Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015161.1 Corchorus capsularis cultivar CVL-1 contig15182, 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: 111251
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:3088 original size:968 final size:960
Alignment explanation
Indices: 1--5398 Score: 6572
Period size: 968 Copynumber: 5.6 Consensus size: 960
* * *
1 ATCCAATGTGGCTGACATTTGGTTCGATGAATATTGATATTTCAAGGAGCCTTTATGCCAAAAAT
1 ATCCAATGTGGCTGACATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGTGCCAAAAAT
* * **
66 TATGCAAAACTGAGTCGGGGCTCCGGAACATGTTTTTAGCCAAAAAC----T-G-T-GTACACGA
66 CATGCAAAATTGAGTCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACTTGATGGTTAGTACACGA
* *
124 TTTCGGCTAAAAACTGACCCTAAAAGTTTTTTCTCAATTTTTTGAAACAATACTCA-TAAAAAAT
131 TTTCGGCTAAAAACTGACCCTAAAAGTTTTTTCTCAACTTTTTGAAACAATACTCAGAAAAAAAT
* * * *
188 ATATAATTCAATGCCAAAAAGATTGACGGGTTTTTCAAGCTTCCAAAATTTTTTTTTCATTTTTT
196 ATATAATTCAATGCCAAAAAGATTGACGGGCTTTTCAAGCTTCTAATATTGTTTTTTCA--TTTT
253 TTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTAAGATACTCGGAAAAAAAAATCCTTATA
259 TTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTAAGATACTC-GAAAAAAAAATCCTTATA
* * * *
318 TCCAATATGGCTGAGATTTGCTTCAATGAATATAGATATTTCAAGGAGTCTTCCTGCCAAAATTC
323 TCCAATATGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATC
* * * * * * * * *
383 ATACGAAATTCAGCCGGTGACTCCGGAACGCGTTTTTAGCCAAAAACTGTGA---TAACGTACAC
388 ATGCAAAACTGAGTCGG-GACTCCGAAACACGTTTTTACCCAAAAACTGTGATGGTTA-GTACAC
* * * * ** * *
445 GATTTTGGCGAAAAACTGACCCGAACAGTTTTTTCTCACCTTTCTGCGACAATACTCAGAAAAAA
451 GATTTCGGCCAAAAACTGACCCGAAAAGTTATTTCTCAATTTTTTGCAACAATACTCAGAAAAAA
* * *
510 TATATAATTCAATGCCAAAAAGATTGACGGGATTTTCAAGATTCTAATATTGTTTTTTCATTTTT
516 TATATAATTCAATGCCAAAAAGATTGACGGGCTTTTCAAGCTTCTAATATCGTTTTTTCATTTTT
* * * * *
575 TTTCGGAATTAATTTATAATTAAATTGAAACAAGATTAAGATACTCGAAAAAATACAAATCCTTA
581 TTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTAAGATGCTCG-TAAAA-ACAAATCCTTA
* * * * * * *
640 TATCCAATATGACTGAGATTTGGTTCGATGAATATAAATATTTCAAGGAATCTTTCTGCCAAGAA
644 TATCCAATGTGGCTGACATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGTGCCAAAAA
* * * * * * *
705 TCATGAAAAACTGAGTCGGGGTTCCCGAAACACGTTTTTACCCCTAAAGCCGTGATGGTTAGTAC
709 TCATGCAAAATTGAGTCGGGGCT-CCGGAACGCGTTTTTA-GCC-AAA-AC---AT-G-TAGTAC
* * * ** *
770 ACGATTTCGGCCAAAAACTGACCCGAAAAGTTATTTCTCAATTTTTTGCCAGAATACTCAG-AAA
765 ACGATTTCGGCTAAAAACTGACCCTAAAAGTTTTTTCTCAATTTTTTGAAACAATACTCAGAAAA
* * * * * *
834 AATATATAATTTAACG-CAAAATAGATTGTCGTGCTTTTCAAGGTTCTAATATCG-TTTTTTCAT
830 AATATATAATTCAATGCCAAAA-AGATTGACGGGTTTTTCAAGCTTCTAATATCGTTTTTTTCA-
*
897 TTTTTTTCCGAATTAATTTCTAATTAAATCGAAACTAA-ATTCAGATGCTCGTAAAAACAAATCC
893 TTTTTTTCCGAATTAATTTCTAATTAAATCGAAAC-AAGATTAAGATGCTCGTAAAAACAAATCC
961 TTAT
957 TTAT
*
965 ATCCAATGTGGCTGACATTTGGTTCGATGAATATAGATATTTCAAGGAGCCTTTGTGCCAAAAAT
1 ATCCAATGTGGCTGACATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGTGCCAAAAAT
* *
1030 TATGCAAAACTGAGTCGGGGCTCCGGAACGCGTTTTTAGCCAAAATACTATGATGGTTAGTACAC
66 CATGCAAAATTGAGTCGGGGCTCCGGAACGCGTTTTTAGCCAAAA-ACT-TGATGGTTAGTACAC
* * * * * * ** *
1095 GATTTTGGCAAAAAACTGAACCGAAATG-TTTTTCTCAACTTTCTGCGACAATACT--TAAAAAA
129 GATTTCGGCTAAAAACTGACCCTAAAAGTTTTTTCTCAACTTTTTGAAACAATACTCAGAAAAAA
*
1157 ATATATAATTCAATGCCAAAAAGATTGAAGGGCTTTTCAAGCTTCTAATATTGTTTTTTCATTTT
194 ATATATAATTCAATGCCAAAAAGATTGACGGGCTTTTCAAGCTTCTAATATTGTTTTTTCATTTT
* *
1222 TTTCCGAATTAATTTCTAACTAAATTGAAACAAGATTAAGATACTCGAAAAAAAAATCCTTATAT
259 TTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTAAGATACTCGAAAAAAAAATCCTTATAT
* *
1287 CCAATATGGCTGAGATTTGGTTCGATGAATACAGATATTTCAAAGAGTCTTTCTGCCAAAAATCA
324 CCAATATGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCA
* * *
1352 TGCAAAACTGAGTCGGAACTCCGGAAACACGTTTTTACCCCAAAACTCGTGAT-ATATA-TACAC
389 TGCAAAACTGAGTCGGGACTCC-GAAACACGTTTTTACCCAAAAACT-GTGATGGT-TAGTACAC
* * *
1415 GATTTTGGCCAAAAACTGACCCGAAAAGTTATTTCTCAATTTTTTGCCAGAATACTCA-AAAAAA
451 GATTTCGGCCAAAAACTGACCCGAAAAGTTATTTCTCAATTTTTTGCAACAATACTCAGAAAAAA
* * * * *
1479 TATATAATTTAACG-CAAAATAGATTGTCGTGCTTTTCAAGGTTCTAATATCGTTTTTTCATTTT
516 TATATAATTCAATGCCAAAA-AGATTGACGGGCTTTTCAAGCTTCTAATATCGTTTTTTCATTTT
* *
1543 TTTTCCGAATTAATTTCTGATTAAATCGAAACTAA-ATTCAGATGCTCGTAAAAATCAAATCCTT
580 TTTTCCGAATTAATTTCTAATTAAATCGAAAC-AAGATTAAGATGCTCGTAAAAA-CAAATCCTT
*
1607 ATATCCAATGTGGCTGACATTTGGTTCGATGAATATAGATATTTCAAGGAGCCTTTGTGCCAAAA
643 ATATCCAATGTGGCTGACATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGTGCCAAAA
* * *
1672 ATTATGCAAAACTGAGTCGGGGCTCCGGAACGCGTTTTTAGCCAAAA-ACTGT-GTACACCATTT
708 ATCATGCAAAATTGAGTCGGGGCTCCGGAACGCGTTTTTAGCCAAAACA-TGTAGTACACGATTT
