Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021806.1 Corchorus olitorius cultivar O-4 contig21839, 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: 68672
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:6 original size:1 final size:1
Alignment explanation
Indices: 1--27 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
28 AATTGATGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:7368 original size:14 final size:15
Alignment explanation
Indices: 7351--7383 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
7341 ATTTTAAAGA
7351 ATTAATTT-ATGAAT
1 ATTAATTTAATGAAT
*
7365 ATTAATTTAATTAAT
1 ATTAATTTAATGAAT
7380 ATTA
1 ATTA
7384 TTTTTAGTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (15 bp):
ATTAATTTAATGAAT
Found at i:7553 original size:86 final size:88
Alignment explanation
Indices: 7436--7600 Score: 271
Period size: 86 Copynumber: 1.9 Consensus size: 88
7426 CATGCTTGGA
* *
7436 TTTTCTTAAAAATTAGGAGATTTGACTTAGTACGTAATTGTTATATGAATTCATGACATGAGTAA
1 TTTTCTTAAAAATTAGAAGATTTGACTTAGTACATAATTGTTATATGAATTCATGACATGAGTAA
*
7501 GACAT-TTTTTTATGCGATAACT
66 AACATATTTTTTATGCGATAACT
*
7523 TTTTCTTAAAGATT-GAAGATTTGACTTAGTACATAATTGTTATATGAATTCATGACATGAGTAA
1 TTTTCTTAAAAATTAGAAGATTTGACTTAGTACATAATTGTTATATGAATTCATGACATGAGTAA
7587 AACATCATTTTTTA
66 AACAT-ATTTTTTA
7601 ACCCTGCAAA
Statistics
Matches: 72, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
86 52 0.72
87 13 0.18
88 7 0.10
ACGTcount: A:0.35, C:0.09, G:0.15, T:0.42
Consensus pattern (88 bp):
TTTTCTTAAAAATTAGAAGATTTGACTTAGTACATAATTGTTATATGAATTCATGACATGAGTAA
AACATATTTTTTATGCGATAACT
Found at i:12072 original size:397 final size:397
Alignment explanation
Indices: 11190--12173 Score: 1640
Period size: 397 Copynumber: 2.5 Consensus size: 397
11180 ATGGTGATAG
11190 TGTTAGGGATTCACATGTGAGGTAAACATCCCACATCATAAAGAGATGGATTGTTAGAGTCCCTT
1 TGTTAGGGATTCACATGTGAGGTAAACATCCCACATCATAAAGAGATGGATTGTTAGAGTCCCTT
*
11255 ATATACATGAAGGACCCAAGAAACCATTAGTCTAGACTTTTGGGTTCGGGTTGATGTCCGACATG
66 ATATACATGAAGGACCCAAGAAACCATTAGTCTAGACTTTTGGGTTCGGGTTGGTGTCCGACATG
* *
11320 TATATGGGCTACTCGGTGGGCCTTGCTGGAGCAGACAGGGCCTGGTTCCTCTCCCAACAAGTGGT
131 TATATGGGCTACTCGGTGGGCCTTGCTGGAGCAGACAGGGCCCGGTTCCTCTCCCAACAAGTGAT
* *
11385 ATCAGAGCTCGGTTAGACTCGATCAGTGTGGCCCATGAGCACGGTAAACCTGGTGTCCGTGTCCC
196 ATCAGAGCTCGGTTAGACTCGATCAGTGTGGCCCATGAGCACGGTAAACCTGGTAT-CGTGTACC
* *
11450 CGCCAGGGGTGTGCGATTGTGGAGTGTTGTGCTTGCACTCTACGGGTTAAGTCTTGGATGACCGG
260 AGCCAGGGGTGTGCAATTGTGGAGTGTTGTGCTTGCACTCTACGGGTTAAGTCTTGGATGACCGG
*
11515 TAATTGGCTTAAGACTTGACGGGTTGGGCCGCACGGGGGAGAGATGAGGACTCACAAGTGAATCG
325 TAATTGGCTTAAGACTTGACAGGTTGGGCCGCACGGGGGAGAGATGAGGACTCACAAGTGAATCG
11580 GGGGAGAT
390 GGGGAGAT
* * * **
11588 TGTTAAGGGATTCACATGTGAGG-AAACATCCCACATCATGAAGAGATGGGTTGTTGGAGTAGCT
1 TGTT-AGGGATTCACATGTGAGGTAAACATCCCACATCATAAAGAGATGGATTGTTAGAGTCCCT
* *
11652 TATATACATGAAGGACCCAAGAAACCATTAGTCTAGACTTTTGGGTTCGAGTTGGTGTCCAACAT
65 TATATACATGAAGGACCCAAGAAACCATTAGTCTAGACTTTTGGGTTCGGGTTGGTGTCCGACAT
