Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020808.1 Corchorus olitorius cultivar O-4 contig20841, 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: 145329
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1040 original size:331 final size:327
Alignment explanation
Indices: 1--1658 Score: 1735
Period size: 331 Copynumber: 5.1 Consensus size: 327
** * * * * * *
1 ATATCGTTTTTGCTTTTTTTTCCGAGTTAAATTCTAATTAAATCGAAATAATATTCAGATGCTCG
1 ATATCGTTTTT-CCATTTTTTCCGAATTAATTTATAATTAAATCGAAACAAGATTCAGATACTCG
** * * * *
66 TAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGACTGGATGAACATAAATATTTCAATGA
65 TAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGA
* * * * *
131 GTCTATGCACCAAAAATCATGTAAAATTGAGCTAGGACTCCGGAACTCGTTTTTAGCAAAAACCG
130 GTAT-TGCGCCAAAAATCATG-AAAATTGA-CCAGGACTTCGGAACACGTTTTTAGCAAAAACC-
* **
196 GTGATGGTTAGTACACGATTTCGGCTAAAATTTTTGCAAAAAC-AGACCCGAAAAGTTTTCCCTC
191 GTGATGGTTAGTACATGATTTCGGCTAAAA-TTTTGCAAAAACTA-ACCCGAAAAGTTTTTTCTC
* *
260 -TTTTTCTTTCCACAATACTCATAAAAAATATATAATTCAACACCAAAGAA-ATTGAAGGGTTTT
254 AATTTT-TTTCCACAATACTCAGAAAAAATATATAATTCAACACCAAA-AAGATTGAAGGGTTTT
323 TCACGCTTCTA
317 TCACGCTTCTA
* * * * * *
334 ATATCGTTTTTCCATTTTTTTCCGAATTTATTTCTAATTAAATCAAAATAAGATTCAGATGCTTG
1 ATATCGTTTTTCCA-TTTTTTCCGAATTAATTTATAATTAAATCGAAACAAGATTCAGATACTCG
* *
399 TAAAAACAAATCCTTATATCCAATGTGGCTGAGAATTGGTTCGATGAATATAGATATTTGAAGGA
65 TAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGA
* * * * * *
464 GTCTTTGCGCAAAAAATTATGCAAAATTGAGTC-GAGACTCCAGAACACGTTTTTAGCCAAAAAC
130 GT-ATTGCGCCAAAAATCATG-AAAATTGA-CCAG-GACTTCGGAACACGTTTTTAG-CAAAAAC
* * * * *
528 CGTGAT-G-AAGTACACGATTTTGGC--------T--AAAAACTGACCCGAAAAAATTTTTTCTC
190 CGTGATGGTTAGTACATGATTTCGGCTAAAATTTTGCAAAAACTAACCCG-AAAAGTTTTTTCTC
* * * * * * *
581 AATTTTTTTCCATAATACACAGAAAAAATATATAATTCAACACCAAAAAGTTTCATGGGCTTTAC
254 AATTTTTTTCCACAATACTCAGAAAAAATATATAATTCAACACCAAAAAGATTGAAGGGTTTTTC
646 ACGCTTCTA
319 ACGCTTCTA
* * * *
655 ATATCGTTTTTCCATTTTTTTCGAATTAATTTTTAATTAAATCGAAATAAGATTCAGATCCTCGT
1 ATATCGTTTTTCCATTTTTTCCGAATTAATTTATAATTAAATCGAAACAAGATTCAGATACTCGT
* ** *
720 AAAAACAAATCCTTATGTCCAATGTGGCTGAGATTTGACTCGATGAACATAGATATTTCAAGGAG
66 AAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAG
* * *
785 TATATGCAG-AAAAAATCATGTAAAATTGAGCCAGGAC-TCTGGAACTCATTTTTAGCAAAAACC
131 TAT-TGC-GCCAAAAATCATG-AAAATTGA-CCAGGACTTC-GGAACACGTTTTTAGCAAAAACC
* ** *
848 GGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAACTAACCCGAAAAGTTTTCCCTCT
191 -GTGATGGTTAGTACATGATTTCGGCTAAAATTTTGCAAAAACTAACCCGAAAAGTTTTTTCTCA
* *
913 ATTTTTTTCCGCAATACTCAGAAAAAATATATAATTCAACGCCAAAGAA-ATTGAAGGGTTTTTC
255 ATTTTTTTCCACAATACTCAGAAAAAATATATAATTCAACACCAAA-AAGATTGAAGGGTTTTTC
977 ACGCTTCTA
319 ACGCTTCTA
* * * *
986 ATATCGTTTTTCCATTTTTTCCAAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGT
1 ATATCGTTTTTCCATTTTTTCCGAATTAATTTATAATTAAATCGAAACAAGATTCAGATACTCGT
* * *
1051 AAAAACAAATCCTTATATCCAATGTGGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGAC
66 AAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAG
* * * * * *
1116 TCTTTCTGCCAAAAATCATGCAAATCTGAACAGGGACTTCGAAACGCGTTTTTAGCAAAAACCGT
131 TATTGC-GCCAAAAATCATGAAAAT-TGACCA-GGACTTCGGAACACGTTTTTAGCAAAAACCGT
* * * * *
1181 GATAGTTAGTACATGATTTCGGC--------T--AAAAACTTACCTGAACAGTTTTTTTATCAAT
193 GATGGTTAGTACATGATTTCGGCTAAAATTTTGCAAAAACTAACCCGAAAAG-TTTTTTCTCAAT
* * * * *
1236 TTTTTGCCACAATACTCTGATAAAGTATATAATTCAACACCAAAAAGATTGACGGGTTTTTCACG
257 TTTTTTCCACAATACTCAGAAAAAATATATAATTCAACACCAAAAAGATTGAAGGGTTTTTCACG
1301 CTTCTA
322 CTTCTA
* * * * * *
1307 ATATCATTTTTGCATTTTTTTTCCGAATTAATTTATTATTAAATCAAAACAATATTCAAATACTC
1 ATATCGTTTTTCCA--TTTTTTCCGAATTAATTTATAATTAAATCGAAACAAGATTCAGATACTC
* *
1372 GTAAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGGTTCGATAAATATAGATTTTTCAAG
64 GT-AAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAG
* * * * *
1437 GAGTTTTTGCGCCAAAAATTATGCAAAATTCAACCGGGGCTTCGGAACACGTTTTTAGCCAAAAA
128 GAG-TATTGCGCCAAAAATCATG-AAAATT-GACCAGGACTTCGGAACACGTTTTTAG-CAAAAA
* * *
1502 CCGTGATGGTTAATACATGATTTCGTCTAAAATTTTGCAAAAACTAACTCGAAAAGTTTTTTCTC
189 CCGTGATGGTTAGTACATGATTTCGGCTAAAATTTTGCAAAAACTAACCCGAAAAGTTTTTTCTC
* * * *
1567 AATTTTTTTCCACAATATTCAG--AAAACATATAATTTAACGCCAAAACA-ATTGAAGGGTTTTT
254 AATTTTTTTCCACAATACTCAGAAAAAATATATAATTCAACACCAAAA-AGATTGAAGGGTTTTT