* *
1735 CGGCTAAAAACTGACCCTAAAAGTTTTTCCTCAATTTTTTGAAACAATACTCATAAAAAATATAT
772 CGGCTAAAAACTGACCCTAAAAGTTTTTTCTCAATTTTTTGAAACAATACTCAGAAAAAATATAT
* *
1800 AATTCAATGCCAAAAAGTTTGACGGGTTTTTCAAGCTTCTAATATCGTTTTATATCATTTTTTTT
837 AATTCAATGCCAAAAAGATTGACGGGTTTTTCAAGCTTCTAATATCGTTTT-TTTCA-TTTTTTT
* * * * **
1865 CCGAATTAATTTCTGATTAAATCGAAACAAGATTAAGATACTCGGAGTAAAAGAAATTTTTAT
900 CCGAATTAATTTCTAATTAAATCGAAACAAGATTAAGATGCTCGTA--AAAACAAATCCTTAT
* * * * * * **
1928 ATCCAATATGGCTCAGATTTGGTTCGATGAATATTGATATTTGAAGGAGTGTTCCTGCCAAAAAT
1 ATCCAATGTGGCTGACATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGTGCCAAAAAT
* * * * * *
1993 CATACAAAATTGAGCCGGTGACTCTGGAACGCGTTTTTAGCCAAAAACTGTGATAGTTAGTAAAC
66 CATGCAAAATTGAGTCGG-GGCTCCGGAACGCGTTTTTAGCCAAAAACT-TGATGGTTAGTACAC
* * * **
2058 GATTTTGACGAAAAACTGA-CCTGAAAAGTTTTTTCTCAACTTTTTGCGACAATACT-A-AAAAA
129 GATTTCGGCTAAAAACTGACCCT-AAAAGTTTTTTCTCAACTTTTTGAAACAATACTCAGAAAAA
*
2120 TATATATAATTCAATGCCAAAAAGATTGACGGGCTTTTCAAGCTTCTAATATTGTTTTTTCATTT
193 AATATATAATTCAATGCCAAAAAGATTGACGGGCTTTTCAAGCTTCTAATATTGTTTTTTCATTT
* *
2185 TTTTCCGAATTAATTTCTAACTAAATTGAAACAAGATTAAGATACTCGAAAAAATAAATCCTTAT
258 TTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTAAGATACTCGAAAAAA-AAATCCTTAT
* *
2250 ATCCAATATGGCTGAGATTTGGTTCGATGGATATAGATATTTCAAGGAGTCTATCTGCCAAAAAT
322 ATCCAATATGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAAT
* * * * * *
2315 CATGCAAAACTGGGACGGGGCTCCCGAAACACGTTTTTACCCCAAAACTCGTGATGGTCAATACA
387 CATGCAAAACTGAGTCGGGACT-CCGAAACACGTTTTTACCCAAAAACT-GTGATGGTTAGTACA
** *
2380 CGATTTCGGCCAAAAACTGACCCGAAAAGTTATTTCTCAATTTTTTAAAACAATACTCATAAAAA
450 CGATTTCGGCCAAAAACTGACCCGAAAAGTTATTTCTCAATTTTTTGCAACAATACTCAGAAAAA
*
2445 ATATATAATTCAATGCCAAAAATATTGACGGGCTTTTCAAGCTTCTAATATCGTTTTTT-ATCAT
515 ATATATAATTCAATGCCAAAAAGATTGACGGGCTTTTCAAGCTTCTAATATCGTTTTTTCAT--T
* * * **
2509 TTTTTTCCGAATTAATTTCTGATTAAATCGAAACAAGATTAAGATACTCGGAAAAA-AGATATTT
578 TTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTAAGATGCTCGTAAAAACA-A-ATCC
* * * * **
2573 TTATATCCAATATGGCTCAGATTTGGTTCGATGAATATTGATATTTCAAGGAGTCTTCCTGCCAA
641 TTATATCCAATGTGGCTGACATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGTGCCAA
* * *
2638 AAATCATACAAAATTGAGCCGGTGACTCCGGAACGCGTTTTTAGCCAAAACATGT-G-ACACGAT
706 AAATCATGCAAAATTGAGTCGG-GGCTCCGGAACGCGTTTTTAGCCAAAACATGTAGTACACGAT
** * * ** **
2701 TTTTG-TGAAAAACTAACCCGAAAAGTTTTTTCTCAACATTTTGCGACAATACTCAGAAAAAATA
770 TTCGGCT-AAAAACTGACCCTAAAAGTTTTTTCTCAATTTTTTGAAACAATACTCAGAAAAAATA
* * *
2765 TATAATTCAATGCCAAAAAGATTGACGGGCTTTTCAAGCCTCTAATATTGTTTTTTTCATTTTTT
834 TATAATTCAATGCCAAAAAGATTGACGGGTTTTTCAAGCTTCTAATATCGTTTTTTTCATTTTTT
* * * *
2830 TCCGAATTAATTTCTAATTGAATCGAAACACGATTCAGATGCTCCTAAAAACAAATCCTTAT
899 TCCGAATTAATTTCTAATTAAATCGAAACAAGATTAAGATGCTCGTAAAAACAAATCCTTAT
* * * * * *
2892 ATTCACTGCGGCTAACATTTGGTTCGATAAATATATATATTTCAAGGAGTCTTTGTGCCAAAAAT
1 ATCCAATGTGGCTGACATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGTGCCAAAAAT
* * *
2957 CATGCAAAATTGAGAT-GGGTCTCCGGAACGCGTTTTTAGCAAAAAACTATAATGGTTAGTACAC
66 CATGCAAAATTGAG-TCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACT-TGATGGTTAGTACAC
* *
3021 GATTTCGGCTAATAACTGACACACTAAAAGTTTTTTCTCAATTTTTTGAAACAATACTCAG-AAA
129 GATTTCGGCTAAAAACTGAC-C-CTAAAAGTTTTTTCTCAACTTTTTGAAACAATACTCAGAAAA
* * *
3085 AAATATACAATTCAATGCCAAAAAGATTGACGGGTTTTTCAAGCTTCTGATATAAT-TTTTTTCA
192 AAATATATAATTCAATGCCAAAAAGATTGACGGGCTTTTCAAGCTTCT-A-ATATTGTTTTTTCA
*
3149 TTTTTTT-CGAATTAATTTCTGATTAAATCGAAAC-AGAATTAAGATACTCGAAAAAAAAACAAA
255 TTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAG-ATTAAGATACTCG---AAAAAA-AAA
3212 TCCTTATATCCAATATGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTCTGC
315 TCCTTATATCCAATATGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTCTGC
* *
3277 CATAAATCATGCAAAACTGAGTC-GGAGCTCCGGAAACACGTTTTTACCCCAAAACCCT-TGATG
380 CAAAAATCATGCAAAACTGAGTCGGGA-CTCC-GAAACACGTTTTTA-CCCAAAA-ACTGTGATG
* * * *
3340 GTTAGTACACGGTTTCGGCCAAAAACTGACCCGAAAAGTTATTTCTCAATTTTTTTCCCAGAATA
441 GTTAGTACACGATTTCGGCCAAAAACTGACCCGAAAAGTTATTTCTCAA-TTTTTTGCAACAATA
* * * * * *
3405 CTCAGAAAAAATATATAATTTAACG-CAAAATAGATTGTCGTGCTTTTCAAGGTTCTAATATCGG
505 CTCAGAAAAAATATATAATTCAATGCCAAAA-AGATTGACGGGCTTTTCAAGCTTCTAATATCGT
*
3469 TTTTTCATATTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACTAGATTCAA-ATGCTCGTAA
569 TTTTTC--ATTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATT-AAGATGCTCGTAA
* *
3533 AAACAAATCCTTATATCCAATGTGGTTGACATTTGGTTCGATGAATATAGATATTTCAAGGAGCC
631 AAACAAATCCTTATATCCAATGTGGCTGACATTTGGTTCGATGAATATAGATATTTCAAGGAGTC
* *