* *
11717 GTATATGGGCTACTCGGTGGGCCTTGTTGAAGCAGACAGGGCCCGGTTCCTCTCCCAACAAGTGA
130 GTATATGGGCTACTCGGTGGGCCTTGCTGGAGCAGACAGGGCCCGGTTCCTCTCCCAACAAGTGA
* *
11782 TATCAGAGCTCGGTTAGACTCGATCGGTGTGGCCCATGAGCACGGTGAACCT-G-AT-GTG-ACC
195 TATCAGAGCTCGGTTAGACTCGATCAGTGTGGCCCATGAGCACGGTAAACCTGGTATCGTGTACC
*
11843 ATCCAGGGGTGTGCAATTGTGTGAAGTGTTG-GACCCTTGCACT-TCACGGGTTAAGTCTTGGAT
260 AGCCAGGGGTGTGCAATTGTG-G-AGTGTTGTG---CTTGCACTCT-ACGGGTTAAGTCTTGGAT
*
11906 GGCCGGTAATTGGCTTAAGACTTGACAGGTTGGGCCGCACGGGGGAGAGATGAGGACTCACAAGT
319 GACCGGTAATTGGCTTAAGACTTGACAGGTTGGGCCGCACGGGGGAGAGATGAGGACTCACAAGT
11971 GAATCGGGGGAGAT
384 GAATCGGGGGAGAT
11985 TGTTAGGGATTCACATGTGAGGTAAACATCCCACATCATAAAGAGATGGATTGTTAGAGTCCCTT
1 TGTTAGGGATTCACATGTGAGGTAAACATCCCACATCATAAAGAGATGGATTGTTAGAGTCCCTT
12050 ATATACATGAAGGACCCAAGAAACCATTAGTCTAGACTTTTGGGTTCGGGTTGGTGTCCGACATG
66 ATATACATGAAGGACCCAAGAAACCATTAGTCTAGACTTTTGGGTTCGGGTTGGTGTCCGACATG
* *
12115 TATATGGGCTACTCGATGGGCCTTGCTGGAGCAGACAGGGCCCGGTTCTTCTCCCAACA
131 TATATGGGCTACTCGGTGGGCCTTGCTGGAGCAGACAGGGCCCGGTTCCTCTCCCAACA
12174 GATAGATCTA
Statistics
Matches: 546, Mismatches: 32, Indels: 17
0.92 0.05 0.03
Matches are distributed among these distances:
393 20 0.04
394 5 0.01
395 7 0.01
396 20 0.04
397 263 0.48
398 213 0.39
399 18 0.03
ACGTcount: A:0.24, C:0.20, G:0.30, T:0.26
Consensus pattern (397 bp):
TGTTAGGGATTCACATGTGAGGTAAACATCCCACATCATAAAGAGATGGATTGTTAGAGTCCCTT
ATATACATGAAGGACCCAAGAAACCATTAGTCTAGACTTTTGGGTTCGGGTTGGTGTCCGACATG
TATATGGGCTACTCGGTGGGCCTTGCTGGAGCAGACAGGGCCCGGTTCCTCTCCCAACAAGTGAT
ATCAGAGCTCGGTTAGACTCGATCAGTGTGGCCCATGAGCACGGTAAACCTGGTATCGTGTACCA
GCCAGGGGTGTGCAATTGTGGAGTGTTGTGCTTGCACTCTACGGGTTAAGTCTTGGATGACCGGT
AATTGGCTTAAGACTTGACAGGTTGGGCCGCACGGGGGAGAGATGAGGACTCACAAGTGAATCGG
GGGAGAT
Found at i:16127 original size:33 final size:33
Alignment explanation
Indices: 16072--16173 Score: 152
Period size: 33 Copynumber: 3.1 Consensus size: 33
16062 GCTCTTACAA
* *
16072 ACAATGAAGTT-AAGGGCCTTCATCACGTCGTT
1 ACAATGAAGTTCACGGGCCTTCATCACGCCGTT
* *
16104 CCAATGAAGTTCACGGGCCTTCATCACGCCTTT
1 ACAATGAAGTTCACGGGCCTTCATCACGCCGTT
*
16137 ACAATGAAGTTCACGGGCCTTCATCACGCCTTT
1 ACAATGAAGTTCACGGGCCTTCATCACGCCGTT
16170 ACAA
1 ACAA
16174 GTTGAGCAAA
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
32 10 0.16
33 54 0.84
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.26
Consensus pattern (33 bp):
ACAATGAAGTTCACGGGCCTTCATCACGCCGTT
Found at i:17511 original size:40 final size:40
Alignment explanation
Indices: 17456--17536 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
17446 ACCAAGTTCA
*
17456 AAAGTTAAAAGCAAATAAGAGATATTCAATTCAAGCACAC
1 AAAGTTAAAAACAAATAAGAGATATTCAATTCAAGCACAC
17496 AAAGTTAAAAACAAATAAGAGATATTCAATTCAAGCACAC
1 AAAGTTAAAAACAAATAAGAGATATTCAATTCAAGCACAC
17536 A
1 A
17537 TATTTCTCCC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.54, C:0.15, G:0.11, T:0.20
Consensus pattern (40 bp):
AAAGTTAAAAACAAATAAGAGATATTCAATTCAAGCACAC
