:44
Alignment explanation
Indices: 28316--28455 Score: 138
Period size: 44 Copynumber: 3.2 Consensus size: 44
28306 ATATACCAAC
* * * *
28316 ATTTTATAGGGAGGTTATCAAAATTTCGT-AGTGTGCTTACCAAC
1 ATTTCATATGGAGGTTATCAAAATTTCGTAAG-GTGCTTATCAAA
* * * * * *
28360 ATTCCATATGGTGGTTATTAAAATATCATAATGTGCTTATCAAA
1 ATTTCATATGGAGGTTATCAAAATTTCGTAAGGTGCTTATCAAA
* * *
28404 ATTTGATATGGAGGTTATCAAAATTTCGTAAGGAGCTTATTAAA
1 ATTTCATATGGAGGTTATCAAAATTTCGTAAGGTGCTTATCAAA
*
28448 TTTTCATA
1 ATTTCATA
28456 GTTTCGTTAT
Statistics
Matches: 74, Mismatches: 21, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
44 73 0.99
45 1 0.01
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.39
Consensus pattern (44 bp):
ATTTCATATGGAGGTTATCAAAATTTCGTAAGGTGCTTATCAAA
Found at i:28549 original size:22 final size:22
Alignment explanation
Indices: 28498--28566 Score: 68
Period size: 22 Copynumber: 3.1 Consensus size: 22
28488 ACCACATGGA
* *
28498 GAGGTTATTAAAATATCAT-AG
1 GAGGTTATCAAAATTTCATAAG
* * * *
28519 TGTGTTTATCAAAATTTTATATG
1 -GAGGTTATCAAAATTTCATAAG
28542 GAGGTTATCAAAATTTCATAAG
1 GAGGTTATCAAAATTTCATAAG
28564 GAG
1 GAG
28567 TTTAATAAAT
Statistics
Matches: 36, Mismatches: 10, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
22 35 0.97
23 1 0.03
ACGTcount: A:0.38, C:0.06, G:0.19, T:0.38
Consensus pattern (22 bp):
GAGGTTATCAAAATTTCATAAG
Found at i:28561 original size:44 final size:44
Alignment explanation
Indices: 27879--28561 Score: 120
Period size: 44 Copynumber: 15.4 Consensus size: 44
27869 TTTCTTAGAA
* ** * *
27879 AGGTTATCAAAATTTCATAGTGTGGTTA-CTAAAATTACACATGA
1 AGGTTATCAAAATTTCATAGTGTGTTTATC-AAAATTTTATATGG
* * * ** *
27923 AGGTTAT-AAAAATTCGATAGTATGGTTATCAAAATTACATAGGG
1 AGGTTATCAAAATTTC-ATAGTGTGTTTATCAAAATTTTATATGG
* * * * * ** *
27967 AGATTAACAAAATTTCATAGGGAGGTTATCGTAATTTTATAGTGT
1 AGGTTATCAAAATTTCATAGTGTGTTTATCAAAATTTTATA-TGG
* * * *
28012 A-GTTATCAAAATTTCATAGTATTGTTT-TCAAAATTCTGTAAGG
1 AGGTTATCAAAATTTCATAGT-GTGTTTATCAAAATTTTATATGG
* ** * * * **
28055 AGATTAAAAAAATTTCGTAAG-GATG-TTATCAAAAATTCATAAAG
1 AGGTTATCAAAATTTCAT-AGTG-TGTTTATCAAAATTTTATATGG
* * * *
28099 CGTTTATCCAAATTTCATA-TG-GTAGTTATCAAAATTTCATGA-GG
1 AGGTTATCAAAATTTCATAGTGTGT--TTATCAAAATTTTAT-ATGG
* * * * * *
28143 TGATTATCGAAATTTCATGAG-GATCAGATTATCAAAATTTCA-AAGG
1 AGGTTATCAAAATTTCAT-AGTG-T--GTTTATCAAAATTTTATATGG
** * *
28189 AGGGTTATCATACTTTTACA-AG-GAGGTTTTATCAAAAATTTATAAT-G
1 A-GGTTATCA-AAATTT-CATAGTG-TG-TTTATCAAAATTTTAT-ATGG
* * *** * * * * *
28236 AGGTCATCGAAATTTCATAGAAAG-TAATCACAATTTGACAGTGT
1 AGGTTATCAAAATTTCATAGTGTGTTTATCAAAATTTTATA-TGG
* * * * * *
28280 A-TTTATCAAATTTTCATGGTATGATTATATACCAACATTTTATAGGG
1 AGGTTATCAAAATTTCATAGTGTG-TT-TAT--CAAAATTTTATATGG
* * * * **
28327 AGGTTATCAAAATTTCGTAGTGTGCTTACCAACATTCCATATGG
1 AGGTTATCAAAATTTCATAGTGTGTTTATCAAAATTTTATATGG
* * * * * *
28371 TGGTTATTAAAATATCATAATGTGCTTATCAAAATTTGATATGG
1 AGGTTATCAAAATTTCATAGTGTGTTTATCAAAATTTTATATGG
* * * * *
28415 AGGTTATCAAAATTTCGTAAG-GAGCTTAT-TAAATTTTCATA-GTT