3598 TTTGTGCCAAAAATTATGCAAAATTGAGTCGAGGCTCCGGAACGCGTTTTTAGCCAAAA-ACTGT
696 TTTGTGCCAAAAATCATGCAAAATTGAGTCGGGGCTCCGGAACGCGTTTTTAGCCAAAACA-TGT
* * *
3662 A-TACATGATTTCGGCTAAAAACTGACCCTAAAAGTTTTATCTTAATTTTTTGAAACAATACTCA
760 AGTACACGATTTCGGCTAAAAACTGACCCTAAAAGTTTTTTCTCAATTTTTTGAAACAATACTCA
* * *
3726 TAAAAAATATATAATTCAATGCCAAAAAGATTGACGGGTTTTTCAAGTTTCTAATATCATTTTTT
825 GAAAAAATATATAATTCAATGCCAAAAAGATTGACGGGTTTTTCAAGCTTCTAATATCGTTTTTT
* *** *
3791 TCA-TTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTAAGACACTTGAAAGAAAAAAA
890 TCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTAAG--A--TGCTCG---TAAA
3855 AACAAATCCTTAT
948 AACAAATCCTTAT
* *
3868 ATCCAATGTGGCTGACATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGTGCTATAAAT
1 ATCCAATGTGGCTGACATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGTGCCAAAAAT
*
3933 CATGCAAAATTGAGTCGGGGTTCCGGAACGCGTTTTTAGCCAAAAAC----T-G-T-GTACACGA
66 CATGCAAAATTGAGTCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACTTGATGGTTAGTACACGA
*
3991 TTTCGGCTAAAAACTGACCCTAAAAGTTTTTTCTCAATTTTTTGAAACAATACTCAG-AAAAAAT
131 TTTCGGCTAAAAACTGACCCTAAAAGTTTTTTCTCAACTTTTTGAAACAATACTCAGAAAAAAAT
* * * *
4055 ATATAATTCAATGTCAATAAGATTGACGGGTTTTTCAAGCTTCTAATTTTGTTTTTTCATTTTTT
196 ATATAATTCAATGCCAAAAAGATTGACGGGCTTTTCAAGCTTCTAATATTGTTTTTTCATTTTTT
*
4120 T-CGAATTAATTTCTAATTAAATTGAAACAAGATTAAGATACTCGGAAAAAAAATTTAAAAAAAA
261 TCCGAATTAATTTCTAATTAAATCGAAACAAGATTAAGATACTC-G-------------------
* *
4184 AAAAAAAAAAGCAAATCCTTATATCAAATATGACTGAGATTTGGTTCGATGAATATAGATATTTC
306 ----AAAAAA--AAATCCTTATATCCAATATGGCTGAGATTTGGTTCGATGAATATAGATATTTC
* * * * * * * *
4249 AAGGAGTCTTCCTGCAAAAAATCATGCAAAATTGAGCCGGTGAATCCGGAACGCGTTTTTAACCA
365 AAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGTCGG-GACTCCGAAACACGTTTTTACCCA
* * * * * *
4314 AAAACTATGATGGTTAGTACACGATTTTGGCGAAAAACTGACCCGAAAAGTTTTTTCTGAACTTT
429 AAAACTGTGATGGTTAGTACACGATTTCGGCCAAAAACTGACCCGAAAAGTTATTTCTCAATTTT
* * * *
4379 TTGCGACAATACTCAGAAAAAATATATAATTCAATGCCAAAAATATTGACAGACTTTTCAAGCTT
494 TTGCAACAATACTCAGAAAAAATATATAATTCAATGCCAAAAAGATTGACGGGCTTTTCAAGCTT
* * * * *
4444 CTAATATTGTTTTTTC-GTTTTTTTCCGAATTAACTTCTTATTAAATCGAAACAAGATTTAGATG
559 CTAATATCGTTTTTTCATTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTAAGATG
* * * *
4508 CTCCTAAAAACAAATCCTTATATGCAATGTGGCTGACATTTGGTTCAATAAATATAGATATTTCA
624 CTCGTAAAAACAAATCCTTATATCCAATGTGGCTGACATTTGGTTCGATGAATATAGATATTTCA
* *
4573 AGGAGTGTTTGTGCC-AAAATCATGCAAAATTGAGTCGGGGCTCCGGAACGCGCTTTTAGCCAAA
689 AGGAGTCTTTGTGCCAAAAATCATGCAAAATTGAGTCGGGGCTCCGGAACGCGTTTTTAGCC-AA
* *
4637 AACTGTGATGATTAGTACACGATTTCAGCTAATAACTGACCCTAAAAGTTTTTTCTCAATTTTTT
753 AAC----ATG--TAGTACACGATTTCGGCTAAAAACTGACCCTAAAAGTTTTTTCTCAATTTTTT
* * * *
4702 AAAATAATACTCAGAAAAAATATATAATTCAATGCCAAAAAGATTGACGCGTTTTTCAATCTTCT
812 GAAACAATACTCAGAAAAAATATATAATTCAATGCCAAAAAGATTGACGGGTTTTTCAAGCTTCT
* * * * * *
4767 GATATCATTTTTCTCATTTTTTTCCGAATTAATTTCTGATTAAATCGAAACAAGATTAATATACT
877 AATATCGTTTTTTTCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTAAGATGCT
4832 CGATTAAAAAAAAAACAAATCCTTAT
942 CG--T-----AAAAACAAATCCTTAT
* * * ***
4858 ATCCAATATGGCTGAGATTTGATTCGATGAATATAGATATTTCAAGGAGTCTTCCCGCCAAAAAT
1 ATCCAATGTGGCTGACATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGTGCCAAAAAT
* * * * *
4923 TATGCAAAATTAAGTCGGTGCCTCCGGAACGCGTTTTTAGCCAAAAACGGTGATGGTTAGTTCAC
66 CATGCAAAATTGAGTCGG-GGCTCCGGAACGCGTTTTTAGCCAAAAAC-TTGATGGTTAGTACAC
* * * **
4988 GATTTTGGCGT-AAAACTGACCCGAAAAGTTTTTTCTGAACTTTTTGCGACAATACTCAGAAAAA
129 GATTTCGGC-TAAAAACTGACCCTAAAAGTTTTTTCTCAACTTTTTGAAACAATACTCAG-AAAA
* *
5052 AAAAATATAATTCAATGCCAAAAAGATTGACGGGCTTTTCAAGTTTCTAATATTGTTTTTTCATT
192 AAATATATAATTCAATGCCAAAAAGATTGACGGGCTTTTCAAGCTTCTAATATTGTTTTTTCA-T
* * *
5117 TTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTT
256 TTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTAAGATACTCG-AAAAAAAAATCCTT
* * *
5182 ATATCCAATGTGGCTGACATTTGGTTCGATAAATATAGATATTTCAAGGAGTCTTTCTGCCAAAA
320 ATATCCAATATGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAA
* * * * * * *
5247 ATCATGCAAAATTAAGTCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACTGTAATGGTTAGTACA
385 ATCATGCAAAACTGAGTCGGGACTCCGAAACACGTTTTTACCCAAAAACTGTGATGGTTAGTACA
* * * *
5312 CGATTTCGGCTAAAAACTGACCCTAAAAGTTTTTTCTCAATTTTTTGAAACAATACTCAGAAAAA
450 CGATTTCGGCCAAAAACTGACCCGAAAAGTTATTTCTCAATTTTTTGCAACAATACTCAGAAAAA
5377 ATATATAATTCAATGCCAAAAA
515 ATATATAATTCAATGCCAAAAA
5399 AAACAATTAT
Statistics
Matches: 3866, Mismatches: 431, Indels: 261
0.85 0.09 0.06
Matches are distributed among these distances:
958 56 0.01
959 45 0.01
960 12 0.00
961 52 0.01
962 2 0.00
963 173 0.04