Found at i:23420 original size:33 final size:33
Alignment explanation
Indices: 23360--23451 Score: 114
Period size: 33 Copynumber: 2.8 Consensus size: 33
23350 GCTCTTACAA
** *
23360 ACAATGAAGTT-ACATGCCTTCATCACACCGTT
1 ACAATGAAGTTCACGGGCCTTCATCACACAGTT
* * *
23392 CCAATGAAGTTCACGGGCTTTCATCACACATTT
1 ACAATGAAGTTCACGGGCCTTCATCACACAGTT
*
23425 ACAATGAAGTTCATGGGCCTTCATCAC
1 ACAATGAAGTTCACGGGCCTTCATCAC
23452 GGCTTTACAA
Statistics
Matches: 50, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
32 10 0.20
33 40 0.80
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.28
Consensus pattern (33 bp):
ACAATGAAGTTCACGGGCCTTCATCACACAGTT
Found at i:27543 original size:131 final size:131
Alignment explanation
Indices: 27407--27940 Score: 583
Period size: 131 Copynumber: 4.1 Consensus size: 131
27397 ACAATAATTA
* * * * *
27407 AAAGTCGTTGTCTTAGTAATTTTGATGGTATTTTAC-CTAACAAATTTTTTAATTGTTTCCAATA
1 AAAGTCGTTGCCTAAGTGATTTTGATGGTATTTTACAC-AAC-AATTTTTTAGTTGTTGCCAATA
* * * * * *
27471 CTTACAGTTTTCGTAACAATAAAAAC-AAAGTCGTTGTGAAATCATAATCTATTCGTAACAATTT
64 CTTACAATATTCGTAACAACAAAAACTAAAGTCGTTGCGAAATCATAAACTATTCGTAACAACTT
27535 TAT
129 TAT
* * ** *
27538 TAAGTCGTTGCCTAAGTGATTTTGATGGTAATTTACACAACAATTTTTTAGTCATTGCCAATGCT
1 AAAGTCGTTGCCTAAGTGATTTTGATGGTATTTTACACAACAATTTTTTAGTTGTTGCCAATACT
* *
27603 TACAGAT-TTCGTAACAAGAGAAAC-AAAGTCGTTGCGAAATCATAAACTATTCGTAACAACTTT
66 TACA-ATATTCGTAACAACAAAAACTAAAGTCGTTGCGAAATCATAAACTATTCGTAACAACTTT
27666 AT
130 AT
** ** * * **
27668 AAAAACGTTGCCTAAGTGATTTTGATAATATTTTACACAACACTCTTTTAGTTGTTGCCAATGTT
1 AAAGTCGTTGCCTAAGTGATTTTGATGGTATTTTACACAACAATTTTTTAGTTGTTGCCAATACT
** * * *
27733 TACAATATTCGTAACAACAAATTCTGAAGTTGTTGCGAAATCATAAACTATTCATAACAACTTTA
66 TACAATATTCGTAACAACAAAAACTAAAGTCGTTGCGAAATCATAAACTATTCGTAACAACTTTA
27798 T
131 T
** * * * * * *
27799 AAAAACATTGCGTAAGTGATTTTGATGGTATTTTATACAATACTTTTTTAGTTGTTGCCAATATT
1 AAAGTCGTTGCCTAAGTGATTTTGATGGTATTTTACACAACAATTTTTTAGTTGTTGCCAATACT
** * * * * *
27864 TACAATATTCGTAACAACAAATTCTTAAAGTTGTTGTGAAATCTTAATCTACTCGTAACAACTTT
66 TACAATATTCGTAACAACAAAAAC-TAAAGTCGTTGCGAAATCATAAACTATTCGTAACAACTTT
27929 AT
130 AT
27931 -AAGTCGTTGC
1 AAAGTCGTTGC
27941 ACAATCAATT
Statistics
Matches: 347, Mismatches: 51, Indels: 10
0.85 0.12 0.02
Matches are distributed among these distances:
129 2 0.01
130 147 0.42
131 161 0.46
132 37 0.11
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (131 bp):
AAAGTCGTTGCCTAAGTGATTTTGATGGTATTTTACACAACAATTTTTTAGTTGTTGCCAATACT
TACAATATTCGTAACAACAAAAACTAAAGTCGTTGCGAAATCATAAACTATTCGTAACAACTTTA
T
Found at i:27952 original size:131 final size:130
Alignment explanation
Indices: 27425--27932 Score: 581
Period size: 130 Copynumber: 3.9 Consensus size: 130
27415 TGTCTTAGTA
* * * * *
27425 ATTTTGATGGTATTTTAC-CTAACAAATTTTTTAATTGTTTCCAATACTTACAGTTTTCGTAACA
1 ATTTTGATGGTATTTTACAC-AAC-ACTTTTTTAGTTGTTGCCAATACTTACAATATTCGTAACA
* * * * * * **
27489 ATAAAAACAAAGTCGTTGTGAAATCATAATCTATTCGTAACAATTTTATTAAGTCGTTGCCTAAG
64 ACAAATACAAAGTCGTTGCGAAATCATAAACTATTCGTAACAACTTTATAAAAACGTTGCCTAAG