** *
1629 TTCGCTTTTA
318 CACGCTTCTA
*
1639 A-ATTCGTATTTCCATTTTTT
1 ATA-TCGTTTTTCCATTTTTT
1659 TACTCAATTG
Statistics
Matches: 1113, Mismatches: 161, Indels: 105
0.81 0.12 0.08
Matches are distributed among these distances:
319 10 0.01
320 178 0.16
321 166 0.15
322 21 0.02
323 43 0.04
324 92 0.08
325 40 0.04
330 39 0.04
331 244 0.22
332 68 0.06
333 162 0.15
334 36 0.03
335 14 0.01
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (327 bp):
ATATCGTTTTTCCATTTTTTCCGAATTAATTTATAATTAAATCGAAACAAGATTCAGATACTCGT
AAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAG
TATTGCGCCAAAAATCATGAAAATTGACCAGGACTTCGGAACACGTTTTTAGCAAAAACCGTGAT
GGTTAGTACATGATTTCGGCTAAAATTTTGCAAAAACTAACCCGAAAAGTTTTTTCTCAATTTTT
TTCCACAATACTCAGAAAAAATATATAATTCAACACCAAAAAGATTGAAGGGTTTTTCACGCTTC
TA
Found at i:1328 original size:653 final size:653
Alignment explanation
Indices: 1--1658 Score: 2254
Period size: 653 Copynumber: 2.5 Consensus size: 653
* * * *
1 ATATCGTTTTTGC-TTTTTTTTCCGAGTTAAATTCTAATTAAATCGAAATAATATTCAGATGCTC
1 ATATCGTTTTTGCATTTTTTTTCCGAATTAATTTTTAATTAAATCGAAATAATATTCAGATACTC
* * *
65 GTAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGACTGGATGAACATAAATATTTCAATG
66 GTAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGACTCGATGAACATAGATATTTCAAGG
* * * *
130 AGTCTATGCACCAAAAATCATGTAAAATTGAGCTAGGACTCCGGAACTCGTTTTTAGCAAAAACC
131 AGTATATGCAGCAAAAATCATGTAAAATTGAGCCAGGACTCTGGAACTCGTTTTTAGCAAAAACC
195 GGTGATGGTTAGTACACGATTTCGGCTAAAATTTTTGCAAAAAC-AGACCCGAAAAGTTTTCCCT
196 GGTGATGGTTAGTACACGATTTCGGCTAAAA-TTTTGCAAAAACTA-ACCCGAAAAGTTTTCCCT
* *
259 CT-TTTTCTTTCCACAATACTCATAAAAAATATATAATTCAACACCAAAGAAATTGAAGGGTTTT
259 CTATTTT-TTTCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAGAAATTGAAGGGTTTT
* *
323 TCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTTATTTCTAATTAAATCAAAATAAGAT
323 TCACGCTTCTAATATCGTTTTTCCA-TTTTTTCCAAATTTATTTCTAATTAAATCAAAACAAGAT
* * *
388 TCAGATGCTTGTAAAAACAAATCCTTATATCCAATGTGGCTGAGAATTGGTTCGATGAATATAGA
387 TCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTAAGAATTGGTTAGATGAATATAGA
* * * *
453 TATTTGAAGGAGTCTTTGCGCAAAAAATTATGCAAAATTGAGTCGAGACTCCAGAACACGTTTTT
452 TATTTCAAGGACTCTTTGCGCAAAAAATCATGCAAAATTGAGACGAGACTCCAGAACACGTTTTT
* *
518 AGCCAAAAACCGTGATGAAGTACACGATTTTGGCTAAAAACTGACCCGAAAAAATTTTTTCTCAA
517 AGCCAAAAACCGTGATGAAGTACACGATTTCGGCTAAAAACTGACCCGAAAAAATTTTTTATCAA
* * * *
583 TTTTTTTCCATAATACACAGAAAAAATATATAATTCAACACCAAAAAGTTTCATGGGCTTTACAC
582 TTTTTTGCCACAATACACAGAAAAAATATATAATTCAACACCAAAAAGATTCACGGGCTTTACAC
648 GCTTCTA
647 GCTTCTA
* * *
655 ATATCGTTTTTCCA-TTTTTTT-CGAATTAATTTTTAATTAAATCGAAATAAGATTCAGATCCTC
1 ATATCGTTTTTGCATTTTTTTTCCGAATTAATTTTTAATTAAATCGAAATAATATTCAGATACTC
*
718 GTAAAAACAAATCCTTATGTCCAATGTGGCTGAGATTTGACTCGATGAACATAGATATTTCAAGG
66 GTAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGACTCGATGAACATAGATATTTCAAGG
* *
783 AGTATATGCAGAAAAAATCATGTAAAATTGAGCCAGGACTCTGGAACTCATTTTTAGCAAAAACC
131 AGTATATGCAGCAAAAATCATGTAAAATTGAGCCAGGACTCTGGAACTCGTTTTTAGCAAAAACC
848 GGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAACTAACCCGAAAAGTTTTCCCTCT
196 GGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAACTAACCCGAAAAGTTTTCCCTCT
*
913 ATTTTTTTCCGCAATACTCAGAAAAAATATATAATTCAACGCCAAAGAAATTGAAGGGTTTTTCA
261 ATTTTTTTCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAGAAATTGAAGGGTTTTTCA
*
978 CGCTTCTAATATCGTTTTTCCATTTTTTCCAAATTTATTTCTAATTAAATCGAAACAAGATTCAG
326 CGCTTCTAATATCGTTTTTCCATTTTTTCCAAATTTATTTCTAATTAAATCAAAACAAGATTCAG
*
1043 ATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTAAGATTTGGTTAGATGAATATAGATATT
391 ATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTAAGAATTGGTTAGATGAATATAGATATT
* * * *
1108 TCAAGGACTCTTT-CTGCCAAAAATCATGC-AAATCTGA-ACAGGGACTTC-GAAACGCGTTTTT
456 TCAAGGACTCTTTGC-GCAAAAAATCATGCAAAAT-TGAGAC-GAGACTCCAG-AACACGTTTTT
* * * * * **
1169 AG-CAAAAACCGTGATAGTTAGTACATGATTTCGGCTAAAAACTTACCTGAACAGTTTTTTTATC
517 AGCCAAAAACCGTGAT-G-AAGTACACGATTTCGGCTAAAAACTGACCCGAAAAAATTTTTTATC
* * * * * * *
1233 AATTTTTTGCCACAATACTCTGATAAAGTATATAATTCAACACCAAAAAGATTGACGGGTTTTTC
580 AATTTTTTGCCACAATACACAGAAAAAATATATAATTCAACACCAAAAAGATTCACGGGCTTTAC
1298 ACGCTTCTA
645 ACGCTTCTA
* * * *
1307 ATATCATTTTTGCATTTTTTTTCCGAATTAATTTATT-ATTAAATCAAAACAATATTCAAATACT
1 ATATCGTTTTTGCATTTTTTTTCCGAATTAATTT-TTAATTAAATCGAAATAATATTCAGATACT