964 361 0.09
965 211 0.05
966 289 0.07
967 97 0.03
968 481 0.12
969 411 0.11
970 320 0.08
971 119 0.03
972 28 0.01
973 33 0.01
975 1 0.00
976 115 0.03
977 120 0.03
978 84 0.02
980 5 0.00
981 44 0.01
982 118 0.03
985 68 0.02
986 73 0.02
987 98 0.03
988 7 0.00
989 120 0.03
990 129 0.03
991 27 0.01
996 1 0.00
997 1 0.00
998 1 0.00
999 56 0.01
1000 1 0.00
1001 60 0.02
1002 8 0.00
1003 39 0.01
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.33
Consensus pattern (960 bp):
ATCCAATGTGGCTGACATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGTGCCAAAAAT
CATGCAAAATTGAGTCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACTTGATGGTTAGTACACGA
TTTCGGCTAAAAACTGACCCTAAAAGTTTTTTCTCAACTTTTTGAAACAATACTCAGAAAAAAAT
ATATAATTCAATGCCAAAAAGATTGACGGGCTTTTCAAGCTTCTAATATTGTTTTTTCATTTTTT
TCCGAATTAATTTCTAATTAAATCGAAACAAGATTAAGATACTCGAAAAAAAAATCCTTATATCC
AATATGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATG
CAAAACTGAGTCGGGACTCCGAAACACGTTTTTACCCAAAAACTGTGATGGTTAGTACACGATTT
CGGCCAAAAACTGACCCGAAAAGTTATTTCTCAATTTTTTGCAACAATACTCAGAAAAAATATAT
AATTCAATGCCAAAAAGATTGACGGGCTTTTCAAGCTTCTAATATCGTTTTTTCATTTTTTTTCC
GAATTAATTTCTAATTAAATCGAAACAAGATTAAGATGCTCGTAAAAACAAATCCTTATATCCAA
TGTGGCTGACATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGTGCCAAAAATCATGCA
AAATTGAGTCGGGGCTCCGGAACGCGTTTTTAGCCAAAACATGTAGTACACGATTTCGGCTAAAA
ACTGACCCTAAAAGTTTTTTCTCAATTTTTTGAAACAATACTCAGAAAAAATATATAATTCAATG
CCAAAAAGATTGACGGGTTTTTCAAGCTTCTAATATCGTTTTTTTCATTTTTTTCCGAATTAATT
TCTAATTAAATCGAAACAAGATTAAGATGCTCGTAAAAACAAATCCTTAT
Found at i:3909 original size:321 final size:316
Alignment explanation
Indices: 1--5398 Score: 5961
Period size: 321 Copynumber: 16.7 Consensus size: 316
* * * * *
1 ATCCAATGTGGCTGACATTTGGTTCGATGAATATTGATATTTCAAGGAGCCTTTATGCCAAAAAT
1 ATCCAATATGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAAT
* * **
66 TATGCAAAACTGAGTCGGGGCTCCGGAACATGTTTTTAGCCAAAAAC-TG-T-GTACACGATTTC
66 CATGCAAAATTGAGTC-GGGCTCCGGAACGCGTTTTTAGCCAAAAACTTGTTAGTACACGATTTC
* * *
128 GGCTAAAAACTGACCCTAAAAGTTTTTTCTCAATTTTTTGAAACAATACTCATAAAAAATATATA
130 GGCTAAAAACTGACCCGAAAAGTTTTTTCTCAATTTTTTGCAACAATACTCAGAAAAAATATATA
* * *
193 ATTCAATGCCAAAAAGATTGACGGGTTTTTCAAGCTTCCAAAATTTTTTTTTCATTTTTTTTTCC
195 ATTCAATGCCAAAAAGATTGACGGGCTTTTCAAGCTTCTAATA-TTTTTTTTCA--TTTTTTTCC
258 GAATTAATTTCTAATTAAATCGAAACAAGATTAAGATACT-CGGAAAAAA-AAATCCTTAT
257 GAATTAATTTCTAATTAAATCGAAACAAGATTAAGATACTGC-GAAAAAACAAATCCTTAT
* * * *
317 ATCCAATATGGCTGAGATTTGCTTCAATGAATATAGATATTTCAAGGAGTCTTCCTGCCAAAATT
1 ATCCAATATGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAAT
* * * * *
382 CATACGAAATTCAGCCGGTGACTCCGGAACGCGTTTTTAGCCAAAAACTGTGATAACGTACACGA
66 CATGCAAAATTGAGTCGG-G-CTCCGGAACGCGTTTTTAGCCAAAAACT-TG-TTA-GTACACGA
* * * ** * *
447 TTTTGGCGAAAAACTGACCCGAACAGTTTTTTCTCACCTTTCTGCGACAATACTCAGAAAAAATA
126 TTTCGGCTAAAAACTGACCCGAAAAGTTTTTTCTCAATTTTTTGCAACAATACTCAGAAAAAATA
* *
512 TATAATTCAATGCCAAAAAGATTGACGGGATTTTCAAGATTCTAATATTGTTTTTTCATTTTTTT
191 TATAATTCAATGCCAAAAAGATTGACGGGCTTTTCAAGCTTCTAATATT-TTTTTTCA-TTTTTT
* * *
577 TCGGAATTAATTTATAATTAAATTGAAACAAGATTAAGATACT-CGAAAAAATACAAATCCTTAT
254 TCCGAATTAATTTCTAATTAAATCGAAACAAGATTAAGATACTGCG-AAAAA-ACAAATCCTTAT
* * * *
641 ATCCAATATGACTGAGATTTGGTTCGATGAATATAAATATTTCAAGGAATCTTTCTGCCAAGAAT
1 ATCCAATATGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAAT
* * * * * * **
706 CATGAAAAACTGAGTCGGGGTTCCCGAAACACGTTTTTACCCCTAAAGCCGTGATGGTTAGTACA
66 CATGCAAAATTGAGTC-GGGCT-CCGGAACGCGTTTTTA-GCC-AAAAAC-T--T-GTTAGTACA
* * * *
771 CGATTTCGGCCAAAAACTGACCCGAAAAGTTATTTCTCAATTTTTTGCCAGAATACTCAG-AAAA
123 CGATTTCGGCTAAAAACTGACCCGAAAAGTTTTTTCTCAATTTTTTGCAACAATACTCAGAAAAA
* * * * * *
835 ATATATAATTTAACG-CAAAATAGATTGTCGTGCTTTTCAAGGTTCTAATATCGTTTTTTCATTT
188 ATATATAATTCAATGCCAAAA-AGATTGACGGGCTTTTCAAGCTTCTAATAT-TTTTTTTCA-TT
* * *
899 TTTTTCCGAATTAATTTCTAATTAAATCGAAACTAA-ATTCAGATGCT-CGTAAAAACAAATCCT
250 TTTTTCCGAATTAATTTCTAATTAAATCGAAAC-AAGATTAAGATACTGCGAAAAAACAAATCCT
962 TAT
314 TAT
* * * *
965 ATCCAATGTGGCTGACATTTGGTTCGATGAATATAGATATTTCAAGGAGCCTTTGTGCCAAAAAT
1 ATCCAATATGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAAT
* *
1030 TATGCAAAACTGAGTCGGGGCTCCGGAACGCGTTTTTAGCCAAAATACTATGATGGTTAGTACAC
66 CATGCAAAATTGAGTC-GGGCTCCGGAACGCGTTTTTAGCCAAAA-AC--T--T-GTTAGTACAC
* * * * * * * *
1095 GATTTTGGCAAAAAACTGAACCGAAATG-TTTTTCTCAACTTTCTGCGACAATACTTA-AAAAAA
124 GATTTCGGCTAAAAACTGACCCGAAAAGTTTTTTCTCAATTTTTTGCAACAATACTCAGAAAAAA
*
1158 TATATAATTCAATGCCAAAAAGATTGAAGGGCTTTTCAAGCTTCTAATATTGTTTTTTCATTTTT
189 TATATAATTCAATGCCAAAAAGATTGACGGGCTTTTCAAGCTTCTAATATT-TTTTTTCATTTTT
* *