27554 TG
129 TG
* * ** *
27556 ATTTTGATGGTAATTTACACAACAATTTTTTAGTCATTGCCAATGCTTACAGAT-TTCGTAACAA
1 ATTTTGATGGTATTTTACACAACACTTTTTTAGTTGTTGCCAATACTTACA-ATATTCGTAACAA
*
27620 GAGAA-ACAAAGTCGTTGCGAAATCATAAACTATTCGTAACAACTTTATAAAAACGTTGCCTAAG
65 CA-AATACAAAGTCGTTGCGAAATCATAAACTATTCGTAACAACTTTATAAAAACGTTGCCTAAG
27684 TG
129 TG
** * **
27686 ATTTTGATAATATTTTACACAACACTCTTTTAGTTGTTGCCAATGTTTACAATATTCGTAACAAC
1 ATTTTGATGGTATTTTACACAACACTTTTTTAGTTGTTGCCAATACTTACAATATTCGTAACAAC
* * * * * *
27751 AAATTCTGAAGTTGTTGCGAAATCATAAACTATTCATAACAACTTTATAAAAACATTGCGTAAGT
66 AAATAC-AAAGTCGTTGCGAAATCATAAACTATTCGTAACAACTTTATAAAAACGTTGCCTAAGT
27816 G
130 G
* * *
27817 ATTTTGATGGTATTTTATACAATACTTTTTTAGTTGTTGCCAATATTTACAATATTCGTAACAAC
1 ATTTTGATGGTATTTTACACAACACTTTTTTAGTTGTTGCCAATACTTACAATATTCGTAACAAC
* * * * * *
27882 AAATTCTTAAAGTTGTTGTGAAATCTTAATCTACTCGTAACAACTTTATAA
66 AAATAC--AAAGTCGTTGCGAAATCATAAACTATTCGTAACAACTTTATAA
27933 GTCGTTGCAC
Statistics
Matches: 329, Mismatches: 41, Indels: 13
0.86 0.11 0.03
Matches are distributed among these distances:
129 4 0.01
130 144 0.44
131 142 0.43
132 39 0.12
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (130 bp):
ATTTTGATGGTATTTTACACAACACTTTTTTAGTTGTTGCCAATACTTACAATATTCGTAACAAC
AAATACAAAGTCGTTGCGAAATCATAAACTATTCGTAACAACTTTATAAAAACGTTGCCTAAGTG
Found at i:28457 original size:21 final size:21
Alignment explanation
Indices: 28427--28489 Score: 108
Period size: 21 Copynumber: 3.0 Consensus size: 21
28417 TAGAACTACT
*
28427 ACTCTTAGAACCTGAAATAAA
1 ACTCTTAGAACCAGAAATAAA
*
28448 ACTTTTAGAACCAGAAATAAA
1 ACTCTTAGAACCAGAAATAAA
28469 ACTCTTAGAACCAGAAATAAA
1 ACTCTTAGAACCAGAAATAAA
28490 TAGGCTTACC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.51, C:0.17, G:0.10, T:0.22
Consensus pattern (21 bp):
ACTCTTAGAACCAGAAATAAA
Found at i:29688 original size:1 final size:1
Alignment explanation
Indices: 29684--29712 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
29674 CAAACGTTGC
29684 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
29713 CCAGAAACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:31473 original size:23 final size:22
Alignment explanation
Indices: 31400--31571 Score: 109
Period size: 22 Copynumber: 7.5 Consensus size: 22
31390 GGGAGATTAA
* *
31400 CAAAATCTCACAGAGAA-GTTAT
1 CAAAATTTCATAG-GAAGGTTAT
*
31422 CAAAA-ATCATAGGAAGGTTA-
1 CAAAATTTCATAGGAAGGTTAT
31442 CAAAATTTCATAGGAAGGTTTAT
1 CAAAATTTCATAGGAAGG-TTAT
* **
31465 TAAAATTTCATAGTTAGGTTAT
1 CAAAATTTCATAGGAAGGTTAT
**
31487 CAAAATTTCATATTTCATAGGTATATTAT
1 CAAAATTTCATA--GGA-AGG----TTAT
** *
31516 CAAAATTTCATAACATGGTTAT
1 CAAAATTTCATAGGAAGGTTAT
* *
31538 CAAAATTTTATAAGGTA-GTTAT
1 CAAAATTTCAT-AGGAAGGTTAT
31560 CAAAATTTCATA
1 CAAAATTTCATA
31572 AAATTATTCA
Statistics
Matches: 120, Mismatches: 18, Indels: 25
0.74 0.11 0.15
Matches are distributed among these distances:
20 8 0.07
21 21 0.17
22 52 0.43
23 16 0.13
25 3 0.03
26 2 0.02
27 2 0.02
29 16 0.13