1 AGGTTATCAAAATTTCAT-AGTGTGTTTATCAAAATTTT-ATATG-G
** * * * * * * **
28459 TCGTTATTAAATTTTCCGTAGGTGTGCTTA-CCACA---TGGA--G
1 AGGTTATCAAAATTT-CATA-GTGTGTTTATCAAAATTTTATATGG
* *
28499 AGGTTATTAAAATATCATAGTGTGTTTATCAAAATTTTATATGG
1 AGGTTATCAAAATTTCATAGTGTGTTTATCAAAATTTTATATGG
28543 AGGTTATCAAAATTTCATA
1 AGGTTATCAAAATTTCATA
28562 AGGAGTTTAA
Statistics
Matches: 452, Mismatches: 137, Indels: 100
0.66 0.20 0.15
Matches are distributed among these distances:
38 8 0.02
39 6 0.01
40 11 0.02
41 1 0.00
42 4 0.01
43 47 0.10
44 248 0.55
45 33 0.07
46 32 0.07
47 29 0.06
48 30 0.07
49 3 0.01
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.37
Consensus pattern (44 bp):
AGGTTATCAAAATTTCATAGTGTGTTTATCAAAATTTTATATGG
Found at i:28757 original size:22 final size:22
Alignment explanation
Indices: 28716--28769 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
28706 TAACAAAATG
28716 GAATTTCATAGTGTAGTTATCA
1 GAATTTCATAGTGTAGTTATCA
* *
28738 GAATTTTATAGTGT-GATTATTA
1 GAATTTCATAGTGTAG-TTATCA
*
28760 AAATTTCATA
1 GAATTTCATA
28770 TGGATGTCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 1 0.04
22 26 0.96
ACGTcount: A:0.35, C:0.06, G:0.15, T:0.44
Consensus pattern (22 bp):
GAATTTCATAGTGTAGTTATCA
Found at i:28882 original size:2 final size:2
Alignment explanation
Indices: 28875--28914 Score: 62
Period size: 2 Copynumber: 19.5 Consensus size: 2
28865 TGTACATGTA
*
28875 AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT ACT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT A
28915 AAAGTACGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 33 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:30229 original size:22 final size:22
Alignment explanation
Indices: 30070--30286 Score: 115
Period size: 22 Copynumber: 9.8 Consensus size: 22
30060 GATTTTCTTG
*
30070 TCATTGTGTGGTTATCAAAATT
1 TCATAGTGTGGTTATCAAAATT
* * *
30092 TCATAAG-ATGGTTATTATAATT
1 TCAT-AGTGTGGTTATCAAAATT
*
30114 TCATGAG-GAGGTTATCAAAATT
1 TCAT-AGTGTGGTTATCAAAATT
* * *
30136 CCATAGTGTGGTTACCAAATTT
1 TCATAGTGTGGTTATCAAAATT
*
30158 TCATA-TG-GAACTTATCAAAATT
1 TCATAGTGTG--GTTATCAAAATT
* * *
30180 TAAT-GGGAAGGTTATCAAAATT
1 TCATAGTG-TGGTTATCAAAATT
*
30202 TCATAGTGTGGTTACCAAAATT
1 TCATAGTGTGGTTATCAAAATT
* * *
30224 TAATAG-GATCACGTTATTAAAATT
1 TCATAGTG-T--GGTTATCAAAATT
* * * **
30248 TCTTAG-GAAGGTCATTGAAATT
1 TCATAGTG-TGGTTATCAAAATT
30270 TCATAGTGTGGTTATCA
1 TCATAGTGTGGTTATCA
30287 CAAACTTTAT
Statistics
Matches: 144, Mismatches: 39, Indels: 24
0.70 0.19 0.12
Matches are distributed among these distances:
20 1 0.01
21 5 0.03
22 117 0.81
23 4 0.03
24 17 0.12
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38
Consensus pattern (22 bp):
TCATAGTGTGGTTATCAAAATT
Found at i:30341 original size:22 final size:21
Alignment explanation
Indices: 30316--30686 Score: 137
Period size: 22 Copynumber: 16.7 Consensus size: 21
30306 ATCAAAGAGA
*
30316 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAG-GAGG
*
30338 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAG-GAGG