** * * *
1371 CGTAAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGGTTCGATAAATATAGATTTTTCAA
65 CGT-AAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGACTCGATGAACATAGATATTTCAA
* * * * * * * * *
1436 GGAGTTTTTGC-GCCAAAAATTATGCAAAATTCAACCGGGGCT-TCGGAACACGTTTTTAGCCAA
129 GGAGTATATGCAG-CAAAAATCATGTAAAATTGAGCCAGGACTCT-GGAACTCGTTTTTAG-CAA
* * * * *
1499 AAACC-GTGATGGTTAATACATGATTTCGTCTAAAATTTTGCAAAAACTAACTCGAAAAGTTTTT
191 AAACCGGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAACTAACCCGAAAAGTTTTC
* * * * *
1563 TCTCAATTTTTTTCCACAATATTCAG--AAAACATATAATTTAACGCCAAA-ACAATTGAAGGGT
256 CCTCTATTTTTTTCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAGA-AATTGAAGGGT
** * *
1625 TTTTTTCGCTTTTAA-ATTCGTATTTCCATTTTTT
320 TTTTCACGCTTCTAATA-TCGTTTTTCCATTTTTT
1659 TACTCAATTG
Statistics
Matches: 893, Mismatches: 93, Indels: 37
0.87 0.09 0.04
Matches are distributed among these distances:
650 20 0.02
651 146 0.16
652 225 0.25
653 260 0.29
654 57 0.06
655 177 0.20
656 8 0.01
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (653 bp):
ATATCGTTTTTGCATTTTTTTTCCGAATTAATTTTTAATTAAATCGAAATAATATTCAGATACTC
GTAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGACTCGATGAACATAGATATTTCAAGG
AGTATATGCAGCAAAAATCATGTAAAATTGAGCCAGGACTCTGGAACTCGTTTTTAGCAAAAACC
GGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAACTAACCCGAAAAGTTTTCCCTCT
ATTTTTTTCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAGAAATTGAAGGGTTTTTCA
CGCTTCTAATATCGTTTTTCCATTTTTTCCAAATTTATTTCTAATTAAATCAAAACAAGATTCAG
ATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTAAGAATTGGTTAGATGAATATAGATATT
TCAAGGACTCTTTGCGCAAAAAATCATGCAAAATTGAGACGAGACTCCAGAACACGTTTTTAGCC
AAAAACCGTGATGAAGTACACGATTTCGGCTAAAAACTGACCCGAAAAAATTTTTTATCAATTTT
TTGCCACAATACACAGAAAAAATATATAATTCAACACCAAAAAGATTCACGGGCTTTACACGCTT
CTA
Found at i:5250 original size:22 final size:22
Alignment explanation
Indices: 5215--5265 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
5205 TTAACAATTA
* *
5215 TTGAAGAATAAAATTCCACTAC
1 TTGAAAAATAAAATACCACTAC
* *
5237 TTGAAAAATGAAATACTACTAC
1 TTGAAAAATAAAATACCACTAC
5259 TTAGAAA
1 TT-GAAA
5266 TTAAAAAAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.49, C:0.14, G:0.10, T:0.27
Consensus pattern (22 bp):
TTGAAAAATAAAATACCACTAC
Found at i:6013 original size:17 final size:16
Alignment explanation
Indices: 5959--6009 Score: 66
Period size: 17 Copynumber: 3.1 Consensus size: 16
5949 GATCACCTCC
*
5959 AGATCACTAGTGATCTA
1 AGATCACCAGTGATC-A
5976 AGATCACCAGTGATGCA
1 AGATCACCAGTGAT-CA
*
5993 AGATCACCGGTGATCA
1 AGATCACCAGTGATCA
6009 A
1 A
6010 AGATTACATG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
16 3 0.10
17 27 0.87
18 1 0.03
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.22
Consensus pattern (16 bp):
AGATCACCAGTGATCA
Found at i:18930 original size:20 final size:19
Alignment explanation
Indices: 18905--18948 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
18895 TTTTTATAAA
18905 TAAAAAATAATAA-AAATTAT
1 TAAAAAATAA-AAGAAA-TAT
*
18925 TAAAAATTAAAAGAAATAT
1 TAAAAAATAAAAGAAATAT
18944 TAAAA
1 TAAAA
18949 TAAAAATGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.27
Consensus pattern (19 bp):
TAAAAAATAAAAGAAATAT
Found at i:18952 original size:17 final size:18
Alignment explanation
Indices: 18907--18954 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 18
18897 TTTATAAATA
18907 AAAAATAATAAAAATTATT
1 AAAAATAA-AAAAATTATT
18926 AAAAATTAAAAGAAA-TATT
1 AAAAA-TAAAA-AAATTATT
18945 -AAAATAAAAA
1 AAAAATAAAAA
18955 TGAGAAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
16 1 0.04
17 5 0.19
18 4 0.15
19 11 0.41
20 6 0.22
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (18 bp):
AAAAATAAAAAAATTATT
Found at i:42382 original size:19 final size:21
Alignment explanation
Indices: 42344--42382 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
42334 ACTGCAAATG
42344 GGAAAAGATCATATCAAAAAA
1 GGAAAAGATCATATCAAAAAA
*
42365 GGAAAA-AT-ATATCCAAAA
1 GGAAAAGATCATATCAAAAA
42383 GCTGTGCACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 2 0.12
21 6 0.35
ACGTcount: A:0.62, C:0.10, G:0.13, T:0.15
Consensus pattern (21 bp):
GGAAAAGATCATATCAAAAAA
Found at i:62796 original size:84 final size:84
Alignment explanation
Indices: 62655--62820 Score: 224
Period size: 84 Copynumber: 2.0 Consensus size: 84