1223 TTCCGAATTAATTTCTAACTAAATTGAAACAAGATTAAGATACT-CGAAAAAA-AAATCCTTAT
253 TTCCGAATTAATTTCTAATTAAATCGAAACAAGATTAAGATACTGCGAAAAAACAAATCCTTAT
* *
1285 ATCCAATATGGCTGAGATTTGGTTCGATGAATACAGATATTTCAAAGAGTCTTTCTGCCAAAAAT
1 ATCCAATATGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAAT
* * * * * *
1350 CATGCAAAACTGAGTCGGAACTCCGGAAACACGTTTTTACCCCAAAACTCGTGATATATATACAC
66 CATGCAAAATTGAGTCGG-GCTCCGG-AACGCGTTTTTAGCCAAAAACT--TG-T-TA-GTACAC
* * * * *
1415 GATTTTGGCCAAAAACTGACCCGAAAAGTTATTTCTCAATTTTTTGCCAGAATACTCA-AAAAAA
124 GATTTCGGCTAAAAACTGACCCGAAAAGTTTTTTCTCAATTTTTTGCAACAATACTCAGAAAAAA
* * * * * *
1479 TATATAATTTAACG-CAAAATAGATTGTCGTGCTTTTCAAGGTTCTAATATCGTTTTTTCATTTT
189 TATATAATTCAATGCCAAAA-AGATTGACGGGCTTTTCAAGCTTCTAATAT-TTTTTTTCA-TTT
* * * *
1543 TTTTCCGAATTAATTTCTGATTAAATCGAAACTAA-ATTCAGATGCT-CGTAAAAATCAAATCCT
251 TTTTCCGAATTAATTTCTAATTAAATCGAAAC-AAGATTAAGATACTGCG-AAAAAACAAATCCT
1606 TAT
314 TAT
* * * *
1609 ATCCAATGTGGCTGACATTTGGTTCGATGAATATAGATATTTCAAGGAGCCTTTGTGCCAAAAAT
1 ATCCAATATGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAAT
* * *
1674 TATGCAAAACTGAGTCGGGGCTCCGGAACGCGTTTTTAGCCAAAAAC-TG-T-GTACACCATTTC
66 CATGCAAAATTGAGTC-GGGCTCCGGAACGCGTTTTTAGCCAAAAACTTGTTAGTACACGATTTC
* * * *
1736 GGCTAAAAACTGACCCTAAAAGTTTTTCCTCAATTTTTTGAAACAATACTCATAAAAAATATATA
130 GGCTAAAAACTGACCCGAAAAGTTTTTTCTCAATTTTTTGCAACAATACTCAGAAAAAATATATA
* * *
1801 ATTCAATGCCAAAAAGTTTGACGGGTTTTTCAAGCTTCTAATATCGTTTTATATCATTTTTTTTC
195 ATTCAATGCCAAAAAGATTGACGGGCTTTTCAAGCTTCTAATAT--TTTT-TTTCA-TTTTTTTC
* * * **
1866 CGAATTAATTTCTGATTAAATCGAAACAAGATTAAGATACT-CGGAGTAAAAGAAATTTTTAT
256 CGAATTAATTTCTAATTAAATCGAAACAAGATTAAGATACTGC-GA-AAAAACAAATCCTTAT
* * * * *
1928 ATCCAATATGGCTCAGATTTGGTTCGATGAATATTGATATTTGAAGGAGTGTTCCTGCCAAAAAT
1 ATCCAATATGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAAT
* * * *
1993 CATACAAAATTGAGCCGGTGACTCTGGAACGCGTTTTTAGCCAAAAACTGTGATAGTTAGTAAAC
66 CATGCAAAATTGAGTCGG-G-CTCCGGAACGCGTTTTTAGCCAAAAAC--T--T-GTTAGTACAC
* * * * * *
2058 GATTTTGACGAAAAACTGACCTGAAAAGTTTTTTCTCAACTTTTTGCGACAATACT-A-AAAAAT
124 GATTTCGGCTAAAAACTGACCCGAAAAGTTTTTTCTCAATTTTTTGCAACAATACTCAGAAAAA-
2121 ATATATAATTCAATGCCAAAAAGATTGACGGGCTTTTCAAGCTTCTAATATTGTTTTTTCATTTT
188 ATATATAATTCAATGCCAAAAAGATTGACGGGCTTTTCAAGCTTCTAATATT-TTTTTTCATTTT
* * *
2186 TTTCCGAATTAATTTCTAACTAAATTGAAACAAGATTAAGATACT-CGAAAAAATAAATCCTTAT
252 TTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTAAGATACTGCGAAAAAACAAATCCTTAT
* *
2250 ATCCAATATGGCTGAGATTTGGTTCGATGGATATAGATATTTCAAGGAGTCTATCTGCCAAAAAT
1 ATCCAATATGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAAT
* * * * * * * *
2315 CATGCAAAACTGGGACGGGGCTCCCGAAACACGTTTTTACCCCAAAACTCGTGATGGTCAATACA
66 CATGCAAAATTGAGTC-GGGCT-CCGGAACGCGTTTTTAGCCAAAAACT--TG-T--T-AGTACA
* * ** *
2380 CGATTTCGGCCAAAAACTGACCCGAAAAGTTATTTCTCAATTTTTTAAAACAATACTCATAAAAA
123 CGATTTCGGCTAAAAACTGACCCGAAAAGTTTTTTCTCAATTTTTTGCAACAATACTCAGAAAAA
*
2445 ATATATAATTCAATGCCAAAAATATTGACGGGCTTTTCAAGCTTCTAATATCGTTTTTTATCATT
188 ATATATAATTCAATGCCAAAAAGATTGACGGGCTTTTCAAGCTTCTAATAT--TTTTTT-TCATT
* * * **
2510 TTTTTCCGAATTAATTTCTGATTAAATCGAAACAAGATTAAGATACT-CGGAAAAAAGATATTTT
250 TTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTAAGATACTGC-GAAAAAACAAATCCT
2574 TAT
314 TAT
* * *
2577 ATCCAATATGGCTCAGATTTGGTTCGATGAATATTGATATTTCAAGGAGTCTTCCTGCCAAAAAT
1 ATCCAATATGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAAT
* * *
2642 CATACAAAATTGAGCCGGTGACTCCGGAACGCGTTTTTAGCC-AAAACATG-T-G-ACACGATTT
66 CATGCAAAATTGAGTCGG-G-CTCCGGAACGCGTTTTTAGCCAAAAACTTGTTAGTACACGATTT
** * ** *
2703 TTG-TGAAAAACTAACCCGAAAAGTTTTTTCTCAACATTTTGCGACAATACTCAGAAAAAATATA
129 CGGCT-AAAAACTGACCCGAAAAGTTTTTTCTCAATTTTTTGCAACAATACTCAGAAAAAATATA
*
2767 TAATTCAATGCCAAAAAGATTGACGGGCTTTTCAAGCCTCTAATATTGTTTTTTTCATTTTTTTC
193 TAATTCAATGCCAAAAAGATTGACGGGCTTTTCAAGCTTCTAATA-T-TTTTTTTCATTTTTTTC
* * * * **
2832 CGAATTAATTTCTAATTGAATCGAAACACGATTCAGATGCT-CCTAAAAACAAATCCTTAT
256 CGAATTAATTTCTAATTAAATCGAAACAAGATTAAGATACTGCGAAAAAACAAATCCTTAT
* * ** * * * * *
2892 ATTCACTGCGGCTAACATTTGGTTCGATAAATATATATATTTCAAGGAGTCTTTGTGCCAAAAAT
1 ATCCAATATGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAAT
*
2957 CATGCAAAATTGAGAT-GGGTCTCCGGAACGCGTTTTTAGCAAAAAACTATAATGGTTAGTACAC
66 CATGCAAAATTGAG-TCGGG-CTCCGGAACGCGTTTTTAGCCAAAAAC--T--T-GTTAGTACAC
* * *
3021 GATTTCGGCTAATAACTGACACACTAAAAGTTTTTTCTCAATTTTTTGAAACAATACTCAGAAAA
124 GATTTCGGCTAAAAACTGAC-C-CGAAAAGTTTTTTCTCAATTTTTTGCAACAATACTCAGAAAA
* * *
3086 AATATACAATTCAATGCCAAAAAGATTGACGGGTTTTTCAAGCTTCTGATATAATTTTTTTCATT
187 AATATATAATTCAATGCCAAAAAGATTGACGGGCTTTTCAAGCTTCT-A-ATATTTTTTTTCATT
*
3151 TTTTT-CGAATTAATTTCTGATTAAATCGAAAC-AGAATTAAGATACT-CGAAAAAAAAACAAAT