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.35
Consensus pattern (22 bp):
CAAAATTTCATAGGAAGGTTAT
Found at i:31502 original size:29 final size:29
Alignment explanation
Indices: 31469--31527 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
31459 GTTTATTAAA
* *
31469 ATTTCATAGTTAGGTTATCAAAATTTCAT
1 ATTTCATAGGTAGATTATCAAAATTTCAT
*
31498 ATTTCATAGGTATATTATCAAAATTTCAT
1 ATTTCATAGGTAGATTATCAAAATTTCAT
31527 A
1 A
31528 ACATGGTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.44
Consensus pattern (29 bp):
ATTTCATAGGTAGATTATCAAAATTTCAT
Found at i:33825 original size:13 final size:12
Alignment explanation
Indices: 33807--33851 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 12
33797 ATATTATTAC
33807 TGTTTTATTAAAT
1 TGTTTTA-TAAAT
33820 TGTTTTATAAAT
1 TGTTTTATAAAT
*
33832 GGTTTTAAATAAAT
1 TGTTTT--ATAAAT
33846 TGTTTT
1 TGTTTT
33852 GGGTGCATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 10 0.36
13 7 0.25
14 11 0.39
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.58
Consensus pattern (12 bp):
TGTTTTATAAAT
Found at i:37937 original size:28 final size:28
Alignment explanation
Indices: 37906--37962 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
37896 CAAAACCCAA
37906 AAGAAATTAGCATTTTGCATTAGTAATT
1 AAGAAATTAGCATTTTGCATTAGTAATT
37934 AAGAAATTAGCATTTTGCATTAGTAATT
1 AAGAAATTAGCATTTTGCATTAGTAATT
37962 A
1 A
37963 GGCATTAGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.39
Consensus pattern (28 bp):
AAGAAATTAGCATTTTGCATTAGTAATT
Found at i:40313 original size:22 final size:22
Alignment explanation
Indices: 40275--40546 Score: 178
Period size: 21 Copynumber: 12.6 Consensus size: 22
40265 ATTCAGTAAT
* *
40275 AGTAATTAGT-AAAGAGTGAAG
1 AGTAATCAGTAAAAGAGTAAAG
*
40296 AGTAATCTGTAAAAGAGTAAAG
1 AGTAATCAGTAAAAGAGTAAAG
* *
40318 AGTAATCAGTAAAAGAG-CAAT
1 AGTAATCAGTAAAAGAGTAAAG
** ** **
40339 AGTAATCAGTTTAAGAACAATT
1 AGTAATCAGTAAAAGAGTAAAG
*
40361 AGTAAAT-GGT--AAGAGTAAAG
1 AGT-AATCAGTAAAAGAGTAAAG
* *
40381 AATAATAGTAGTAAGTAAAGAGTAAAG
1 AGTAAT--CAGT-A--AAAGAGTAAAG
*
40408 TGTAATCA--AGAAAGAGTAATA-
1 AGTAATCAGTA-AAAGAGTAA-AG
*
40429 A-TATTCAGT-AAAGAGTAAAG
1 AGTAATCAGTAAAAGAGTAAAG
*
40449 AGTAATCA--AGAAAGAGT-AAT
1 AGTAATCAGTA-AAAGAGTAAAG
40469 AGTAATCAGTAAAAGAGTAAAG
1 AGTAATCAGTAAAAGAGTAAAG
*
40491 AGTAATCAGTAAAAGAGT-AAT
1 AGTAATCAGTAAAAGAGTAAAG
*
40512 AGTAATCAGT-AAAGAGTAAAA
1 AGTAATCAGTAAAAGAGTAAAG
*
40533 AGTAGTCAGTAAAA
1 AGTAATCAGTAAAA
40547 TGGTAATGAC
Statistics
Matches: 198, Mismatches: 30, Indels: 45
0.73 0.11 0.16
Matches are distributed among these distances:
19 4 0.02
20 40 0.20
21 75 0.38
22 61 0.31
23 3 0.02
25 1 0.01
27 14 0.07
ACGTcount: A:0.52, C:0.04, G:0.21, T:0.22
Consensus pattern (22 bp):
AGTAATCAGTAAAAGAGTAAAG
Found at i:40428 original size:41 final size:41
Alignment explanation
Indices: 40377--40536 Score: 223
Period size: 41 Copynumber: 3.9 Consensus size: 41
40367 TGGTAAGAGT
* * * *
40377 AAAGAATAATAGTAGTAAGTAAAGAGTAAAGTGTAATCAAG
1 AAAGAGTAATAGTAATCAGTAAAGAGTAAAGAGTAATCAAG