62645 TCAGTGCTTA
** * *
62655 TCAACGGAATAAAGCTTTCTGGACTAACTTGTTCTGAGTTAGAGCCACTTCCATTGTCAAAGCTG
1 TCAACGGAATAAAGCTTTCCAGACCAACTTGTTCCGAGTTAGAGCCACTTCCATTGTCAAAGCTG
*
62720 TCCCCTTCAACAACATTTT
66 TCACCTTCAACAACATTTT
* * * * * *
62739 TCAACGGAATAAGGCTTTCCATACCAGCTTGTTCCGAGTTTGAGCCACTTCCATTGTCAATGTTG
1 TCAACGGAATAAAGCTTTCCAGACCAACTTGTTCCGAGTTAGAGCCACTTCCATTGTCAAAGCTG
*
62804 TCACCTTCAACAGCATT
66 TCACCTTCAACAACATT
62821 CTGGGACACC
Statistics
Matches: 70, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
84 70 1.00
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (84 bp):
TCAACGGAATAAAGCTTTCCAGACCAACTTGTTCCGAGTTAGAGCCACTTCCATTGTCAAAGCTG
TCACCTTCAACAACATTTT
Found at i:63253 original size:111 final size:111
Alignment explanation
Indices: 63069--63275 Score: 281
Period size: 111 Copynumber: 1.9 Consensus size: 111
63059 TCCAAACTTC
* * * * *
63069 CACAATGGTTTCCAGCCTTACAATCTCCAAGGTTCTTTCTGACTGCACTACGACGTTTGAAATTC
1 CACAATGGTTTCCAGCCTTACAATCTCCAAGGTTCTTTCTCACAGCACTACGAAGCTTGAAATCC
*
63134 AAAAAAGTTGTGTCTTCAGTTT-TGTGGCTGCAATTCTCCAGATTTT
66 AAAAAAGTTGTGTCTTCAATTTGT-TGGCTGCAATTCTCCAGATTTT
* * * *
63180 CACAATGGTTTCCAGTCTTACCATCTTCAAGGTTCTTTCTCACAGCACTACGAAGCTTGATATCC
1 CACAATGGTTTCCAGCCTTACAATCTCCAAGGTTCTTTCTCACAGCACTACGAAGCTTGAAATCC
** *
63245 GCAGAAGTTGTGTCTTCAATTTGTTGGCTGC
66 AAAAAAGTTGTGTCTTCAATTTGTTGGCTGC
63276 TATTATCCTT
Statistics
Matches: 82, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
111 81 0.99
112 1 0.01
ACGTcount: A:0.23, C:0.24, G:0.18, T:0.35
Consensus pattern (111 bp):
CACAATGGTTTCCAGCCTTACAATCTCCAAGGTTCTTTCTCACAGCACTACGAAGCTTGAAATCC
AAAAAAGTTGTGTCTTCAATTTGTTGGCTGCAATTCTCCAGATTTT
Found at i:84369 original size:12 final size:12
Alignment explanation
Indices: 84362--84395 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
84352 GCATCAAAAA
84362 AAGAATCATAAC
1 AAGAATCATAAC
84374 AAGAATCATAAC
1 AAGAATCATAAC
84386 AAGAATCATA
1 AAGAATCATA
84396 TATTATTTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.59, C:0.15, G:0.09, T:0.18
Consensus pattern (12 bp):
AAGAATCATAAC
Found at i:84442 original size:13 final size:13
Alignment explanation
Indices: 84424--84448 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
84414 TTCTTCTCTT
84424 AATTGCATCAATG
1 AATTGCATCAATG
84437 AATTGCATCAAT
1 AATTGCATCAAT
84449 AAACCCAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (13 bp):
AATTGCATCAATG
Found at i:87063 original size:33 final size:33
Alignment explanation
Indices: 87021--87086 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
87011 AAGTTTTTTA
87021 ATTAAAATAGTAAAATGATTCCATATCCAGAGT
1 ATTAAAATAGTAAAATGATTCCATATCCAGAGT
*
87054 ATTAAAATAGTAAAATGGTTCCATATCCAGAGT
1 ATTAAAATAGTAAAATGATTCCATATCCAGAGT
87087 TTTGTCGTGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.30
Consensus pattern (33 bp):
ATTAAAATAGTAAAATGATTCCATATCCAGAGT
Found at i:89226 original size:18 final size:18
Alignment explanation
Indices: 89203--89291 Score: 99
Period size: 18 Copynumber: 4.9 Consensus size: 18
89193 ACTGCAATTG
*
89203 TCACCATTGAGAAATGCT
1 TCACCATTGAGAAATGTT
*
89221 TCACCACTGAGAAATGTT
1 TCACCATTGAGAAATGTT
89239 TCACCATTGAGAAATGTT
1 TCACCATTGAGAAATGTT
* * * **
89257 TCA-CTTTCACCACTTGTT
1 TCACCATTGA-GAAATGTT
89275 TCACCATTGAGAAATGT
1 TCACCATTGAGAAATGT
89292 GACCAGTCAG
Statistics
Matches: 56, Mismatches: 13, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.07
18 48 0.86
19 4 0.07
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (18 bp):
TCACCATTGAGAAATGTT
Found at i:97024 original size:1 final size:1
Alignment explanation
Indices: 97020--97049 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
97010 ATTAAAAATT
97020 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
97050 CTAGCTCTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:105480 original size:56 final size:57
Alignment explanation
Indices: 105409--105524 Score: 198
Period size: 56 Copynumber: 2.1 Consensus size: 57
105399 TTATTTTGTA
105409 GAATAATTAAGTAGAGATAGGGGGATAGGATTTATTATAACATTTATTGTGTG-AAG
1 GAATAATTAAGTAGAGATAGGGGGATAGGATTTATTATAACATTTATTGTGTGAAAG
* * *
105465 GAATAATTAAGTAGAGATAGTGGGATATGATTTATTATAATATTTATTGTGTGAAAG
1 GAATAATTAAGTAGAGATAGGGGGATAGGATTTATTATAACATTTATTGTGTGAAAG
105522 GAA
1 GAA
105525 ACAGATAATT
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