250 TTTTTCCGAATTAATTTCTAATTAAATCGAAACAAG-ATTAAGATACTGCG---AAAAAACAAAT
3213 CCTTAT
311 CCTTAT
*
3219 ATCCAATATGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTCTGCCATAAAT
1 ATCCAATATGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAAT
* * * *
3284 CATGCAAAACTGAGTCGGAGCTCCGGAAACACGTTTTTACCCCAAAACCCTTGATGGTTAGTACA
66 CATGCAAAATTGAGTCGG-GCTCCGG-AACGCGTTTTTA-GCCAAAA-AC-T--T-GTTAGTACA
* * * * * *
3349 CGGTTTCGGCCAAAAACTGACCCGAAAAGTTATTTCTCAATTTTTTTCCCAGAATACTCAGAAAA
123 CGATTTCGGCTAAAAACTGACCCGAAAAGTTTTTTCTCAA-TTTTTTGCAACAATACTCAGAAAA
* * * * * **
3414 AATATATAATTTAACG-CAAAATAGATTGTCGTGCTTTTCAAGGTTCTAATATCGGTTTTTCATA
187 AATATATAATTCAATGCCAAAA-AGATTGACGGGCTTTTCAAGCTTCTAATAT-TTTTTTTC--A
* * *
3478 TTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACTAGATTCAA-ATGCT-CGTAAAAACAAAT
248 -TTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATT-AAGATACTGCGAAAAAACAAAT
3541 CCTTAT
311 CCTTAT
* * * * *
3547 ATCCAATGTGGTTGACATTTGGTTCGATGAATATAGATATTTCAAGGAGCCTTTGTGCCAAAAAT
1 ATCCAATATGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAAT
* *
3612 TATGCAAAATTGAGTCGAGGCTCCGGAACGCGTTTTTAGCCAAAAAC-TG-TA-TACATGATTTC
66 CATGCAAAATTGAGTCG-GGCTCCGGAACGCGTTTTTAGCCAAAAACTTGTTAGTACACGATTTC
* * * * *
3674 GGCTAAAAACTGACCCTAAAAGTTTTATCTTAATTTTTTGAAACAATACTCATAAAAAATATATA
130 GGCTAAAAACTGACCCGAAAAGTTTTTTCTCAATTTTTTGCAACAATACTCAGAAAAAATATATA
* * *
3739 ATTCAATGCCAAAAAGATTGACGGGTTTTTCAAGTTTCTAATATCATTTTTTTCA-TTTTTTCTG
195 ATTCAATGCCAAAAAGATTGACGGGCTTTTCAAGCTTCTAATAT--TTTTTTTCATTTTTTTCCG
* *
3803 AATTAATTTCTAATTAAATCGAAACAAGATTAAGACACTTGAAAGAAAAAAAAACAAATCCTTAT
258 AATTAATTTCTAATTAAATCGAAACAAGATTAAGATAC-TG--CG---AAAAAACAAATCCTTAT
* * * * *
3868 ATCCAATGTGGCTGACATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGTGCTATAAAT
1 ATCCAATATGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAAT
*
3933 CATGCAAAATTGAGTCGGGGTTCCGGAACGCGTTTTTAGCCAAAAAC-TG-T-GTACACGATTTC
66 CATGCAAAATTGAGTC-GGGCTCCGGAACGCGTTTTTAGCCAAAAACTTGTTAGTACACGATTTC
* *
3995 GGCTAAAAACTGACCCTAAAAGTTTTTTCTCAATTTTTTGAAACAATACTCAGAAAAAATATATA
130 GGCTAAAAACTGACCCGAAAAGTTTTTTCTCAATTTTTTGCAACAATACTCAGAAAAAATATATA
* * * *
4060 ATTCAATGTCAATAAGATTGACGGGTTTTTCAAGCTTCTAATTTTGTTTTTTCATTTTTTT-CGA
195 ATTCAATGCCAAAAAGATTGACGGGCTTTTCAAGCTTCTAATATT-TTTTTTCATTTTTTTCCGA
*
4124 ATTAATTTCTAATTAAATTGAAACAAGATTAAGATACT-CGGAAAAAAAATTTAAAAAAAAAAAA
259 ATTAATTTCTAATTAAATCGAAACAAGATTAAGATACTGC-G-----------------------
4188 AAAAAAGCAAATCCTTAT
300 AAAAAA-CAAATCCTTAT
* * * *
4206 ATCAAATATGACTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTCCTGCAAAAAAT
1 ATCCAATATGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAAT
* * *
4271 CATGCAAAATTGAGCCGGTGAATCCGGAACGCGTTTTTAACCAAAAACTATGATGGTTAGTACAC
66 CATGCAAAATTGAGTCGG-G-CTCCGGAACGCGTTTTTAGCCAAAAAC--T--T-GTTAGTACAC
* * * * *
4336 GATTTTGGCGAAAAACTGACCCGAAAAGTTTTTTCTGAACTTTTTGCGACAATACTCAGAAAAAA
124 GATTTCGGCTAAAAACTGACCCGAAAAGTTTTTTCTCAATTTTTTGCAACAATACTCAGAAAAAA
* * * *
4401 TATATAATTCAATGCCAAAAATATTGACAGACTTTTCAAGCTTCTAATATTGTTTTTTCGTTTTT
189 TATATAATTCAATGCCAAAAAGATTGACGGGCTTTTCAAGCTTCTAATATT-TTTTTTCATTTTT
* * * * **
4466 TTCCGAATTAACTTCTTATTAAATCGAAACAAGATTTAGATGCT-CCTAAAAACAAATCCTTAT
253 TTCCGAATTAATTTCTAATTAAATCGAAACAAGATTAAGATACTGCGAAAAAACAAATCCTTAT
* * * * * * *
4529 ATGCAATGTGGCTGACATTTGGTTCAATAAATATAGATATTTCAAGGAGTGTTTGTGCC-AAAAT
1 ATCCAATATGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAAT
*
4593 CATGCAAAATTGAGTCGGGGCTCCGGAACGCGCTTTTAGCCAAAAACTGTGATGATTAGTACACG
66 CATGCAAAATTGAGTC-GGGCTCCGGAACGCGTTTTTAGCCAAAAAC--T--TG-TTAGTACACG
* * * ** *
4658 ATTTCAGCTAATAACTGACCCTAAAAGTTTTTTCTCAATTTTTTAAAATAATACTCAGAAAAAAT
125 ATTTCGGCTAAAAACTGACCCGAAAAGTTTTTTCTCAATTTTTTGCAACAATACTCAGAAAAAAT
* * * * *
4723 ATATAATTCAATGCCAAAAAGATTGACGCGTTTTTCAATCTTCTGATATCATTTTTCTCATTTTT
190 ATATAATTCAATGCCAAAAAGATTGACGGGCTTTTCAAGCTTCTAATAT--TTTTTTTCATTTTT
* *
4788 TTCCGAATTAATTTCTGATTAAATCGAAACAAGATTAATATACT-CGATTAAAAAAAAAACAAAT
253 TTCCGAATTAATTTCTAATTAAATCGAAACAAGATTAAGATACTGCG-------AAAAAACAAAT
4852 CCTTAT
311 CCTTAT
* * *
4858 ATCCAATATGGCTGAGATTTGATTCGATGAATATAGATATTTCAAGGAGTCTTCCCGCCAAAAAT
1 ATCCAATATGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAAT
* * *
4923 TATGCAAAATTAAGTCGGTGCCTCCGGAACGCGTTTTTAGCCAAAAACGGTGATGGTTAGTTCAC
66 CATGCAAAATTGAGTCGG-G-CTCCGGAACGCGTTTTTAGCCAAAAAC--T--T-GTTAGTACAC
* * * *
4988 GATTTTGGCGT-AAAACTGACCCGAAAAGTTTTTTCTGAACTTTTTGCGACAATACTCAGAAAAA
124 GATTTCGGC-TAAAAACTGACCCGAAAAGTTTTTTCTCAATTTTTTGCAACAATACTCAG--AAA
* *
5052 AAAAATATAATTCAATGCCAAAAAGATTGACGGGCTTTTCAAGTTTCTAATATTGTTTTTTCATT