* *
40418 AAAGAGTAATAATATTCAGTAAAGAGTAAAGAGTAATCAAG
1 AAAGAGTAATAGTAATCAGTAAAGAGTAAAGAGTAATCAAG
40459 AAAGAGTAATAGTAATCAGTAAAAGAGTAAAGAGTAATC-AG
1 AAAGAGTAATAGTAATCAGT-AAAGAGTAAAGAGTAATCAAG
*
40500 TAAAAGAGTAATAGTAATCAGTAAAGAGTAAAAAGTA
1 --AAAGAGTAATAGTAATCAGTAAAGAGTAAAGAGTA
40537 GTCAGTAAAA
Statistics
Matches: 108, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
41 56 0.52
42 32 0.30
43 20 0.19
ACGTcount: A:0.54, C:0.04, G:0.21, T:0.21
Consensus pattern (41 bp):
AAAGAGTAATAGTAATCAGTAAAGAGTAAAGAGTAATCAAG
Found at i:40447 original size:7 final size:7
Alignment explanation
Indices: 40435--40536 Score: 59
Period size: 7 Copynumber: 14.6 Consensus size: 7
40425 AATAATATTC
40435 AGTAAAG
1 AGTAAAG
40442 AGTAAAG
1 AGTAAAG
40449 AGTAATCA-
1 AGTAA--AG
40457 AG-AAAG
1 AGTAAAG
*
40463 AGT-AAT
1 AGTAAAG
**
40469 AGTAATC
1 AGTAAAG
40476 AGTAAAAG
1 AGT-AAAG
40484 AGTAAAG
1 AGTAAAG
**
40491 AGTAATC
1 AGTAAAG
40498 AGTAAAAG
1 AGT-AAAG
*
40506 AGT-AAT
1 AGTAAAG
**
40512 AGTAATC
1 AGTAAAG
40519 AGTAAAG
1 AGTAAAG
*
40526 AGTAAAA
1 AGTAAAG
40533 AGTA
1 AGTA
40537 GTCAGTAAAA
Statistics
Matches: 72, Mismatches: 15, Indels: 16
0.70 0.15 0.16
Matches are distributed among these distances:
5 1 0.01
6 12 0.17
7 46 0.64
8 12 0.17
9 1 0.01
ACGTcount: A:0.55, C:0.04, G:0.22, T:0.20
Consensus pattern (7 bp):
AGTAAAG
Found at i:40770 original size:72 final size:72
Alignment explanation
Indices: 40622--40771 Score: 207
Period size: 72 Copynumber: 2.1 Consensus size: 72
40612 AAATGGTATT
*
40622 CAGTAATTAAAGTGAAAAAATGGTAAAAATGGTATTCAGTAATTAAAGTGAAAAAAGAGTAAAAA
1 CAGTAATTAAAGTGAAAAAATGGTAAAAATGGTATTCAGTAATTAAAGTGAAAAAAGAGAAAAAA
* **
40687 TGGTATT
66 TGGAAAC
*
40694 CAGTAATTAAAGTGAAAAAA-GAGTAAAAATGGTATTTAGTAATTAAAGT-AAAAAAG-GCAAAA
1 CAGTAATTAAAGTGAAAAAATG-GTAAAAATGGTATTCAGTAATTAAAGTGAAAAAAGAG--AAA
40756 AAATGGAAAC
63 AAATGGAAAC
40766 CAGTAA
1 CAGTAA
40772 AAAAAATATA
Statistics
Matches: 70, Mismatches: 5, Indels: 6
0.86 0.06 0.07
Matches are distributed among these distances:
70 1 0.01
71 8 0.11
72 61 0.87
ACGTcount: A:0.54, C:0.04, G:0.19, T:0.23
Consensus pattern (72 bp):
CAGTAATTAAAGTGAAAAAATGGTAAAAATGGTATTCAGTAATTAAAGTGAAAAAAGAGAAAAAA
TGGAAAC
Found at i:40771 original size:36 final size:36
Alignment explanation
Indices: 40601--40749 Score: 250
Period size: 36 Copynumber: 4.2 Consensus size: 36
40591 TAAAAAGATT
*
40601 AAAAAA-ATTAAAAATGGTATTCAGTAATTAAAGTG
1 AAAAAAGAGTAAAAATGGTATTCAGTAATTAAAGTG
40636 AAAAAATG-GTAAAAATGGTATTCAGTAATTAAAGTG
1 AAAAAA-GAGTAAAAATGGTATTCAGTAATTAAAGTG
40672 AAAAAAGAGTAAAAATGGTATTCAGTAATTAAAGTG
1 AAAAAAGAGTAAAAATGGTATTCAGTAATTAAAGTG
*
40708 AAAAAAGAGTAAAAATGGTATTTAGTAATTAAAGT-
1 AAAAAAGAGTAAAAATGGTATTCAGTAATTAAAGTG
40743 AAAAAAG
1 AAAAAAG
40750 GCAAAAAAAT
Statistics
Matches: 109, Mismatches: 2, Indels: 6
0.93 0.02 0.05
Matches are distributed among these distances:
35 14 0.13
36 95 0.87
ACGTcount: A:0.54, C:0.02, G:0.17, T:0.26
Consensus pattern (36 bp):