56 50 0.89
57 6 0.11
ACGTcount: A:0.39, C:0.01, G:0.25, T:0.35
Consensus pattern (57 bp):
GAATAATTAAGTAGAGATAGGGGGATAGGATTTATTATAACATTTATTGTGTGAAAG
Found at i:109515 original size:3 final size:3
Alignment explanation
Indices: 109509--109540 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
109499 TGACGATGAT
*
109509 GAA GAA GAA GAA GAA GAA GCA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
109541 TAGTGAAGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.62, C:0.03, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:113584 original size:21 final size:19
Alignment explanation
Indices: 113541--113596 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 19
113531 TGTTTAGCAA
*
113541 TGTATAGATGAGATTACAC
1 TGTACAGATGAGATTACAC
* *
113560 TGTACATATTAGATTAGCTAC
1 TGTACAGATGAGATTA-C-AC
113581 TGTACAGATGAGATTA
1 TGTACAGATGAGATTA
113597 TTAGAGCAGC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
19 13 0.43
20 1 0.03
21 16 0.53
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.34
Consensus pattern (19 bp):
TGTACAGATGAGATTACAC
Found at i:117901 original size:2 final size:2
Alignment explanation
Indices: 117894--117930 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
117884 AATGCAATGG
117894 AT AT AT AT AT 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 AT AT AT AT AT A
117931 ATACATAAGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:118260 original size:3 final size:3
Alignment explanation
Indices: 118252--118287 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
118242 ATTTATTAAT
118252 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
118288 GATAATTAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:121653 original size:42 final size:42
Alignment explanation
Indices: 121594--121674 Score: 153
Period size: 42 Copynumber: 1.9 Consensus size: 42
121584 TCAGGATCAG
121594 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
*
121636 GATTTGAGTTGAGTATTTCTTAATTTACAGAGAATTTTC
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTC
121675 AAGACTTAGC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.30, C:0.07, G:0.16, T:0.47
Consensus pattern (42 bp):
GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
Found at i:127394 original size:18 final size:20
Alignment explanation
Indices: 127354--127399 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 20
127344 TAAATAAATT
127354 AAGAGAAAAAAAAAGAAGAA
1 AAGAGAAAAAAAAAGAAGAA
127374 AAGAGAATAAAAAAAAGAAAGAA
1 AAGAG-A-AAAAAAAAG-AAGAA
127397 AAG
1 AAG
127400 CAAAAAACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 5 0.22
21 1 0.04
22 9 0.39
23 8 0.35
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (20 bp):
AAGAGAAAAAAAAAGAAGAA
Found at i:136177 original size:7 final size:7
Alignment explanation
Indices: 136165--136196 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
136155 TTCTACTGAA
136165 TTCCCAT
1 TTCCCAT
136172 TTCCCAT
1 TTCCCAT
136179 TTCCCAT
1 TTCCCAT
*
136186 TACCCAT
1 TTCCCAT
136193 TTCC
1 TTCC
136197 ACTTTTGTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.16, C:0.44, G:0.00, T:0.41
Consensus pattern (7 bp):
TTCCCAT
Found at i:144470 original size:322 final size:322
Alignment explanation
Indices: 142966--145294 Score: 3097
Period size: 321 Copynumber: 7.3 Consensus size: 322
142956 AAAGATTTGT
* * * * * * * *
142966 TTTTTGGAGTTGAATTATATATTTTTTCTAAATATT-TTGCAAAAATTTCAGAAAAAA-CT-TTC
1 TTTTTGGCGTTGAATTATATA-CTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAATTTCTTC
* * *
143028 GGGTCAGTTTTTAGACGAAATCGTGTACTAACCATCACGG-TTTTTGACTAAAAACGGGTTTCGG
65 GGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTTG-CTAAAAACGCGTTTTGG
* * * * * * *
143092 GGCCCTGGCTCAGTTTTACAAGATTTTTGACAAAAAGACTCCTT-AAATTATCTATATTCATCTA
129 GGCCCCGACTAAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAA-TATCTATATTCATCTA
* * * * ** *
143156 ACTAAATCTCAGCCACAATGGATTTAATGATTTGTTTTTACGAATATCTGAATCTTGTTTCGATT
193 ACCAAATCTCAGCCACAATGGATTTAAGGATTGGTATTTACGAGCATCTGAATCTTGTTTTGATT
* * * * * * * *** * *
143221 AAATTAGAAATTAATTCGGAAAAAGAAT-GAAAAATGATTTTGGAAGCGTGAAAAGCCGGTT-AA
258 TAATTAGAAATAAATTC-TAAAAAAAATGGAAAAACGATATTAGAATATTGAAAAACC-CTTCAA
143284 TCA
321 T-A
* ** * * * *
143287 -TTATGGAATTGAATTATATATTTTTTCTGAATATT-TTGCAAAAAATTGAGAAAAAACTT-TTC