186 AAATATATAATTCAATGCCAAAAAGATTGACGGGCTTTTCAAGCTTCTAATATT-TTTTTTCA-T
* * *
5117 TTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCT-CGTAAAAACAAATCCT
249 TTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTAAGATACTGCGAAAAAACAAATCCT
5181 TAT
314 TAT
* * *
5184 ATCCAATGTGGCTGACATTTGGTTCGATAAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAAT
1 ATCCAATATGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAAT
*
5249 CATGCAAAATTAAGTCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACTGTAATGGTTAGTACACG
66 CATGCAAAATTGAGTC-GGGCTCCGGAACGCGTTTTTAGCCAAAAAC--T--T-GTTAGTACACG
* *
5314 ATTTCGGCTAAAAACTGACCCTAAAAGTTTTTTCTCAATTTTTTGAAACAATACTCAGAAAAAAT
125 ATTTCGGCTAAAAACTGACCCGAAAAGTTTTTTCTCAATTTTTTGCAACAATACTCAGAAAAAAT
5379 ATATAATTCAATGCCAAAAA
190 ATATAATTCAATGCCAAAAA
5399 AAACAATTAT
Statistics
Matches: 4340, Mismatches: 563, Indels: 351
0.83 0.11 0.07
Matches are distributed among these distances:
313 2 0.00
314 61 0.01
315 143 0.03
316 159 0.04
317 208 0.05
318 106 0.02
319 93 0.02
320 209 0.05
321 524 0.12
322 353 0.08
323 362 0.08
324 413 0.10
325 221 0.05
326 268 0.06
327 349 0.08
328 220 0.05
329 106 0.02
330 28 0.01
331 122 0.03
332 13 0.00
333 97 0.02
337 11 0.00
338 84 0.02
339 25 0.01
344 1 0.00
345 1 0.00
346 1 0.00
347 123 0.03
348 37 0.01
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.33
Consensus pattern (316 bp):
ATCCAATATGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAAT
CATGCAAAATTGAGTCGGGCTCCGGAACGCGTTTTTAGCCAAAAACTTGTTAGTACACGATTTCG
GCTAAAAACTGACCCGAAAAGTTTTTTCTCAATTTTTTGCAACAATACTCAGAAAAAATATATAA
TTCAATGCCAAAAAGATTGACGGGCTTTTCAAGCTTCTAATATTTTTTTTCATTTTTTTCCGAAT
TAATTTCTAATTAAATCGAAACAAGATTAAGATACTGCGAAAAAACAAATCCTTAT
Found at i:5418 original size:26 final size:26
Alignment explanation
Indices: 5389--5495 Score: 214
Period size: 26 Copynumber: 4.1 Consensus size: 26
5379 ATATAATTCA
5389 ATGCCAAAAAAAACAATTATCAAAGT
1 ATGCCAAAAAAAACAATTATCAAAGT
5415 ATGCCAAAAAAAACAATTATCAAAGT
1 ATGCCAAAAAAAACAATTATCAAAGT
5441 ATGCCAAAAAAAACAATTATCAAAGT
1 ATGCCAAAAAAAACAATTATCAAAGT
5467 ATGCCAAAAAAAACAATTATCAAAGT
1 ATGCCAAAAAAAACAATTATCAAAGT
5493 ATG
1 ATG
5496 AACAGACACA
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 81 1.00
ACGTcount: A:0.57, C:0.15, G:0.08, T:0.20
Consensus pattern (26 bp):
ATGCCAAAAAAAACAATTATCAAAGT
Found at i:9459 original size:36 final size:36
Alignment explanation
Indices: 9419--9496 Score: 147
Period size: 36 Copynumber: 2.2 Consensus size: 36
9409 TAAAGATCGA
9419 ACCCTAGCTACTGAAATTAAGAATTAAGAGTTCAGC
1 ACCCTAGCTACTGAAATTAAGAATTAAGAGTTCAGC
*
9455 ACCCTAGCTACTGAAATTAAGAATTAAGAGTTGAGC
1 ACCCTAGCTACTGAAATTAAGAATTAAGAGTTCAGC
9491 ACCCTA
1 ACCCTA
9497 ACACCAAGTT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.24
Consensus pattern (36 bp):
ACCCTAGCTACTGAAATTAAGAATTAAGAGTTCAGC
Found at i:27103 original size:2 final size:2
Alignment explanation
Indices: 27096--27128 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
27086 ACTAAAACCC
27096 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 A
27129 AAATAAGCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28924 original size:25 final size:25
Alignment explanation
Indices: 28875--28925 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
28865 TTAGTAGAAT
*
28875 AATTGTAAAAGTTTATTTCTAAAAA
1 AATTGTAAAAGTATATTTCTAAAAA
28900 AATTGTAAAAGAATATATTT-TAAAAA
1 AATTGTAAAAG--TATATTTCTAAAAA
28926 TTCTAATATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 11 0.48
26 6 0.26
27 6 0.26
ACGTcount: A:0.53, C:0.02, G:0.08, T:0.37
Consensus pattern (25 bp):
AATTGTAAAAGTATATTTCTAAAAA
Found at i:33205 original size:16 final size:16
Alignment explanation
Indices: 33181--33215 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
33171 ATTTTCTTCT
33181 TCTCCATATTCTATTG
1 TCTCCATATTCTATTG
* *
33197 TCTCTATATTCTCTTG
1 TCTCCATATTCTATTG
33213 TCT
1 TCT
33216 TTTCCATACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.14, C:0.26, G:0.06, T:0.54
Consensus pattern (16 bp):
TCTCCATATTCTATTG
Found at i:38525 original size:15 final size:15
Alignment explanation
Indices: 38505--38536 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
38495 TACCTTCTGC
*
38505 TGAGAGTTTATATTT
1 TGAGAGTTTACATTT
38520 TGAGAGTTTACATTT
1 TGAGAGTTTACATTT
38535 TG
1 TG
38537 CTTAGAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.03, G:0.22, T:0.50
Consensus pattern (15 bp):
TGAGAGTTTACATTT
Found at i:41226 original size:23 final size:23
Alignment explanation
Indices: 41196--41242 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
41186 GTACTAACCC
41196 CGGTATCCAGTAACTCCATTGTA