AAAAAAGAGTAAAAATGGTATTCAGTAATTAAAGTG
Found at i:40821 original size:26 final size:26
Alignment explanation
Indices: 40788--40841 Score: 92
Period size: 27 Copynumber: 2.1 Consensus size: 26
40778 TATAGGTAAG
40788 AAAATGGTAATAAGT-AAAAAGAGTA
1 AAAATGGTAATAAGTAAAAAAGAGTA
40813 AAAATTGGTAATAAGTAAAAAAGAGTA
1 AAAA-TGGTAATAAGTAAAAAAGAGTA
40840 AA
1 AA
40842 GGTAATCAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 4 0.15
26 11 0.41
27 12 0.44
ACGTcount: A:0.61, C:0.00, G:0.19, T:0.20
Consensus pattern (26 bp):
AAAATGGTAATAAGTAAAAAAGAGTA
Found at i:41019 original size:26 final size:26
Alignment explanation
Indices: 40963--41013 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
40953 ATTTAATTAG
40963 AAAGAGTAAAAAATGGTAATAAGTAA
1 AAAGAGTAAAAAATGGTAATAAGTAA
* *
40989 AAAGAGT-ACAAATGGTAATCAGTAA
1 AAAGAGTAAAAAATGGTAATAAGTAA
41014 TCAAGAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.57, C:0.04, G:0.20, T:0.20
Consensus pattern (26 bp):
AAAGAGTAAAAAATGGTAATAAGTAA
Found at i:44472 original size:39 final size:39
Alignment explanation
Indices: 44382--44712 Score: 500
Period size: 39 Copynumber: 8.4 Consensus size: 39
44372 ATAAAACTGA
* * * * *
44382 GAAAAGATGACTTGTTTCCAGTCAATCCTTGGTAACTACT
1 GAAAAGATGACCTGTTTCCAGTCAA-CTTTGATAAATGCT
*
44422 GAAAAAATGACCTGTTTCCAGTCAACTTTGATAAATGCT
1 GAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATGCT
**
44461 GAAAAGATGACCTGTTTCCAGTCAACCCTGATAAATGCT
1 GAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATGCT
* ***
44500 AAAAAGATGACCTGTTTCCAGTCAACTTTGATAAACATT
1 GAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATGCT
* *
44539 GAAAAGATTACTTGTTTCCAGTCAACTTTGATAAATGCT
1 GAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATGCT
*
44578 GAAAAGATGACTTGTTTCCAGTCAACTTTGATAAATGCT
1 GAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATGCT
44617 GAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATGCT
1 GAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATGCT
*
44656 GAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATACTT
1 GAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATGC-T
44696 GAAAAGATGACCTGTTT
1 GAAAAGATGACCTGTTT
44713 GAGGTCGATG
Statistics
Matches: 266, Mismatches: 24, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
39 225 0.85
40 41 0.15
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (39 bp):
GAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATGCT
Found at i:53790 original size:38 final size:37
Alignment explanation
Indices: 53729--53848 Score: 133
Period size: 38 Copynumber: 3.3 Consensus size: 37
53719 ATTGAAAACT
*
53729 AAAACTTGATGGGAACTTTCCCAATTTAGAAACTTTG
1 AAAACCTGATGGGAACTTTCCCAATTTAGAAACTTTG
*
53766 AAAACCTGAATGGGAACTTCCCCAATTT-GAAAAC-TT-
1 AAAACCTG-ATGGGAACTTTCCCAATTTAG-AAACTTTG
* * *
53802 AAAAACTGGTGGGAACTTTCCCAATTTAAAAAACTTTG
1 AAAACCTGATGGGAACTTTCCCAATTT-AGAAACTTTG
53840 --AACCTGATG
1 AAAACCTGATG
53849 AAATTCTTTT
Statistics
Matches: 69, Mismatches: 8, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