*
30360 TTAACAAAATTTCATAAGGAGG
1 TTATCAAAATTTCAT-AGGAGG
* *
30382 TTA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCAT-AGGAGG
* ** *
30404 TTTTCAAAATTTCATAAAAAGA
1 TTATCAAAATTTCAT-AGGAGG
*
30426 TTATAAAAGTCTCAATTTCATA--AGG
1 TTAT-CAA-----AATTTCATAGGAGG
* * * *
30451 AGTACCAACA-TTCGATAGAAGG
1 -TTATCAAAATTTC-ATAGGAGG
*
30473 TTATC-AAATCTCATA-GAGTG
1 TTATCAAAATTTCATAGGAG-G
*
30493 ATTATCGAAATTTCATAGAGATCGG
1 -TTATCAAAATTTCATAG-GA--GG
*
30518 ATTATCAAAATTT-ATAGGAAGA
1 -TTATCAAAATTTCATAGG-AGG
**
30540 TTATCAAAATTTCATAGTGTTG
1 TTATCAAAATTTCATAG-GAGG
* *
30562 TTATGAAAATTTCAAAGCGAGG
1 TTATCAAAATTTCATAG-GAGG
* * * *
30584 TTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCAT-AGGAGG
* *
30606 TTATCAAAATTTTAATAGAGGGG
1 TTATCAAAA-TTTCATAG-GAGG
* * *
30629 TCAACAAAATTTTATAGAGAGG
1 TTATCAAAATTTCATAG-GAGG
*
30651 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCAT-AGGAGG
*
30673 TTATCAAATTTTCA
1 TTATCAAAATTTCA
30687 AAATGTCATT
Statistics
Matches: 261, Mismatches: 58, Indels: 60
0.69 0.15 0.16
Matches are distributed among these distances:
19 5 0.02
20 10 0.04
21 25 0.10
22 161 0.62
23 24 0.09
24 7 0.03
25 17 0.07
26 3 0.01
27 1 0.00
28 8 0.03
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (21 bp):
TTATCAAAATTTCATAGGAGG
Found at i:31102 original size:23 final size:23
Alignment explanation
Indices: 31050--31151 Score: 118
Period size: 23 Copynumber: 4.5 Consensus size: 23
31040 AAATTTGTAG
* *
31050 TTATCAAGATTTCATAAGGAGG-
1 TTATCAAAATTTCATAGGGAGGT
*
31072 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTCATAGGGAGGT
* *
31095 TTATCAAAATTTTATAGGAAGGT
1 TTATCAAAATTTCATAGGGAGGT
* *
31118 TTATCAAAATTTCATAGAGA-GA
1 TTATCAAAATTTCATAGGGAGGT
*
31140 TTATCACAATTT
1 TTATCAAAATTT
31152 AATGGTGTGA
Statistics
Matches: 70, Mismatches: 9, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
22 31 0.44
23 39 0.56
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.37
Consensus pattern (23 bp):
TTATCAAAATTTCATAGGGAGGT
Found at i:31448 original size:22 final size:22
Alignment explanation
Indices: 30796--31448 Score: 282
Period size: 22 Copynumber: 30.0 Consensus size: 22
30786 TTATGGAGTA
* *
30796 ATCAAAATTTC--AGGGAGGAT
1 ATCAAAATTTCATAAGGAGGTT
* *
30816 ATCAAAATTTCATATGAAGGTT
1 ATCAAAATTTCATAAGGAGGTT
*
30838 ATCAAAATTTCAT-AGTTTA-GTT
1 ATCAAAATTTCATAAG--GAGGTT
* *
30860 TTCAAATTTTCATAA-GAGGGTT
1 ATCAAAATTTCATAAGGA-GGTT
* * * *
30882 ATCAAAATTTTAT-AGTATGTAG
1 ATCAAAATTTCATAAGGAGGT-T
* *
30904 ATCAAAATTTCATATGAAGGTT
1 ATCAAAATTTCATAAGGAGGTT
30926 ATCAAAATTTCATAA-GAGGATT
1 ATCAAAATTTCATAAGGAGG-TT
* * *
30948 ATCAAAATTTCAT-AGTATGTAG
1 ATCAAAATTTCATAAGGAGGT-T
* *
30970 ATCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATAAGGAGGTT
* *
30992 AACAAAATTTCATAATGAGGTT
1 ATCAAAATTTCATAAGGAGGTT
* **
31014 ATAAAAAAATCAT-AGAGAGGTT
1 ATCAAAATTTCATAAG-GAGGTT
* *
31036 AT-AAAAATT--T--GTA-GTT
1 ATCAAAATTTCATAAGGAGGTT
*
31052 ATCAAGATTTCATAAGGAGGTT