1 CGGTATCCAGTAACTCCATTGTA
41219 CGGTATCCAGTAACTCCATTGTA
1 CGGTATCCAGTAACTCCATTGTA
41242 C
1 C
41243 CCTGACTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.30
Consensus pattern (23 bp):
CGGTATCCAGTAACTCCATTGTA
Found at i:42356 original size:13 final size:13
Alignment explanation
Indices: 42338--42362 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42328 TTGTCAATAA
42338 GAATGAATGAAAT
1 GAATGAATGAAAT
42351 GAATGAATGAAA
1 GAATGAATGAAA
42363 ATTATTATTA
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:0.56, C:0.00, G:0.24, T:0.20
Consensus pattern (13 bp):
GAATGAATGAAAT
Found at i:45638 original size:3 final size:3
Alignment explanation
Indices: 45625--45656 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
45615 TTTGCGGTGG
45625 TTC TT- TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
45657 CTCCTTTCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:52990 original size:17 final size:18
Alignment explanation
Indices: 52961--52997 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
52951 GAGGTACATA
52961 TAATCATTAATTATAGAT
1 TAATCATTAATTATAGAT
52979 TAATCA-TAATTATAGAT
1 TAATCATTAATTATAGAT
52996 TA
1 TA
52998 TACATATGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.43
Consensus pattern (18 bp):
TAATCATTAATTATAGAT
Found at i:55931 original size:18 final size:18
Alignment explanation
Indices: 55908--55943 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
55898 TTACGAAGGC
*
55908 AGGCGGTTGGTGAGGCGG
1 AGGCGGTTGATGAGGCGG
55926 AGGCGGTTGATGAGGCGG
1 AGGCGGTTGATGAGGCGG
55944 TGGTTCATGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.14, C:0.11, G:0.58, T:0.17
Consensus pattern (18 bp):
AGGCGGTTGATGAGGCGG
Found at i:60927 original size:3 final size:3
Alignment explanation
Indices: 60919--60943 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
60909 AACACCCATA
60919 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
60944 TTGGAAAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:63311 original size:59 final size:58
Alignment explanation
Indices: 63242--63358 Score: 225
Period size: 58 Copynumber: 2.0 Consensus size: 58
63232 GGGTCAATAA
63242 GATGTGAACTCTACTAGAATTAATATTACCCTTTTTTTAATACTAATAAAATAATTAGT
1 GATGTGAACTCTACTAGAATTAATATTA-CCTTTTTTTAATACTAATAAAATAATTAGT
63301 GATGTGAACTCTACTAGAATTAATATTACCTTTTTTTAATACTAATAAAATAATTAGT
1 GATGTGAACTCTACTAGAATTAATATTACCTTTTTTTAATACTAATAAAATAATTAGT
63359 TGAGCATACC
Statistics
Matches: 58, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
58 30 0.52
59 28 0.48
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (58 bp):
GATGTGAACTCTACTAGAATTAATATTACCTTTTTTTAATACTAATAAAATAATTAGT
Found at i:75051 original size:13 final size:13
Alignment explanation
Indices: 75033--75059 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
75023 GTTGCATCAG
75033 ATATGAACAAAGA
1 ATATGAACAAAGA
75046 ATATGAACAAAGA
1 ATATGAACAAAGA
75059 A
1 A
75060 CTTGTTACTA
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:0.07, G:0.15, T:0.15
Consensus pattern (13 bp):
ATATGAACAAAGA
Found at i:85694 original size:9 final size:9
Alignment explanation
Indices: 85671--85704 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
85661 CCGATGAGGA
*
85671 AACAGCAGC
1 AACAGCAAC
*
85680 AGCAGCAAC
1 AACAGCAAC
85689 AACAGCAAC
1 AACAGCAAC
85698 AACAGCA
1 AACAGCA
85705 GATGTTGATG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.50, C:0.32, G:0.18, T:0.00
Consensus pattern (9 bp):
AACAGCAAC
Found at i:94131 original size:19 final size:19
Alignment explanation
Indices: 94107--94144 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
94097 GTACTTTGTA
94107 TATTAAAGTATGATCATAC
1 TATTAAAGTATGATCATAC
94126 TATTAAAGTATGATCATAC
1 TATTAAAGTATGATCATAC
94145 ATTTGCCTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.37
Consensus pattern (19 bp):
TATTAAAGTATGATCATAC
Found at i:95871 original size:2 final size:2
Alignment explanation
Indices: 95866--95894 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
95856 TGCGTGTGTT
95866 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
95895 GGTTGAAATC
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
Found at i:98271 original size:23 final size:23
Alignment explanation
Indices: 98223--98271 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
98213 GATTTTATTA
***
98223 TTATAATAGAATTAGAATTTTCT
1 TTATAATAGAATTAGAATTGAAT
98246 TTATAATAGAA-TAGAATTAGAAT
1 TTATAATAGAATTAGAATT-GAAT
98269 TTA
1 TTA
98272 ATCGCATGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.45, C:0.02, G:0.10, T:0.43
Consensus pattern (23 bp):
TTATAATAGAATTAGAATTGAAT
Done.