35 17 0.25
36 18 0.26
37 12 0.17
38 22 0.32
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (37 bp):
AAAACCTGATGGGAACTTTCCCAATTTAGAAACTTTG
Found at i:53805 original size:73 final size:74
Alignment explanation
Indices: 53704--53841 Score: 201
Period size: 73 Copynumber: 1.9 Consensus size: 74
53694 TGAAAATGAC
* *
53704 GGGAACTTTCCCTAAATTGAAAACT-AAAACTTGATGGGAACTTTCCCAATTT-AGAAACTTTGA
1 GGGAACTTTCCCCAAATTGAAAACTAAAAAC-TGATGGGAACTTTCCCAATTTAAAAAACTTTGA
53767 AAACCTGAAT
65 AAACCTGAAT
* *
53777 GGGAAC-TTCCCCAATTTGAAAACTTAAAAACTGGTGGGAACTTTCCCAATTTAAAAAACTTTGA
1 GGGAACTTTCCCCAAATTGAAAAC-TAAAAACTGATGGGAACTTTCCCAATTTAAAAAACTTTGA
53841 A
65 A
53842 CCTGATGAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
72 15 0.26
73 27 0.47
74 16 0.28
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.28
Consensus pattern (74 bp):
GGGAACTTTCCCCAAATTGAAAACTAAAAACTGATGGGAACTTTCCCAATTTAAAAAACTTTGAA
AACCTGAAT
Found at i:53826 original size:35 final size:35
Alignment explanation
Indices: 53666--53833 Score: 153
Period size: 38 Copynumber: 4.6 Consensus size: 35
53656 TGCTTTGGAC
* * * *
53666 GGGAACTTTCCCACTTTGAAAACTAAACTGAAAATGAC
1 GGGAACTTTCCCAATTTGAAAACTTAA---AAACTGAT
*
53704 GGGAACTTTCCCTAAATTGAAAAC-T-AAAACTTGAT
1 GGGAACTTTCCC-AATTTGAAAACTTAAAAAC-TGAT
*
53739 GGGAACTTTCCCAATTT-AGAAACTTTGAAAACCTGAAT
1 GGGAACTTTCCCAATTTGA-AAAC-TT-AAAAACTG-AT
* *
53777 GGGAACTTCCCCAATTTGAAAACTTAAAAACTGGT
1 GGGAACTTTCCCAATTTGAAAACTTAAAAACTGAT
*
53812 GGGAACTTTCCCAATTTAAAAA
1 GGGAACTTTCCCAATTTGAAAA
53834 ACTTTGAACC
Statistics
Matches: 109, Mismatches: 12, Indels: 21
0.77 0.08 0.15
Matches are distributed among these distances:
33 1 0.01
34 11 0.10
35 36 0.33
36 8 0.07
37 5 0.05
38 38 0.35
39 10 0.09
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.27
Consensus pattern (35 bp):
GGGAACTTTCCCAATTTGAAAACTTAAAAACTGAT
Found at i:58057 original size:16 final size:16
Alignment explanation
Indices: 58017--58079 Score: 56
Period size: 16 Copynumber: 3.9 Consensus size: 16
58007 TTAAACGGTA
*
58017 AAAAAGAAATTAAAAG
1 AAAAAGAAATTAAATG
* **
58033 GAATGGAAATTAAATG
1 AAAAAGAAATTAAATG
*
58049 AAAAAGAAA-TAAATACA
1 AAAAAGAAATTAAAT--G
58066 AAAAAGAAATTAAA
1 AAAAAGAAATTAAA
58080 AGGAAATTAA
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
15 5 0.14
16 18 0.50
17 9 0.25
18 4 0.11
ACGTcount: A:0.70, C:0.02, G:0.13, T:0.16
Consensus pattern (16 bp):
AAAAAGAAATTAAATG
Found at i:60831 original size:51 final size:51
Alignment explanation
Indices: 60774--60875 Score: 195
Period size: 51 Copynumber: 2.0 Consensus size: 51
60764 AAAATTACCC
60774 TCAAAGTGTAATGGCCTATCATTTTTCCATGTTTAGTGTAAGATTAAACAT
1 TCAAAGTGTAATGGCCTATCATTTTTCCATGTTTAGTGTAAGATTAAACAT
*
60825 TCAAAGTGTAATGGCCTATCATTTTTCCATGTTTAGTGTAAGGTTAAACAT
1 TCAAAGTGTAATGGCCTATCATTTTTCCATGTTTAGTGTAAGATTAAACAT
60876 AATTCCTCAT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (51 bp):
TCAAAGTGTAATGGCCTATCATTTTTCCATGTTTAGTGTAAGATTAAACAT
Done.