1 TTTTTGGCGTTGAATTATATA-CTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAATTTCTTC
* * * * ** * *
143349 GGGTCAGTTTTTAACCGAAGTCGTTTAATAACCATCACTATTTTTGGCTAAAAACGCGTTTCGGG
65 GGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTTGCTAAAAACGCGTTTTGGG
* ** * **
143414 ACCTTGTCTAAGTTTTGCATGATTTCTT-GCAGAAAGACTCCTTGAAAGGTCTATATTCATCTAA
130 GCCCCGACTAAGTTTTGCATGATTT-TTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAA
** *
143478 CCAAATCTCAATCACAATGGATTTATGGATTGGTATTTACGAGCATCTGAATCTTGTTTTGATTT
194 CCAAATCTCAGCCACAATGGATTTAAGGATTGGTATTTACGAGCATCTGAATCTTGTTTTGATTT
* ** *
143543 AATTAGAAATAAATTCTTAAAAAAAATGGAAAAATGATATTAGAAGCTTGAAAAACACTTCAATA
259 AATTAGAAATAAATTC-TAAAAAAAATGGAAAAACGATATTAGAATATTGAAAAACCCTTCAATA
*
143608 TTTTTGGCGTTGAATTATATAC-TTTCTGAGTATTTTGGCCAAAAAATTGAGAAAAAATTTCTTC
1 TTTTTGGCGTTGAATTATATACTTTTCTGAGTATTGTGG-CAAAAAATTGAGAAAAAATTTCTTC
* * * *
143672 GGGTCAGTTTTTAGCCGAAATCGTGTACGTTA-CATCACGGTATTTTGCTAAAAACGTGATTTGG
65 GGGTCAGTTTTTAGCCGAAATCGTGTAC-TAACCATCACGGTTTTTTGCTAAAAACGCGTTTTGG
** * *
143736 GGCCCTAACTAAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATAATGATCTAA
129 GGCCCCGACTAAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAA
*
143801 CCAAATCTCAGCCACAATGGATCTAAGGATTGGTATTTACGAGCATCTGAATCTTGTTTTGATTT
194 CCAAATCTCAGCCACAATGGATTTAAGGATTGGTATTTACGAGCATCTGAATCTTGTTTTGATTT
* * ** *
143866 AATTAGAAACAAATTCT--------T--AAAAA-AATATTAGAAGCTTGAAAAACCATTCAATA
259 AATTAGAAATAAATTCTAAAAAAAATGGAAAAACGATATTAGAATATTGAAAAACCCTTCAATA
*
143919 TTTTTGGCGTTGAATTATATACTTTTCCGAGTATTGTGGCAAAAAATTGAGAAAAAATTTCTTCG
1 TTTTTGGCGTTGAATTATATACTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAATTTCTTCG
* *
143984 GATCAGTTTTTAGCCGAAATCTTGTACT-ACCATCACGGTTTTTTGCTAAAAACGCGTTTTGGGG
66 GGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTTGCTAAAAACGCGTTTTGGGG
*
144048 CCCCGAC-ACAGTTTTGCATGATTTTTGGTAGAAAGACTCCTTGAAATATCTATATTCATCTAAC
131 CCCCGACTA-AGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAAC
* * *
144112 CAAATATCAGCCACAATGGATTTAAGGATCGGTATTTACGAGCATCTAAATCTTGTTTTGATTTA
195 CAAATCTCAGCCACAATGGATTTAAGGATTGGTATTTACGAGCATCTGAATCTTGTTTTGATTTA
144177 ATTAGAAATAAATTCTAAAAAAAATTGG-AAAACGATATTAGAATATTGAAAAACCCTTCAATA
260 ATTAGAAATAAATTCTAAAAAAAA-TGGAAAAACGATATTAGAATATTGAAAAACCCTTCAATA
*
144240 TTTTTGGCGTTGAATTATATACTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAATTTATTCG
1 TTTTTGGCGTTGAATTATATACTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAATTTCTTCG
* * *
144305 GGTAAGTTTTTAGCCGAAATCGTGTACTAACCTTCACGGTTTTTTGCTAAAAACGCGTTTTAGGG
66 GGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTTGCTAAAAACGCGTTTTGGGG
* *
144370 CCCCGACTAAGTTTTGCATTATTTTTGGCAGAAAGACTCCTTGAAATATTTATATTCATCTAACC
131 CCCCGACTAAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACC
* * * *
144435 AAATCTCAACCACAATGGATATGAGGATTGGTATTTACGAGAATCTGAATCTTGTTTTGATTTAA
196 AAATCTCAGCCACAATGGATTTAAGGATTGGTATTTACGAGCATCTGAATCTTGTTTTGATTTAA
144500 TTAGAAATAAATTCT-AAAAAAATGGAAAAACGATATTAGAATATTGAAAAACCCTTCAATA
261 TTAGAAATAAATTCTAAAAAAAATGGAAAAACGATATTAGAATATTGAAAAACCCTTCAATA
* * * * *
144561 TTTTTGGCGTTGAATTATATATTTTTCTGATTATTTTGGCAAAAAATTGAG-AAAAGTTCTGTTC
1 TTTTTGGCGTTGAATTATATACTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAATT-TCTTC
* * *
144625 GGGTCAGTTTTTAGCCGAAATCGTGTATTAACCATAACGGTTTTTTGCTAAAAACGCGTTTTAGG
65 GGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTTGCTAAAAACGCGTTTTGGG
*
144690 GCCCCGACTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAAC
130 GCCCCGACTAAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAAC
* * * *
144755 CAAATATCAGCCACAATTGATTTAAGGATCGGTATTTACGAGCATCTGAATCTTGTTTTGATTAA
195 CAAATCTCAGCCACAATGGATTTAAGGATTGGTATTTACGAGCATCTGAATCTTGTTTTGATTTA
*
144820 ATTAGAAATAAATTCTAAAAAAAATGGAAAAACTATATTAGAATATTGAAAAACCCTTCAATA
260 ATTAGAAATAAATTCTAAAAAAAATGGAAAAACGATATTAGAATATTGAAAAACCCTTCAATA
*
144883 TTTTTGGCATTGAATTATATACTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAATTTCTTCG
1 TTTTTGGCGTTGAATTATATACTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAATTTCTTCG
* ** *
144948 GATCAGTTTTTAGCCGAAATCGTG---T-ACCATCATAGTTTTTTACTAAAAACGCGTTTTGGGG
66 GGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTTGCTAAAAACGCGTTTTGGGG
* * * *
145009 CCTCGACTCAGTTTTGCATGATTTTTGGCCGAAAGACTCCTTGAAATGTCTATATTCATCTAACC