1 ATCAAAATTTCATAAGGAGGTT
* *
31074 ATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATAAGGAGG-TT
*
31097 ATCAAAATTTTAT-AGGAAGGTTT
1 ATCAAAATTTCATAAGG-AGG-TT
*
31120 ATCAAAATTTCAT-AGAGAGATT
1 ATCAAAATTTCATAAG-GAGGTT
* * *
31142 ATCACAATTT-A-ATGGTGTGATT
1 ATCAAAATTTCATAAGGAG-G-TT
* * * *
31164 ATCAACATTTCA-GAGTGTGATT
1 ATCAAAATTTCATAAG-GAGGTT
*
31186 A-CTAACAA-TTCATATGGAGGTT
1 ATC-AA-AATTTCATAAGGAGGTT
* * * * *
31208 TTTAAATTTTCATAACGTGGTT
1 ATCAAAATTTCATAAGGAGGTT
* * **
31230 ATCAATATATCATTTGGAGGTT
1 ATCAAAATTTCATAAGGAGGTT
* * *
31252 ATCAACATCTCAT-AGCGTTGGTT
1 ATCAAAATTTCATAAG-G-AGGTT
** *
31275 ATCAAAATTTCATTGGGAAGTT
1 ATCAAAATTTCATAAGGAGGTT
* * *
31297 ATCCAAATTTCATTATGAGGTCT
1 ATCAAAATTTCATAAGGAGGT-T
* *
31320 -TCAAAATTT-TTTAGAGAGGTT
1 ATCAAAATTTCATAAG-GAGGTT
* *
31341 AACAAAATTTCATAAGAAGGTT
1 ATCAAAATTTCATAAGGAGGTT
** * **
31363 AAAAAAAATT-ATAAAAAGGTT
1 ATCAAAATTTCATAAGGAGGTT
* * * *
31384 CTCGAAATTTCAT-AGTATCGTT
1 ATCAAAATTTCATAAGGA-GGTT
*
31406 ATTAAAATTTCAT-AGGAAGGTT
1 ATCAAAATTTCATAAGG-AGGTT
31428 ATCAAAATTTCATAAGGAGGT
1 ATCAAAATTTCATAAGGAGGT
31449 CATAAAAAAT
Statistics
Matches: 473, Mismatches: 115, Indels: 88
0.70 0.17 0.13
Matches are distributed among these distances:
16 5 0.01
17 6 0.01
18 1 0.00
19 2 0.00
20 14 0.03
21 44 0.09
22 322 0.68
23 74 0.16
24 5 0.01
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.36
Consensus pattern (22 bp):
ATCAAAATTTCATAAGGAGGTT
Found at i:31458 original size:23 final size:22
Alignment explanation
Indices: 31409--31456 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
31399 TATCGTTATT
* *
31409 AAAATTTCATAGGAAGGTTATC
1 AAAATTTCATAGGAAGGTCATA
31431 AAAATTTCATAAGG-AGGTCATA
1 AAAATTTCAT-AGGAAGGTCATA
31453 AAAA
1 AAAA
31457 ATAGTGTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 20 0.87
23 3 0.13
ACGTcount: A:0.48, C:0.08, G:0.17, T:0.27
Consensus pattern (22 bp):
AAAATTTCATAGGAAGGTCATA
Found at i:49101 original size:13 final size:13
Alignment explanation
Indices: 49083--49108 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
49073 CTTGGCATGA
49083 GTGATGATTTTTG
1 GTGATGATTTTTG
49096 GTGATGATTTTTG
1 GTGATGATTTTTG
49109 TTGTTACCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.31, T:0.54
Consensus pattern (13 bp):
GTGATGATTTTTG
Found at i:51830 original size:15 final size:15
Alignment explanation
Indices: 51799--51833 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
51789 CATGGTAAAA
*
51799 ATTTTTTCTAACCAT
1 ATTTTTTCTAAACAT
*
51814 ATTTTTTCTAAATAT
1 ATTTTTTCTAAACAT
51829 ATTTT
1 ATTTT
51834 ATATAGTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.29, C:0.11, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTTTTTCTAAACAT
Found at i:57116 original size:2 final size:2
Alignment explanation
Indices: 57073--57101 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
57063 ATTTCTATTC
57073 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
57102 TAATCTCTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.