131 CCCCGACTAAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACC
* * *
145074 AAATATCAGCGACAATGGATTTAAGGATTGGTATTTACGAGCTTCTGAATCTTGTTTTGATTTAA
196 AAATCTCAGCCACAATGGATTTAAGGATTGGTATTTACGAGCATCTGAATCTTGTTTTGATTTAA
* * * *
145139 TTAGAAACAAATTCTAAAAAAACATGGAAAAATGATATTAGAATTTTAAAAAACCCTTCAATA
261 TTAGAAATAAATTCTAAAAAAA-ATGGAAAAACGATATTAGAATATTGAAAAACCCTTCAATA
* *
145202 TTTTTGGCGTTGAATTATATACTTTTCTGAGAATTATGGCAAAAAATTGAGAAAAAA-TTCATTC
1 TTTTTGGCGTTGAATTATATACTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAATTTC-TTC
* *
145266 GGCTCATTTTTTAGCCGAAATCGTGTACT
65 GGGTCAGTTTTTAGCCGAAATCGTGTACT
145295 TCACGGTTTT
Statistics
Matches: 1800, Mismatches: 170, Indels: 75
0.88 0.08 0.04
Matches are distributed among these distances:
309 2 0.00
310 165 0.09
311 100 0.06
312 19 0.01
314 1 0.00
318 177 0.10
319 118 0.07
320 75 0.04
321 587 0.33
322 365 0.20
323 189 0.10
324 2 0.00
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (322 bp):
TTTTTGGCGTTGAATTATATACTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAATTTCTTCG
GGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTTGCTAAAAACGCGTTTTGGGG
CCCCGACTAAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACC
AAATCTCAGCCACAATGGATTTAAGGATTGGTATTTACGAGCATCTGAATCTTGTTTTGATTTAA
TTAGAAATAAATTCTAAAAAAAATGGAAAAACGATATTAGAATATTGAAAAACCCTTCAATA
Found at i:144898 original size:643 final size:643
Alignment explanation
Indices: 142966--145292 Score: 3104
Period size: 643 Copynumber: 3.6 Consensus size: 643
142956 AAAGATTTGT
* * * * * * *
142966 TTTTTGG-AGTTGAATTATATATTTTTTCTAAATATT-TTGCAAAAATTTCAGAAAAAA-CT-TT
1 TTTTTGGCA-TTGAATTATATA-CTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAATTTCTT
* * *
143027 CGGGTCAGTTTTTAGACGAAATCGTGTACTAACCATCACGG-TTTTTGACTAAAAACGGGTTTCG
64 CGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTTG-CTAAAAACGCGTTTTG
* * * * * * *
143091 GGGCCCTGGCTCAGTTTTACAAGATTTTTGACAAAAAGACTCCTT-AAATTATCTATATTCATCT
128 GGGCCCCGACTAAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAA-TATCTATATTCATCT
* * * * *
143155 AACTAAATCTCAGCCACAATGGATTTAATGATTTGTTTTTACGA-ATATCTGAATCTTGTTTCGA
192 AACCAAATCTCAGCCACAATGGATTTAAGGATTGGTATTTACGAGA-ATCTGAATCTTGTTTTGA
* ** * * * * * *
143219 TTAAATTAGAAATTAATTCGGAAAAAGAATGAAAAATGATTTTGGAAGCGTGAAAAGCCGGTT-A
256 TTTAATTAGAAACAAATTC-TAAAAA-AATGAAAAATGATATTAGAAGCTTGAAAAACC-CTTCA
* ** * *
143283 ATCA-TTATGGAATTGAATTATATATTTTTTCTGAATATTTT-GCAAAAAATTGAGAAAAAA--C
318 AT-ATTTTTGGCGTTGAATTATATA-CTTTTCTGAGTATTTTGGCAAAAAATTGAGAAAAAATTC
* * * * ** *
143344 TTTTCGGGTCAGTTTTTAACCGAAGTCGTTTAATAACCATCACTATTTTTGGCTAAAAACGCG-T
381 TATTCGGGTCAGTTTTTAGCCGAAATCGTGTAATAACCATCACGGTTTTTTGCTAAAAACGCGTT
* ** * * **
143408 TTCGGGACCTTGTCTAAGTTTTGCATGATTTCTT-GCAGAAAGACTCCTTGAAAGGTCTATATTC
446 TTAGGG-CCCCGACTCAGTTTTGCATGATTT-TTGGCAGAAAGACTCCTTGAAATATCTATATTC
* ** * *
143472 ATCTAACCAAATCTCAATCACAATGGATTTATGGATTGGTATTTACGAGCATCTGAATCTTGTTT
509 ATCTAACCAAATATCAGCCACAATGGATTTAAGGATCGGTATTTACGAGCATCTGAATCTTGTTT
** *
143537 TGATTTAATTAGAAATAAATTCTTAAAAAAAATGGAAAAA-TGATATTAGAAGCTTGAAAAACAC
574 TGATTTAATTAGAAATAAATTC-TAAAAAAAATGGAAAAACT-ATATTAGAATATTGAAAAACCC
143601 TTCAATA
637 TTCAATA
* *
143608 TTTTTGGCGTTGAATTATATAC-TTTCTGAGTATTTTGGCCAAAAAATTGAGAAAAAATTTCTTC
1 TTTTTGGCATTGAATTATATACTTTTCTGAGTATTGTGG-CAAAAAATTGAGAAAAAATTTCTTC
* * * *
143672 GGGTCAGTTTTTAGCCGAAATCGTGTACGTTA-CATCACGGTATTTTGCTAAAAACGTGATTTGG
65 GGGTCAGTTTTTAGCCGAAATCGTGTAC-TAACCATCACGGTTTTTTGCTAAAAACGCGTTTTGG
** * *
143736 GGCCCTAACTAAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATAATGATCTAA
129 GGCCCCGACTAAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAA
* *
143801 CCAAATCTCAGCCACAATGGATCTAAGGATTGGTATTTACGAGCATCTGAATCTTGTTTTGATTT
194 CCAAATCTCAGCCACAATGGATTTAAGGATTGGTATTTACGAGAATCTGAATCTTGTTTTGATTT
* *
143866 AATTAGAAACAAATTCT-------T-AAAAA-AATATTAGAAGCTTGAAAAACCATTCAATATTT
259 AATTAGAAACAAATTCTAAAAAAATGAAAAATGATATTAGAAGCTTGAAAAACCCTTCAATATTT
* * * *
143922 TTGGCGTTGAATTATATACTTTTCCGAGTATTGTGGCAAAAAATTGAGAAAAAATT-TCTTCGGA
324 TTGGCGTTGAATTATATACTTTTCTGAGTATTTTGGCAAAAAATTGAGAAAAAATTCTATTCGGG
* * *
143986 TCAGTTTTTAGCCGAAATCTTGTACT-ACCATCACGGTTTTTTGCTAAAAACGCGTTTTGGGGCC
389 TCAGTTTTTAGCCGAAATCGTGTAATAACCATCACGGTTTTTTGCTAAAAACGCGTTTTAGGGCC
* *
144050 CCGACACAGTTTTGCATGATTTTTGGTAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAA
454 CCGACTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAA
*
144115 ATATCAGCCACAATGGATTTAAGGATCGGTATTTACGAGCATCTAAATCTTGTTTTGATTTAATT
519 ATATCAGCCACAATGGATTTAAGGATCGGTATTTACGAGCATCTGAATCTTGTTTTGATTTAATT
*
144180 AGAAATAAATTCTAAAAAAAATTGG-AAAACGATATTAGAATATTGAAAAACCCTTCAATA
584 AGAAATAAATTCTAAAAAAAA-TGGAAAAACTATATTAGAATATTGAAAAACCCTTCAATA
* *
144240 TTTTTGGCGTTGAATTATATACTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAATTTATTCG
1 TTTTTGGCATTGAATTATATACTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAATTTCTTCG
* * *
144305 GGTAAGTTTTTAGCCGAAATCGTGTACTAACCTTCACGGTTTTTTGCTAAAAACGCGTTTTAGGG
66 GGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTTGCTAAAAACGCGTTTTGGGG
* *
144370 CCCCGACTAAGTTTTGCATTATTTTTGGCAGAAAGACTCCTTGAAATATTTATATTCATCTAACC
131 CCCCGACTAAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACC
* * *
144435 AAATCTCAACCACAATGGATATGAGGATTGGTATTTACGAGAATCTGAATCTTGTTTTGATTTAA
196 AAATCTCAGCCACAATGGATTTAAGGATTGGTATTTACGAGAATCTGAATCTTGTTTTGATTTAA
* * **
144500 TTAGAAATAAATTCTAAAAAAATGGAAAAACGATATTAGAATATTGAAAAACCCTTCAATATTTT
261 TTAGAAACAAATTCTAAAAAAAT-GAAAAATGATATTAGAAGCTTGAAAAACCCTTCAATATTTT
* * * *
144565 TGGCGTTGAATTATATATTTTTCTGATTATTTTGGCAAAAAATTGAG-AAAAGTTCTGTTCGGGT
325 TGGCGTTGAATTATATACTTTTCTGAGTATTTTGGCAAAAAATTGAGAAAAAATTCTATTCGGGT
* *
144629 CAGTTTTTAGCCGAAATCGTGTATTAACCATAACGGTTTTTTGCTAAAAACGCGTTTTAGGGCCC
390 CAGTTTTTAGCCGAAATCGTGTAATAACCATCACGGTTTTTTGCTAAAAACGCGTTTTAGGGCCC
144694 CGACTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAA
455 CGACTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAA
* *
144759 TATCAGCCACAATTGATTTAAGGATCGGTATTTACGAGCATCTGAATCTTGTTTTGATTAAATTA
520 TATCAGCCACAATGGATTTAAGGATCGGTATTTACGAGCATCTGAATCTTGTTTTGATTTAATTA
144824 GAAATAAATTCTAAAAAAAATGGAAAAACTATATTAGAATATTGAAAAACCCTTCAATA
585 GAAATAAATTCTAAAAAAAATGGAAAAACTATATTAGAATATTGAAAAACCCTTCAATA
144883 TTTTTGGCATTGAATTATATACTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAATTTCTTCG
1 TTTTTGGCATTGAATTATATACTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAATTTCTTCG
* ** *
144948 GATCAGTTTTTAGCCGAAATCGTG---T-ACCATCATAGTTTTTTACTAAAAACGCGTTTTGGGG
66 GGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTTGCTAAAAACGCGTTTTGGGG
* * * *
145009 CCTCGACTCAGTTTTGCATGATTTTTGGCCGAAAGACTCCTTGAAATGTCTATATTCATCTAACC
131 CCCCGACTAAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACC
* * **
145074 AAATATCAGCGACAATGGATTTAAGGATTGGTATTTACGAGCTTCTGAATCTTGTTTTGATTTAA
196 AAATCTCAGCCACAATGGATTTAAGGATTGGTATTTACGAGAATCTGAATCTTGTTTTGATTTAA
** *
145139 TTAGAAACAAATTCTAAAAAAACATGGAAAAATGATATTAGAATTTTAAAAAACCCTTCAATATT
261 TTAGAAACAAATTCT-AAAAAA-AT-GAAAAATGATATTAGAAGCTTGAAAAACCCTTCAATATT
* *
145204 TTTGGCGTTGAATTATATACTTTTCTGAGAATTATGGCAAAAAATTGAGAAAAAATTC-ATTCGG
323 TTTGGCGTTGAATTATATACTTTTCTGAGTATTTTGGCAAAAAATTGAGAAAAAATTCTATTCGG
* *
145268 CTCATTTTTTAGCCGAAATCGTGTA
388 GTCAGTTTTTAGCCGAAATCGTGTA
145293 CTTCACGGTT
Statistics
Matches: 1498, Mismatches: 151, Indels: 73
0.87 0.09 0.04
Matches are distributed among these distances:
631 2 0.00
632 292 0.19
633 226 0.15
634 38 0.03
635 1 0.00
639 163 0.11
640 17 0.01
641 125 0.08
642 148 0.10
643 302 0.20
644 174 0.12
645 10 0.01
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (643 bp):
TTTTTGGCATTGAATTATATACTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAATTTCTTCG
GGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTTGCTAAAAACGCGTTTTGGGG
CCCCGACTAAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACC
AAATCTCAGCCACAATGGATTTAAGGATTGGTATTTACGAGAATCTGAATCTTGTTTTGATTTAA
TTAGAAACAAATTCTAAAAAAATGAAAAATGATATTAGAAGCTTGAAAAACCCTTCAATATTTTT
GGCGTTGAATTATATACTTTTCTGAGTATTTTGGCAAAAAATTGAGAAAAAATTCTATTCGGGTC
AGTTTTTAGCCGAAATCGTGTAATAACCATCACGGTTTTTTGCTAAAAACGCGTTTTAGGGCCCC
GACTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAAT
ATCAGCCACAATGGATTTAAGGATCGGTATTTACGAGCATCTGAATCTTGTTTTGATTTAATTAG
AAATAAATTCTAAAAAAAATGGAAAAACTATATTAGAATATTGAAAAACCCTTCAATA
Found at i:145307 original size:1 final size:1
Alignment explanation
Indices: 145301--145329 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
145291 TACTTCACGG
145301 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
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
Done.